title: NC-miR_4d_rep2

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: NC-miR incorporated in sCA were administered on days 1, 2, and 3, and the rectum was excised day 4

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: text file with FPKM

extract_protocol:
Total RNA was extracted from colorectum with miRNeasy Mini Kit (Qiagen) and processed according to the manufacturer’s protocol. The quality of the RNAs was estimated by using the RNA 6000 Nano LabChip Kit (p/n 5065-4476) on the Agilent 2100 Bioanalyzer (G2940BA; Agilent Technologies, Santa Clara, CA).
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: ΜiR-29a and miR-29b, NC-miR loaded in sCA were systemically administered from the tail vein on the 1st, 2nd and 3rd days after the 2% DSS administration was started, and the rectum of the mouse was collected on the 4th day.

value: BALB/c

value: Seven weeks old

value: colorectum

tag: trans-gene


title: NC-miR_2d_rep2

status: Public on Aug 10 2018

type: SRA

description: NC-miR incorporated in sCA were administered on days 1, 2, and 3, and the rectum was excised day 2

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: age

tag: tissue


title: normal_rep1

description: the rectum from the non-tretaed normal mice was excised day 0

value: normal


title: NC-miR_2d_rep1

source_name: NC-miR incorporated in sCA were administered on days 1, 2, and 3, and the rectum was excised day 2


title: normal_rep2

source_name: the rectum from the non-tretaed normal mice was excised day 0


title: HNF-1β KO clone#1

city: Minneapolis

first: Siu Chiu

last: Chan

state: MN

address: MCB-5148 420 Washington Ave SE

department: Medicine

country: USA

institute: University of Minnesota

description: Sample name: HNF1bKO-1_S16

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence quality was accessed via FastQC, and none of the preprocessing (trimming, filtering or masking) is necessary.
Raw paired-reads were mapped to mouse genome (GRCm8) using HiSAT2 with Ensembl (GRCm38.83) reference and following parameters: --dta-cufflinks --threads 8
Various Picard tools (CleanSam, Sort, CollectInsertSizeMetrics) have been used to clean the resulted sam files.
Read counts per gene were calculated using featureCounts (Liao Y. et al, Bioinformatics 2013) and following parameters: -p 8
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw counts of reads mapped per gene for each Sample.

source_name: mIMCD3 cells

growth_protocol: mIMCD3 WT and HNF-1β deficient cells were maintained in DMEM with 10% FBS until 80-90% confluent and changed to fresh medium for 24hrs, cells were fully confluent for total RNA harvesting.

extract_protocol:
Total RNA was isolated using a Qiagen RNA Easy kit.
RNA samples passed the quality control (RIN>8) were used to create a polyA barcoded RNAseq libraries using standard Illumina TruSeq protocols.

tag: genotype

value: HNF-1beta -/-

tag: cell line


title: 29b_4d_rep1

description: miR-29b incorporated in sCA were administered on days 1, 2, and 3, and the rectum was excised on day 4


title: NC-miR_4d_rep1

source_name: NC-miR incorporated in sCA were administered on days 1, 2, and 3, and the rectum was excised day 4


title: 29a_4d_rep2

description: miR-29a incorporated in sCA were administered on days 1, 2, and 3, and the rectum was excised on day 4


title: 29a_4d_rep1

source_name: miR-29a incorporated in sCA were administered on days 1, 2, and 3, and the rectum was excised on day 4


title: Bmi1.AIN.2

status: Public on Aug 09 2018

city: Bronx

first: Wenge

last: Li

state: NY

address: 1300 Morris Park Avenue

institute: Albert Einstein College of Medicine

description: barcode: CGTACTAG-TATCCTCT (N702-N503)

data_processing:
RNA-seq reads were aligned to the mm9 genome assembly using STAR (v2.4.2a) in per-sample 2-pass mode. The alignment was performed with default parameters, except --outFilterMultimapNmax 1 --outFilterMismatchNmax 3 --alignIntronMax 50000
The number of reads aligned to each defined gene was quantified using HTSeq-count (v0.6.1) with unstranded and union overlap resolution modes. Raw counts were normalized by converting the raw expression values to TPM (Transcript Per Million mapped reads) units using edgeR.
Supplementary_files_format_and_content: tab deliminated text files include count and tpm values for each sample
Genome_build: mm9

source_name: Intestinal Stem Cells

growth_protocol: BmicreERT2, Rosa26RFP mouse was fed on highly purified AIN76A diet at weaning and until 3 months of age

extract_protocol:
Isolated intestinal crypts were dispersed into single cell suspensions for FACS. Bmi1 cells exhibited high endogenous red fluorescence and Epcam+ and CD45- markers. Bmi1 cells were sorted and collected in bulk for RNA-seq. Total RNA was isolated using the TRI-Regent protocol.
RNA-seq libraries were prepared with a SMART-Seq v4 ultra low input RNA kit (Clontech) according to manufacturer's instructions.  Final library quality was verified with the Bioanalyzer assay (Agilent, Santa Clara, CA).
library construction protocol:paired end sequencing libraries were constructed using a NEXTERA XT-library prep kit (Illumina).

treatment_protocol: BmicreERT2, Rosa26RFP mouse was fed with AIN76A diet

tag: cell type

value: Bmi1 cell

value: BmicreERT2, Rosa26RFP

value: 3 months old

tag: diet

value: intestine

tag: gender

value: male


title: Bmi1.NWD2.2

description: barcode: TCCTGAGC-AGAGTAGA (N704-N504)

growth_protocol: BmicreERT2, Rosa26RFP mouse was fed on highly purified NWD2 diet at weaning and until 3 months of age

treatment_protocol: BmicreERT2, Rosa26RFP mouse was fed with NWD2 diet


title: Bmi1.NWD2.1

description: barcode: AGGCAGAA-AGAGTAGA (N703-N504)


title: Bmi1.NWD1.3

description: barcode: TAAGGCGA-AGAGTAGA (N701-N504)

growth_protocol: BmicreERT2, Rosa26RFP mouse was fed on highly purified NWD1 diet at weaning and until 3 months of age

treatment_protocol: BmicreERT2, Rosa26RFP mouse was fed with NWD1 diet


title: Lgr5.AIN.VdrKO.3

description: barcode: TAGGCATG-AGAGTAGA (N706-N504)

growth_protocol: Lgr5EGFPcre-ERT2/VdrKO mouse was fed on highly purified AIN76A diet at weaning and until 3 months of age

extract_protocol:
Isolated intestinal crypts were dispersed into single cell suspensions for FACS.  Lgr5 cells were the highest 2-3% subpopulation of Lgr5 fluorescent cells from Lgr5EGFP-creERT2 mice. Lgr5 cells were sorted and collected in bulk for RNA-seq. Total RNA was isolated using the TRI-Regent protocol.
RNA-seq libraries were prepared with a SMART-Seq v4 ultra low input RNA kit (Clontech) according to manufacturer's instructions.  Final library quality was verified with the Bioanalyzer assay (Agilent, Santa Clara, CA).
library construction protocol:paired end sequencing libraries were constructed using a NEXTERA XT-library prep kit (Illumina).

treatment_protocol: Lgr5EGFPcre-ERT2/VdrKO mouse was fed with AIN76A diet

value: Lgr5 cell

value: Vitamin D receptor knock out (VdrKO)


title: Bmi1.NWD1.1

description: barcode: AGGCAGAA-TATCCTCT (N703-N503)


title: Bmi1.AIN.1

description: barcode: TAAGGCGA-TATCCTCT (N701-N503)


title: Bmi1.NWD1.2

description: barcode: TCCTGAGC-TATCCTCT (N704-N503)

value: female


title: Lgr5.AIN.VdrKO.1

description: barcode: TCCTGAGC-CTCTCTAT (N704-N502)


title: Lgr5.AIN.VdrKO.2

description: barcode: GGACTCCT-TATCCTCT (N705-N503)


title: Lgr5.AINlowVitD.2

description: barcode: TAGGCATG-CTCTCTAT (N706-N502)

growth_protocol: Lgr5EGFPcre-ERT2 mice were fed on highly purified AINlowVitD diet at weaning and until 3 months of age

treatment_protocol: Lgr5EGFPcre-ERT2 mouse was fed with AINlowVitD diet

value: AINlowVitD (AIN + 0.11 IU/g body weight Vitamin D)


title: Lgr5.AINlowVitD.1

description: barcode: GGACTCCT-GCGTAAGA (N705-N517)


title: Lgr5.NWD1VitD.3

description: barcode: CGTACTAG-AGAGTAGA (N702-N504)

growth_protocol: Lgr5EGFPcre-ERT2 mice were fed on highly purified NWD1VitD diet at weaning and until 3 months of age

treatment_protocol: Lgr5EGFPcre-ERT2 mouse was fed with NWD1VitD diet

value: NWD1VitD (NWD1 + 2.3 IU/g body weight Vitamin D)


title: Lgr5.NWD1VitD.2

description: barcode: TCCTGAGC-AGAGTAGA (N704-N504)


title: Lgr5.AINlowVitD.3

description: barcode: AGGCAGAA-GCGTAAGA (N703-N517)


title: Lgr5.NWD1Ca.3

description: barcode: TAAGGCGA-TATCCTCT (N701-N503)

growth_protocol: Lgr5EGFPcre-ERT2 mice were fed on highly purified NWD1Ca diet at weaning and until 3 months of age

treatment_protocol: Lgr5EGFPcre-ERT2 mouse was fed with NWD1Ca diet

value: NWD1Ca (NWD1 + 7.0 mg/g body weight Calcium)


title: 29b_4d_rep2

source_name: miR-29b incorporated in sCA were administered on days 1, 2, and 3, and the rectum was excised on day 4


title: Lgr5.NWD2.1

description: barcode: CGTACTAG-CTCTCTAT (N702-N502)

growth_protocol: Lgr5EGFPcre-ERT2 mice were fed on highly purified NWD2 diet at weaning and until 3 months of age

treatment_protocol: Lgr5EGFPcre-ERT2 mouse was fed with NWD2 diet


title: Lgr5.NWD1.3

description: barcode: TAAGGCGA-CTCTCTAT (N701-N502)

growth_protocol: Lgr5EGFPcre-ERT2 mice were fed on highly purified NWD1 diet at weaning and until 3 months of age

treatment_protocol: Lgr5EGFPcre-ERT2 mouse was fed with NWD1 diet


title: Lgr5.NWD1.2

description: barcode: TCCTGAGC-GCGTAAGA (N704-N517)


title: Lgr5.NWD1.1

description: barcode: AGGCAGAA-GCGTAAGA (N703-N517)


title: Lgr5.NWD2.3

description: barcode: TCCTGAGC-CTCTCTAT (N704-N502)


title: Lgr5.NWD1Ca.1

description: barcode: TAAGGCGA-GCGTAAGA (N701-N517)


title: Lgr5.AIN.3

description: barcode: CGTACTAG-GCGTAAGA (N702-N517)

growth_protocol: Lgr5EGFPcre-ERT2 mice were fed on highly purified AIN76A diet at weaning and until 3 months of age

treatment_protocol: Lgr5EGFPcre-ERT2 mouse was fed with AIN76A diet


title: Lgr5.NWD1VitD.1

description: barcode: AGGCAGAA-TATCCTCT (N703-N503)


title: Lgr5.AIN.2

description: barcode: CGTACTAG-CTCTCTAT (N702-N502)


title: Lgr5.NWD2.2

description: barcode: AGGCAGAA-CTCTCTAT (N703-N502)


title: Lgr5.AIN.1

description: barcode: TAAGGCGA-GCGTAAGA (N701-N517)


title: RNA-seq, 6-week-old Fmr1 KO mice, cerebral cortex, m6A-IP, replicate 2

city: Atlanta

first: Feiran

last: Zhang

state: GA

address: 615 Michael St NE

department: Human Genetics

institute: Emory University

description: Illumina HiSeq

data_processing:
For m6A-IP-seq, reads were first aligned to mouse genome (mm9) by Bowtie v2.2.4, using the local, sensitive and non-deterministic mode.
Genome-based m6A peaks were identified by HOMER findPeaks, using the factor mode and additional settings (peak size = 100 nt; fragment length = 100 nt; maximum distance used to stitch peaks together = 50; fold change threshold = 3; local fold change = disabled; size of region to search for control tags = 1x peak size; p-value threshold = 0.0001; and false-discovery rate (FDR) threshold = 0.001).
High-confidence peaks found in both biological replicates were annotated by HOMER annotatePeaks.pl.
The annotation of boundary genes were corrected using a Python script.
For exome-based peak calling, reads were re-aligned to mouse genome (mm9) byTophat v2.0.13.
Exome-based m6A peaks were identified and annotated by R using MeTPeak package (v1.1; fold enrichment ≥ 2).
Differential methylation (DM) in m6A-RIP-seq data of WT and Fmr1 KO cortex was analyzed by R using MeTDiff package (v1.1.0; fold enrichment ≥ 2)
Tiled data files (TDF) for the Integrative Genomics Viewer (IGV) were generated by igvtools.
The genome-wide coverage data were normalized by 1,000,000/total read count, and were visualized by IGV.
FPKM values were calculated by Cufflinks v2.2.1.
Differentially expressed genes were identified by Cuffdiff (v2.2.1).
Genome_build: mm9
Supplementary_files_format_and_content: For m6A-IP-seq, peak files with quantitative and statictic data, as well as tag density files, are included. For RNA-seq, gene expression values in Cufflinks-normalized fpkm_tracking format were included.

molecule: polyA RNA

source_name: Cerebral cortex

extract_protocol:
Total RNA was extracted from fresh cerebral cortex tissue by using TRIzol Reagent (Thermo Fisher) and Phase Lock Gel, Heavy (QuantaBio) per manufacturer’s protocol.
The non-IP (RNA-seq) libraries for m6A-IP were generated from about 50 ng of poly(A)+ RNA fragments from duplicated samples per condition. The m6A-IP libraries were generated from all anti-m6A immunoprecipitated and free m6A eluted fragments of poly(A)+ RNA from duplicated samples per condition.The TruSeq LT RNA Library Preparation Kit v2 (Illumina) was used and the manufacturer’s protocol was followed. An Agilent 2100 BioAnalyzer and DNA1000 kit were used to quantify amplified cDNA and to control the quality of the libraries.

value: Fmr1 KO (Fmr1tm1Cgr), C57BL/6J

value: 6 weeks

tag: treatment of rna sample

value: Poly(A) selection; anti-m6A immunoprecipitation

tag: biological replicate no.


title: RNA-seq, 6-week-old Fmr1 KO mice, cerebral cortex, non-IP, replicate 1

description: Illumina HiSeq

value: Poly(A) selection


title: RNA-seq, 6-week-old WT mice, cerebral cortex, m6A-IP, replicate 2

description: Illumina HiSeq

value: Wild-type, C57BL/6J


title: RNA-seq, 6-week-old WT mice, cerebral cortex, non-IP, replicate 1

description: Illumina HiSeq


title: RNA-seq, 6-week-old WT mice, cerebral cortex, non-IP, replicate 2

description: Illumina HiSeq


title: DM023

city: New York

first: Donna

last: Farber

department: Department of of Surgical Sciences and Microbiology and Immunology

institute: Columbia University

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming.
We map the reads to a reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm9) using Tophat [1] (version 2.1.0) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). {reference: Trapnell C et al 2009 Bioinformatics}
To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.
We estimate the relative abundance (aka expression level) of genes and splice isoforms using cufflinks [2] (version 2.0.2) with default settings. {reference: Trapnell C et al 2010 Nature Biotech}
We test for differentially expressed genes under various conditions using DEseq [3]. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Genome_build: Human: NCBI/build37.2
Supplementary_files_format_and_content: 1) sampleName.counts_stranded.txt: number of counts for each gene (counts file can be used in Deseq)

organism: Homo sapiens

source_name: individual 3

growth_protocol: primary cells

extract_protocol:
total RNA was extracted using DNA/RNA all prep kit from QIAGEN, sent to Columbia Genome center which further processed the RNA by doing poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation.
Illumina TruSeq RNA prep kit, Libraries are then sequenced using Illumina HiSeq2000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane

value: Lymph nodes

value: T cells

tag: cd69 expression

value: positive

tag: donor id number


title: RNA-seq, 6-week-old Fmr1 KO mice, cerebral cortex, non-IP, replicate 2

description: Illumina HiSeq


title: RNA-seq, 6-week-old Fmr1 KO mice, cerebral cortex, m6A-IP, replicate 1

description: Illumina HiSeq


title: RNA-seq, 6-week-old WT mice, cerebral cortex, m6A-IP, replicate 1

description: Illumina HiSeq


title: DM024

source_name: individual 2


title: DM020

value: Bone marrow


title: Lgr5.NWD1Ca.2

description: barcode: CGTACTAG-CTCTCTAT (N702-N502)

value: 3 months old

value: intestine


title: DM019

source_name: individual 1


title: DM012

value: negative


title: DM011


title: DM009


title: DM010


title: DM008


title: DM007


title: 121_Wang_HiC_BWX4152_1mMIPTG_30m

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

description: parS∆9 no a.b., ∆spo0J (remains wt parS at -1˚)::spec, yvbJ::Pspank (optRBS) spo0J(∆parS) (cat), smc (F66Y) loxP-kan-loxP

library_source: genomic

data_processing:
Library strategy: HiC-Seq
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Hi-C, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Bacillus subtilis (PY79) genome was divided into restriction fragments (2398 HindIII fragments). Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genome of Bacillus subtilis (PY79) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Genome_build: NC_022898.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices.
Supplementary_files_format_and_content: header information: 10kb bins of B. subtilis genome
Supplementary_files_format_and_content: column information: 10kb bins of B. subtilis genome
Supplementary_files_format_and_content: normalized Hi-C interaction scores

molecule: genomic DNA

organism: Bacillus subtilis PY79

source_name: Bacillus subtilis PY79

growth_protocol: Bacillus subtilis strains were derived from the prototrophic strain PY79 (Youngman et al 1983, PMID: 6300908). Cells were grown in defined rich medium (CH) (Harwood and Cutting 1990, Molecular Biological Methods for Bacillus) at specified temperature.

extract_protocol:
Hi-C experiments were performed using HindIII according to previous publications (Le et al, 2013, PMID: 24158908; Wang et al 2015, PMID: 26253537).
Standard library construction protocol was used for Illumina Nextseq500 sequencing platform. Illumina Truseq indexes were used.

treatment_protocol:
Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 30 min, fixed by 3% formaldehyde for 30min at room temperature
None

tag: protocol

value: CH, 37C, 1mM IPTG

tag: time point

value: 30 min

value: parSdelta9 no a.b., deltaspo0J (remains wt parS at -1 degree)::spec, yvbJ::Pspank (optRBS) spo0J(deltaparS) (cat), smc (F66Y) loxP-kan-loxP

tag: restriction enzyme

value: HindIII


title: 124_Wang_HiC_BWX4152_1mMIPTG_60m

treatment_protocol:
Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 60 min, fixed by 3% formaldehyde for 30min at room temperature
None

value: 60 min


title: 123_Wang_HiC_BWX4152_1mMIPTG_50m

treatment_protocol:
Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 50 min, fixed by 3% formaldehyde for 30min at room temperature
None

value: 50 min


title: 120_Wang_HiC_BWX4152_1mMIPTG_20m

treatment_protocol:
Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 20 min, fixed by 3% formaldehyde for 30min at room temperature
None

value: 20 min


title: 122_Wang_HiC_BWX4152_1mMIPTG_40m

treatment_protocol:
Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 40 min, fixed by 3% formaldehyde for 30min at room temperature
None

value: 40 min


title: 119_Wang_HiC_BWX4152_0IPTG

treatment_protocol:
Cells were growing in CH medium at 22˚C, fixed by 3% formaldehyde for 30min at room temperature
None

value: CH, 22C, no IPTG


title: DM022


title: 117_Wang_HiC_BWX4149_1mMIPTG_50m

description: parS∆9 no a.b., ∆spo0J (remains wt parS at -1˚)::spec, yvbJ::Pspank (optRBS) spo0J(∆parS) (cat), smc (K12R) loxP-kan-loxP

value: parSdelta9 no a.b., deltaspo0J (remains wt parS at -1 degree)::spec, yvbJ::Pspank (optRBS) spo0J(deltaparS) (cat), smc (K12R) loxP-kan-loxP


title: DM021


title: 118_Wang_HiC_BWX4149_1mMIPTG_60m


title: 116_Wang_HiC_BWX4149_1mMIPTG_40m


title: 113_Wang_HiC_BWX4149_0IPTG


title: 112_Wang_HiC_BWX4078_1mMIPTG_60m

description: parS∆9 no a.b., ∆spo0J (remains wt parS at -1˚)::spec, yvbJ::Pspank (optRBS) spo0J(∆parS) (cat), smc (R57A) loxP-kan-loxP

value: parSdelta9 no a.b., deltaspo0J (remains wt parS at -1 degree)::spec, yvbJ::Pspank (optRBS) spo0J(deltaparS) (cat), smc (R57A) loxP-kan-loxP


title: 111_Wang_HiC_BWX4078_1mMIPTG_50m


title: 107_Wang_HiC_BWX4078_0IPTG


title: 106_Wang_HiC_BWX4077_1mMIPTG_40m

description: parS∆9 no a.b., ∆spo0J (remains wt parS at -1˚)::spec, yvbJ::Pspank (optRBS) spo0J(∆parS) (cat), smc (WT) loxP-kan-loxP

value: parSdelta9 no a.b., deltaspo0J (remains wt parS at -1 degree)::spec, yvbJ::Pspank (optRBS) spo0J(deltaparS) (cat), smc (WT) loxP-kan-loxP


title: 110_Wang_HiC_BWX4078_1mMIPTG_40m


title: 109_Wang_HiC_BWX4078_1mMIPTG_30m


title: 104_Wang_HiC_BWX4077_1mMIPTG_30m


title: 103_Wang_HiC_BWX4077_1mMIPTG_25m

treatment_protocol:
Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 25 min, fixed by 3% formaldehyde for 30min at room temperature
None

value: 25 min


title: 108_Wang_HiC_BWX4078_1mMIPTG_20m


title: 105_Wang_HiC_BWX4077_1mMIPTG_35m

treatment_protocol:
Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 35 min, fixed by 3% formaldehyde for 30min at room temperature
None

value: 35 min


title: Medulla_IBA_rep4

city: Aurora

first: Kent

middle: Augustus

last: Riemondy

state: Colorado

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
21-M153_S25_L003_R1_001

data_processing:
RNA-Seq libraries were trimmed with bcl2fastq (illumina 4000 libraries)  or cutadapt (illumina 2500) to remove illumina adapters. Reads were then aligned with STAR  in two-pass mode against the spetri2 genome supplemented with a custom transcriptome built with all the brain and additionally neonate and testes RNA-Seq libraries. PCR duplicates were marked using picard, and intron junctions were split and trimmed using GATK SplitNTrim. HaplotypeCaller was used to identify variants, followed by base recalibration with variants identified from Haplotype Caller. This process was repeated another two times to establish properly recalibrated quality scores. Variant calls from all samples were merged and filtered to identify variants with a minimum variant allele frequency > 0.05 and < 0.95. Variants were annotated with SNPeff using ensembl85 annotations. For each variant the read count for each allele was enumerated. RNA editing events were called from A-to-G variants with significant (FDR <0.01) variant allele frequencies associated with hibernation state in an ANOVA-like analysis.
Hyperedited reads were identified following the approach described in Porath et al. Nature Communications 2014. Hyperedited sites supported by less than two reads were excluded.
A novel transcriptome assembly was generated using Stringtie and TACO on Hisat2 alignments from brain, testes, and neonatal RNA-Seq libraries. Only genomic contigs of at least 10kbp were used for HISAT2 alignments and generating the transcriptome
Genome_build: spetri2
Supplementary_files_format_and_content: Processed data format and content is described in supplied readme.txt

organism: Ictidomys tridecemlineatus

growth_protocol: Animal housing and sample collection were performed as described previously (Grabek K. et al. eLife 2015).

extract_protocol:
RNA was extracted as described previously (Grabek K. et al. eLife 2015).
Illumina TruSeq mRNA Strand Specific

value: IBA

tag: Sex

value: F

tag: tb at sac'ing

value: Medulla


title: Medulla_Ent_rep5

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
26-M164_S30_L003_R1_001

value: Ent


title: 102_Wang_HiC_BWX4077_1mMIPTG_20m

value: CH, 37C, 1mM IPTG


title: Medulla_IBA_rep5

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
27-M163_S31_L003_R1_001


title: Medulla_SpD_rep4

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
6-M83_S6_L001_R1_001

value: SpD


title: Medulla_SpD_rep1

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
18-M77_S22_L003_R1_001

value: M


title: Medulla_IBA_rep3

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
15-M78_S15_L001_R1_001


title: Medulla_SpD_rep2

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
24-M79_S28_L003_R1_001


title: Medulla_SpD_rep5

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
12-M84_S12_L001_R1_001


title: Medulla_LT_rep5

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
28-M74_S32_L003_R1_001

value: LT


title: Medulla_IBA_rep2

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
9-M70_S9_L001_R1_001


title: Medulla_LT_rep4

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
22-M72_S26_L003_R1_001


title: Medulla_LT_rep2

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
10-M67_S10_L001_R1_001


title: Medulla_LT_rep3

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
16-M68_S20_L003_R1_001


title: 114_Wang_HiC_BWX4149_1mMIPTG_20m

value: HindIII


title: Medulla_Ent_rep4

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
20-M66_S24_L003_R1_001


title: Medulla_LT_rep1

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
4-M65_S4_L001_R1_001


title: Medulla_IBA_rep1

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
3-M69_S3_L001_R1_001


title: Medulla_Ar_rep4

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
19-M58_S23_L003_R1_001

value: Ar


title: Medulla_Ent_rep3

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
14-M62_S14_L001_R1_001


title: Medulla_Ar_rep5

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
25-M61_S29_L003_R1_001


title: 101_Wang_HiC_BWX4077_0IPTG

description: parS∆9 no a.b., ∆spo0J (remains wt parS at -1˚)::spec, yvbJ::Pspank (optRBS) spo0J(∆parS) (cat), smc (WT) loxP-kan-loxP


title: Medulla_Ar_rep3

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
13-M57_S13_L001_R1_001


title: Medulla_Ent_rep1

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
2-M55_S2_L001_R1_001


title: Medulla_Ar_rep1

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
1-M53_S1_L001_R1_001


title: Medulla_SpD_rep3

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
30-M80_S34_L003_R1_001


title: Medulla_Ent_rep2

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
8-M59_S8_L001_R1_001


title: Medulla_Ar_rep2

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
7-M54_S7_L001_R1_001


title: Testes_rep2

description:
processed data file:
transcriptome.gtf
T77O_31_CGATGT_L004_R1_001

source_name: Testes

value: SA

value: testes


title: Medulla_SA_rep5

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
29-M34_S33_L003_R1_001


title: Neonate_tail

description:
processed data file:
transcriptome.gtf
P1_T_35_GTGGCC_L004_R1_001

value: neonate


title: Medulla_SA_rep3

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
17-M32_S21_L003_R1_001


title: Medulla_SA_rep2

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
11-M31_S11_L001_R1_001


title: Neonate_head

description:
processed data file:
transcriptome.gtf
P1_H_33_CAGATC_L004_R1_001


title: Medulla_SA_rep1

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
5-M30_S5_L001_R1_001


title: Hypothalamus_IBA_rep5

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
57-H163_S70_L008_R1_001

value: Hypothalamus


title: Hypothalamus_Ent_rep5

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
56-H164_S69_L008_R1_001


title: Medulla_SA_rep4

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
23-M33_S27_L003_R1_001


title: Neonate_middle

description:
processed data file:
transcriptome.gtf
P1_M_34_CCGTCC_L004_R1_001


title: Forebrain_IBA_rep5

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B163_9_ATGTCA_L001_R1_001

value: Forebrain


title: Forebrain_SpD_rep5

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B84_7_AGTCAA_L001_R1_001


title: Forebrain_SpD_rep4

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B83_1_ACAGTG_L001_R1_001


title: Hypothalamus_SpD_rep4

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
36-H83_S40_L005_R1_001


title: Hypothalamus_SpD_rep3

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
60-H80_S73_L008_R1_001


title: Hypothalamus_SpD_rep2

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
54-H79_S67_L008_R1_001


title: Forebrain_SpD_rep3

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B80_25_ACAGTG_L003_R1_001


title: Hypothalamus_IBA_rep3

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
45-H78_S49_L005_R1_001


title: Forebrain_SpD_rep1

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B77_13_CAGATC_L002_R1_001


title: Hypothalamus_SpD_rep1

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
48-H77_S61_L008_R1_001


title: Forebrain_IBA_rep3

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B78_27_CTTGTA_L003_R1_001


title: Hypothalamus_LT_rep5

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
58-H74_S71_L008_R1_001


title: Forebrain_SpD_rep2

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B79_19_ACTGAT_L002_R1_001


title: Forebrain_LT_rep5

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B74_29_TTAGGC_L003_R1_001


title: Testes_rep1

description:
processed data file:
transcriptome.gtf
T77D_32_TGACCA_L004_R1_001


title: Hypothalamus_LT_rep4

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
52-H72_S65_L008_R1_001


title: Hypothalamus_SpD_rep5

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
42-H84_S46_L005_R1_001


title: Hypothalamus_IBA_rep4

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
51-H153_S64_L008_R1_001


title: Forebrain_IBA_rep1

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B69_15_GTGGCC_L002_R1_001


title: Hypothalamus_IBA_rep1

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
33-H69_S37_L005_R1_001


title: Forebrain_IBA_rep2

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B70_21_ATCACG_L003_R1_001


title: Forebrain_LT_rep4

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B72_23_TAGCTT_L003_R1_001


title: Forebrain_IBA_rep4

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B153_3_CTTGTA_L001_R1_001


title: Hypothalamus_IBA_rep2

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
39-H70_S43_L005_R1_001


title: Forebrain_Ent_rep5

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B66_28_GTGAAA_L003_R1_001


title: Hypothalamus_LT_rep2

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
40-H67_S44_L005_R1_001


title: Hypothalamus_LT_rep3

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
46-H68_S59_L008_R1_001


title: Forebrain_LT_rep2

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B67_11_CGATGT_L002_R1_001


title: Hypothalamus_Ent_rep4

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
50-H66_S63_L008_R1_001


title: Forebrain_LT_rep1

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B65_5_TTAGGC_L001_R1_001


title: Forebrain_Ent_rep3

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B62_16_GTTTCG_L002_R1_001


title: Forebrain_Ent_rep4

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B64_22_ACTTGA_L003_R1_001


title: Hypothalamus_Ar_rep5

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
55-H61_S68_L008_R1_001


title: Hypothalamus_Ent_rep3

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
44-H64_S48_L005_R1_001


title: Forebrain_Ar_rep5

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B61_30_GATCAG_L003_R1_001


title: Forebrain_Ent_rep2

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B59_10_GTCCGC_L001_R1_001


title: Forebrain_Ar_rep4

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B58_24_GGCTAC_L003_R1_001


title: Hypothalamus_Ar_rep4

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
49-H60_S62_L008_R1_001


title: Hypothalamus_Ent_rep2

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
38-H62_S42_L005_R1_001


title: Forebrain_Ent_rep1

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B55_4_GTGAAA_L001_R1_001


title: Forebrain_LT_rep3

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B68_17_CGTACG_L002_R1_001


title: Forebrain_Ar_rep3

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B57_18_GAGTGG_L002_R1_001


title: Forebrain_Ar_rep2

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B54_12_TGACCA_L002_R1_001


title: Hypothalamus_Ar_rep2

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
37-H54_S41_L005_R1_001


title: Hypothalamus_Ar_rep1

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
31-H53_S35_L005_R1_001


title: Hypothalamus_SA_rep4

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
53-H33_S66_L008_R1_001


title: Hypothalamus_Ar_rep3

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
43-H57_S47_L005_R1_001


title: Hypothalamus_SA_rep5

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
59-H34_S72_L008_R1_001


title: Forebrain_SA_rep3

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B32_14_CCGTCC_L002_R1_001


title: Forebrain_Ar_rep1

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B53_6_GATCAG_L001_R1_001


title: Forebrain_SA_rep5

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B34_26_GCCAAT_L003_R1_001


title: Forebrain_SA_rep4

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B33_20_ATTCCT_L002_R1_001


title: Forebrain_SA_rep1

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B30_2_GCCAAT_L001_R1_001


title: Forebrain_SA_rep2

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B31_8_AGTTCC_L001_R1_001


title: Hypothalamus_LT_rep1

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
34-H65_S38_L005_R1_001


title: Hypothalamus_SA_rep3

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
47-H31_S60_L008_R1_001


title: DNase-seq human heart explant 24hr

status: Public on Aug 08 2018

city: Baltimore

first: Dongwon

last: Lee

state: MD

address: 733 N Broadway, MRB 572

department: Institute of Genetic Medicine

institute: Johns Hopkins University School of Medicine

description:
adult_heart_chaklab2_peaks.narrowPeak
adult_heart_chaklab2_treat_pileup.bigWig

data_processing:
First 20 bp of Dnase-seq raw reads were mapped to hg19 with Bowtie, with 2 mismatches allowed and mapping up to 4 sites
Bam files from the same indviduals were combined
Peaks and read density signals were calculated using MACS2 (ver. 2.1.0.20150731) with the parameters “-g hs –nomodel –shift -50 –extsize 100"
To identify all potential open chromatin regions in heart tissues (all_heart_dhs_sumiits.e300.bed), three additional heart DNase-seq data sets were obtained from the ENCODE and the Roadmap Epigenomics projects (GSM1027322, ENCFF000SPN, and ENCFF000SPP)
The mapped reads provided by the consortia were used to call peaks using the same pipeline as described above
The 600 bp regions centered at the identified summits from all five samples were merged using bedtools (v2.24.0) to generate all_heart_dhs_summits.e300.bed
Genome_build: hg19
Supplementary_files_format_and_content: bam; narrowPeak; bed

source_name: heart explant 24hr

extract_protocol:
Cells from the frozen human tissues were processed as previously described in Song & Crawford, 2010 (PMID: 20150147).
DNase-seq libraries were constructed as previously described in Song & Crawford, 2010 (PMID: 20150147)

value: heart left ventricle

value: female

tag: time

value: 24 hrs postmortem

tag: developmental stage

value: adult


title: DNase-seq human heart explant 12hr

source_name: heart explant 12hr

tag: tissue

value: 12 hrs postmortem


title: Hypothalamus_Ent_rep1

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
32-H59_S36_L005_R1_001

value: Ent


title: Hypothalamus_SA_rep2

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
41-H30_S45_L005_R1_001

value: F


title: DNase-seq human heart autopsy 24hr

description:
adult_heart_chaklab1_peaks.narrowPeak
adult_heart_chaklab1_treat_pileup.bigWig

source_name: heart autopsy 24hr


title: DNase-seq human heart autopsy 5hr

source_name: heart autopsy 5hr

value: 5 hrs postmortem


title: SAM24345515 vismo_6d

city: South San Francisco

first: Robert

last: Piskol

state: CA

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: K14Cre-ER; Ptch1fl/fl; p53fl/fl;Lgr5GFP

extract_protocol: Tumour cells were collected in FACS buffer, centrifuged for 8 minutes at 500g, and were lysed in RLT lysis buffer. Total RNA was extracted with the RNeasy Midi kit (Qiagen). The concentration and integrity of RNA samples was determined with the Bioanalyzer RNA 6000 Pico Kit (Agilent).

value: skin

tag: tissue diagnosis

value: Carcinoma Basal Cell

tag: strain/genotype

value: K14Cre-ER; Ptch1fl/fl; p53fl/fl;Lgr5GFP

tag: treatment

value: vismodegib - 6 days


title: SAM24346043 vismo_6d


title: SAM24350083 vismo_14d

value: vismodegib - 14 days


title: SAM24346042 vismo_6d


title: SAM24345517 vismo_6d


title: SAM24345521 vismo_6d


title: SAM24350082 vismo_14d


title: SAM24346044 vismo_6d


title: SAM24345519 vismo_6d


title: SAM24345520 vismo_6d


title: SAM24346045 MCT

value: control


title: SAM24345516 MCT


title: SAM24345518 MCT


title: SAM24345522 MCT


title: SAM24350084 vismo_14d


title: Hypothalamus_SA_rep1

description:
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
35-H29_S39_L005_R1_001

value: SA


title: SAM17865147 LCM BCC ki67+

description: sample_id: SAM17865147

source_name: laser capture micro-dissected (LCM) tumour nests from fresh frozen skin of K14Cre-ER; Ptch1fl/fl; p53fl/fl mice

extract_protocol: Tumour nests were collected in RLT lysis buffer and total RNA was extracted with the RNeasy Micro kit (Qiagen). The concentration and integrity of RNA samples was determined with the NanoDrop 8000 (Thermo Scientific) and the Bioanalyzer RNA 6000 Pico Kit (Agilent), respectively.

value: LCM BCC ki67+

value: K14Cre-ER; Ptch1fl/fl; p53fl/fl; Lgr5GFP

value: Skin

value: Carcinoma Basal Cell Ki67+


title: SAM17865168 LCM BCC ki67+

description: sample_id: SAM17865168


title: SAM17865145 LCM BCC ki67+

description: sample_id: SAM17865145


title: SAM17865157 LCM BCC + vismo

description: sample_id: SAM17865157

value: LCM BCC + vismo

value: Vismodegib


title: SAM17865144 LCM BCC ki67+

description: sample_id: SAM17865144


title: SAM17865155 LCM BCC + vismo

description: sample_id: SAM17865155


title: adult mourin lung GLI2+ stromal cells

city: San Francisco

first: Peng

last: Tien

address: 513 Parnassus Ave, Health Sciences East 1350

department: Department of Pulmonary Medicine

institute: University of California San Francisco

description: single cell RNA sequencing of adult mourin lung GLI2+ stromal cells

data_processing:
Data were processed according to the 10x Cellranger pipeline.
BAM files were generated with v1.1 10X Genomics Cellranger software using default parameters.
Gene-barcode matrices were generated from Cellranger v1.1 using default parameteres.
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger outputs a .mtx file with the gene-barcode matrix. This matrix contains the counts of molecules per cell (UMI/cell) as determined after filtering and counting by Cellranger. The matrix is in market exchange format while the row (gene names) and columns (cell barcodes) are provided as TSV files. File formats are documented in Cellranger software manual.

source_name: adult mourin lung GLI2+ stromal cells

extract_protocol:
Whole lung was dissected from the adult mouse and tracheally perfused with a digestion cocktail of Collagenase Type I (225 U/ml, Thermo Fisher), Dispase (15 U/ml, Thermo Fisher) and Dnase (50 U/ml, Sigma) and removed from the chest. The lung was further diced with razor blades and the mixture was incubated for 45 mins at 37 °C and vortexed intermittently. The mixture was then washed with FACS buffer (2% FBS in DMEM-F12). The mixture was passed through a 70 µm cell strainer and resuspended in RBC lysis buffer, before passing through a 40 µm cell strainer. Cells suspensions were incubated with the appropriate antibodies in FACS buffer for 30 min at 4 °C and washed with FACS buffer. The following antibodies were used at 1:200 for staining: Rat anti-CD45-PE-Cy7 and Rat anti-Epcam-BV421. DAPI (0.2 µg/ml) was used to exclude dead cells. Doublets and dead cells were excluded based on forward scatter, side scatter and DAPI fluorescence. Cells were sorted into FACS buffer. FACS analysis was performed by FACSDiva.
cDNA libraries were prepared for sequencing using standard protocol for the 10x Single Cell instrument.

value: lung

value: adult


title: SAM17865146 LCM BCC ki67+

description: sample_id: SAM17865146


title: SAM17865154 LCM BCC + vismo

description: sample_id: SAM17865154


title: SAM17865153 LCM BCC + vismo

description: sample_id: SAM17865153


title: run1692_lane12_read1_indexN711-S506=Jul25_Cell_46

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

description: Single cell RNA-seq

data_processing:
Raw fastq data was quality trimmed to a minimum Phred score of 20 using trimmomatic.
Reads were then filtered against mouse ribosomal sequences using bowtie2, followed by full genome and transcriptome alignment to mouse reference mm10 using STAR.
Apparent PCR duplicates and unassignable reads were removed using Picard Mark Duplicates.
SNPs for CAST/EiJ mice were obtained from release-1505-GRCm38 from Sanger Institute’s ftp site (ftp://ftp-mouse.sanger.ac.uk/). SNPs with quality score of at least 100, reported by Sanger, were retained for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Allele distributions (*subset.txt files): Only Sanger SNPs with a coverage of at least 30 in at least one sample were included for further analysis. The allele counts are summarized in the allele distribution files (*_subset.txt): each position in the Ig kappan (top section) and lambda (bottom section) loci is listed with its coordinates and V or J segment name, the overall sequencing depth at that position (ACGT bases only), and the percent of B6, CAST, or unassigned alleles. Allele counting was performed using samtools mpileup. When cells do not express these loci, the processed data files will contain no data beyond the header.
Supplementary_files_format_and_content: Summary statistics (*summary.txt files): Summary files for each cell over each V and J segment in the Ig kappa (top section) and lamda (bottom section) loci were compiled giving the sequencing depth, number of heptamer/nonamer motifs found, allelic specificity of the expression, and any splicing observed between that segment and other segments in the same locus. Read counts and splicing instances were obtained using bedtools; motif instances were found by string matches to the motif sequence with wildcards for spacer sequences (regex); allelic expression was determined from all SNPs with coverage of at least 10 on a segment from the allele distribution files.

source_name: Small Pre-B cells

extract_protocol:
B6 X CAST small pre-B cells were FACs sorted for CD19+B220+IgM-CD43low, and used for bulk or single cell sorting and sequencing.
Bulk sorted CD19+B220+IgM-CD43low small pre-B cells were single cell sorted on pre-primed C1 Fluidic Chips. Cells were lysed, RT performed (Clontech SMARTer) and cDNAs transferred to 96 well plates. Libraries were prepared using Nextera XT (Illumina) then tagmented. Pooled libraries were purified with AMPure magnetic separation assayed for quality with Qubit® dsDNA HS (Life Tecnologies) and sequenced (75bp paired).

tag: cell type

value: Small Pre-B cells

tag: strain

value: B6 x CAST F1 hybrid

tag: genotype

value: wildtype


title: run1687_lane12_read1_indexN706-S506=Jul26_Cell_6

description: Single cell RNA-seq


title: run1692_lane12_read1_indexN708-S504=Jul25_Cell_36

description: Single cell RNA-seq


title: run1692_lane12_read1_indexN710-S505=Jul25_Cell_45

description: Single cell RNA-seq


title: run1692_lane12_read1_indexN703-S508=Jul25_Cell_64

description: Single cell RNA-seq


title: run1692_lane12_read1_indexN709-S504=Jul25_Cell_44

description: Single cell RNA-seq


title: run1692_lane12_read1_indexN704-S504=Jul25_Cell_4

description: Single cell RNA-seq


title: run1692_lane12_read1_indexN712-S505=Jul25_Cell_61

description: Single cell RNA-seq


title: run1687_lane12_read1_indexN707-S507=Jul26_Cell_7

description: Single cell RNA-seq


title: run1692_lane12_read1_indexN701-S508=Jul25_Cell_48

description: Single cell RNA-seq


title: run1692_lane12_read1_indexN706-S503=Jul25_Cell_27

description: Single cell RNA-seq


title: run1692_lane12_read1_indexN711-S504=Jul25_Cell_60

description: Single cell RNA-seq


title: run1692_lane12_read1_indexN709-S503=Jul25_Cell_51

description: Single cell RNA-seq


title: run1692_lane12_read1_indexN705-S503=Jul25_Cell_19

description: Single cell RNA-seq


title: run1687_lane12_read1_indexN712-S506=Jul26_Cell_54

description: Single cell RNA-seq


title: run1687_lane12_read1_indexN708-S502=Jul26_Cell_50

description: Single cell RNA-seq


title: run1692_lane12_read1_indexN709-S517=Jul25_Cell_65

description: Single cell RNA-seq


title: run1692_lane12_read1_indexN706-S505=Jul25_Cell_13

description: Single cell RNA-seq


title: SAM17865156 LCM BCC + vismo

description: sample_id: SAM17865156

value: Carcinoma Basal Cell


title: run1687_lane12_read1_indexN707-S502=Jul26_Cell_42

description: Single cell RNA-seq


title: run1687_lane12_read1_indexN706-S517=Jul26_Cell_41

description: Single cell RNA-seq


title: run1687_lane12_read1_indexN708-S504=Jul26_Cell_36

description: Single cell RNA-seq


title: run1687_lane12_read1_indexN703-S503=Jul26_Cell_3

description: Single cell RNA-seq


title: run1687_lane12_read1_indexN710-S504=Jul26_Cell_52

description: Single cell RNA-seq


title: run1687_lane12_read1_indexN706-S502=Jul26_Cell_34

description: Single cell RNA-seq


title: run1687_lane12_read1_indexN701-S507=Jul26_Cell_55

description: Single cell RNA-seq


title: run1687_lane12_read1_indexN703-S502=Jul26_Cell_10

description: Single cell RNA-seq


title: run1687_lane12_read1_indexN702-S502=Jul26_Cell_2

description: Single cell RNA-seq


title: 115_Wang_HiC_BWX4149_1mMIPTG_30m

description: parS∆9 no a.b., ∆spo0J (remains wt parS at -1˚)::spec, yvbJ::Pspank (optRBS) spo0J(∆parS) (cat), smc (K12R) loxP-kan-loxP

value: CH, 37C, 1mM IPTG

value: 30 min

value: parSdelta9 no a.b., deltaspo0J (remains wt parS at -1 degree)::spec, yvbJ::Pspank (optRBS) spo0J(deltaparS) (cat), smc (K12R) loxP-kan-loxP

value: HindIII


title: run1687_lane12_read1_indexN711-S508=Jul26_Cell_32

description: Single cell RNA-seq


title: rna_D3_null1_R2

description: bulk RNA-seq

data_processing:
Raw fastq data was quality trimmed to a minimum Phred score of 20 using trimmomatic.
Reads were then filtered against mouse ribosomal sequences using bowtie2, followed by full genome and transcriptome alignment to mouse reference mm10 using STAR.
Apparent PCR duplicates and unassignable reads were removed using Picard Mark Duplicates.
SNPs for CAST/EiJ mice were obtained from release-1505-GRCm38 from Sanger Institute’s ftp site (ftp://ftp-mouse.sanger.ac.uk/). SNPs with quality score of at least 100, reported by Sanger, were retained for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Allele distributions (*subset.txt files): Only Sanger SNPs with a coverage of at least 30 in at least one sample were included for further analysis. The allele counts are summarized in the allele distribution files (*_subset.txt): each position in the Ig kappan (top section) and lambda (bottom section) loci is listed with its coordinates and V or J segment name, the overall sequencing depth at that position (ACGT bases only), and the percent of B6, CAST, or unassigned alleles. Allele counting was performed using samtools mpileup. When cells do not express these loci, the processed data files will contain no data beyond the header.
Supplementary_files_format_and_content: Summary statistics (*summary.txt files): Summary files for each cell over each V and J segment in the Ig kappa (top section) and lamda (bottom section) loci were compiled giving the sequencing depth, number of heptamer/nonamer motifs found, allelic specificity of the expression, and any splicing observed between that segment and other segments in the same locus. Read counts and splicing instances were obtained using bedtools; motif instances were found by string matches to the motif sequence with wildcards for spacer sequences (regex); allelic expression was determined from all SNPs with coverage of at least 10 on a segment from the allele distribution files.
Supplementary_files_format_and_content: Raw expression count table (bulk D3 null samples): Raw read counts per gene were obtained for all regular RNA-seq (non-single-cell) data using htseq-count. Gene annotations for mm10 from iGenomes were supplemented with the Ig kappa and lambda segments.

source_name: Ccnd3-/- pro-B Rep 1

value: pro-B


title: run1311_lane12_read2_indexN712-S517=Nov19_Cell_41

description: Single cell RNA-seq


title: run1311_lane12_read2_indexN709-S503=Nov19_Cell_59

description: Single cell RNA-seq


title: run1311_lane12_read2_indexN708-S504=Nov19_Cell_36

description: Single cell RNA-seq


title: run1692_lane12_read1_indexN707-S502=Jul25_Cell_42

description: Single cell RNA-seq


title: run1692_lane12_read1_indexN710-S508=Jul25_Cell_24

description: Single cell RNA-seq


title: run1311_lane12_read2_indexN708-S503=Nov19_Cell_51

description: Single cell RNA-seq


title: run1687_lane12_read1_indexN709-S506=Jul26_Cell_30

description: Single cell RNA-seq


title: run1687_lane12_read1_indexN710-S507=Jul26_Cell_31

description: Single cell RNA-seq


title: run1311_lane12_read2_indexN708-S505=Nov19_Cell_29

description: Single cell RNA-seq


title: rna_SpreB_cross

description: bulk RNA-seq

source_name: WT small pre-B cells

value: small pre-B cells


title: run1311_lane12_read2_indexN708-S502=Nov19_Cell_58

description: Single cell RNA-seq


title: rna_D3_null2_R2

description: bulk RNA-seq

source_name: Ccnd3-/- pro-B Rep 2


title: Gli2+RSmoY_2899

data_processing:
FASTQC for  quality control, Cuadapt and Sickle for triming adaptors
reads were aligned and mapped using HISAT and Stringtie
DESeq was use to call differential gene expression, in Rstudio
Genome_build: UCSC mus musculus mm10

source_name: Lung stroma

extract_protocol:
Whole lung was dissected from the adult mouse and tracheally perfused with a digestion cocktail of Collagenase Type I (225 U/ml, Thermo Fisher), Dispase (15 U/ml, Thermo Fisher) and Dnase (50 U/ml, Sigma) and removed from the chest. The lung was further diced with razor blades and the mixture was incubated for 45 mins at 37 ºC and vortexed intermittently. The mixture was then washed with FACS buffer (2% FBS in DMEM-F12). The mixture was passed through a 70 µm cell strainer and resuspended in RBC lysis buffer, before passing through a 40 µm cell strainer. Cells suspensions were incubated with the appropriate antibodies in FACS buffer for 30 min at 4 ºC and washed with FACS buffer. DAPI (0.2 µg/ml) was used to exclude dead cells. Doublets and dead cells were excluded based on forward scatter, side scatter and DAPI fluorescence. YFP+ cells were sorted by endogenous YFP fluorescence. Cells were sorted into FACS buffer. FACS analysis was performed by FACSDiva (BD Biosciences). The RNA was extracted by PicoPure RNA Isolation Kit (Applied Biosystems) from the sorted cells, and the amount and quality of extracted RNA was measured by RNA 6000 Pico Kit (Agilent). The Bulk RNA-seq was done in GENEWIZ.
RNA sequencing library preparation used the NEBNext Ultra RNA Library Prep Kit for Illumina by following manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, mRNA were first enriched with Oligod(T) beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized.  cDNA fragments were end repaired and adenylated at 3’ends,and universal adapter was ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative  PCR (Applied Biosystems, Carlsbad, CA, USA).
The sequencing libraries were multiplexed and clustered on one lane of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument according to manufacturer’s instructions.  The samples were sequenced using a 2x150 Paired End (PE) configuration.  Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.

treatment_protocol: Tamoxifen (Sigma) was dissolved in corn oil and administered intraperitoneally at 200mg/kg per day x 5 days for activating hedgehog signaling in the GLI2+ stromal cells of the Gli2creERT2-tdt:R26RYFP/SmoM2 murine lung.

value: administered intraperitoneally with tamoxifen for labelling the Hh-activated GLI2+ cells


title: run1687_lane12_read1_indexN704-S503=Jul26_Cell_11

description: Single cell RNA-seq


title: run1311_lane12_read2_indexN710-S508=Nov19_Cell_24

description: Single cell RNA-seq


title: Gli2+RSmoY_2896


title: run1311_lane12_read2_indexN712-S506=Nov19_Cell_62

description: Single cell RNA-seq


title: run1311_lane12_read2_indexN710-S504=Nov19_Cell_60

description: Single cell RNA-seq


title: run1687_lane12_read1_indexN704-S502=Jul26_Cell_18

description: Single cell RNA-seq


title: Gli2+RSmoY_88


title: run1311_lane12_read2_indexN709-S506=Nov19_Cell_30

description: Single cell RNA-seq


title: Gli2+RSmoY_2888


title: Gli2+RY_89

value: control


title: Gli2+RY_2754


title: Gli2+RY_2893


title: run1311_lane12_read2_indexN705-S506=Nov19_Cell_46

description: Single cell RNA-seq


title: run1311_lane12_read2_indexN705-S517=Nov19_Cell_33

description: Single cell RNA-seq


title: run1311_lane12_read2_indexN706-S503=Nov19_Cell_27

description: Single cell RNA-seq


title: run1311_lane12_read2_indexN701-S502=Nov19_Cell_42

description: Single cell RNA-seq


title: run1289_lane12_read2_indexN709-S506=Nov18_Cell_30

description: Single cell RNA-seq


title: Gli2+RY_90


title: run1289_lane12_read2_indexN711-S508=Nov18_Cell_32

description: Single cell RNA-seq


title: run1289_lane12_read2_indexN711-S503=Nov18_Cell_75

description: Single cell RNA-seq


title: run1289_lane12_read2_indexN709-S517=Nov18_Cell_73

description: Single cell RNA-seq


title: run1289_lane12_read2_indexN709-S505=Nov18_Cell_37

description: Single cell RNA-seq


title: run1289_lane12_read2_indexN709-S504=Nov18_Cell_52

description: Single cell RNA-seq


title: run1289_lane12_read2_indexN707-S505=Nov18_Cell_21

description: Single cell RNA-seq


title: run1289_lane12_read2_indexN707-S507=Nov18_Cell_7

description: Single cell RNA-seq


title: run1289_lane12_read2_indexN706-S506=Nov18_Cell_6

description: Single cell RNA-seq


title: run1289_lane12_read2_indexN707-S517=Nov18_Cell_57

description: Single cell RNA-seq


title: run1289_lane12_read2_indexN711-S507=Nov18_Cell_39

description: Single cell RNA-seq


title: run1289_lane12_read2_indexN705-S503=Nov18_Cell_19

description: Single cell RNA-seq


title: run1289_lane12_read2_indexN704-S505=Nov18_Cell_45

description: Single cell RNA-seq


title: run1289_lane12_read2_indexN704-S504=Nov18_Cell_4

description: Single cell RNA-seq


title: run1289_lane12_read2_indexN704-S502=Nov18_Cell_18

description: Single cell RNA-seq


title: run1311_lane12_read2_indexN705-S505=Nov19_Cell_5

description: Single cell RNA-seq


title: run1289_lane12_read2_indexN702-S508=Nov18_Cell_64

description: Single cell RNA-seq


title: run1289_lane12_read2_indexN703-S504=Nov18_Cell_44

description: Single cell RNA-seq


title: bpc1,2,3,4,6 BA rep3

city: Chapel Hill

first: Carly

middle: Michelle

last: Shanks

state: NC

address: Genome Sciences Building, Room 4163

institute: UNC Chapel Hill

description:
BPC-bpcBAresponse.edgeR_de_total.txt
RPKM-BPC.txt
Bpc-BA-rep3

data_processing:
The sequencing data was first checked for quality control using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Sequences were aligned to the Arabidopsis Col-0 genome assembly (TAIR10) with TopHat version 2.0.11 and Bowtie version 1.1.0
SAMtools version 0.1.18 was used to create the BAM files and 87-95% of the reads mapped to the TAIR10 genome
FeatureCounts was used to map the number of single-mapped reads that overlap with the annotated genes
The counts files were used as inputs for EdgeR version 3.0. The false discovery rate for differentially expressed genes was set to 5% using the Benjamini and Hochberg method
Genome_build: TAIR10
Supplementary_files_format_and_content: The results files contain the LogFC for the differentially expressed genes for WT compared to the bpc1,2,3,4,6 mutant and WT and bpc1,2,3,4,6 mutants treated with cytokinin for every gene in the Arabidopsis genome. The files were created using EdgeR with the input counts files made using featureCounts. The counts files were normalized with RUV-seq to make consistency between the biological replicates.
Supplementary_files_format_and_content: RPKM-BPC file is the tab-delimited text files include RPKM values for each sample replicates (The RPKM output derived from featureCounts)

organism: Arabidopsis thaliana

source_name: bpc1,2,3,4,6 BA, whole roots

growth_protocol: Arabidospis seedlings were grown vertically on square plates on 1/2 MS media with phytogel at 24 hour light 22 degree celcius.

extract_protocol:
Total RNA was extracted with the Quiagen RNeasy Plus kit, DNAse treated with the TURBO DNA-freeTM kit (Life Technologies), and RNA was cleaned with RNeasy Plus kit (Qiagen)
Libraries were created with the KAPA Stranded mRNA-Seq Kit with KAPA mRNA Capture Beads for Illumina platforms, KAPA Pure Beads, and KAPA Single-Indexed Adapter Kit, Set A (1.5 µM) (Kappa Biosystems)

treatment_protocol: For each treatment of either WT Arabiodpsis (Col-0) or bpc1,2,3,4,6 mutants, 12 whole seedlings were suspended in liquid 1/2 MS media supplemented with 5µM BA (Benzyladenine, synthetic cytokinin) or 0.01% 5N NaOH as a vehicle control for 1 hour with gentle shaking. Seedlings were removed from the liquid and whole root tissue was cut with a razor blade and the tissue was frozen in liquid nitrogen

value: bpc1,2,3,4,6 mutant

value: BA

value: 10 days old

value: seedlings

tag: number of seedlings


title: run1289_lane12_read2_indexN701-S502=Nov18_Cell_42

description: Single cell RNA-seq


title: run1289_lane12_read2_indexN706-S502=Nov18_Cell_34

description: Single cell RNA-seq


title: bpc1,2,3,4,6 NaOH rep3

description:
BPC-wtVSbpc.edgeR_de_total.txt
BPC-bpcBAresponse.edgeR_de_total.txt
RPKM-BPC.txt
Bpc-NaOH-rep3

source_name: bpc1,2,3,4,6 NaOH, whole roots

value: NaOH


title: bpc1,2,3,4,6 BA rep2

description:
BPC-bpcBAresponse.edgeR_de_total.txt
RPKM-BPC.txt
Bpc-BA-rep2


title: WT BA rep2

description:
BPC-wtBAresponse.edgeR_de_total.txt
RPKM-BPC.txt
Col-BA-rep2

source_name: WT BA, whole roots

value: WT


title: WT NaOH rep3

description:
BPC-wtVSbpc.edgeR_de_total.txt
BPC-wtBAresponse.edgeR_de_total.txt
RPKM-BPC.txt
Col-NaOH-rep3

source_name: WT NaOH, whole roots


title: bpc1,2,3,4,6 BA rep1

description:
BPC-bpcBAresponse.edgeR_de_total.txt
RPKM-BPC.txt
Bpc-BA-rep1


title: bpc1,2,3,4,6 NaOH rep2

description:
BPC-wtVSbpc.edgeR_de_total.txt
BPC-bpcBAresponse.edgeR_de_total.txt
RPKM-BPC.txt
Bpc-NaOH-rep2


title: bpc1,2,3,4,6 NaOH rep1

description:
BPC-wtVSbpc.edgeR_de_total.txt
BPC-bpcBAresponse.edgeR_de_total.txt
RPKM-BPC.txt
Bpc-NaOH-rep1


title: WT BA rep3

description:
BPC-wtBAresponse.edgeR_de_total.txt
RPKM-BPC.txt
Col-BA-rep3


title: WT NaOH rep2

description:
BPC-wtVSbpc.edgeR_de_total.txt
BPC-wtBAresponse.edgeR_de_total.txt
RPKM-BPC.txt
Col-NaOH-rep2


title: WT BA rep1

description:
BPC-wtBAresponse.edgeR_de_total.txt
RPKM-BPC.txt
Col-BA-rep1


title: Mx1-Cre, Cbfb+/56M, rep2

city: Bethesda

first: Pu

middle: Paul

last: Liu

address: 49 Convent Dr.

department: TFGB

institute: NHGRI/NIH

description:
LTKI_2
Processed data file: TZ_Chd7_RNAseq_Processed_Counts.txt

data_processing:
The raw data was processed using RTA version 1.18.64 and CASAVA 1.8.2 for base calling.
RNA sequencing raw reads were aligned to the mouse genome reference (GRCm38) and transcript reference (GRCm38.78) using STAR (version 2.4).
RSEM to obtain RNA-seq count and to estimate relative transcript abundance at the gene level from the aligned reads.
DESeq2 was implemented in R to perform differential expression analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: TZ_Chd7_RNAseq_Processed_Counts.txt: Tab-delimited text file includes transcript per million read counts for each sample.

source_name: Bone marrow C-KIT+ cells, Mx1-Cre, Cbfb+/56M

extract_protocol:
Bone marrow cells were extracted from pIpC-treated mice and c-KIT+ cells were selected using Stemcell's EasySep Mouse CD117 positive selection kit. Total RNA was extracted using Qiagen AllPrep kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/variation

tag: genotype/variation

value: Mx1-Cre, Cbfb+/56M

value: Bone marrow

value: C-KIT+


title: Mx1-Cre, Cbfb+/56M, rep1

description:
LTKI_1
Processed data file: TZ_Chd7_RNAseq_Processed_Counts.txt


title: run1289_lane12_read2_indexN705-S506=Nov18_Cell_46

description: Single cell RNA-seq

value: Small Pre-B cells

value: B6 x CAST F1 hybrid

value: wildtype


title: Mx1-Cre, Cbfb+/56M, rep3

description:
LTKI_3
Processed data file: TZ_Chd7_RNAseq_Processed_Counts.txt


title: Chd7f/f, Mx1-Cre, Cbfb+/56M, rep1

description:
LTd_1
Processed data file: TZ_Chd7_RNAseq_Processed_Counts.txt

source_name: Bone marrow C-KIT+ cells, Chd7f/f, Mx1-Cre, Cbfb+/56M

value: Chd7f/f, Mx1-Cre, Cbfb+/56M


title: WT, rep3

description:
LTwt_3
Processed data file: TZ_Chd7_RNAseq_Processed_Counts.txt

source_name: Bone marrow C-KIT+ cells, WT


title: WT, rep1

description:
LTwt_1
Processed data file: TZ_Chd7_RNAseq_Processed_Counts.txt


title: run1289_lane12_read2_indexN701-S517=Nov18_Cell_1

description: Single cell RNA-seq


title: siTRPS1_rep1

status: Public on Aug 07 2018

city: Jena

first: Bjoern

last: von Eyss

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute on Aging

data_processing:
Adapter removal & quality filtering were performed using cutadapt (version 1.12) using the following parameters: cutadapt --discard-trimmed -m 20 -q 10
All data processing steps (quality filtering, alignment, peak calling, IDR) were performed using a publicly available ATAC-Seq pipeline (https://github.com/kundajelab/atac_dnase_pipelines).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *bw: Normalized (per million reads) bigWig files were generated using the pipelines' MACS2 output.

growth_protocol: T47D cells were cultured in DMEM (+GlutaMAX, Thermo Scientific) supplemented with 10% FBS (Sigma) and 1% penicillin-streptomycin (Sigma) and 1 µl/ml human insulin solution (Sigma).

extract_protocol:
50,000 cells were used per reaction. Nuclei were isolated after resuspension and centrifugation in Lysis buffer (10 mM Tris.Cl, pH 7.4, 10 mM NaCl, 3 mMMgCl2, 1% (v/v) Igepal CA-630. The 50 µl transposase reaction with isolated nuclei (plus 25 µl TD, 2.5 µl TDE1 and 22.5µl H2O) was incubated at 37°C for 30 min. DNA was purified using a MinElutePCR purification column (Qiagen).
The transposed DNA fragments were preamplified by a first PCR reaction with 5 cycles containing barcoded Nextera PCR primers. The optimal number of cycles was determined by a SybrGreen qPCR reaction containing a 5 µl aliquot from the first PCR. The second PCR was then carried out with 8 cycles and the libraries were first purified by MinElutePCR purification column (Qiagen) and then further size-selected by AMPure XP beads to obtain libraries with a size distribution between 150-1000 base pairs.

treatment_protocol: To investigate chromatin changes after TRPS1 depletion, TRPS1 was depleted in T47D breast cancer cells using 20 nM siRNAs targeting TRPS1 (Dharmacon, SmartPool) or a non-targeting control (20 nM) from the same company.

tag: cell line

value: breast cancer cell line

tag: construct/sirna

tag: induction by

tag: replicate


title: siTRPS1_rep2


title: siCtrl_rep2

value: siCtrl


title: WT NaOH rep1

description:
BPC-wtVSbpc.edgeR_de_total.txt
BPC-wtBAresponse.edgeR_de_total.txt
RPKM-BPC.txt
Col-NaOH-rep1


title: Chd7f/f, Mx1-Cre, Cbfb+/56M, rep3

description:
LTd_3
Processed data file: TZ_Chd7_RNAseq_Processed_Counts.txt


title: 3T3-Dppa4-2

city: Sacramento

first: Paul

last: Knoepfler

address: 2425 Stockton Blvd, Room 633

department: Cell Biology and Human Anatomy

institute: University of California Davis

description: ChIP sample

data_processing:
Bases were called with Casava 1.8 (bcl2fastq 1.8)
Reads were aligned to the mouse genome (mm9) using BWA Version 0.7.13-r1126
Files were converted to .BAM using Samtools Version 1.3
Peaks were called using MACS Version 1.4.2, with the input sample used as the background control
Genome_build: mm9
Supplementary_files_format_and_content: BED files, with chromosome and coordinates for each significant peak

source_name: 3T3 cells

growth_protocol: 3T3 cells were cultured in DMEM supplemented with 10% FBS and 1% Glutamine. E14 cells were cultured under feeder-free conditions in 2i media with 2% FBS on gelatin-coated plates. P19 cells were cultured in DMEM supplemented with 10% FBS and 1% Glutamine.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with the DPPA4 antibody (R&D systems AF3730).
Libraries were prepared with the Nextera library prep kit

value: 3T3 cells ectopically expressing Dppa4


title: P19-Dppa4-2

description: ChIP sample

source_name: P19 cells

value: embryonic carcinoma cells


title: E14 Input

description: Input control

source_name: E14 cells

value: embryonic stem cells


title: E14-Dppa4-1

description: ChIP sample


title: 3T3-Dppa4-1

description: ChIP sample


title: P19-Dppa4-1

description: ChIP sample


title: NOK_siPAX9_B

first: Maria

middle: Irene

last: Morasso

state: Maryland

address: Bldg 50

institute: NIAMS NIH

data_processing:
Demultiplex and Convert to FastQ: CASAVA 1.8.2
Map to hg19 transcriptome: tophat 2.1.0
Calculate RPKM: Partek GS 6.6
Genome_build: hg19
Supplementary_files_format_and_content: Excel format, containing gene level RPKM values

extract_protocol:
RNA was harvested 48hs after siRNA transfection or viral transduction and sequencing was performed using Illumina.
cDNA library preparation for RNA-seq analysis was performed on samples using the Mondrian SP kit (Illumina, San Diego, CA). Sequencing was performed using the Illumina HiSeq 2000.

treatment_protocol: All cells were cultured at 37°C in the presence of 5% CO2. NOK culture was performed as described. HEK were from LONZA. NOK cells were maintained in defined keratinocyte serum free media (KSFM) (GIBCO) supplemented with antibiotics. HEK cells where cultured in KGM-Gold™ Keratinocyte Growth Medium (LONZA). For siRNA experiments, primary cells were transfected with the corresponding siRNAs next day after plating and imaged/harvested as indicated. siRNA was transfected at a concentration of 8 pmol cm-2 using HiPerfect transfection reagent (QIAGEN) according to manufacturer’s instructions. siRNAs were from GE Dharmacon siGENOME SMARTpool for human PAX9 M-012242-01-0005, PITX1 M-017246-01-0005, PITX2 M-017315-02-0005, SOX2 M-011778-00-0005 and non-targeting control siRNA D-001206-13. For adenoviral transduction, cells where incubated with MOI 10 adeno-GFP (control), adeno-h-SOX2 (NM_003106) and adeno-h-PITX1 (Genbank RefSeq: BC009412.1) for 24 hs. Adenoviruses were from Vector Biolabs.

value: NOK

value: Human normal oral keratinocytes

tag: transfected with


title: 3T3-Input

description: Input control


title: NOK_siPAX9_C


title: WT, rep2

description:
LTwt_2
Processed data file: TZ_Chd7_RNAseq_Processed_Counts.txt


title: NOK_siPITX2_B


title: NOK_siPITX2_C


title: Chd7f/f, Mx1-Cre, Cbfb+/56M, rep2

description:
LTd_2
Processed data file: TZ_Chd7_RNAseq_Processed_Counts.txt


title: siCtrl_rep1


title: P19 Input

description: Input control


title: NOK_siPAX9_A


title: NOK_siPITX1_C


title: NOK_siPITX2_A


title: NOK_siPITX1_B


title: NOK_siPITX1_A


title: NOK_siSOX2_B


title: NOK_siSOX2_C


title: NOK_siCON_C

value: siCON


title: NOK_siSOX2_A


title: NOK_siCON_B


title: NOK_siCON_A


title: E14-Dppa4-2

description: ChIP sample


title: HEK_adSOX2_A

value: HEK

value: Human epidermal keratinocytes


title: HEK_adPitx1_B


title: HEK_adPitx1_A


title: HEK_adSOX2_C


title: igfbp3_tss_wt

data_processing:
Library strategy: 4C-Seq
For 4C-Seq analyses, the publicly available w4CSeq analysis pipeline was used (https://github.com/WGLab/w4CSeq) using default settings.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *bedgraph: Bedgraph files were generated as part of the w4CSeq analysis pipeline.

growth_protocol: MCF7 cells were cultured in DMEM (+GlutaMAX, Thermo Scientific) supplemented with 10% FBS (Sigma) and 1% penicillin-streptomycin (Sigma).

extract_protocol:
3 million MCF7 and TRPS1 KO cells were cross-linked with 1% (v/v) formaldehyde (Sigma) in culture medium for 10 min at room temperature. Cells were lysed in lysis buffer (10 mM Tris-HCl (pH 8.0), 10 mM NaCl) containing 0.5% (v/v) NP-40. Nuclei were digested with 800 U EcoRI (NEB) in Cutsmart buffer (NEB) supplemented with 0.3% SDS and 2% Triton X-100, overnight at 37°C while shaking. The first ligation was carried out with 100 U T4 DNA ligase (Thermo Scientific) at 16°C overnight. After decross-linking and phenol/chloroform extraction, 25 mg of the 3C library was digested with 100 U DpnII in DpnII buffer (NEB) overnight at 37°C while shaking. After a second ligation carried out with 200 U T4 ligase at 16°C overnight, DNA was extracted with phenol/chloroform and purified with the ChIP DNA clean and concentratorTM kit (Zymo Research).
Per PCR (50 µl reaction), 100 ng DNA were used as template to amplify libraries of the IGFBP3 TSS using specific primer (Fw: AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTGAGAAATAAAGTTCCTGCCTTGC ; Rev: CAAGCAGAAGACGGCATACGACTTCCTTGGTCCAAATCCGC) and Phusion hot start II polymerase (Thermo Scientific) as recommended by the manufacturer. PCR reactions were pooled and purified with Agencourt AMPure XP Beads (Beckman Coulter). In total, 1 µg of genomic DNA was amplified in 10 reactions. Equal amounts of specific libraries were combined and sequenced on an Illumina Hiseq 2500 with 75 cycles.

treatment_protocol: To generate TRPS1 KO cells by CRISPR, MCF7 cells were transfected with a pX461 vector (carrying WT Cas9 and not the nickase version) carrying a sgRNA sequence that targets human TRPS1. Transfection was performed using Lipofectamine 3000. Transfected (GFP+) cells were sorted by flow cytometry into a 96-well plate as single cells. The Knockout of TRPS1 was verified by Western Blot and Sanger Sequencing.

value: WT


title: wtHTT-IN3

city: Lund

first: Per

last: Brattas

address: Sölvegatan 17

country: Sweden

institute: Lund University

description: Striatal tissue collected 3 weeks after unilateral injection of AAV-wtHTT

data_processing:
Adaptor sequences were removed using cutadapt
Reads obtained from mouse tissue were mapped to the mouse genome using STAR_2.4.0j (for microRNAs 1 mismatches per 20nt were allowed)
Reads were quantified using the Rsubread package for R using miRbase annotation (miRNAs)
Genome_build: mm10 for mouse tissue
Supplementary_files_format_and_content: txt files containing abundance measurements of miRNA features from miRBase, repeats annotation from repeatMasker. Whitespace separated. Columns: [Geneid- Chr- Start- End- Strand- Length - #reads mapping to feature]

source_name: freshly dissected tissue

growth_protocol: All stereotactic injections into the striatum were performed as described before with minor changes (Malmevik, J. et al. Identification of the miRNA targetome in hippocampal neurons using RIP-seq. Scientific reports 5, 12609 (2015)). All mice were adult C57BL/6 females aged 9 to 10 weeks old at the time of surgery. Injections were unilateral, always on the right side of the brain with a total of 1 µl injected. The injection coordinates were: AP: +0,9 mm; ML: +/-1.8 mm; DV (from dura): -2.7 mm.

extract_protocol:
smallRNA was extracted using the miRNeasy Mini kit from Qiagen
NEBNext Multiplex Small RNA Library Prep Set for Illumina

treatment_protocol: Striatal tissue was harvested 3 weeks after virus injection and immediately lysed for RNA extraction and smallRNA sequencing.

tag: lentiviral mediated overexpression

value: wtHTT


title: wtHTT-RIP1

treatment_protocol: Striatal tissue was harvested 3 weeks after virus injection and immediately lysed for AGO2-RIPseq.


title: wtHTT-RIP2

treatment_protocol: Strital tissue was harvested 3 weeks after virus injection and immediately lysed for AGO2-RIPseq


title: HEK_adSOX2_B


title: wtHTT-RIP3


title: wtHTT-IN2


title: wtHTT-IN1


title: t47d_trps1

data_processing:
FASTQ files were processed (adapter removal, length filter, quality filter) using cutadapt (version 1.12) with the following options: --discard-trimmed -m 25 -q 10
FASTQ files were aligned to hg19 using bowtie2 (version 2.2.9) using the --local option
Peak calling was performed using MACS2 (version 2.1.1) using the following settings: B --nomodel --SPMR -g hs --extsize 147. The resulting normalized (per million reads) bedgraph files were converted to bigWig files using bdg2bw.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *bw: The MACS2-derived normalized (per million reads) bedgraph files were converted to bigWig files using bdg2bw.

growth_protocol: MCF7 and T47D cells were cultured in DMEM (+GlutaMAX, Thermo Scientific) supplemented with 10% FBS (Sigma) and 1% penicillin-streptomycin (Sigma). T47D culture medium was additionally supplemented with 1 µl/ml human insulin solution (Sigma).

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 min at RT. Nuclei were extracted using hypotonic buffer (20 mM Tris, pH 7.4, 2 mM MgCl2, 5% glycerol) and lysed with ChIP lysis buffer (20 mM Tris pH 7.4, 150 mM NaCl, 1% NP40, 0.5% DOC, 0.1% SDS, 1 mM EDTA). Chromatin was sonicated to obtain fragments of 200 bp. Equilibration of beads (Dynabeads, Thermo Scientific) with antibodies (2 μg for ChIP, 10 μg for ChIP-Seq) was performed overnight, following immunoprecipitation of chromatin for 6h. After extensive washing, bound chromatin was eluted using ChIP elution buffer (50 M Tris, pH 8.0, 1 mM EDTA, 1% SDS, 50 mM NaHCO3) and de-crosslinked and RNase A/Proteinase K (Roth) digested over night. DNA was purified by phenol/chloroform extraction and ethanol precipitation.
ChIP-Seq libraries were generated according to the manufacturer’s protocol (NEBNext Ultra II DNA Library Prep Kit for Illumina, NEB) using Dual Index Primers (NEBNext Multiplex Oligos for Illumina, NEB). The number of PCR cycles varied between 9-12 PCR cycles. The optimal PCR cycle number was determined beforehand using a qPCR machine with 10% of the material used for the final amplification.

treatment_protocol: For YAP ChIP, an MCF7 cell line carrying a doxycycline-inducible YAP 5SA allele was used. YAP 5SA was induced by adding 1 µg/ml doxycycline for 18 hours and subsequently subjected to formaldehyde crosslinking. For generating TRPS1 KO cells by CRISPR, MCF7 cells were transfected with a pX461 vector (carrying WT Cas9 and not the nickase version) carrying a sgRNA sequence that targets human TRPS1. Transfection was performed using Lipofectamine 3000. Transfected (GFP+) cells were sorted by flow cytometry into a 96-well plate as single cells. The Knockout of TRPS1 was verified by Western Blot and Sanger Sequencing.

tag: yap 5sa induced

value: No

tag: chip antibody

value: TRPS1 (self-made affinity-purified antibody raised against aa 920-1281)


title: mtHTT-RIP2

description: Striatal tissue collected 3 weeks after unilateral injection of AAV-mtHTT

value: mHTT


title: HEK_adGFP_C

source_name: HEKdGFP

value: adGFP


title: HEK_adPitx1_C