title: ume6DELTA_dCas9_E-ChRP_ALP1_inaccessible_target-mmgRNA

value: Contains gRNA with 3nt mismatch in PAM-distal region to inaccessible portion of ALP1 locus


title: 254706910151_b3 - col0_rep2 vs dgk5.1_rep2

status: Public on Sep 25 2019

type: RNA

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Is the dgk5.1 mutant impaired in its response to flagellin?

hyb_protocol: dgk5.1_rep2 Cy5 / col0_rep2 Cy3 : 20pmol. (Hybridation_CAGE_proto.doc)

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

molecule: total RNA

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, total RNA  .

growth_protocol: seedling - Media: Murashige-Skoog liquid media supplemented with vitamins. Temperature: 22°C Light: 16h light / 8h dark

extract_protocol: dgk5.1_rep2:200mg. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: ecotype

value: columbia

tag: genotype

value: dgk5 mutant

tag: age

value: 15.9day dev.stage (Boyes et al. Plant Cell 2001):boyes:1.03

extract_protocol: col0_rep2:200mg. (Qiagen_RNeasy.pdf)

value: wildtype


title: OCI-Ly1-ID3-sg1-02 [ATAC-seq]

type: SRA

city: Cambridge

first: Candace

last: Patterson

state: MA

address: 75 Ames St

country: USA

institute: The Broad Institute

description:
ID3g1_2
20170705_ID3g1_ATAC_Ad2_11_21_CO4516-2_S11

library_source: genomic

data_processing:
Samples were sequenced on an Illumina NextSeq 500, 35 base pair cycles in paired-end mode. ATAC-seq reads in fastq format were trimmed to remove adapter sequences using skewer v0.2.2.
Trimmed reads were aligned to hg19 using bowtie2 v2.3.3.1 (Langmead and Salzberg, 2012)
Alignments were filtered using samtools v1.9 (Li and Durbin, 2009) to remove duplicate reads and retain only proper pairs with mapping quality greater than 30
Reads mapping to blacklisted regions were removed using samtools v1.9.
Reads were converted to bed format and reads on the forward and reverse strands were shifted +4 and -5 bp respectively.
MACS2 v2.1.1 (Zhang et al., 2008) was used to call peaks
IDR v2.0.4.2 was used to filter enriched regions at an IDR of less than 0.05 to produce high-confidence peak and summit sets. High-confidence summits were expanded to 500bp and a count matrix was generated with Rsubread v1.30.9 (Chen et al., 2016).
This matrix was imported to R and chromVAR (Schep et al., 2017) was used in conjunction with motifs in the JASPAR2018 (10.18129/B9.bioc.JASPAR2018) (Khan et al., 2018) and chromVARmotifs (https://github.com/GreenleafLab/chromVARmotifs) R packages to generate motif-level measures of differential accessibility.
Genome_build: hg19
Supplementary_files_format_and_content: tab-separated values (differential accessibility z−score); bigwig containing 10bp binned Tn5 insertion counts normalized to millions of reads in peaks.

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
ATAC-seq was performed on 50,000 cells as described (Buenrostro et al., 2013).
Transposition reactions were performed for 1 hr at 37° C, followed by purification and sample barcoding by PCR.

tag: cell line

tag: genotype/variation

value: ID3 knocked-out


title: OCI-Ly1-ID3-sg2-01 [ATAC-seq]

description:
ID3g2_1
20170702_ID3g2_ATAC_Ad2_12_23_CO4516_S12


title: ume6DELTA_dCas9_E-ChRP_ALP1_accessible_target-mmgRNA

city: Eugene

first: Jeffrey

middle: N

last: McKnight

state: OR

address: 1229 University of Oregon, 1318 Franklin Blvd, Rm 273 Onyx Bridge

department: Institute of Molecular Biology

institute: University of Oregon

data_processing:
Basecalling was performed by Illumina CASAVA software package
Reads were mapped to S. cerevisiae genome (Saccharomyces_cerevisiae.EF4.65.dna.toplevel.fa) with Bowtie2
Dyads were calculated by taking the midpoint of paired-end reads from fragments between 100 and 200 bp
Data were normalized such that average value at a genomic position was 1.0
Genome_build: Saccharomyces_cerevisia.EF4.65
Supplementary_files_format_and_content: tab-delimited chromosome/position/normalized dyad counts; coverage file (chr, position, count)

organism: Saccharomyces cerevisiae

growth_protocol:
exponentially-growing W303 yeast cells
grown to mid-log

extract_protocol:
cells were crosslinked with 1% formaldehyde for 20 min, spheroplasted, digested with micrococcal nuclease, crosslinks reversed overnight at 65 degrees with proteinase K treatment, phenol-chloroform extracted, RNase-treated, mononucleosome band gel-extracted and CIP-treated
CIP-treated nucleosome-sized DNA footprints were converted to libraries with NuGEN Ovation Ultralow kit

tag: strain background

value: W303 ume6

tag: e-chrp added

tag: spytagged-factor

tag: expression promoter

value: ADH1 (on pRS416)

tag: molecule subtype

value: Nucleosomal DNA

tag: treatment

value: Contains gRNA with 3nt mismatch in PAM-distal region to accessible portion of ALP1 locus


title: ume6DELTA_dCas9_E-ChRP_ALP1_accessible_target-lower_MNase

value: Contains perfect-match gRNA to accessible portion of ALP1 locus


title: OCI-Ly1-ID3-sg1-01 [ATAC-seq]

description:
ID3g1_1
20170702_ID3g1_ATAC_Ad2_11_21_CO4516_S11


title: ume6DELTA_dCas9_E-ChRP_ALP1_inaccessible_target_MNase

value: Contains perfect-match gRNA to inaccessible portion of ALP1 locus


title: ume6DELTA_dCas9_E-ChRP_ALP1_accessible_target-higher_MNase


title: OCI-Ly1-vene-resistant-01 [ATAC-seq]

description:
ABTr_1
20170702_ABTr_ATAC_Ad2_2_3_CO4516_S2

value: OCI-Ly1 resistant to venetoclax


title: Control siRNA anti-H3K27ac antibody

city: Daejeon

first: Chang Gon

last: Kim

address: 291 Daehak-ro

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description:
Control siRNA treated CD8+ T cell
Control siRNA specific peaks.txt

data_processing:
Alignment: Bowtie2 (for RNA-seq)
Assembly: EdgeR (for RNA-seq)
Additional processing: abundance measurement (for RNA-seq)
Mapping: BWA-mem (for ChIP-seq)
Filtering: reads with MAPQ < 10 were removed, PCR duplicates were removed by Picard
Additional processing: ChIP peaks were identified by MACS
Genome_build: hg38, mm9
Supplementary_files_format_and_content: Normal colon 1/2/3, MC38-OVA 1/2/3: raw read counts (.txt)  Control siRNA specific peaks: specific peaks in H3K27ac ChIP-seq in control siRNA-transfected CD8+ T cells

source_name: CD8+ T cells

extract_protocol: H3K27ac was purified with anti-H3K27ac antibody and RNA was extracted from cells using TRIZOL reagent.

tag: harvest time

value: Cells from Homo sapiens

value: Control siRNA transfection


title: OCI-Ly1-parental-01 [ATAC-seq]

description:
Ly1_1
20170702_Ly1_ATAC_Ad2_1_1_CO4516_S1


title: Ume6_E-ChRP_13hr_GAL_MNase

value: W303 WT

value: GAL (integrated at HO locus)

value: 2% galactose added for 13hr


title: 254706910151_b1 - col0_rep1 vs dgk5.1_rep1

hyb_protocol: dgk5.1_rep1 Cy5 / col0_rep1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: dgk5.1_rep1:200mg. (Qiagen_RNeasy.pdf)

value: columbia

extract_protocol: col0_rep1:200mg. (Qiagen_RNeasy.pdf)


title: 254706910151_b4 - dgk5.1_rep2 vs col0_rep2

hyb_protocol: col0_rep2 Cy5 / dgk5.1_rep2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: dgk5 mutant


title: 1092Y-ENDO

city: New York

first: Natalia

last: Teleshova

state: NY

address: 1230 York Avenue

institute: Population Council

description: counts.matrix" column "1092Y.ENDO

library_source: transcriptomic

data_processing:
Input adapter trimming using Cutadapt version 1.9.1 with -a AAAAAAAAAAAAA -a TTTTTTTTTTTTT -a AGATCGGAAGAG -a CTCTTCCGATCT
Aligning the input reads to reference genome using STAR_2.4.2a
Quality assesment on aligned data using FastQC v0.11.5
Quality assesment on aligned data using QualiMap  v.2.2
Count reads on exon level (-f exon) and gene level (default no -f) using featureCounts v1.5.0-p2
Genome_build: Hsapiens/GRCh37
Supplementary_files_format_and_content: .counts summarizing count information of gene presented after aligning samples to the reference genome

source_name: endocervix

extract_protocol:
Tissue RNA was extracted using total RNAase Fibrous Tissue Mini Kit (Qiagen, Valencia, CA). The concentration and purity of the extracted RNA were assessed by the Agilent Bioanalyzer (Agilent, Santa Clara, CA). RNA was labeled and sequenced at the RU Genomics center by using Illumina TruSeq technology (75bp, >30M coverage).
100 ng of total RNA was used to generate RNA-Seq libraries using Illumina TruSeq stranded mRNA LT kit (Cat# RS-122-2101).

treatment_protocol: Tissue from subjects undergoing hysterectomies for non-malignant conditions were stored in RNAlater at -80°C before RNA extraction

tag: tissue

value: mucosa

tag: mestrual phase

value: Secretory


title: 1097D-ENDO [re-analysis]

description:
counts.matrix" column "1097D.ENDO
GSM2671179


title: 1092Y-ECTO

description: counts.matrix" column "1092Y.ECTO

source_name: ectocervix


title: ume6DELTA_dCas9_E-ChRP_noTarget-2_MNase

value: no gRNA


title: ume6_delete_Ume6_E-ChRP_GGSx11_Linker_MNase_rep3

value: W303 ume6

value: possesses flexible GGSx11 linker


title: 1086S-ENDO [re-analysis]

description:
counts.matrix" column "1086S.ENDO
GSM2671177


title: Spycatcher_E-ChRP_Reb1-Spytag_13hrs_RAF_MNase_rep1

value: Nucleosomal DNA

value: 2% raffinose added for 13hr


title: 1076I-ECTO [re-analysis]

description:
counts.matrix" column "1076I.ECTO
GSM2671174


title: Spycatcher_E-ChRP_Reb1-Spytag_13hrs_RAF_MNase_rep2


title: 1063V-ECTO [re-analysis]

description:
counts.matrix" column "1063V.ECTO
GSM2671169


title: 1063V-ENDO [re-analysis]

description:
counts.matrix" column "1063V.ENDO
GSM2671170


title: Spycatcher_E-ChRP_Reb1-Spytag_13hrs_GAL_MNase_rep2


title: Ume6_E-ChRP_13hr_RAF_MNase


title: Spycatcher_E-ChRP_Reb1-Spytag_13hrs_GAL_MNase_rep3


title: Engrailed_E-ChRP_13hrs_RAF_MNase


title: 1060S-ENDO

description: counts.matrix" column "1060S.ENDO


title: Spycatcher_E-ChRP_Reb1-Spytag_13hrs_GAL_MNase_rep1


title: Engrailed_E-ChRP_13hrs_GAL_MNase


title: 1060S-ECTO

description: counts.matrix" column "1060S.ECTO


title: 1076I-ENDO [re-analysis]

description:
counts.matrix" column "1076I.ENDO
GSM2671175


title: Ume6_E-ChRP_Pre-Induction_H3K23ac-2

data_processing:
Basecalling was performed by Illumina CASAVA software package
Reads were mapped to S. cerevisiae genome (Saccharomyces_cerevisiae.EF4.65.dna.toplevel.fa) with Bowtie2
Data were normalized such that average value at a genomic position was 1.0
Only R1 reads were aligned from paired-end reads
Genome_build: Saccharomyces_cerevisia.EF4.65
Supplementary_files_format_and_content: tab-delimited chromosome/position/normalized dyad counts; coverage file (chr, position, count)

extract_protocol:
cells were crosslinked with 1% formaldehyde for 20 min, lysed by bead beating for 4 minutes, chromatin was sheared to ~300bp mean fragment length using Bioruptor high setting, ChIP was performed, crosslinks were reversed, protein was digested, RNA was degraded, DNA was recovered by Qiagen PCR Purification
Libraries were made with NuGEN Ovation Ultralow kit

value: W303, Ume6-FLAG

value: GAL (integrated at HO)

tag: chip antibody

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat#

tag: chip antibody lot#

value: treated with 2% raffinose 13hr


title: Ume6_E-ChRP_Post-Induction_H3K23ac-1

value: treated with 2% galactose 13hr


title: 1084Q-ECTO

description: counts.matrix" column "1084Q.ECTO

value: Proliferative


title: ume6_delete_Ume6_E-ChRP_2micron_rep1

growth_protocol: grown to mid-log; exponentially-growing W303 yeast cells

value: ADH1 (on pRS416)


title: 1072E-ENDO

description: counts.matrix" column "1072E.ENDO


title: Spycatcher_E-ChRP_Reb1-Spytag_13hrs_RAF_MNase_rep3

value: W303 WT

value: GAL (integrated at HO locus)


title: 1073F-ENDO [re-analysis]

description:
counts.matrix" column "1073F.ENDO
GSM2671173


title: 1089V-ENDO

description: counts.matrix" column "1089V.ENDO


title: ume6_delete_Ume6_D513N_E-ChRP_2micron_rep1

value: Chd1-Ume6 [catalytically-inactive]

value: contains catalytically inactive Chd1 core


title: 1084Q-ENDO

description: counts.matrix" column "1084Q.ENDO

value: mucosa


title: 1062U-ENDO

description: counts.matrix" column "1062U.ENDO

value: Secretory


title: 1072E-ECTO

description: counts.matrix" column "1072E.ECTO


title: Spycatcher_E-ChRP_Reb1-Spytag_Post-Induction_rep3

value: 2% galactose added for 2 hr


title: Spycatcher_E-ChRP_Reb1-Spytag_Post-Induction_rep2


title: 1069B-ENDO

description: counts.matrix" column "1069B.ENDO


title: 1068A-ENDO [re-analysis]

description:
counts.matrix" column "1068A.ENDO
GSM2671172


title: Engrailed_D513N_E-ChRP_rep1

value: Chd1-Engrailed [catalytically-inactive]

value: GPD (on pRS426)


title: 1068A-ECTO [re-analysis]

description:
counts.matrix" column "1068A.ECTO
GSM2671171


title: 1059R-ENDO [re-analysis]

description:
counts.matrix" column "1059R.ENDO
GSM2671168


title: Engrailed_E-ChRP_rep2

value: Nucleosomal DNA


title: Engrailed_E-ChRP_rep3


title: 1077J-ECTO [re-analysis]

description:
counts.matrix" column "1077J.ECTO
GSM2671176


title: Spycatcher_E-ChRP_Ume6-Spytag_Post-Induction_rep2


title: 1059R-ECTO [re-analysis]

description:
counts.matrix" column "1059R.ECTO
GSM2671167


title: 1040Y-ENDO [re-analysis]

description:
counts.matrix" column "1040Y.ENDO
GSM2671164


title: Ume6_E-ChRP_Pre-Induction_H3K23ac-1

value: W303, Ume6-FLAG


title: 1040Y-ECTO [re-analysis]

description:
counts.matrix" column "1040Y.ECTO
GSM2671163


title: shTyr rep2

first: Doowon

last: Huh

state: New York

institute: Rockefeller University

data_processing:
Library strategy: Ribosome profiling
For the ribosome footprinting data, reads were first subjected to linker removal and quality trimming (cutadapt v1.17).
The reads were then distributed among the samples based on their assigned barcodes using fastx_barcode_splitter (using --eol and --mismatches 1).
The reads were then collapsed and UMIs were extracted in two steps (2 at the 5' end and 5 at the 3' end) using UMI Tools.
The reads were then aligned against a reference database of rRNAs and tRNAs as to remove contaminants (using bowtie 2.3.4.1).
STAR was then used to align the remaining reads to the human transcriptome
PCR duplicates were then removed using UMI Tools
Xtail (Xiao et al., 2016) was used to count RPFs, estimate translation efficiency, and perform statistical comparisons
For RNA-seq data analysis, reads were first subjected to quality trimming and adapter removal.
STAR (v2.5.2a) was used to align the reads to the human transcriptome
The number of reads mapping to each gene was counted using htseq-count.
Genome_build: hg38
Supplementary_files_format_and_content: A normalized count table was generated

source_name: MCF10A cells

growth_protocol: MCF10A cells were grown in MCF10A media

extract_protocol:
RNA was extracted using TRIzol
This procedure was conducted as described by (McGlincy and Ingolia, 2017). Briefly, cells were washed and flash frozen with liquid N2 before being lysed with lysis buffer containing cycloheximide (Alfa Aesar). Lysate was digested with RNase I (Lucigen) before ribosomes were isolated through ultracentrifugation through a sucrose cushion. The ribosome pellet was resuspended in a solubilization buffer containing 0.5% SDS and 1mM EDTA and TRIzol before RNA was extracted using the Direct-zol kit (Zymo Research). RNA was separated on a 15% TBE-Urea gel before RNA between 17nt and 34nt were gel extracted. Barcoded pre-adenylated linkers were ligated using T4 RNA ligase 2 truncated K227Q (NEB) and rRNA was depleted using the Ribo-Zero gold kit (Illumina) according to the manufacturer's protocol. RNA was converted to cDNA using SuperScript III (Life Technologies) and the RT product was circularized by CircLigase II (Epicentre). A PCR library was amplified and sequenced using Illumina Nextseq 500.

treatment_protocol: Experimental cells stably express a hairpin against tRNA-Tyr-GUA and control cells express a control hairpin

tag: cell type

tag: barcode

value: TCTAG


title: RPF: All RPF reads for the samples (multiplexed)

description: Multiplexed raw data is submitted for this sample. For demultiplexing RPF reads, refer to McGlincy and Ingolia, Methods, 2017 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5582988/).


title: shTyr rep1

value: TAGAC


title: WT_rep1

source_name: WT


title: Ume6_E-ChRP_Post-Induction_rep3


title: Ume6_E-ChRP_Post-Induction_rep1


title: Ume6_E-ChRP_Post-Induction_rep2


title: shControl rep1

value: GATCA


title: WT_Galactose_rep1


title: shControl rep2

value: GCATA


title: Ume6_E-ChRP_Pre-Induction_rep2


title: Ume6_E-ChRP_Pre-Induction_rep3


title: Ume6_E-ChRP_Pre-Induction_rep1


title: ume6_delete_Ume6_E-ChRP_no_Linker_rep2

value: W303 ume6

value: E-ChRP lacks GGSx11 linker


title: ume6_delete_Ume6_E-ChRP_GGSx11_Linker_rep2

value: ADH1 (on pRS416)


title: Spycatcher_E-ChRP_Ume6-Spytag_Pre-Induction_rep1

value: W303 WT

value: GAL (integrated at HO locus)


title: ume6_delete_Ume6_E-ChRP_GGSx11_Linker_rep1


title: Spycatcher_E-ChRP_Ume6-Spytag_Post-Induction_rep1


title: Ume6_E-ChRP_Post-Induction_H3K23ac-2

value: GAL (integrated at HO)

value: Millipore

value: treated with 2% galactose 13hr


title: Spycatcher_E-ChRP_Reb1-Spytag_Pre-Induction_rep1


title: Engrailed_E-ChRP_rep1


title: Spycatcher_E-ChRP_Reb1-Spytag_Post-Induction_rep1

value: 2% galactose added for 2 hr


title: 051917CD2+GFPred

city: Boston

first: Stephen

last: Gisselbrecht

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics, Department of Medicine

institute: Brigham and Women's Hospital

data_processing:
Reads were filtered for the presence of common primer sequences, indicating that they originated from a barcoded end of a library element, and barcode sequences were extracted. Barcode lookup produced a table of insert read counts per library element per sample. These steps used a custom Perl program, available upon request.
Within each experiment, triplicate low-GFP mesodermal cell readcounts were compared to readcounts from input cell populations (not sorted for GFP status) with the original DESeq package and commands estimateSizeFactors, estimateVarianceFunctions, and nbinomTest.
Genome_build: n/a
Supplementary_files_format_and_content: count tables (reads per library insert barcode in each sorted cell sample)
Supplementary_files_format_and_content: DESeq results from nbinomTest give average corrected abundance is experimental and control conditions, fold change, and raw and adjusted p-values for each library element.

organism: Drosophila melanogaster

source_name: low-GFP mesodermal cells

growth_protocol: Transformant male flies containing random picks from a pool of silencer reporter constructs were crossed to twi:CD2 virgin females in population cages. Embryos were collected for 2.25 hours from pre-layed cages and aged 11 hours at 18°.

extract_protocol:
Total genomic DNA from sorted cells was used as template for nested PCR recovery of barcoded library inserts with common vector primers.
Size-selected amplicons were sheared by sonication, end-repaired, and A-tailed before ligation of Illumina PE adaptors and PCR enrichment.

treatment_protocol: Single-cell suspensions were prepared from dechorionated embryos and stained with Alexa647-anti-rat CD2 (Biorad MCA154A647), then CD2-positive and -negative populations were sorted as controls before low-GFP CD2+ populations were sorted to provide informative pools of silencers.

tag: strain

value: reporter insertion pool crossed to twi:CD2

tag: cell population


title: 051817CD2+GFPred


title: WT_rep2

tag: strain background


title: 051717CD2+GFPred


title: 051717 CD2+

source_name: mesodermal cells


title: 051217CD2+GFPred


title: 051817 CD2+


title: 051917 CD2+


title: 051217 CD2+


title: ume6_delete_Ume6_E-ChRP_no_Linker_rep1

tag: e-chrp added


title: 051017CD2+GFPred


title: Light7-1 total RNA

city: Porto Alegre

first: Felipe

middle: dos Santos

last: Maraschin

state: RS

address: Av. Bento Goncalves 9500, Instituto de Biociencias - Departamento de Botânica - UFRGS, Prédio 43.423, sala 216

department: Botany

country: Brazil

institute: UFRGS

description:
Athaliana_counts_edit.txt
sample name in processed data file:
HXZ-7

data_processing:
The raw reads were filtered before data analysis, the presence of adapters and quality of reads were determined using FastQC software (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Based on these data, the Trim Galore! software (http://www.bioinformatics.babraham.ac.uk/ projects/trim_galore/) was used to eliminate sequences of reads with a quality below 30, as well as the adapters. The cleaned reads were anchored  with TopHat2 (Kim et al., 2013) to the reference genome of Arabidopsis thaliana (http://plants.ensembl.org/Arabidopsis_thaliana/Info/Index). During mapping, zero mismatches and unique mapped reads were allowed. The counting tables of the reads mapped to each gene were generated by the Subread software (Liao et al., 2013)
HiSeq Control Software 2.2.58
RTA 1.18.64.0
CASAVA-1.8.2
Genome_build: TAIR10
Supplementary_files_format_and_content: text file with raw counts

source_name: Light7-1 total RNA

growth_protocol: Seeds were surface sterilized and cold-stratified at 4°C for two days in complete darkness to synchronize germination. Plants were grown on half-strength sucrose-free Murashige and Skoog (Sigma-Aldrich, M5519) media supplemented with 1.5% (w/v) agar and 0.05% (w/v) MES, pH 5.7, on vertically oriented 12-cm-square plates. Seedlings were grown at 21°C ± 2°C under long days photoperiod (16-hour light and 8-hour dark) with white light illumination (130µmol m−2s for the RNA seq analysis in a modified D-Root system (Silva-Navas et al., 2015). For dark grown plants, the plates were completely covered with aluminum foil. Roots of 4 and 7 days-old seedlings were used for RNA isolation.

extract_protocol:
Roots were immeadiately frozen in liquid N2 (two independent biological samples, composed of approximately 70 seedling each) and total RNA was isolated using NucleoSpin® RNA Macherey-Nagel) according to the manufacturer’s instructions. RNA concentrations were verified using the Nanodrop spectrophotometer (Thermo Scientific). Samples with concentrations ranging from 250 ng to 1 µg of RNA were precipitated with 3M NaOAc, 5mg/mL glycogen and ethanol and the pellet was kept in 70% ethanol for shipping.
RNAseq sequencing was performed by Fasteris SA, Switzerland. Library preparation followed RiboZero treatment.

value: primary root

tag: ecotype

tag: light condition

value: shoot-light/root-dark

tag: duration

value: 7 days


title: Light7-2 total RNA

description:
Athaliana_counts_edit.txt
sample name in processed data file:
HXZ-8

source_name: Light7-2 total RNA


title: Light4-2 total RNA

description:
Athaliana_counts_edit.txt
sample name in processed data file:
HXZ-6

source_name: Light4-2 total RNA

value: 4 days


title: 051117 CD2+


title: 051117CD2+GFPred


title: Dark7-2 total RNA

description:
Athaliana_counts_edit.txt
sample name in processed data file:
HXZ-4

source_name: Dark7-2 total RNA

value: shoot-dark/root-dark


title: Spycatcher_E-ChRP_Ume6-Spytag_rep1

tag: spytagged-factor

tag: expression promoter

tag: molecule subtype

value: Nucleosomal DNA


title: Dark7-1 total RNA

description:
Athaliana_counts_edit.txt
sample name in processed data file:
HXZ-3

source_name: Dark7-1 total RNA

tag: tissue


title: Light4-1 total RNA

description:
Athaliana_counts_edit.txt
sample name in processed data file:
HXZ-5

source_name: Light4-1 total RNA


title: Dark4-2 total RNA

description:
Athaliana_counts_edit.txt
sample name in processed data file:
HXZ-2

source_name: Dark4-2 total RNA


title: 10/17 CD2-

source_name: non-mesodermal cells


title: Dark4-1 total RNA

description:
Athaliana_counts_edit.txt
sample name in processed data file:
HXZ-1

source_name: Dark4-1 total RNA


title: 10/17 GFP-CD2+


title: 10/16 CD2-


title: i3CBEs_3CBEdel_sti_iCBE_2_1

first: Frederick

middle: W

last: Alt

address: 1 Blackfan Circle

department: PCMM

institute: Boston Children's Hospital

data_processing:
Library strategy: 3C-HTGTS
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt and bait sequences shorter than 50nt.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files were generated for displaying (Jane et al., 2018)

organism: Mus musculus

source_name: CH12F3 murine lymphoma cells

extract_protocol:
About 10 million cells were crosslinked with 2% formaldehyde for 10 minutes at room temperature and quenched with glycine at a final concentration of 125 mM. Then, the crosslinked cells were lysed in the 3C lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, protease inhibitors) and nuclei were digested with NlaIII enzyme (NEB, R0125) at 37 ℃ overnight.  They were then brought to 16℃, 100U of T4 ligase added  (Promega, M1801) and they incubated again overnight at 16℃.  The ligated products were de-crosslinked with Proteinase K (Roche, #03115852001) at 56 ℃ overnight and the 3C templates were purified by phenol/chloroform.
Libraries were prepared using 3C samples by HTGTS (Jane et al., 2018).

treatment_protocol: Purified B cells were stimulated with either aCD40/IL4 for 48 hrs; CH12F3 cell lines were cultured in lymphocyte medium R15 and stimulated with anti-CD40+IL4+TGF-β for 24 hrs.

value: CH12F3 murine lymphoma cells

tag: genotype

tag: activation

tag: treatment

value: cytokine stimulation

tag: target locus

value: AID-/-; non-coding alele deletion; Ia deletion; three CBE insertion with the convergent orientation as 3'CBE downstream of Cg2a


title: i3CBEs_3CBEdel_sti_iCBE_2_2

tag: cell type


title: i3CBEs_sti_iCBE_2_2


title: 10/16 GFP-CD2+


title: 10/16 CD2+


title: 10/15 CD2-


title: 10/15 CD2+


title: 10/15 GFP-CD2+


title: 10/10 GFP-CD2+


title: i3CBEc-3'CBEsD_1

data_processing:
Library strategy: CSR-HTGTS-Seq
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
We removed potential duplicates by comparing the coordinates of the end of the bait alignment and the start of the prey alignment across all reads. A read will be marked as a duplicate if it has a bait alignment offset within 2nt and a prey alignment offset within 2nt of another read’s bait and prey alignments.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt and bait sequences shorter than 50nt.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

extract_protocol:
DNA was extracted overnight at 56 degree Celcius in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, prior to DNA fragmentation
Translocation libraries were prepared using CSR-HTGTS-Seq (Dong et al., 2015)

treatment_protocol: CH12F3 cell lines were cultured in lymphocyte medium R15 and stimulated with anti-CD40+IL4+TGF-β for 72 hrs.

value: 3'BCEs deletion in three CBEs inserted cells


title: CH12F3NCD_6

value: non-coding IgH Sm-Sa deletion


title: 10/9 CD2+


title: i3CBEc_3

value: three CBEs insertion with the convergent orientation as 3'CBEs in non-coding IgH Sm-Sa deletion cells


title: 10/10 CD2+


title: i3CBEc_1


title: 051017 CD2+


title: i3CBEc-3'CBEsD_2


title: 10/9 CD2-


title: i3CBEc_2


title: CH12F3NCD_4


title: 10/8 CD2-


title: IaD-i3CBEc_3

value: three CBEs insertion downstream of Cg2a in Ia deleted cells


title: 10/10 CD2-


title: 10/8 CD2+


title: i3CBEs_sti_iCBE_2_1


title: CH12F3NCD_5


title: 10/8 GFP-CD2+


title: IaD-i3CBEc_2


title: i3CBEc-3'CBEsD_3


title: IaD_6

value: I-alpha-delta

value: Ia deletion in non-coding IgH Sm-Sa deletion cells


title: IaD_5


title: IaD 1


title: IaD 2


title: IaD-i3CBEc_1


title: 10/9 GFP-CD2+


title: 10/17 CD2+


title: CH12F3NCD 2


title: IaD 3


title: IaD_4


title: CH12F3NCD 1


title: Iadel-i3CBEc_iEm_2-3


title: Iadel_sti_iEm_2-3

value: I-alpha-delta-AID-/-

value: AID-/-; non-coding alele deletion; Ia deletion


title: Iadel_sti_iCBE_2-2


title: OCI-Ly1-vene-resistant-02 [ATAC-seq]

description:
ABTr_2
20170705_ABTr_ATAC_Ad2_2_3_CO4516-2_S2

tag: cell line

tag: genotype/variation

value: OCI-Ly1 resistant to venetoclax


title: ume6_delete_Ume6_E-ChRP_no_Linker_MNase_rep3

value: W303 ume6

value: ADH1 (on pRS416)

value: possesses no flexible linker between Chd1 and Ume6


title: Iadel-i3CBEc_iCBE_2-2


title: Control_fetal_lung_rep9 [mRNA]

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description:
Ctrl_F427
Gene expression data from fetal lung, E18.5, from control mother.

hyb_protocol: According to the Affymetrix expression protocol (HWS kit).

scan_protocol: According to the Affymetrix expression protocol with GeneChip Scanner 3000 7G.

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.3.0.187) including median polish and Sketch-Quantile normalisation.

label: Biotin

source_name: Fetal lung, E18.5, from control mother

label_protocol: Ovation PicoSL WTA System V2 and Encore Biotin Module (Nugen).

growth_protocol: Animals housed under spf conditions.

extract_protocol: miRNeasy (Qiagen).

treatment_protocol: Mice were treated as described in the paper. Briefly, eight-week-old virgin females were mated with each one proven male breeder for 24h. To allow proper implantation of the fertilized oocyte, mice were exposed from gestational day (GD) 2.5 to smoke or filtered air until GD 17.5.

tag: strain/background

value: Balb/c

value: WT

value: fetal lung

tag: age

tag: gender

value: female

value: untreated mother


title: Control_fetal_lung_rep4 [mRNA]

description:
Ctrl_M386
Gene expression data from fetal lung, E18.5, from control mother.

value: male


title: Control_fetal_lung_rep5 [mRNA]

description:
Ctrl_M421
Gene expression data from fetal lung, E18.5, from control mother.


title: Control_fetal_lung_rep8 [mRNA]

description:
Ctrl_F381
Gene expression data from fetal lung, E18.5, from control mother.


title: Control_fetal_lung_rep1 [mRNA]

description:
Ctrl_M141
Gene expression data from fetal lung, E18.5, from control mother.


title: Smoke_fetal_lung_rep11 [mRNA]

description:
Smoke_F444
Gene expression data from fetal lung, E18.5, from mother exposed to smoke during pregnancy.

source_name: Fetal lung, E18.5, from mother exposed to smoke during pregnancy


title: Smoke_fetal_lung_rep12 [mRNA]

description:
Smoke_F445
Gene expression data from fetal lung, E18.5, from mother exposed to smoke during pregnancy.


title: Control_fetal_lung_rep2 [mRNA]

description:
Ctrl_M187
Gene expression data from fetal lung, E18.5, from control mother.


title: Control_fetal_lung_rep3 [mRNA]

description:
Ctrl_M307
Gene expression data from fetal lung, E18.5, from control mother.


title: Control_fetal_lung_rep6 [mRNA]

description:
Ctrl_F181
Gene expression data from fetal lung, E18.5, from control mother.


title: Control_fetal_lung_rep7 [mRNA]

description:
Ctrl_F301
Gene expression data from fetal lung, E18.5, from control mother.


title: i3CBEc_sti_iEm_1-2

value: CH12F3 murine lymphoma cells

value: cytokine stimulation

value: AID-/-; non-coding allele deletion; three CBE insertion with the convergent orientation as 3'CBE downstream of Cg2a


title: CH12F3NCdel_sti_iCBE_1-2

value: AID-/-; non-coding allele deletion


title: CH12F3NCdel_sti_iCBE_1-1


title: i3CBEc_sti_iCBE_1-1

value: AID-/-; non-coding allele deletion; three CBEs insertion with the convergent orientation as 3'CBE downstream of Cg2a


title: CH12F3NCD 3

value: non-coding IgH Sm-Sa deletion


title: CH12F3NCdel_sti_iEm_1-2


title: i3CBEc_sti_iCBE_1-2


title: Smoke_fetal_lung_rep9 [mRNA]

description:
Smoke_F201
Gene expression data from fetal lung, E18.5, from mother exposed to smoke during pregnancy.


title: Splenic_aCD40_IL4_3RR_1

source_name: Splenic mature B cells

value: Splenic mature B cells

value: AID-deficient primary splenic B cells


title: Splenic_aCD40_IL4_3RR_2


title: 20171129 MPRA RNA barcode reads, 8 forskolin, biological replicate 1

city: Los Angeles

first: Jessica

middle: Elizabeth

last: Davis

state: CA

address: 607 Charles E Young Dr E

department: CHEMISTRY AND BIOCHEMISTRY

institute: UCLA

description:
20171129_R8_1_BC
total RNA
MPRA barcode reads used for expression analysis

data_processing:
Library strategy: targeted amplicon sequencing
Variant-barcode mapping reads were merged with BBMerge version 9.00. All bbmerge files are presented here following the different libraries. A custom python script was used to map unique barcodes to variants lacking synthesis errors. Briefly, this script searched the last 150 bp of merged reads for sequences perfectly matching the variants designed. The first 20 bp of each merged read was determined to be a barcode and each barcode was then mapped to the most common sequence associated with it, only retaining barcodes that appeared more than twice in merged reads. In order to differentiate between mapped barcodes that are associated with variants with sequencing errors and another variant in the library, we used a Levenshtein distance cut-off of 13 between variants that share a common barcode. This cut-off represented 1% of the total bootstrapped distances between perfect variants in the library. Barcodes mapped to perfect variants were kept if all other variants associated with a barcode fell below this cut-off. This barcode-mapping output is indicated in uniqueSP2345.txt and barcode_statistics_followup.txt and is used in downstream MPRA expression analysis.
MPRA barcode reads were processed using a custom python script to isolate barcode sequences from reads and determine their total number of reads. Briefly, the first 20 sequences were extracted from each read, reverse complemented to match the barcode format from barcode mapping and then the occurence of each of these barcodes was summed as their total number of reads per indexed sample.
Downstream MPRA expression analysis involves only retaining barcodes present in the barcode mapping tables per library. Then barcodes in the DNA sample per each MPRA (indicated by date) are only retained with greater than 6 reads and. Barcode expression is determined by normalizing reads per RNA sample per condition (indicate with the format R#N in which R stands for RNA, # indicates the forskolin concentration and N indicates the replicate). Variants are only analalyzed if they contain at least 8 barcodes in the DNA sample. For 20171129 the nomenclature follows the biological replicate and then the technical replicate (DNA_1_1_BC are barcode reads for the DNA sample, biological replicate 1, technical replicate 1).
Supplementary_files_format_and_content: Barcode mapping tables consisting of barcodes and their associated variants: barcode_statistics_followup.txt; uniqueSP2345.txt

growth_protocol: DMEM with 1% Penicillin-streptomycin and 10% FBS (Thermo Fisher Scientific)

extract_protocol:
Qiagen RNeasy Midi kit (Qiagen) was used for total RNA extraction. Cells were homogenized by passing the lysate through an 18-gauge needle 10 times and were stored at -80°C. Two days later, lysates were thawed and processed according to the RNeasy Midi Protocol for Isolation of Total RNA from Animal Cells from Qiagen RNeasy Midi/Maxi Handbook (09/2010) (Qiagen) starting at the addition of 1x volume of 70% ethanol to thawed lysates. On-column DNase I digestions were performed with the Qiagen RNase-free DNase Set (Qiagen).
RNA was reverse transcribed using the recommended materials for Superscript IV Reverse Transcriptase (Thermo Fisher Scientific) but with 10 µg total RNA instead of the recommended 5 µg per 20 µL reaction. RNAse A (DNase and protease-free, Thermo Fisher Scientific) was added to each reaction at a final concentration of 100 ng/µL and incubated at 37°C for 30 minutes. Reactions were combined and concentrated using an Amicon Ultra-0.5 mL Centrifugal Filter with a 10 kDa cut-off (Sigma-Aldrich). cDNA was amplified using volumes determined from qPCR for a total of 16 cycles. A second PCR was performed in order to add P5 and P7 illumina flow cell adapter sequences and indices. 0.5 ng cDNA was amplified for a total of 7 cycles. Amplicons were isolated on a 2% TAE gel and bands were confirmed using Agilent’s D1000 ScreenTape and reagents (Agilent) on a 2200 Tapestation system.

treatment_protocol: 2.6 x 106 Hek293T H11 landing pad cells were plated per T75 flask, 6 flasks in total. The next day, the cells were transfected using Lipofectamine 3000 (Thermo Fisher Scientific) along with BxB1 expression vector (Duportet et al., 2014). BxB1 was added to the library mixture at a 1:8 ratio. Cells were passaged after 3 days onto a T875, in which the media was changed to 1 µg/mL puromycin (Life Technologies, Carlsbad, CA) selection media. Cells were passaged at 1:10, 1:20 or at 1:1 as needed during selection every 1-4 days, with 6 passages in total over 16 days of selection. Selected cells were frozen at 5 x 10^6 cells/mL in 5% DMSO (Thermo Fisher Scientific). 2.5 x 10^5 Genomic MPRA library-integrated and selected cells were plated on 2 separate 6-wells, forming the two biological replicates used in the Genomic MPRA. These cells were passaged twice in their expansion, after which cells were frozen at 5 x 10^6 cells/mL in 5% DMSO (Thermo Fisher Scientific). For the Genomic MPRA, 5 aliquots of each replicate, 2.5 x 10^7 cells total, were thawed and grown to cover the initial bottleneck amount 100-fold. 2 days later these cells were trypsinized and plated for stimulation at 3.47 x 10^6 cells per 150 cm plate with 20 mL of media, eight plates total per replicate. Two days later, both replicates were stimulated by adding 20 mL of media with 16 µM forskolin to the 20 mL media already on plates. Cells were stimulated for 3 hours before lysis.

value: H11 BxB1 Landing pad cells


title: 20171129 MPRA RNA barcode reads, 8 forskolin, biological replicate 2

description:
20171129_R8_2_BC
total RNA
MPRA barcode reads used for expression analysis


title: Splenic_aCD40_IL4_3RR_3


title: 20171129 MPRA DNA barcode reads, biological replicate 1, technical replicate 2

description:
20171129_DNA_1_2_BC
genomic DNA
MPRA barcode reads used for expression analysis

extract_protocol:
For genomic DNA isolation, samples were processed according to the Sample Preparation and Lysis Protocol for Cell Cultures from QIAGEN Genomic DNA Handbook (08/2001) using the settings for the Qiagen Blood and Cell Culture DNA Maxi Kit (Qiagen). Pelleted nuclei were frozen at -20°C before G2 buffer was added. Two days later, nuclei were thawed and the remainder of the protocol was followed using Qiagen Protease digestion at 50°C for 60 minutes, and precipitating DNA according to the recommended protocol for vortexing and centrifugation after isopropanol addition followed by washing with cold 70% ethanol.
5 µg gDNA was loaded per 50 µL in a 96-well PCR plate and amplified for 7 cycles, wells were combined and cleaned-up using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA). 0.4x volume of beads were used per sample and after magnetic separation, the supernatant was collected, isolating the amplicons from genomic DNA. Similar as in (Matreyek et al., 2017), 40% of eluted volume was used in a second PCR to add P5 and P7 illumina flow cell adapter sequences and indices and was amplified for 14 cycles. Amplicons were isolated on a 2% TAE gel and bands were confirmed using Agilent’s D1000 ScreenTape and reagents (Agilent) on a 2200 Tapestation system.


title: Splenic_aCD40_IL4_iEm_2


title: Splenic_nonsti_3RR_2


title: Splenic_nonsti_3RR_1


title: 20171129 MPRA DNA barcode reads, biological replicate 2, technical replicate 1

description:
20171129_DNA_2_1_BC
genomic DNA
MPRA barcode reads used for expression analysis


title: 20171129 MPRA DNA barcode reads, biological replicate 2, technical replicate 2

description:
20171129_DNA_2_2_BC
genomic DNA
MPRA barcode reads used for expression analysis


title: Splenic_nonsti_3RR_3


title: 20171129 MPRA DNA barcode reads, biological replicate 1, technical replicate 1

description:
20171129_DNA_1_1_BC
genomic DNA
MPRA barcode reads used for expression analysis


title: Splenic_nonsti_iEm_2


title: 20170320 MPRA RNA barcode reads, 25 forksolin, replicate B

description:
20170320_bc_R25B
total RNA
MPRA barcode reads used for expression analysis

extract_protocol:
Qiagen RNeasy Mini Kits with Qiashredder and on-column DNase I digestions with Qiagen RNase-free DNase Set (Qiagen).
Per sample, RNA was reverse-transcribed using 1.5x the recommended materials for Superscript IV Reverse Transcriptase (Thermo Fisher Scientific. cDNA was amplified with NEBNext Q5 Hot Start HiFi PCR Master Mix (New England Biolabs) using input amounts between samples determined from qPCR for a total of 10 cycles. A second PCR was performed in order to add P5 and P7 Illumina flow cell adapter sequences and indices. 0.5 ng was amplified for a total of 7 cycles. Bands were confirmed using Agilent’s D1000 ScreenTape and reagents (Agilent Technologies) on a 2200 Tapestation system.

treatment_protocol: Two mL of a 1.026 x 105 cells/mL stock of H11 Landing Pad cells were plated per 6-well per biological replicate.  The next day, cells were transfected with libraries using Lipofectamine 3000 (Thermo Fisher Scientific). The next day, 2 mL of media with 2x 25 µM forskolin (Sigma Aldrich) was added to the 2 mL media within each 6-well. Cells were stimulated for 3 hours before lysis.


title: Splenic_nonsti_iEm_1


title: Smoke_fetal_lung_rep10 [mRNA]

description:
Smoke_F202
Gene expression data from fetal lung, E18.5, from mother exposed to smoke during pregnancy.


title: 20170320 MPRA RNA barcode reads, 0 forksolin, replicate B

description:
20170320_bc_R0B
total RNA
MPRA barcode reads used for expression analysis

treatment_protocol: Two mL of a 1.026 x 105 cells/mL stock of H11 Landing Pad cells were plated per 6-well per biological replicate.  The next day, cells were transfected with libraries using Lipofectamine 3000 (Thermo Fisher Scientific). The next day, 2 mL of media with 2x 0 µM forskolin (Sigma Aldrich) was added to the 2 mL media within each 6-well. Cells were stimulated for 3 hours before lysis.


title: Smoke_fetal_lung_rep5 [mRNA]

description:
Smoke_M443
Gene expression data from fetal lung, E18.5, from mother exposed to smoke during pregnancy.


title: Smoke_fetal_lung_rep1 [mRNA]

description:
Smoke_M121
Gene expression data from fetal lung, E18.5, from mother exposed to smoke during pregnancy.


title: Smoke_fetal_lung_rep8 [mRNA]

description:
Smoke_F197
Gene expression data from fetal lung, E18.5, from mother exposed to smoke during pregnancy.


title: Smoke_fetal_lung_rep3 [mRNA]

description:
Smoke_M205
Gene expression data from fetal lung, E18.5, from mother exposed to smoke during pregnancy.


title: Smoke_fetal_lung_rep2 [mRNA]

description:
Smoke_M191
Gene expression data from fetal lung, E18.5, from mother exposed to smoke during pregnancy.


title: Smoke_fetal_lung_rep7 [mRNA]

description:
Smoke_F195
Gene expression data from fetal lung, E18.5, from mother exposed to smoke during pregnancy.


title: Smoke_fetal_lung_rep6 [mRNA]

description:
Smoke_M447
Gene expression data from fetal lung, E18.5, from mother exposed to smoke during pregnancy.


title: CORIN_SUDIPGXIII_C

city: Boston, MA

first: Jamie

last: Anastas

state: United States of America

address: 300 Longwood Ave

department: Newborn Medicine

data_processing:
Sequencing files were selected for quality using Trimgalore v0.4.0 with a minimum length of 35 base pairs and a minimum quality score of 25
Trimmed reads where aligned to hg19 using STAR v2.5.2a
Count tables were generated  on a gene level using featureCounts function in the subread package and  the UCSC hg19 reference gene list.
Genome_build: hg19
Supplementary_files_format_and_content: text file with raw read count

molecule: polyA RNA

source_name: SU-DIPGXIII

growth_protocol: DIPG cells were grown as neurospheres in a glioma stem cell media consisting of a 50:50 mixture of DMEM F12 and Neurobasal A medium containing 20 µg/mL h-EGF, 20 µg/mL FGF-154, B27 without vitamin A, and heparin sulfate, that was supplemented with sodium pyruvate, HEPES buffer, GlutaMAX, and 1x Antibiotic-Antimycotic. Cells were fed every three to four days with fresh media and drugs where indicated and passaged approximately once per week using TrypLE™ Express Enzyme to dissociate spheroids to obtain a single cell suspension.

extract_protocol:
For RNA-seq, total RNA was purified using TRIzol® and then mRNAs were isolated using NEBNext Poly(A) mRNA isolation module (New England Biotechnology, E7490L). mRNAs were fragmented by heating to 95°C for ten minutes in a thermocycler.
Libraries were generated using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biotechnology, E7420L).

treatment_protocol: SU-DIPGXIII cells were treated with  either  0.5 uM of the LSD1 inhibitor, JKD-1-62, the HDAC inhibitor MS-275, the dual LSD1 and HDAC inhibitor, Corin, or the vehicle control, DMSO for one week. Cells were fed with fresh media and compounds every three days.

value: CORIN

value: diffuse intrinsic pontine glioma


title: CORIN_SUDIPGXIII_A


title: CORIN_SUDIPGXIII_B


title: 20170320 MPRA DNA barcode reads

description:
20170320_bc_DNA
plasmid
MPRA barcode reads used for expression analysis

growth_protocol: LB

extract_protocol:
QIAprep (Qiagen, Hilden, Germany) spin miniprep kits
Library plasmids mixed at the same ratio as for transfection were used for DNA normalization in the episomal MPRA. 128 ng of this mixture was amplified for 9 cycles. Amplicons were isolated on a 2% TAE gel, after which they were cleaned-up again. A second PCR was performed in order to add P5 and P7 Illumina flow cell adapter sequences and indices. 0.5 ng was amplified for a total of 7 cycles. Bands were confirmed using Agilent’s D1000 ScreenTape and reagents (Agilent Technologies) on a 2200 Tapestation system.


title: 20170320 MPRA RNA barcode reads, 0 forksolin, replicate A

description:
20170320_bc_R0A
total RNA
MPRA barcode reads used for expression analysis


title: Control_fetal_lung_rep11 [miRNA]

description:
Ctrl_F381
Gene expression data from fetal lung, E18.5, from control mother.

data_processing: RMA probeset summary with standard settings (RMA+DABG) of the Affymetrix Expression Console software (v.1.3.0.187).

label_protocol: FlashTag Biotin HSR kit (Genisphere).

value: Balb/c


title: entinostat_SUDIPGXIII_C

value: entinostat


title: Smoke_fetal_lung_rep4 [mRNA]

description:
Smoke_M207
Gene expression data from fetal lung, E18.5, from mother exposed to smoke during pregnancy.

value: WT

value: fetal lung


title: Control_fetal_lung_rep12 [miRNA]

description:
Ctrl_F427
Gene expression data from fetal lung, E18.5, from control mother.

value: female

value: untreated mother


title: 20170320 MPRA RNA barcode reads, 25 forksolin, replicate A

description:
20170320_bc_R25A
total RNA
MPRA barcode reads used for expression analysis


title: Control_fetal_lung_rep9 [miRNA]

description:
Ctrl_F181
Gene expression data from fetal lung, E18.5, from control mother.


title: K27M-SU-DIPGXIII_K27M

data_processing:
Sequences were aligned to hg19 using Bowtie2
Peaks were called using MACS2 (v2.1). For H3K27ac, H3K27M and H3K27me3 ChIP experiments, peaks were called using the "broad peaks" setting with a cutoff of 0.1. For H3K4me1 ChIP peaks were called using the "narrow peaks" setting with a model, and and cutoff FDR p-value of  0.05.
Bigwigs were generated  by combining the aligned sequences from replicates using the  bamCoverage 2.3.6  function in DeepTools normalizing coverage to 1x, and ignoring duplicates.
Genome_build: hg19

growth_protocol: DIPG cells were grown as neurospheres in a glioma stem cell media consisting of a 50:50 mixture of DMEM F12 and Neurobasal A medium containing 20 µg/mL h-EGF, 20 µg/mL FGF-154,  10 µg/mL PDGFAA, 10 µg/mL PDGFBB, B27 without vitamin A, and heparin sulfate, that was supplemented with sodium pyruvate, HEPES buffer, GlutaMAX, and 1x Antibiotic-Antimycotic. Cells were fed every three to four days with fresh media and drugs where indicated and passaged approximately once per week using TrypLE™ Express Enzyme to dissociate spheroids to obtain a single cell suspension.

extract_protocol:
For H3K27ac, H3K27me3, and H3K4me1 chIP-seq, nuclei were using a hypotonic buffer (25 mM Tris (pH 8.0), 1.5 mM MgCl2, 0.2% NP40, 10 mM KCl). Isolated nuclei were washed in buffer A (0.34 M sucrose, 4 mM MgCl2, 60 mM KCl, 50 mM HEPES (pH 7.4), and digested with micrococcal nuclease I (New England Biotechnology) to obtain mono- and di-nucleosomes. Micrococcal nuclease reactions were stopped by the addition of EGTA to 10 mM, nuclei were then pelleted and chromatin was extracted in 10 mM EDTA. Buffer B (20 mM Tris (pH 8.0), 5 mM EDTA (pH 8), 500 mM NaCl, ) was added to dilute each sample to 100 ng/µl before incubating overnight at 4°C with 5 µg of the following antibodies: H3K27ac (Active Motif, #39135), H3K4me1 (Abcam, ab8895), or H3K27me3 (Millipore, 07-449). Antibody-chromatin complexes were retrieved using Protein G Magnetic Beads (EMD Millipore), followed by extensive washing and elution  in a buffer containing 1% SDS, 50 mM Tris HCl (pH 7.0), and 1 mM EDTA. For H3K27M ChIP-seq 10 million SU-DIPGXIII cells were crosslinked with 1% formaldehyde added directly to the media for 10 minutes at 37°C before quenching with glycine added to acheive a final concentration of 0.11 mM. After pelleting and washing cells in twice with PBS, cells were re-suspended in lysis buffer (50 mM Tris-HCl, 1% SDS, 0.25% sodium deoxycholate) with protease inhibitors added and lysed for 10 minutes on ice. After lysis samples were diluted 1:2.33 with ChIP dilution buffer (50 mM Tris-HCl pH 7.4, 0.01% SDS, 15 0mM NaCl, and 1% Triton-X100)  and then sonicated to 200-3000 base pair fragments. After sonication samples were diluted another 10 fold  in ChIP dilution buffer and H3K27M immunoprecipitation was done overnight using 10 µg of antibody (Millipore, ABE419) followed by retrieval of immunoprecipitated proteins and DNA with protein G beads on a rotator at 4°C for 2 hours. Protein G beads were then washed with 1 mL RIPA wash buffer (0.1% SDS, 0.1% sodium deoxycholate 1% Triton X100, 1 mM EDTA, 10 mM Tris-HCl pH 8.1, 150 mM NaCl), followed by 1 mL RIPA wash buffer with the NaCl concentration increased to 500 mM, and 1 mL LiCl wash buffer (10 mM Tris-HCl, pH 8.1, 250 mM LiCl, 0.5% TritonX-100, 0.5% sodium deoxycholate), and 1 mL of 10 mM Tris-HCl (pH 8.5). ChIP samples were eluted with a solution of 50 mM Tris-HCl (pH 8.0), 0.1% SDS, 150 mM NaCl and 5 mM dithiotreitol (DTT) at 65º C for 1 hour. Eluates were then subjected to treatment RNAse (Roche # 11119915001) at 37°C for 30 minutes followed by treatment with Proteinase K (Sigma# G1508) added to 0.25 mg/mL at 63°C for 3 hours. DNA was then isolated by double sided SPRI bead purification using AMPure XP beads following the manufacturer’s protocol.
Libraries for sequencing were prepared using the NEBNext library preparation kit (New England Biotechnology) and sequenced on an Illumina HiSeq2500 to a length of 50 base pairs except in the case of H3K27M chIP libraries, which were analyzed by paired end sequencing to a length of 40 base pairs.

treatment_protocol: Cells were wither grow  in cancer stem cell growth media or treated with either 0.5 µM Corin, or DMSO for 7 days, adding fresh media and drug at day 3 and day 6.

value: CSC growth media

tag: chip target


title: Control_fetal_lung_rep5 [miRNA]

description:
Ctrl_F257
Gene expression data from fetal lung, E18.5, from control mother.


title: Control_fetal_lung_rep10 [miRNA]

description:
Ctrl_F301
Gene expression data from fetal lung, E18.5, from control mother.


title: entinostat_SUDIPGXIII_B


title: Control_fetal_lung_rep6 [miRNA]

description:
Ctrl_M307
Gene expression data from fetal lung, E18.5, from control mother.

value: male


title: Control_fetal_lung_rep4 [miRNA]

description:
Ctrl_M251
Gene expression data from fetal lung, E18.5, from control mother.


title: entinostat_SUDIPGXIII_A


title: compound7_SUDIPGXIII_C


title: compound7_SUDIPGXIII_A


title: DMSO_SUDIPGXIII_A

value: DMSO


title: input_SUDIPGXIII_CORIN_rep2

data_processing:
Sequences were aligned to hg19 using Bowtie2
Peaks were called using MACS2 (v2.1). For H3K27ac and H3K27me3 ChIP experiments, peaks were called using the "broad peaks" setting with a cutoff of 0.1. For H3K4me1 ChIP peaks were called using the "narrow peaks" setting with a model, and and cutoff FDR p-value of  0.05.
Bigwigs were generated  by combining the aligned sequences from replicates using the  bamCoverage 2.3.6  function in DeepTools normalizing coverage to 1x, smoothing to a length of 50 basepairs, and ignoring duplicates.
Genome_build: hg19
Supplementary_files_format_and_content: bed files with peak coordinates and bigwig files are available on sample records.on sample records.

extract_protocol:
Nuclei were using a hypotonic buffer (25 mM Tris (pH 8.0), 1.5 mM MgCl2, 0.2% NP40, 10 mM KCl). Isolated nuclei were washed in buffer A (0.34 M sucrose, 4 mM MgCl2, 60 mM KCl, 50 mM HEPES (pH 7.4), and digested with micrococcal nuclease I (New England Biotechnology) to obtain mono- and di-nucleosomes. Micrococcal nuclease reactions were stopped by the addition of EGTA to 10 mM, nuclei were then pelleted and chromatin was extracted in 10 mM EDTA. Buffer B (20 mM Tris (pH 8.0), 5 mM EDTA (pH 8), 500 mM NaCl, ) was added to dilute each sample to 100 ng/µl before incubating overnight at 4°C with 5 µg of the following antibodies: H3K27ac (Active Motif, #39135), H3K4me1 (Abcam, ab8895), or H3K27me3 (Millipore, 07-449). Antibody-chromatin complexes were retrieved using Protein G Magnetic Beads (EMD Millipore), followed by extensive washing and elution  in a buffer containing 1% SDS, 50 mM Tris HCl (pH 7.0), and 1 mM EDTA.
Libraries for sequencing were prepared using the NEBNext library preparation kit (New England Biotechnology) and sequenced on an Illumina HiSeq2500 to a length of 50 base pairs.

treatment_protocol: Cells were treated with eithe 0.5 uM Corin, or DMSO for 7 days, adding fresh media and drug at day 3 and day 6.

value: CORIN treated

value: none (input)


title: input_SUDIPGXIII_CORIN_rep1


title: Control_fetal_lung_rep3 [miRNA]

description:
Ctrl_M187
Gene expression data from fetal lung, E18.5, from control mother.


title: Smoke_fetal_lung_rep10 [miRNA]

description:
Smoke_F202
Gene expression data from fetal lung, E18.5, from mother exposed to smoke during pregnancy.


title: Control_fetal_lung_rep8 [miRNA]

description:
Ctrl_M421
Gene expression data from fetal lung, E18.5, from control mother.


title: Control_fetal_lung_rep1 [miRNA]

description:
Ctrl_M141
Gene expression data from fetal lung, E18.5, from control mother.


title: CORIN_SUDIPGXIII_H3K27me3_rep2


title: Smoke_fetal_lung_rep9 [miRNA]

description:
Smoke_F201
Gene expression data from fetal lung, E18.5, from mother exposed to smoke during pregnancy.


title: Smoke_fetal_lung_rep7 [miRNA]

description:
Smoke_F195
Gene expression data from fetal lung, E18.5, from mother exposed to smoke during pregnancy.


title: Control_fetal_lung_rep2 [miRNA]

description:
Ctrl_F146
Gene expression data from fetal lung, E18.5, from control mother.


title: input_SUDIPGXIII_DMSO_rep2

value: DMSO treated


title: Smoke_fetal_lung_rep11 [miRNA]

description:
Smoke_F444
Gene expression data from fetal lung, E18.5, from mother exposed to smoke during pregnancy.


title: input_SUDIPGXIII_DMSO_rep1


title: DMSO_SUDIPGXIII_C


title: Control_fetal_lung_rep7 [miRNA]

description:
Ctrl_M386
Gene expression data from fetal lung, E18.5, from control mother.


title: Smoke_fetal_lung_rep12 [miRNA]

description:
Smoke_F445
Gene expression data from fetal lung, E18.5, from mother exposed to smoke during pregnancy.


title: Smoke_fetal_lung_rep6 [miRNA]

description:
Smoke_M447
Gene expression data from fetal lung, E18.5, from mother exposed to smoke during pregnancy.


title: Smoke_fetal_lung_rep4 [miRNA]

description:
Smoke_M207
Gene expression data from fetal lung, E18.5, from mother exposed to smoke during pregnancy.


title: CORIN_SUDIPGXIII_H3K27me3_rep1


title: compound7_SUDIPGXIII_B


title: DMSO_SUDIPGXIII_B


title: Smoke_fetal_lung_rep2 [miRNA]

description:
Smoke_M191
Gene expression data from fetal lung, E18.5, from mother exposed to smoke during pregnancy.


title: Smoke_fetal_lung_rep8 [miRNA]

description:
Smoke_F197
Gene expression data from fetal lung, E18.5, from mother exposed to smoke during pregnancy.


title: DMSO_SUDIPGXIII_H3K27me3_rep2


title: K27M-SU-DIPGXIII_WCE

value: WCE


title: CORIN_SUDIPGXIII_H3K27ac_rep1


title: CORIN_SUDIPGXIII_H3K27ac_rep2


title: Smoke_fetal_lung_rep5 [miRNA]

description:
Smoke_M443
Gene expression data from fetal lung, E18.5, from mother exposed to smoke during pregnancy.


title: CORIN_SUDIPGXIII_H3K4me1_rep1


title: DMSO_SUDIPGXIII_H3K4me1_rep2


title: CORIN_SUDIPGXIII_H3K4me1_rep2


title: Smoke_fetal_lung_rep3 [miRNA]

description:
Smoke_M205
Gene expression data from fetal lung, E18.5, from mother exposed to smoke during pregnancy.


title: DM-1164

city: Dallas

first: Ronak

last: Lakhia

state: Texas

address: 5323 Harry Hines

institute: UTSW

data_processing:
Strand-specific RNA-Seq libraries were prepared using the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina (n=3 biological replicates for all groups).  After quality check and quantification, libraries were sequenced at the University of Texas Southwestern McDermott Center using a Hiseq2500 Sequencer to generate 51 bp single-end reads.  Before mapping reads were trimmed to remove low-quality regions in the ends.  Trimmed reads were mapped to the mouse genome (mm10) using TopHat version 2.0.12 with the USCS iGenomes GTF file from Ilumina.  Alignments with mapping quality <10 were discarded.  Expression abundance estimation and differential expression gene identification were done using edgeR.  Genes with a P value < 0.05 were considered significantly differentially expressed between the two conditions.
Genome_build: mm10
Supplementary_files_format_and_content: Text file with coutns and differential expression between Pkd2-KO kidneys and PKD2-miR-214 KO kidneys

source_name: Kidney

extract_protocol:
Kidneys were removed, flash frozen on dry ice, and RNA was harvested using Qiazol miRNeasy RNA extraction kit. Illumina TruSeq Stranded Total RNA LT Sample Prep Kit was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Pkhd1Cre; Pkd2 F/F; miR-214null

value: Post-natal day 35


title: DM-952


title: DMSO_SUDIPGXIII_H3K4me1_rep1


title: DMSO_SUDIPGXIII_H3K27ac_rep1


title: SM-868

value: Pkhd1Cre; Pkd2 F/F


title: SM-867


title: DM-864


title: CITiHPCdf2 (II)

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

country: Switzerland

institute: EPFL

data_processing:
tophat --library-type fr-firststrand -p 6 -g 1 --no-novel-juncs --no-novel-indels -G $gtf --transcriptome-index $transcriptome --b2-sensitive -o $localdir $index $reads
Counts of reads on genes were computed using HTseq-count v0.6.1 with default parameters
Counts on Eres were computed using bedtools multicov v2.26.0 (bedtools multicov -split -bams $bam -bed $Eres)
Genome_build: hg19
Supplementary_files_format_and_content: The .txt files contain read counts on genes or endogenous retroelements (EREs)

source_name: day 2 redifferentiation timepoint of CIT_HEP to hepatocyte-like cells

growth_protocol: Human primary hepatocytes were culture in Hepatocyte basal medium (LONZA). Dedifferentiation of primary hepatocytes and iHPC culture was performed in DMEMF12 Ham basal medium 20% FBS supplemented with EGF 10ng/ml, b-FGF 10ng/ml and 3µM CHIR99021. iHPC redifferentiation was performed in hepatocyte basal medium (LONZA) in the presence of 20ng ml-1 Oncostatin M + 1µM Dexamethasone

extract_protocol:
Total RNA from cell lines was isolated using the High Pure RNA Isolation Kit (Roche).
TruSeq stranded RNA sample preparation kit (Illumina).

treatment_protocol: Dedifferentiation of primary hepatocytes was performed by culturing the cells in medium with a cocktail of growth factors and small molecules.

value: iHPC redifferentiation to hepatocyte-like cells

tag: transgenes

value: not applicable

tag: time

value: day 2 after re-differentiation


title: CIT_iHPCp3 (II)

source_name: Citrullinemia induced hepatic progenitor cells passage 3

value: passage 3 induced hepatic progenitor cells

value: day 30 of hepatocyte dedifferentiation, passage 3


title: CNI_iHPCp3 (II)

source_name: Crigler-Najjar induced hepatic progenitor cells passage 3


title: DMSO_SUDIPGXIII_H3K27ac_rep2

value: diffuse intrinsic pontine glioma


title: TSC_RNAseq_KD_control_day3

city: Austin

first: Bum-Kyu

last: Lee

state: TX

address: 2506 Speedway Stop A5000

institute: University of Texas at Austin

description:
RNAseq of control KD in dTSCs (d3)
RNAseq.expression.TPM.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to mouse mm9 genome using bowtie2 for ChIP-seq and ATAC-seq. Salmon was used for mapping reads of RNA-seq.
Peaks of ChIP-seq and ATAC-seq were called using MACS peak caller. Tximport was used for calculating TPM for RNA-seq.
Genome_build: mm9
Supplementary_files_format_and_content: For ChIP-seq and ATAC-seq, tab-delimited text files include information regarding chromosome, peak start, peak end, peak score, and peak center for each peak. For RNA-seq, one tab-delimited text file contains all RNA-seq data. Gene expression was shown as TPM values for each genes.

source_name: Trophoblast stem cells

growth_protocol: Mouse J1 ES cells were cultivated in 0.1% gelatin coated dishes using DMEM (Dulbecco’s modified Eagle’s medium) supplemented with 15% fetal bovine serum (FBS), 2 mM of L-glutamine, 0.1 mM of non-essential amino acid, 1% of nucleoside mix, 0.1 mM of ß-mercaptoethanol, 1000U/ml of recombinant leukemia inhibitory factor and 50 U/ml of Penicillin/Streptomycin. Mouse trophoblast stem cells (TSCs) were maintained in TS cell culture media (mixture of mouse embryonic fibroblast (MEF)-conditioned TS medium with TS basal medium at a ratio of 3:7) supplemented with 25ng/ml Fgf4 and 1ug/ml of heparin. The TS basal medium is composed of RPMI 1640 medium (Gibco) supplemented with 20% FBS, 100 mM β-mercaptoethanol, 2 mM L-glutamine, 1 mM sodium pyruvate, 50 U/mL penicillin/streptomycin.

extract_protocol:
ChIP was performed by cross-linking proteins to DNA using 1% formaldehyde solution in J1 mouse ES cells. Briefly, cells were cross-linked with 1% formaldehyde for 7 min at room temperature, and then formaldehyde was quenched by adding glycine (final 125 mM) for 5 min. After washing cells with PBS two times, fixed cell pellets were resuspended in ChIP dilution buffer and sonicated using a Bioruptor (Diagenode) with a setting of 30 sec on and 1 min off for 10 min (3 times). Sheared chromatins containing average size of 300 bp DNA fragments were used for immunoprecipitation using 10ug of a native antibody against each factor. Immunoprecipitated DNA was sequenced using Illumina sequencers. Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) was performed in in both ESCs and TSCs. Briefly, tagmentation reaction was performed with 50ng of target DNA, and then bPCR-compatible sites and barcode were added into the target DNA by PCR. After cleaning up the PCR products using Zymo DNA clean and concentrator-5 kit, the final product was sequenced using Illumina NextSeq 500 machine. Global gene expression profiles using RNA-seq were performed in both ESCs and TSCs.  Briefly, total RNAs were isolated using the RNeasy plus minikit (Qiagen). mRNAs were enriched from total RNAs, fragmented, and primed. First strand cDNAs were synthesized following by second strand synthesis. The ends of purified double strand cDNAs were repaired, ligated with a barcoded adaptor, and amplified with PCR. Purified final PCR product was sequenced using Illumina NextSeq 500 machine.
ChIP-seq library  was constructed using the NEB ChIP-seq library prep. kit (E6200L ) following by manufacturer’s instructions. ATAC-seq library was constructed using Nextera DNA library prep kit following the manufacturer’s protocol. RNA-seq library was constructed using NEBNext Ultra RNA Library prep kit (NEB, E7530S) according to manufacturer’s instruction
ChIP-Seq, ATAC-seq, and RNA-seq

treatment_protocol: To differentiate TSCs, They were cultivated in TS basal medium without Fgf4 and heparin

value: mouse trophoblast stem cells

tag: strain

value: TS3.5 TS cells


title: Raw264.7_violacein_rep3

city: San Pedro

first: Alfonso

middle: J

last: García-Piñeres

address: Ciudad Universitaria Rodrigo Facio

country: Costa Rica

institute: Universidad de Costa Rica

description: Gene expression data from Raw 264.7 with the treatment of 4 µM violacein  replica 3

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC). Significant cut-off by Fold change, LPE test. Cut-off : in comparison, |fc|≥1.5 & lpe.pval<0.05 probes

label: biotin

source_name: Raw 264.7, violacein treated, rep3

label_protocol: The sense cDNA was  fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: Raw 264.7 cells were seeded into a 24-well plate (1x10^6 live cells/mL per well) and were incubated for 24 h in DMEM medium containing 10 % inactivated FBS, 1 % penicillin and streptomycin in a 5 % CO2 humidified atmosphere at 37 °C

extract_protocol: Total RNA was extracted from  Raw 264.7 cells using RNeasy Mini kit for total RNA isolation (QIAGEN) as per the manufacturer’s instructions

treatment_protocol: The negative controls were treated with fresh medium, while the positive controls were treated with violacein with a final concentration in the well of 4 μmol/L for 4 hours


title: Raw264.7_untreated_rep2

description: Gene expression data from Raw 264.7 without the treatment of violacein replica 2

source_name: Raw 264.7, untreated control rep2


title: Raw264.7_violacein_rep1

description: Gene expression data from Raw 264.7 with the treatment of  4 µM violacein  replica 1

source_name: Raw 264.7, violacein treated, rep1


title: TSC_RNAseq_KD_control_day0

description:
RNAseq of control KD in TSCs (d0)
RNAseq.expression.TPM.txt


title: TSC_RNAseq_KD_Pou3f1_day3

description:
RNAseq of Pou3f1 KD in dTSCs (d3)
RNAseq.expression.TPM.txt


title: Raw264.7_untreated_rep3

description: Gene expression data from Raw 264.7 without the treatment of violacein  replica 3

source_name: Raw 264.7, untreated control rep3


title: CNI_iHPCp1 (II)

source_name: Crigler-Najjar induced hepatic progenitor cells passage 1

value: passage 1 induced hepatic progenitor cells

value: day 20 of hepatocyte dedifferentiation, passage 1


title: Raw264.7_untreated_rep1

description: Gene expression data from Raw 264.7 without the treatment of violacein  replica1

source_name: Raw 264.7, untreated control rep1


title: CIT_iHPCp1 (II)

source_name: Citrullinemia induced hepatic progenitor cells passage 1


title: TSC_RNAseq_KD_Mafk_day3

description:
RNAseq of Mafk KD in dTSCs (d3)
RNAseq.expression.TPM.txt


title: CITiHPCdf5 (II)

source_name: day 5 redifferentiation timepoint of CIT_HEP to hepatocyte-like cells

value: day 5 after re-differentiation


title: TSC_RNAseq_KD_Meis1_day3

description:
RNAseq of Meis1 KD in dTSCs (d3)
RNAseq.expression.TPM.txt


title: SM-871


title: CNI_iHPCd5 (II)

source_name: day 5 de-differentiation timepoint of CNI_HEP to iHPC

value: hepatocyte dedifferentiation

value: day 5 of hepatocyte dedifferentiation


title: CIT_iHPCd8 (II)

source_name: day 8 de-differentiation timepoint of CIT_HEP to iHPC

value: day 8 of hepatocyte dedifferentiation


title: CNI_HEP (II)

source_name: human primary hepatocytes from a Crigler-Najjar metabolic disease donor

value: liver

value: day 0 of hepatocyte dedifferentiation


title: TSC_RNAseq_KD_Hopx_day3

description:
RNAseq of Hopx KD in dTSCs (d3)
RNAseq.expression.TPM.txt


title: OKSM2DFd30 (I)

data_processing:
tophat -p 4 -g 1 --no-novel-juncs --no-novel-indels -G $gtf --transcriptome-index $transcriptome --b2-sensitive $index $reads
Counts of reads on genes were computed using HTseq-count v0.6.1 with default parameters
Counts on Eres were computed using bedtools multicov v2.26.0 (bedtools multicov -split -bams $bam -bed $Eres)
Genome_build: hg19
Supplementary_files_format_and_content: The .txt files contain read counts on genes or endogenous retroelements (EREs)

source_name: Hepatocyte-like cells differentiated from CNI-iPSC clone 2 (day 30 differentiation)

growth_protocol: Human primary hepatocytes were cultured in Hepatocyte basal medium (LONZA). Reprogramming and iPSC culture was performed in mTeSR1 (Stemcell). Differentiation was performed following the protocol described by Si-Tayeb et al. (Hepatology. 2010).

extract_protocol:
Total RNA from cell lines was isolated using the High Pure RNA Isolation Kit (Roche).
TruSeq RNA sample preparation kit (Illumina).

treatment_protocol: Human primary hepatocytes were transduced with a lentiviral vector encoding the 4 classic pluripotency transcription factors OCT4, KLF4, SOX2 and C-MYC (OKSM).

value: hepatocyte-like cells

value: OKSM

value: day 30 of HLC differentiation protocol


title: dTSC_ChIPseq_p300

description: Chromatin IP against p300

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to mouse mm9 genome using bowtie2 for ChIP-seq and ATAC-seq. Tophat2 was used for mapping reads of RNA-seq.
Peaks of ChIP-seq and ATAC-seq were called using MACS peak caller. Cufflinks was used for counting reads in exons for RNA-seq.
Genome_build: mm9
Supplementary_files_format_and_content: For ChIP-seq and ATAC-seq, tab-delimited text files include information regarding chromosome, peak start, peak end, peak score, and peak center for each peak. For RNA-seq, one tab-delimited text file contains all RNA-seq data. Gene expression was shown as log2(FPKM+1) values for each genes.

tag: chip antibody


title: dTSC_ChIPseq_cFos

description: Chromatin IP against cFos

value: cFos


title: CIT_HEP (II)

source_name: human primary hepatocytes from a Citrullinemia metabolic disease donor

value: not applicable


title: OKSM5DFd30 (I)

source_name: Hepatocyte-like cells differentiated from CNI-iPSC clone 5 (day 30 differentiation)


title: dTSC_ChIPseq_Zfpm1

description: Chromatin IP against Zfpm1


title: OKSM2DFd15 (I)

source_name: day 15 differentiation of CNI_iPSC clone 2 to hepatocyte-like cells (HLC)

value: hepatoblasts

value: day 15 of HLC differentiation protocol


title: OKSM5DFd15 (I)

source_name: day 15 differentiation of CNI_iPSC clone 5 to hepatocyte-like cells (HLC)


title: dTSC_ChIPseq_Pcgf5

description: Chromatin IP against Pcgf5

source_name: Trophoblast stem cells

value: mouse trophoblast stem cells


title: dTSC_ChIPseq_Tfap2c

description: Chromatin IP against Tfap2c

value: TS3.5 TS cells


title: dTSC_ChIPseq_Meis1

description: Chromatin IP against Meis1


title: OKSM2DFd0 (I)

source_name: induced pluripotent stem cell clone 2 generated from CNI_HEP p12

value: iPSC passagen 12

value: day 0 of HLC differentiation protocol


title: dTSC_ChIPseq_Foxj2

description: Chromatin IP against Foxj2


title: OKSM2DFd10 (I)

source_name: day 10 differentiation of CNI_iPSC clone 2 to hepatocyte-like cells (HLC)

value: definitive endoderm

value: day 10 of HLC differentiation protocol


title: dTSC_ChIPseq_Ets2

description: Chromatin IP against Ets2


title: OKSM5DFd0 (I)

source_name: induced pluripotent stem cell clone 5 generated from CNI_HEP p30

value: iPSC passage 30


title: REPR_d30 (I)

source_name: day 30 reprogramming timepoint of CNI_HEP to iPSC with OKSM lentiviral vector

value: reprogramming timepoint

value: day 30 after LV-OKSM transduction


title: dTSC_ChIPseq_Hic2

description: Chromatin IP against Hic2


title: dTSC_ChIPseq_Creb3l2

description: Chromatin IP against Creb3l2


title: dTSC_ChIPseq_Bbx

description: Chromatin IP against Bbx

value: Bbx


title: TSC_RNAseq_KD_Maff_day3

description:
RNAseq of Maff KD in dTSCs (d3)
RNAseq.expression.TPM.txt


title: REPR_d10 (I)

source_name: day 10 reprogramming timepoint of CNI_HEP to iPSC with OKSM lentiviral vector

value: day 10 after LV-OKSM transduction


title: 20190705 merged barcode mapping reads follow-up library

description:
bbmerge_assembled_followup
plasmid
Variant-barcode paired reads used for associating barcodes with variants

organism: Escherichia coli

source_name: source: NEB 5-alpha Electrocompetent cells (#C2989K)

extract_protocol:
QIAprep (Qiagen, Hilden, Germany) spin miniprep kits
0.5 ng of plasmid was amplified using primers with P5 and P7 Illumina flow cell adapter sequences for 17 cycles. Amplicons were isolated on a 2% TAE agarose gel and bands were confirmed using Agilent’s D1000 ScreenTape and reagents (Agilent Technologies) on a 2200 Tapestation system.

value: source:NEB 5-alpha Electrocompetent cells (#C2989K)


title: 20160930 merged barcode mapping reads

description:
bbmerge_assembled_3_5
plasmid
Variant-barcode paired reads used for associating barcodes with variants


title: CNI_HEP_2 (I)

source_name: human primary hepatocytes from a Crigler-Najjar metabolic disease donor (technical replicate)

value: liver

value: non-transduced


title: CNI_HEP_1 (I)

value: not applicable


title: CIT_HEP (I)


title: OKSM5DFd10 (I)

source_name: day 10 differentiation of CNI_iPSC clone 5 to hepatocyte-like cells (HLC)

value: OKSM


title: Smoke_fetal_lung_rep1 [miRNA]

description:
Smoke_M121
Gene expression data from fetal lung, E18.5, from mother exposed to smoke during pregnancy.

source_name: Fetal lung, E18.5, from mother exposed to smoke during pregnancy

value: Balb/c

value: WT

value: fetal lung

value: male


title: BMECs-LL RNA-seq

city: Changchun

first: Lixin

last: Xia

state: Jilin

address: No.5333 Xi'an Road,Luyuan District

department: College of Animal Science

country: China

institute: Jilin University

description: all.counts.exp.xlsx

data_processing:
Whole transcriptome libraries preparation and deep sequencing. The sequencing library of each RNA sample was pre- pared by using Ion Total RNA-Seq Kit v2
Raw Data Treatment: Using high-throughput Life technologies Ion Proton Sequencer, the transcript with poly (A)+ RNA of Human were analyzed. Reads sequenced were filtered and mapped to Cattle genome (download from NCBI) using Mapsplice software. The mapped reads was counted to achieve the expression of each gene based on the gene annotation information from NCBI database.
Data Filtering: In order to achieve the best quality of the RNA Sequencing, Novelbio applied the reads filtration to filter the reads with lower quality and short sequence under following criteria: read length > 50; over 30% base quality >13.
Identification of differentially expressed genes :The DE-Seq algorithm was  applied  to  filter  differentially expressed  genes. After  the  significance  analysis  and  FDR  (false discovery  rate)  analysis ,  we  selected  the  differentially expressed  genes  according  to  the FDR threshold set at p < 0.05 and FDR <0.05. And the fold changes of any two groups are more than 2.
All target genes regulated by DERs were predicted by the combination of miRbase (http://www.mirbase.org) and TargetScan (http://www.targetscan.org). All the predicted target genes were intersected with the DEGs obtained by RNA-seq, and then the DEGs and DERs were obtained by a combined analysis.
Genome_build: Btau_5.0.1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ..

organism: Bos taurus

source_name: mammary epithelial cells

growth_protocol: The cattle in both groups were raised under normal similar conditions on a diet of corn and hay with access to feed and water ad libitum.

extract_protocol:
Total RNA from BMECs with high and low milk fat percentages was extracted using TRIzol reagent. Total RNA was further treated with RNase-free DNase I, and RNA longer than 18 nucleotides was recovered. The quality was assessed by the Agilent2200 (Agilent, USA).
The sequencing library of each RNA sample was prepared by using Ion Total RNA-Seq Kit v2

treatment_protocol: The cells were isolated from bovine breast tissue by tissue culture method, and the primary breast epithelial cells were obtained by enzyme digestion.

value: Primary Mammary Epithelial Cells

value: mammary gland

tag: breed

value: Chinese Holstein cows

tag: phenotype

value: high milk fat


title: BMECs-HH RNA-seq

description: all.counts.exp.xlsx

tag: tissue


title: Normal colon 3

description:
Normal colon
Normal colon 3.txt

data_processing:
Alignment: Bowtie2 (for RNA-seq)
Assembly: EdgeR (for RNA-seq)
Additional processing: abundance measurement (for RNA-seq)
Mapping: BWA-mem (for ChIP-seq)
Filtering: reads with MAPQ < 10 were removed, PCR duplicates were removed by Picard
Additional processing: ChIP peaks were identified by MACS
Genome_build: hg38, mm9
Supplementary_files_format_and_content: Normal colon 1/2/3, MC38-OVA 1/2/3: raw read counts (.txt)  Control siRNA specific peaks: specific peaks in H3K27ac ChIP-seq in control siRNA-transfected CD8+ T cells

source_name: Tissue

extract_protocol: H3K27ac was purified with anti-H3K27ac antibody and RNA was extracted from cells using TRIZOL reagent.

tag: harvest time

value: 14 days after implantation

value: No treatment


title: REPR_d18 (I)

source_name: day 18 reprogramming timepoint of CNI_HEP to iPSC with OKSM lentiviral vector

value: reprogramming timepoint

value: day 18 after LV-OKSM transduction


title: Normal colon 2

description:
Normal colon
Normal colon 2.txt

tag: treatment


title: Iadel_sti_4

description: Run-on RNA

data_processing:
Library strategy: GRO-Seq
Reads were aligned using bowtie 2.2.8 with --non-deterministic flag
reads were quantified for specific loci using samtools version 1.8
wig files were produced using RseqQ package
Genome_build: mm9
Supplementary_files_format_and_content: wig files contain peak information for samples

source_name: CH12F3 murine lymphoma cells

extract_protocol:
Briefly, 10 million cells were collected and permeabilized with the buffer (10 mM Tris-HCl pH 7.4, 300 mM sucrose, 10 mM KCl, 5 mM MgCl2, 1 mM EGTA, 0.05% Tween-20, 0.1% NP40 substitute, 0.5 mM DTT, protease inhibitors and Rnase inhibitor). The permeabilized cells were resuspended in 100 ml of storage buffer (10 mM Tris-HCl pH 8.0, 25% (V/V) glycerol, 5 mM MgCl2, 0.1 mM EDTA and 5 mM DTT) for nuclear run-on with 2X run-on mix (5 mM Tris-HCl PH 8.0, 2.5 mM MgCl2, 0.5 mM DTT, 150 mM KCl, 0.5 mM ATP, 0.5 mM CTP, 0.5 mM GTP, 0.5 mM BrUTP, RNase inhibitor, 1% sarkosyl) at 37o for 5 min. RNA was extracted by Trizol and followed by hybrolyzation with NaOH at a final concentration of 0.2 N on ice for 18 min. After quenching with ice-cold Tris-HCl PH6.8 at a final concentration of 0.55 M and exchanging buffer via Bio-Rad P30 columns, the RNA was incubated with Br-dU antibody-conjugated beads (Santa Cruz biotechnology, sc-32323-ac) for 1 hr. The enriched run-on samples were incubated with RppH (NEB, M0356S) and hydroxyl repair with T4 PNK (NEB, M0201S), followed by ligating the 5’ and 3’ RNA adaptor. RT-PCR was performed from the adaptor-ligated RNA to obtain cDNA
Half of the cDNA was subjected to making Groseq libraries by two rounds of PCR with barcode primers.  200-500 bp products from the first round of PCR were subjected to the second round of PCR with the number of PCR cycles determined by test PCR amplification. The second round of PCR products were size-selected by SPRIselect beads (Beckman Coulter, B23318).

value: AID-deficient CH12F3 murine lymphoma cells

tag: genotype

value: IaD-AID-/-

value: with aCD40/IL4/TGFb stimulation


title: 20161206 merged barcode mapping reads

description:
bbmerge_assembled_2_4
plasmid
Variant-barcode paired reads used for associating barcodes with variants

tag: cell type

value: source:NEB 5-alpha Electrocompetent cells (#C2989K)


title: Normal colon 1

description:
Normal colon
Normal colon 1.txt


title: MC38-OVA 3

description:
MC38-OVA
MC38-OVA 3.txt


title: Iadel_sti_3

description: Run-on RNA


title: Iadel_nonsti_2

description: Run-on RNA

value: without stimulation


title: Iadel_nonsti_1

description: Run-on RNA


title: PD Patient # 29

city: Lille

first: Marie-Christine

last: Chartier-Harlin

address: 1 place de Verdun

institute: INSERM

description: Trasncriptomic profiling of peripheral blood mononuclear cells from patients with Parkinson's disease and control subjects

hyb_protocol: Scanned on an Agilent G2505B scanner and Agilent-014850 whole Human genome microarrays 4x44K (Probe Name Version).

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.9.5.3.1).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (Grid: 014850_D_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: PD Patient # 29

label_protocol: Cyanine-3 (Cya3) labeled cRNA was prepared from 1650 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN), Valencia, CA). Dye incorporation and cRNA yield were with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Blood from control and PD subjects was collected in Vacutainer® CPT Cell Preparation Tubes (Becton Dickinson, Le Pont-de-Claix, France) and PBMC from human samples were isolated on a ficoll gradient. Total RNA from 5 x 106 cells was isolated using Rneasy mini-columns (Qiagen, Courtaboeuf, France). RNA concentration was measured by absorbance at 260nm using a Nanodrop ND-1000 spectrophotometer. RNA quality and integrity were checked using the RNA 6000 NanoChip kit on the Agilent 2100 Bioanalyzer (Agilent Technologies, Massy, France). All samples included in the study had a RIN>9.

tag: disease state

value: Parkinson's disease

value: peripheral blood mononuclear cells


title: PD Patient # 30

source_name: PD Patient # 30


title: PD Patient # 27

source_name: PD Patient # 27


title: PD Patient # 28

source_name: PD Patient # 28


title: Primary-2

city: Tokyo

first: REI

last: MIMOTO

address: 3-25-8 Nishishinbashi, Minato-ku

department: Biochemistry

country: Japan

institute: The Jikei University School of Medicine

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: breast cancer tumor

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA extraction was performed using NucleoSpin® RNA XS  following the manufacture's instructuion.

treatment_protocol: CR cells were cultured with J2 cells, CR cells were extracted withoug J2 cells.

tag: cell

value: breast cancer


title: CR cells -1

source_name: conditional reprogramming cell

value: CR cells


title: Primary -1


title: CR cells -2


title: Splenic_aCD40_IL4_Rad21_3

data_processing:
Reads were aligned using bowtie2 with --non-deterministic flag
peaks were called with MACS2 with the following flags: --nomodel --keep-dup all --extsize 51 --nolambda -B --SPMR
wig files were generated using USCS utilities bedGraphToBigWig
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated for displaying

source_name: Splenic mature B cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (IP-202-1012).

value: AID-deficient Splenic mature B cells

tag: passages

value: 0 (primary mature splenic B cells)

value: Rad21 (Abcam, ab992)

value: with aCD40/IL4 stimulation


title: PD Patient # 22

source_name: PD Patient # 22


title: PD Patient # 21

source_name: PD Patient # 21


title: PD Patient # 23

source_name: PD Patient # 23


title: PD Patient # 24

source_name: PD Patient # 24


title: PD Patient # 26

source_name: PD Patient # 26


title: PD Patient # 19

source_name: PD Patient # 19


title: Splenic_nonsti_Rad21_3


title: DMSO_SUDIPGXIII_H3K27me3_rep1

source_name: SU-DIPGXIII

value: DMSO treated

value: diffuse intrinsic pontine glioma


title: PD Patient # 20

source_name: PD Patient # 20


title: Iadel_nonsti_3

description: Run-on RNA


title: PD Patient # 25

source_name: PD Patient # 25


title: Splenic_aCD40_IL4_Rad21_2


title: PD Patient # 18

source_name: PD Patient # 18


title: Splenic_nonsti_Rad21_2


title: Splenic_nonsti_3

description: Run-on RNA

value: AID-deficient splenic mature B cells

value: AID-deficient primary splenic B cells


title: Splenic_aCD40_IL4_Rad21_1


title: Splenic_nonsti_Rad21_1


title: i3CBEs_aCD40_IL4_TGFb_Rad21_3

source_name: CH12F3 murine lymphoma cells


title: i3CBEs_aCD40_IL4_TGFb_Rad21_2


title: PD Patient # 17

source_name: PD Patient # 17


title: i3CBEs_aCD40_IL4_TGFb_Rad21_1


title: PD Patient # 16

source_name: PD Patient # 16


title: PD Patient # 14

source_name: PD Patient # 14


title: CH12F3NCdel_aCD40_IL4_TGFb_Rad21_4


title: CH12F3NCdel_nonsti_Rad21_3


title: CH12F3NCdel_aCD40_IL4_TGFb_Rad21_2


title: CH12F3NCdel_aCD40_IL4_TGFb_Rad21_3


title: CH12F3NCdel_nonsti_Rad21_2


title: CH12F3NCdel_nonsti_Rad21_1


title: CH12F3NCdel_aCD40_IL4_TGFb_Rad21_1


title: CH12F3NCdel_aCD40_IL4_TGFb_NIPBL_2

value: AID-deficient CH12F3 murine lymphoma cells

value: NIPBL (Bethyl, A301-779A)


title: i3CBEs_aCD40_IL4_TGFb_input

value: with aCD40/IL4/TGFb stimulation


title: PD Patient # 13

source_name: PD Patient # 13


title: Splenic_aCD40_IL4_3CBE7_3

data_processing:
Library strategy: 3C-HTGTS
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt and bait sequences shorter than 50nt.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files were generated for displaying (Jane et al., 2018)

extract_protocol:
About 10 million cells were crosslinked with 2% formaldehyde for 10 minutes at room temperature and quenched with glycine at a final concentration of 125 mM. Then, the crosslinked cells were lysed in the 3C lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, protease inhibitors) and nuclei were digested with NlaIII enzyme (NEB, R0125) at 37 ℃ overnight.  They were then brought to 16℃, 100U of T4 ligase added  (Promega, M1801) and they incubated again overnight at 16℃.  The ligated products were de-crosslinked with Proteinase K (Roche, #03115852001) at 56 ℃ overnight and the 3C templates were purified by phenol/chloroform.
Libraries were prepared using 3C samples by HTGTS (Jane et al., 2018).

value: Splenic mature B cells

tag: activation

value: cytokine stimulation

tag: target locus


title: PD Patient # 10

source_name: PD Patient # 10

value: Parkinson's disease


title: BMECs-LL Solexa

source_name: mammary epithelial cells

value: Primary Mammary Epithelial Cells

value: mammary gland

value: Chinese Holstein cows

value: low milk fat


title: PD Patient # 3

source_name: PD Patient # 3

value: peripheral blood mononuclear cells


title: PD Patient # 11

source_name: PD Patient # 11


title: PD Patient # 4

source_name: PD Patient # 4


title: BMECs-HH Solexa


title: Splenic_aCD40_IL4_3CBE7_2

source_name: Splenic mature B cells


title: PD Patient # 9

source_name: PD Patient # 9


title: PD Patient # 7

source_name: PD Patient # 7


title: PD Patient # 5

source_name: PD Patient # 5


title: PD Patient # 2

source_name: PD Patient # 2


title: Splenic_aCD40_IL4_3CBE7_1


title: PD Patient # 15

source_name: PD Patient # 15


title: CH12F3NCdel_nonsti_NIPBL_2

value: without stimulation


title: PD Patient # 8

source_name: PD Patient # 8


title: Raw264.7_violacein_rep2

description: Gene expression data from Raw 264.7 with the treatment of 4 µM violacein  replica 2

source_name: Raw 264.7, violacein treated, rep2

tag: cell line


title: Woodchuck_16

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

institute: F. Hoffmann - La Roche AG

data_processing:
Basecalling and sample de-multiplexing was performed with CASAVA-1.8.4 and default parameters
Reads were quality check with fastqc v0.11.5 default parameters
Reads for each sample/replicate were mapped against the woodchuck genome assembly using the gem-tools rna-mapper v1.6.1 with default options
Transcripts were quantified with gemtools version 1.7.1 using the Monax4B annotation.
Genome_build: Monax4B
http://denovo.cnag.cat/woodchuck
Supplementary_files_format_and_content: Read counts per transcript

organism: Marmota monax

source_name: Kidney

extract_protocol:
Sequencing libraries were prepared from either 100 ng or one µg of total RNA using the Illumina TruSeq RNA Sample preparation Kit v2 according to manufacturer’s instructions. Sequencing libraries were quantified using the Kapa Library Quantification kit (Kapa Biosystems) and quality controlled by capillary electrophoresis on a Bioanalyzer using DNA 1000 chips (Agilent Technologies).
Libraries were sequenced on a HiSeq2500 sequencer (Illumina) for 2 x 125 cycles using version 3 cluster generation kits and version 3 sequencing reagents (Illumina). The PhiX control library (Illumina) was spiked into each sample (at 1%) as a sequencing control.

tag: common name

value: Eastern woodchuck

value: Kidney

tag: individual


title: Splenic_aCD40_IL4_3CBE1_2


title: Woodchuck_18

source_name: Liver

value: Liver


title: Woodchuck_20

source_name: Spleen

value: Spleen


title: Woodchuck_19


title: Woodchuck_15


title: Woodchuck_17


title: Splenic_aCD40_IL4_3CBE1_1

value: AID-deficient primary splenic B cells


title: PD Patient # 1

source_name: PD Patient # 1