title: 72353 mRNA-Seq Pre-B cell Wapl(∆P1,2/∆P1,2)

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

description: mRNA-Seq Pre-B cell Wapl(∆P1,2/∆P1,2)

data_processing:
ChIP-Seq: Sequence reads were uniquely aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 1.0.  CTCF peaks were called by MACS 2.0.  Genome-wide read coverages were normalized to the number of aligned reads, per million (=RPM)., using 'bedtools' and 'kent source utilities'.
RNA-Seq: The number of reads per gene was counted using the featureCounts version 1.5.0 with default settings. Transcripts per million (TPM) values were calculated as described previously. Differential gene expression between ex vivo sorted Wapl+/+ and Wapl_delta_P1,2/_delta_P1,2 pro-B cells was analyzed using R version 3.3.3. and DESeq2 version 2.1.14.1. Regularized log transformations were computed with the blind option set to ‘FALSE’. Genes with an adjusted P value < 0.05, TPM (averaged for each genotype) > 5 at least in of the two genotypes, and a fold-change of > 2 were called as significantly expressed. All transcripts of the V, D and J gene segments at the Igh, Igk and Igl loci were eliminated from the list of significantly regulated genes, although the immunoglobulin and T cell receptor transcripts were included in all TPM calculations. Differential gene expression between ex vivo sorted control and Rag1Cre/+ Eedfl/fl pro-B cells was analyzed as described above, except that only genes with an expression difference of > 3-fold were considered. The control samples consisted of 3 independent experiments performed with Rag1Cre/+ Eedfl/+ pro-B cells and 1 experiment performed with Eedfl/fl pro-B cells.
ATAC-Seq: Read have been aligned using 'bowtie' version 2.1.0. Genome-wide read coverages were normalized to the number of aligned reads, per million (=RPM), using 'bedtools' and 'kent source utilities'.
Hi-C Seq:  The HiCUP pipeline version 0.5.10 with the scorediff parameter set to "10" was used to truncate, align and filter the reads by applying the following software versions: R 3.4.1, Bowtie 2.2.9 (26) and SAMtools 1.4 (37). Contact matrix files have  been produced with Juicer tools 1.8.9.
3C-Seq: We analyzed the 3C-seq data with the captureC 2.0 program, using cutadapt 1.16 and trim_galore 0.4.2. The 3C-seq data were further analyzed with r3Cseq 1.32 with minor modifications to adjust for a larger viewing range required for the Igh locus and for the insertion of the CBE array by generating a modified genome version.
Genome_build: mm9 (RNA-Seq, ChIP-Seq, Hi-C-Seq, 3C-Seq); mm10 (VDJ-Seq)
Supplementary_files_format_and_content: bed = MACS peak coordinates in BED format; bigwig = read coverage (reads per million) in bigWIG format; density bigwig = bigWig Track format of read density coverage in reads per million after extension to 150 base pairs; bedGraph = bedGraph track of read density coverage, normalized (RPM) and scaled to track with lowest counts; txt = normalized count values, such as TPMs or VDJ-Seq normalized counts, in ASCII text format tab delimited; hic = binary output format provided by the 'HiCUP' pipeline

source_name: Pre-B cell

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell preparation

value: Ex-vivo FACS sorted from bone marrow


title: 72354 mRNA-Seq Pre-B cell Wapl(∆P1,2/∆P1,2)

status: Public on Jul 01 2020

type: SRA

description: mRNA-Seq Pre-B cell Wapl(∆P1,2/∆P1,2)

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: strain

tag: genotype


title: 73767 mRNA-Seq Immature B cell Igh(+/∆890)

description: mRNA-Seq Immature B cell Igh(+/∆890)

source_name: Immature B cell


title: 73770 mRNA-Seq Immature B cell Igh(+/∆890)

description: mRNA-Seq Immature B cell Igh(+/∆890)


title: 73772 mRNA-Seq Immature B cell Igh(V8-8-inv/∆890)


title: 73768 mRNA-Seq Immature B cell Igh(V8-8/∆890)

description: mRNA-Seq Immature B cell Igh(V8-8/∆890)


title: 73771 mRNA-Seq Immature B cell Igh(V8-8-inv/∆890)


title: 71451 mRNA-Seq Immature B cell Igh(CBE-inv/+)

description: mRNA-Seq Immature B cell Igh(CBE-inv/+)

value: Igh(CBE-inv/+)


title: 72350 mRNA-Seq Pro-B cell Wapl(∆P1,2/∆P1,2)

description: mRNA-Seq Pro-B cell Wapl(∆P1,2/∆P1,2)

source_name: Pro-B cell


title: 72351 mRNA-Seq Pre-B cell Wapl(+/+)

description: mRNA-Seq Pre-B cell Wapl(+/+)


title: 72347 mRNA-Seq Pro-B cell Wapl(+/+)

description: mRNA-Seq Pro-B cell Wapl(+/+)


title: 71450 mRNA-Seq Immature B cell Igh(CBE-inv/+)

description: mRNA-Seq Immature B cell Igh(CBE-inv/+)


title: 72352 mRNA-Seq Pre-B cell Wapl(+/+)

description: mRNA-Seq Pre-B cell Wapl(+/+)


title: 72349 mRNA-Seq Pro-B cell Wapl(∆P1,2/∆P1,2)

description: mRNA-Seq Pro-B cell Wapl(∆P1,2/∆P1,2)


title: LANS-Set2_darkToLight_20min_H3_ChIP_Rep1

city: Chapel Hill

first: Austin

middle: J

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

department: Genetics

country: USA

institute: University of North Carolina at Chapel Hill

library_source: genomic

data_processing:
For ChIP: Reads from the sequencer were demultiplexed using bcl2fastq (v2.20.0). Sequencing adapters on reads were trimmed using cutadapt (v1.12) using options -a GATCGGAAGAGC -A GATCGGAAGAGC and --minimum-length 36 in paired mode. After trimming, reads were filtered for quality using the fastq_quality_filter in FASTX-Toolkit (v0.0.12), with options -Q 33, -p 90, and -q 20. In-house scripts were used to limit potential PCR duplicates by limiting reads with the same sequence to a maximum of 5 copies and discarding the copies beyond that limit. Since the previous filtering steps may remove one end of a read pair but not the other, both read-pair fastq files were synced using in-house scripts to ensure proper order for alignment. As the ChIP experiments contained S. pombe spike-in, a chimeric S. cerevisae-S. pombe genome (sacCer3-ASM294v2) was generated using the genomeGenerate tool in STAR (v2.5.2b). This chimeric genome contains the full sequence of both species, allowing reads to align to their best overall fit between the two species. Once generated, read alignment was done using STAR (v2.5.2b) and options --outFilterMismatchNmax 2, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --outSAMtype BAM Unsorted, --outFilterType BySJout, --outFilterScoreMin 1, and --outFilterMultimapNmax 1. Post-alignment, Samtools (v1.31) and bedtools (2.26) were used to generate bigWig files for downstream analyses. To account for S. pombe spike-in, the bigwig signal was normalized by the total number of S. pombe reads per million, using the -scale option within the bedtools genomecov tool. Normalized H3K36me3 signal was obtained by dividing H3K36me3 spike-in normalized signal by H3 spike-in normalized signal for each base pair for each replicate. Some regions were devoid of any H3 signal, and these regions were flagged and excluded from further analyses regardless of H3K36me3 signal.  Deeptools (v2.5.4) was used to generate metagene plots using the normalized H3K36me3 signal. Deeptools was also used to obtain base pair by base pair signal over regions of interest such as genes, introns, and exons. This data was used to calculate the average signal per gene, excluding those regions flagged for lacking H3 signal. We set out to understand H3K36me3 signals over time, however differing levels of normalized H3K36me3 signal within genes made analysis difficult. To account for these differences, we scaled the average signal per gene throughout the time course between 0 (no signal) and 1 (the maximum signal of a gene over the time course). This yielded a relative (proportional) scale for each gene as a fraction of its maximum signal and allowed for easier comparisons of patterns within and across treatments. To yield a comprehensive gene value for plotting, H3K36me3 signal (for both mean or proportional) was the mean of all the replicates for the gene.
For RNA: Reads from the sequencer were demultiplexed using bcl2fastq (v2.20.0). Reads were trimmed using cutadapt (v1.12) using options -a GATCGGAAGAGC -A GATCGGAAGAGC and --minimum-length 36 to remove any sequencing adapters. After trimming, reads were filtered for quality using the fastq_quality_filter in FASTX-Toolkit (v0.0.12), with options -Q 33, -p 90, and -q 20. Reads were aligned to the sacCer3 genome using STAR (v2.5.4b) with options --quantMode TranscriptomeSAM, --outFilterMismatchNmax 2, --alignIntronMax 1000000, --alignIntronMin 20, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --outSAMtype BAM Unsorted, --outFilterType BySJout, and --outFilterMultimapNmax 1. To calculate the RNA abundance values, Salmon (v0.8.1) tool quant was used with options -l SR, --incompatPrior 0.0 to account for read strandedness. Samtools (v1.3.1), bedtools (v2.26), and R (v3.3.1) were used to interconvert files for downstream analyses. DESeq2 (v1.14.1) was used to determine which genes had differential expression. Venn diagrams were made using R package Vennerable (v3.0).
Genome_build: sacCer3-ASM294v2
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files for ChIP contain spike-in (S. pombe) scaled ChIP-seq signal for H3 or H3K36me3. Those ending with "normalizedByH3" contain H3K36me3 ChIP-seq signal that is normalized by matched H3 signal (spike-in scaled H3K36me3 / spike-in scaled H3). Bigwigs for RNA contain read depth normalized, non-stranded RNA-seq signal.
Supplementary_files_format_and_content: sf files contain the gene expression data (TPM) as determined by sailfish for all replicates in either Light to Dark (LtD) or Dark to Light (DtL) treatments.
Supplementary_files_format_and_content: Differential abundance files contain the DESeq2 differential genes between 0min and all other timepoints across Light to Dark (LtD) or Dark to Light (DtL) treatments.
Supplementary_files_format_and_content: Model value matrices contain the GLMM model prediction values, errors, and credible intervals for each gene across the time course. High confidence genes are those where credible interval does not cross zero, and are labeled as having a non-zero trend in the table.
Supplementary_files_format_and_content: Histone value matrices contain the average, spike-in scaled, H3 normalized H3K36me3 ChIP-seq signal for each gene and replicate.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: For ChIP-seq: Cells (either WT, set2∆, set2∆ expressing LANS-Set2, rph1∆, or rph1∆ expressing LANS-Set2) were resuspended in YPD (WT, set2∆, and rph1∆) or SC−LEU (set2∆ expressing LANS-Set2 and rph1∆ expressing LANS-Set2) and grown overnight at 30 °C. In the morning cell density was measured at OD600 and cultures were diluted in appropriate media to a final volume of 70 mL and final OD600 of 0.35. Cultures were maintained at 30 °C until the OD600 reached 0.8−1.0.  For RNA-seq: Cells (either WT, rph1∆, or set2∆ expressing LANS-Set2) were resuspended in YPD (WT and rph1∆) or SC−LEU (set2∆ expressing LANS-Set2) and grown overnight at 30 °C. In the morning cell density was measured at OD600 and cultures were diluted in appropriate media to a final volume of 70 mL and final OD600 of 0.3. Cultures were maintained at 30 °C until the OD600 reached 0.8−1.0.

extract_protocol:
For ChIP-seq: Cells were fixed with a 1% final concentration of formaldehyde, the fixation was quenched, cells were washed, and pellets were frozen at −80 °C. After the completion of each time course, cells were lysed using 140 mM FA lysis buffer (50 mM HEPES, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, pH 7.5, containing protease inhibitor cocktail). Lysed cells were sonicated (Diagenode Bioruptor UCD-200) on high intensity 5 times for 5 minutes each (cycles of 30 seconds “ON” and 30 seconds “OFF”) and clarified by centrifuging at full speed for 15 minutes. Overnight immunoprecipitations of S. cerevisiae chromatin with appropriate antibodies were prepared with S. pombe chromatin spike-in control corresponding to 15% of S. cerevisiae chromatin as estimated by Bradford assay (Bio-Rad). 50 μL of Protein G Dynabeads were added to each 500 μL immunoprecipitation reaction and reactions were incubated for 2 hours. Washes were performed with 1 mL of 140 mM FA-lysis buffer, 500 mM FA-lysis buffer (50 mM HEPES, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, pH 7.5, containing protease inhibitor cocktail), LiCl solution (250 mM LiCl, 10 mM Tris, 0.5% each of NP-40 and sodium doxycholate and 1 mM EDTA) and TE pH 8.0. Elution buffer (1% SDS, 0.1 M NaHCO3) was used to elute the DNA (15 minutes shaking at 65 °C followed by centrifugation at 2,000 RPM for 2 minutes). 10 μL of 5 M NaCl was added to the eluates and 10% inputs and samples were incubated at 65 °C overnight to carry out de-crosslinking. Samples were treated with RNase for 1 hour and proteinase K for 1hour before ChIP DNA Clean & Concentrator (Zymo Research) to extract the DNA.  For RNA-seq: Cells (10 mL of log-phase cultures) were collected by centrifugation and frozen at −80 °C. , RNA was isolated by acid phenol extraction. RNA (10 μg) was treated with DNase (Promega) and purified (RNeasy column, QIAGEN).
For ChIP-seq: Bar-coded sequencing libraries were prepared as recommended by the manufacturer (KAPA Hyper Prep Kit), pooled and sequenced (Hi-Seq 2500, Illumina). Briefly, extracted DNA was end-repaired and A-tailed and adapters were ligated. Bead-based size selection was performed, libraries were amplified, and bead-based size selection was repeated. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.  For RNA-seq: RNA (2.5 μg) was processed using rRNA depletion beads specific to yeast (Illumina). Bar-coded sequencing libraries were prepared as recommended by the manufacturer (TruSeq Stranded Total RNA Library Preparation Kit, Illumina), pooled and sequenced (Hi-Seq 4000, Illumina). Briefly, libraries were constructed by bead-based rRNA depletion, cDNA synthesis, and PCR. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hi-Seq 4000 following the manufacturer's protocols.

treatment_protocol: For ChIP-seq: WT, set2∆, and rph1∆ cells were collected when the OD600 reached 0.8−1.0. Cells expressing LANS-Set2 (set2∆ and rph1∆) were maintained throughout culturing in 500 μW/cm2 blue light (set2∆ and rph1∆) or in the dark (set2∆) until the OD600 reached 0.8−1.0 when an initial time point was collected then samples were shifted from the dark to light or the light to dark.  For RNA-seq: WT and rph1∆ cells were collected when the OD600 reached 0.8−1.0. set2∆ cells expressing LANS-Set2 were maintained throughout culturing in 500 μW/cm2 blue light or in the dark until the OD600 reached 0.8−1.0 when an initial time point was collected then samples were shifted from the dark to light or the light to dark.

tag: lans-set2 status

value: Dark to Light

tag: time after light change

value: 20 min

tag: chip antibody

value: H3 (EMD Millipore 05-928)

tag: genome build


title: 71447 mRNA-Seq Immature B cell Igh(CBE/+)

description: mRNA-Seq Immature B cell Igh(CBE/+)

value: Igh(CBE/+)


title: 72348 mRNA-Seq Pro-B cell Wapl(+/+)

description: mRNA-Seq Pro-B cell Wapl(+/+)


title: 71449 mRNA-Seq Immature B cell Igh(+/+)

description: mRNA-Seq Immature B cell Igh(+/+)


title: 71448 mRNA-Seq Immature B cell Igh(+/+)

description: mRNA-Seq Immature B cell Igh(+/+)


title: m1_Young1_K18

city: Stanford

first: Michelle

middle: Berkeley

last: Chen

address: 318 Campus Drive

institute: Stanford

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: raw count table

molecule: total RNA

source_name: three-mo mouse BEC

growth_protocol: Mice 3 (young)

extract_protocol:
Brain tissues were dissected using Miltenyi neural dissociation kit. Brain endothelial cells were isolated via FACS.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: primary murine brain endothelial cells


title: LANS-Set2_darkToLight_0min_H3_ChIP_Rep1

value: 0 min


title: m1_AY_Y3_M15


title: 71446 mRNA-Seq Immature B cell Igh(CBE/+)

description: mRNA-Seq Immature B cell Igh(CBE/+)


title: m1_AY_Y3_P2


title: LANS-Set2_lightToDark_90min_H3_ChIP_Rep3

value: Light to Dark

value: 90 min


title: 60671 mRNA-Seq in vitro pro-B cell Wapl(∆P1,2/∆P1,2)

source_name: in vitro pro-B cell

value: 3-days in-vitro expansion


title: 60670 mRNA-Seq in vitro pro-B cell Wapl(∆P1,2/∆P1,2)


title: m1_Young1_M4


title: 60669 mRNA-Seq in vitro pro-B cell Wapl(∆P1,2/∆P1,2)


title: 60667 mRNA-Seq in vitro pro-B cell Wapl(+/+)

description: mRNA-Seq in vitro pro-B cell Wapl(+/+)


title: LANS-Set2_lightToDark_30min_H3_ChIP_Rep3

value: 30 min


title: 52055 mRNA-Seq Immature B cell Igh(890-inv/+)

description: mRNA-Seq Immature B cell Igh(890-inv/+)


title: m1_Young2_N8


title: 60666 mRNA-Seq in vitro pro-B cell Wapl(+/+)

description: mRNA-Seq in vitro pro-B cell Wapl(+/+)


title: 52052 mRNA-Seq Immature B cell Igh(+/+)

description: mRNA-Seq Immature B cell Igh(+/+)


title: 52054 mRNA-Seq Immature B cell Igh(890-inv/+)

description: mRNA-Seq Immature B cell Igh(890-inv/+)


title: 38496 mRNA-Seq Pro-B cells Pax5(+/+)

description: mRNA-Seq Pro-B cells Pax5(+/+)

source_name: Pro-B cells


title: 52053 mRNA-Seq Immature B cell Igh(+/+)

description: mRNA-Seq Immature B cell Igh(+/+)


title: m1_Young2_P16


title: 38494 mRNA-Seq Progenitors Pax5(-/-)

description: mRNA-Seq Progenitors Pax5(-/-)

source_name: Progenitors


title: 38493 mRNA-Seq Progenitors Pax5(-/-)

description: mRNA-Seq Progenitors Pax5(-/-)


title: m1_Young1_D8


title: m1_Young1_J14


title: LANS-Set2_lightToDark_60min_H3_ChIP_Rep2

value: 60 min


title: 38492 mRNA-Seq Pro-B cells Pax5(+/+)

description: mRNA-Seq Pro-B cells Pax5(+/+)


title: LANS-Set2_lightToDark_30min_H3_ChIP_Rep2


title: LANS-Set2_lightToDark_90min_H3_ChIP_Rep2


title: m1_Young2_I2


title: 38497 mRNA-Seq Pro-B cells Pax5(+/+)

description: mRNA-Seq Pro-B cells Pax5(+/+)


title: 38488 mRNA-Seq Pro-B cell Eed(F/F) Rag1-cre

description: mRNA-Seq Pro-B cell Eed(F/F) Rag1-cre

value: Eed(F/F) Rag1-cre


title: m1_Young1_E7


title: 38487 mRNA-Seq Pro-B cell Eed(F/F) Rag1-cre

description: mRNA-Seq Pro-B cell Eed(F/F) Rag1-cre


title: LANS-Set2_lightToDark_0min_H3_ChIP_Rep2


title: m1_AY_Y3_B10


title: 38486 mRNA-Seq Pro-B cell Eed(F/F) Rag1-cre

description: mRNA-Seq Pro-B cell Eed(F/F) Rag1-cre


title: m1_Young1_J2


title: 23356 mRNA-Seq Pro-B cell Eed(F/F) Rag1-cre

description: mRNA-Seq Pro-B cell Eed(F/F) Rag1-cre


title: 38485 mRNA-Seq Pro-B cell Eed(F/+) Rag1-cre

description: mRNA-Seq Pro-B cell Eed(F/+) Rag1-cre

value: Eed(F/+) Rag1-cre


title: 23355 mRNA-Seq Pro-B cell Eed(F/+) Rag1-cre

description: mRNA-Seq Pro-B cell Eed(F/+) Rag1-cre


title: LANS-Set2_lightToDark_90min_H3_ChIP_Rep1


title: m1_Young1_I15


title: 23354 mRNA-Seq Pro-B cell Eed(F/+) Rag1-cre

description: mRNA-Seq Pro-B cell Eed(F/+) Rag1-cre


title: 13021 mRNA-Seq Pro-B cell Eed(F/F) Rag1-cre

description: mRNA-Seq Pro-B cell Eed(F/F) Rag1-cre


title: m1_Young2_E7


title: 13020 mRNA-Seq Pro-B cell Eed(F/F)

description: mRNA-Seq Pro-B cell Eed(F/F)

value: Eed(F/F)


title: m1_Young1_B14


title: m1_Young2_N9


title: LANS-Set2_lightToDark_0min_H3_ChIP_Rep1


title: set2d_H3_ChIP_Rep3


title: 39312 ATAC-Seq BLP (Pax5+) WT

description: ATAC-Seq BLP (Pax5+) WT

source_name: BLP (Pax5+)

extract_protocol: ATAC-seq libraries were prepared using NEBNext High-Fidelity 2x PCR Master Mix (New England Labs #M0541) and Nextera PCR primers.

value: WT


title: 41499 ATAC-Seq Pax5-deficient progenitor Pax5(fl/fl) Rag2(-/-) Vav-Cre

source_name: Pax5-deficient progenitor

value: Pax5(fl/fl) Rag2(-/-) Vav-Cre

value: Ex-vivo FACS sorted from bone marrow


title: LANS-Set2_darkToLight_60min_H3_ChIP_Rep2

value: Dark to Light


title: 39311 ATAC-Seq BLP (Pax5-) WT

description: ATAC-Seq BLP (Pax5-) WT

source_name: BLP (Pax5-)


title: set2d_H3_ChIP_Rep2


title: m1_Young2_G2


title: 39310 ATAC-Seq ALP WT

description: ATAC-Seq ALP WT

source_name: ALP


title: 26277 ATAC-Seq Mature B Pax5(fl/+) CD23-Cre

description: ATAC-Seq Mature B Pax5(fl/+) CD23-Cre

source_name: Mature B

value: Pax5(fl/+) CD23-Cre

value: Ex-vivo MACS-sorted from lymphe node, CD43-


title: 39309 ATAC-Seq LSK WT

description: ATAC-Seq LSK WT

source_name: LSK


title: m1_Young2_C4


title: set2d_H3_ChIP_Rep1

value: H3 (EMD Millipore 05-928)


title: LANS-Set2_lightToDark_30min_H3_ChIP_Rep1


title: m1_AY_Y3_N11

value: primary murine brain endothelial cells


title: 23055 Suz12 ChIP-Seq Rag2(-/-)

description: Suz12 ChIP-Seq Rag2(-/-)

extract_protocol: ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols

value: 4-days in-vitro expansion

value: anti-Suz12 (rabbit mAb clone D39F6; Cell Signaling)


title: 35317 Suz12 ChIP-Seq Pax5(-/-) Rag2(-/-)

description: Suz12 ChIP-Seq Pax5(-/-) Rag2(-/-)

value: in-vitro expansion


title: 102355 Pax5 AB ChIP-Seq Wapl(∆P1/∆P1)

description: Pax5 AB ChIP-Seq Wapl(∆P1/∆P1)

value: anti-Pax5 (rabbit polyclonal Ab, detecting the paired domain (amino acids 17-145) (16); Busslinger laboratory)


title: 73769 mRNA-Seq Immature B cell Igh(V8-8/∆890)

description: mRNA-Seq Immature B cell Igh(V8-8/∆890)


title: m1_Young2_F3


title: 41508 ATAC-Seq Pro-B Rag2(-/-)

description: ATAC-Seq Pro-B Rag2(-/-)

source_name: Pro-B


title: 102354 Pax5 AB ChIP-Seq Wapl(+/+)

description: Pax5 AB ChIP-Seq Wapl(+/+)


title: m1_AY_Y3_M4


title: 102353 Pax5 AB ChIP-Seq Wapl(+/+)

description: Pax5 AB ChIP-Seq Wapl(+/+)


title: WT_H3_ChIP_Rep1


title: LANS-Set2_lightToDark_60min_H3_ChIP_Rep3

value: Light to Dark


title: LANS-Set2_lightToDark_0min_H3_ChIP_Rep3

value: 0 min


title: WT_H3_ChIP_Rep3


title: m1_Young2_B1


title: 35325 H3K27me3 ChIP-Seq Rag1(Cre/Cre)

description: H3K27me3 ChIP-Seq Rag1(Cre/Cre)

value: anti-H3K27me3 (rabbit mAb 9733; Cell Signaling)


title: m1_Young1_D3


title: m1_AY_Y3_K16


title: 102350 H3K27me3 AB ChIP-Seq Wapl(+/+)

description: H3K27me3 AB ChIP-Seq Wapl(+/+)


title: 102351 H3K27me3 AB ChIP-Seq Wapl(∆P1/∆P1)

description: H3K27me3 AB ChIP-Seq Wapl(∆P1/∆P1)


title: m1_Young1_K2


title: 21478 H3K27me3 ChIP-Seq Rag1(Cre/Cre)

description: H3K27me3 ChIP-Seq Rag1(Cre/Cre)


title: 102352 H3K27me3 AB ChIP-Seq Wapl(∆P1/∆P1)

description: H3K27me3 AB ChIP-Seq Wapl(∆P1/∆P1)


title: m1_AY_Y3_L5


title: 21479 H3K27me3 ChIP-Seq Rag1(Cre/+) Eed(fl/fl)

value: Rag1(Cre/+) Eed(fl/fl)


title: 23056 Ezh2 ChIP-Seq Rag2(-/-)

description: Ezh2 ChIP-Seq Rag2(-/-)

value: anti-Ezh2 (rabbit polyclonal Ab, pAb-039-050; Diagenode)


title: 25442 Ezh2 ChIP-Seq WT

description: Ezh2 ChIP-Seq WT

source_name: Stimulated B cells

value: WT

value: 2-days in-vitro stimulation with LPS

value: anti-Ezh2 (rabbit mAb clone D2C9; Cell Signaling)


title: 84326 CTCF AB ChIP-Seq WT

description: CTCF AB ChIP-Seq WT

value: 5-days in-vitro expansion

value: anti-CTCF (rabbit polyclonal Ab 07-729; Merck Millipore)


title: 35320 Ezh2 ChIP-Seq Pax5(-/-) Rag2(-/-)

description: Ezh2 ChIP-Seq Pax5(-/-) Rag2(-/-)


title: 84325 CTCF AB ChIP-Seq WT

description: CTCF AB ChIP-Seq WT


title: WT_H3_ChIP_Rep2


title: 102356 Pax5 AB ChIP-Seq Wapl(∆P1/∆P1)

description: Pax5 AB ChIP-Seq Wapl(∆P1/∆P1)


title: Whole seedlings, GFP-FLAG.CHIP.rep3

city: HONG KONG

first: Huan

last: ZHONG

state: HONG KONG

address: T1012 CHA CHI-MING SCIENCE TOWER

department: BIOLOGY

country: Hong Kong

institute: HKBU

data_processing:
The reference genome sequence used for analyzing the ChIP-Seq data and motif finding was the Arabidopsis thaliana TAIR10 database. Enriched peak regions were identified using MACS-1.4.3 (Feng et al., 2012) with default parameters (-g 1.2e8 -p 1e-5 -w --space 50 -m 10,30 -s 49). Chipseeker (Yu et al., 2015) was applied to calculate average profiles of ChIP peaks binding to TSS regions, perform enrichment analysis, and peak annotation.
Genome_build: A. thaliana Ensemble 41 (TAIR10)
Supplementary_files_format_and_content: 20190704.bzip.counts.xlsx, Supplementary_Tables_S1_S2.BZIP68_CHIPSeq_peaks_v4.xlsx

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis seedlings were growth on 1/2 MS plates containing 3% sucrose and 0.8% agar for 8 days under 16h light/ 8h dark condition(with light 125 umoles/m2 seg )

extract_protocol: Three gram of bZIP68-FLAG or GFP-FLAG seedling per sample was cross-linked with 1% formaldehyde for 10 min, and then incubated with 0.125 M glycine (final concentration) for an extra 5 min. Chromatin extraction and immunoprecipitation was carried out according to the protocol from Joseph Ecker lab (Song et al., 2016). DNA-Protein complexes were pulled down using FLAG antibody (Sigma Aldrich, F1804) which has been bound to Pierce™ ChIP-grade Protein A/G Magnetic Beads (ThermoFisher, 26162). The immune complexes were treated with NaCl, RNase A, proteinase K and 65 degree heating for de-crosslinking. Finally, DNAs were purified using ChIP DNA Clean & Concentrator™ kit (ZYMO research, D5205). Illumina sequencing libraries preparation was carried out according to the manufacturer’s manual (CWBIO, CW2585S, NGS Fast DNA Library Prep Set for Illumina). The libraries were sent to Novogene company (Tianjin, China) and sequenced using the Illumina HiSEQ1500 platform.

tag: tissue

value: whole seedlings

tag: age

value: GFP-FLAG

value: FLAG antibody (Sigma Aldrich, F1804)


title: m1_AY_Y3_K7

value: primary murine brain endothelial cells


title: 89022 CTCF AB ChIP-Seq Igh(CBE-inv/CBE-inv)

description: CTCF AB ChIP-Seq Igh(CBE-inv/CBE-inv)

value: Igh(CBE-inv/CBE-inv)


title: 89021 CTCF AB ChIP-Seq Igh(CBE-inv/CBE-inv)

description: CTCF AB ChIP-Seq Igh(CBE-inv/CBE-inv)


title: 29940 H3K27me3 ChIP-Seq Vav-iCre Pax5(F/F) Rag2(-/-)

value: Vav-iCre Pax5(F/F) Rag2(-/-)

value: in-vitro expansion


title: 102349 H3K27me3 AB ChIP-Seq Wapl(+/+)

description: H3K27me3 AB ChIP-Seq Wapl(+/+)

value: 4-days in-vitro expansion


title: Whole seedlings, GFP-FLAG.CHIP.rep2

description: Supplementary_Tables_S1_S2.BZIP68_CHIPSeq_peaks_v4.xlsx


title: m1_AY_Y3_F8


title: 89019 CTCF AB ChIP-Seq Igh(CBE/CBE)

description: CTCF AB ChIP-Seq Igh(CBE/CBE)

value: Igh(CBE/CBE)


title: 89020 CTCF AB ChIP-Seq Igh(CBE/CBE)

description: CTCF AB ChIP-Seq Igh(CBE/CBE)


title: m1_AY_Y3_E3


title: Whole seedlings, GFP-FLAG.CHIP.rep1


title: EAE-m3076-IL23RKO-GP

city: New York

first: Dan

last: Littman

state: NY

address: 430 East 29th St Room 403

institute: New York University School of Medicine

description: eae.count.csv

data_processing:
The single cell RNA raw sequence reads were aligned to the UCSC Mus musculus genome, mm10, using Kallisto.
Gene expression values were quantified into Transcripts Per Kilobase Million (TPM).
Cells which had fewer than 800 detected genes or more than 3,000 genes were removed.
The gene matrix was normalized by SCTransform regression with percent of mitochondria reads separately.
Genome_build: GRCm38

source_name: spinal cord

extract_protocol:
single cells were sorted into 96-well PCR plate containing dNTP, 3' RT primer, RNase inhibitor, superscript II buffer for cell lysis and storage at -80C.
Libraries from isolated single cells were generated based on the Smart-seq2 protocol (Picelli et al., 2014) with the following modifications. In brief, RNA from sorted single cells was used as template for oligo-dT primed reverse transcription with Superscript II Reverse Transcriptase (Thermo Fisher), and the cDNA library was generated by 20 cycle PCR amplification with IS PCR primer using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) followed by Agencourt AMPure XP bead purification as described. Libraries were tagmented using the Nextera XT Library Prep kit (Illumina) with custom barcode adapters (sequences available upon request). Libraries from 1152 cells with unique barcodes were combined and sequenced on a HiSeq2500 in RapidRun mode, with 2x50 nt reads.

treatment_protocol: Lethally irradiated Rag1 KO mice were reconstituted with equal number of bone marrow cells from both Il23RGfp/+ CD45.1/2 and Il23rGfp/Gfp CD45.1/1 donors. 2 months later, mice were either gavaged with SFB to induced SFB-specific Th17 cells in the SILP, or immunized with MOG/CFA for EAE induction. 15 days after SFB gavage or EAE induction (score 5), mice were euthanized for cell isolation.

tag: mouse id

value: mouse 3076

tag: genotype/variation


title: m1_Young2_P1


title: EAE-m3076-IL23Rhet-GN

description: eae.count.csv


title: Whole seedlings, bZIP68-FLAG.CHIP.rep3


title: m1_AY_Y3_M10


title: EAE-m3076-IL23Rhet-GP

description: eae.count.csv


title: 84328 CTCF AB ChIP-Seq Igh(890-inv/890-inv)

description: CTCF AB ChIP-Seq Igh(890-inv/890-inv)


title: EAE-m3041-IL23RKO-GP

description: eae.count.csv

value: mouse 3041


title: m1_AY_Y3_O2


title: Whole seedlings, bZIP68-FLAG.CHIP.rep2


title: EAE-m3041-IL23Rhet-GN

description: eae.count.csv


title: EAE-m3041-IL23RKO-GN

description: eae.count.csv


title: Whole seedlings, bZIP68-FLAG.CHIP.rep1


title: EAE-m3041-IL23Rhet-GP

description: eae.count.csv


title: m1_AY_Y3_N18


title: hc_ir

city: Bronx

first: Sanjeev

last: Gupta

address: 1300 Morris Park Ave.

department: Medicine

institute: Albert Einstein College of Medicine

data_processing:
Basecalls performed using Ion Torrent Suite version 4.2.1 with following configuration; BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 1000 --barcode-filter-postpone 1
Raw RNA-seq reads were trimmed using fastq_quality_trimmer version 0.0.14 with default parameters
Trimmed RNA-seq reads were aligned to the Rnor5.0 genome assembly using Tophat version 2.0.13 with default parameters
Aligned RNA-seq reads were counted using htseq-count version 0.6.1 with default parameters
Genome_build: Rnor5.0
Supplementary_files_format_and_content: Tab-delimited text files were generated using htseq-count; Scores represent number of aligned sequence fragments per gene

organism: Rattus norvegicus

source_name: fresh isolated hepatocytes

extract_protocol:
Total RNA was isolated with mirVana kit followed by mRNA selection with Dynobeads mRNA Direct micro kit (both Ambion),
RNA libraries were prepared with Ion Total RNA-Seq Kit v2 (Life Technologies) according to the kit manual

value: Primary cells

tag: conditions

value: ischemia reperfusion

tag: treatment

value: ischemia reperfusion alone


title: hc_etn

value: ischemia reperfusion plus treatment

value: Etanercept 9 mg/kg; Nitroglycerin 6µg/kg/min


title: SFB_m3677_SILP_IL23RKO_GP

description: sfb.count.csv

source_name: SILP

value: mouse 3677


title: 71445 mRNA-Seq Immature B cell Igh(+/+)

description: mRNA-Seq Immature B cell Igh(+/+)

source_name: Immature B cell

value: Ex-vivo FACS sorted from bone marrow


title: SFB_m3677_SILP_IL23RKO_GN

description: sfb.count.csv


title: m1_Young2_H8


title: SFB_m3677_SILP_IL23Rhet_GP

description: sfb.count.csv


title: 84327 CTCF AB ChIP-Seq Igh(890-inv/890-inv)

description: CTCF AB ChIP-Seq Igh(890-inv/890-inv)

value: 5-days in-vitro expansion

value: anti-CTCF (rabbit polyclonal Ab 07-729; Merck Millipore)


title: SFB_m3677_SILP_IL23Rhet_GN

description: sfb.count.csv


title: hc_ctrl

value: Healthy

value: untreated control


title: m1_Young1_L15

value: primary murine brain endothelial cells


title: EAE_m3086_SC_IL23Rhet_GP

description: eae.count.csv

value: mouse 3086


title: etn_liv

source_name: Liver

value: Liver


title: EAE_m3086_SC_IL23Rhet_GN

description: eae.count.csv


title: SFB-m3040-SILP-IL23RKO-GP

description: sfb.count.csv

value: mouse 3040


title: SFB-m3040-SILP-IL23RKO-GN

description: sfb.count.csv


title: m1_AY_Y3_O7

source_name: three-mo mouse BEC


title: m1_Young2_H1


title: ir_liv


title: m1_Young1_E4


title: SFB-m3040-SILP-IL23Rhet-GP

description: sfb.count.csv


title: IM-SR-M6_S12: iNICD biological replicate 6

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

description:
DL_M_M6
on dox chow (3 weeks), no washout

data_processing:
RNA-Seq reads were trimmed by cutadapt first, then trimmed read were aligned against mouse genome (mm10) using STAR v2.4.2a. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread: featureCount (5) with mouse GENCODE gene annotation (M15).
All gene-level transcript counts were then imported into the R/Bioconductor package EdgeR, and the trimmed mean of M-values (TMM) normalization method was used to adjust for differences in library size

source_name: Heart

extract_protocol:
Murine right and left atrial tisse was flash frozen separately using liquid nitrogen. Bulk RNA was extracted using Trizol and submitted to either the Genome Technology Access Center (GTAC) at Washington University School of Medicine (St. Louis, MO; for RA) or the Moskowitz Laboratory at the University of Chicago (Chicago, IL; LA) for RNA sequencing.
For the RA, after ribosomal RNA depletion, reverse-transcription with random-priming, library construction and multiplexing, samples were sequenced on an Illumina HiSeq 3000 using indexed libraries multiplexed at 6 samples per lane. For the LA, libraries were prepared from LA RNA starting with 1 μg per sample and using the mRNA‐seq Sample Prep Kit (Illumina) as per recommended instructions. After Ribozero purification and removing only ribosomal RNA, barcoded libraries were prepared according to Illumina's instructions (2013) accompanying the TruSeq RNA Sample prep kit v2 (Part# RS‐122‐2001). Libraries were quantitated using the Agilent Bio‐analyzer (model 2100) and pooled in equimolar amounts.

value: Heart:left atrium

tag: disease state

value: Cardiomyocyte-specific adult Notch gain-of-function


title: ctrl_liv


title: m1_Young2_O1


title: IM-SR-M5_S11: iNICD biological replicate 5

description:
DL_M_M5
on dox chow (3 weeks), no washout


title: m1_AY_Y3_D7


title: Etanercept

extract_protocol:
Total RNA was isolated with mirVana kit followed by ribosomal RNA removal with RiboMinus kit (both Ambion),
RNA libraries were prepared with Ion Total RNA-Seq Kit v2 (Life Technologies) according to the kit manual

value: Liver after partial hepatectomy

value: Etanercept 9 mg/kg in 1 ml

value: adult


title: control

value: Healthy liver


title: IM-SR-M3_S9: iNICD biological replicate 3

description:
DL_F_M3
on dox chow (3 weeks), no washout


title: m1_Young2_O5


title: saline

value: Saline 1ml


title: IM-SR-M2_S8: iNICD biological replicate 2

description:
DL_F_M2
on dox chow (3 weeks), no washout


title: IM-SR-C6_S6: Control biological replicate 6

description:
CL_M_C6
on dox chow (3 weeks), no washout

value: Control


title: IM-SR-C5_S5: Control biological replicate 5

description:
CL_M_C4
on dox chow (3 weeks), no washout


title: IM-SR-M1_S7: iNICD biological replicate 1

description:
DL_F_M1
on dox chow (3 weeks), no washout


title: LANS-Set2_lightToDark_60min_H3_ChIP_Rep1

source_name: Saccharomyces cerevisiae

value: Light to Dark

value: 60 min

value: H3 (EMD Millipore 05-928)


title: m1_Young2_J18


title: Mkx-ko rep2

city: Hangzhou

first: HONGWEI

last: OUYANG

state: Zhejiang

address: 866 Yu Hang Tang Road,Hangzhou, Zhejiang, P.R.China.

country: China

institute: Zhejiang University

data_processing:
Clean reads were obtained from the raw reads by removing the adaptor sequences, reads with >5% ambiguous bases (noted as N) and low-quality reads containing more than 20 percent of bases with qualities of <13.
The clean reads were then aligned to mouse genome (mm9) using the MapSplice program (v2.1.6)
Differentially expressed genes was identified with EB-Seq algorithm
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample

source_name: Tail tendon

extract_protocol:
Tail tendons were isolated and minced, and RNA was harvested using Trizol reagent.
cDNA library was prepared using the Ion Total RNA-Seq Kit v2(Life Technologies Corporation, Carlsbad, USA) according to the manufacturers protocol.

value: tail tendon

value: Mkx-/-


title: IM-SR-C3_S3: Control biological replicate 3

description:
CL_F_C3
on dox chow (3 weeks), no washout


title: IM-SR-C4_S4: Control biological replicate 4

description:
CL_F_C5
on dox chow (3 weeks), no washout


title: IM-SR-C2_S2: Control biological replicate 2

description:
CL_F_C2
on dox chow (3 weeks), no washout


title: IM-SR-C1_S1: Control biological replicate 1

description:
CL_F_C1
on dox chow (3 weeks), no washout


title: SFB-m3040-SILP-IL23Rhet-GN

description: sfb.count.csv


title: m1_Young2_E15

value: primary murine brain endothelial cells


title: IM-SR-M4_S10: iNICD biological replicate 4

description:
DL_M_M4
on dox chow (3 weeks), no washout


title: WT rep3

value: WT


title: m1_Young2_C5


title: Mm.plasma.TraPR.Lexo.R4

city: San Francisco

first: Stefan

last: Oberlin

address: 505 Parnassus Ave

department: Department of Microbiology and Immunology

institute: University of California, San Francisco

description: processed data file: Mm_plasma_miRNA_counts.csv

data_processing:
Illumina Casava1.8 software used for basecalling.
Trimming of reads with Trimmomatic 0.36
Mapping to the Arabidopsis thaliana genome (TAIR10) with Bowtie 1.2.1.1
Mapping to the Drosophila melanogaster genome (BDGP6) with Bowtie 1.2.1.1
Mapping to the Mus musculus genome (GRCm38) with Bowtie 1.2.1.1
Read counting to miRBase annotation with Rsubread 1.26.1
Read normalization with DEseq2.
Genome_build: TAIR10
Genome_build: BDGP6
Genome_build: GRCm38
Supplementary_files_format_and_content: comma separated text files of library and log2 normalized miRNA read counts

extract_protocol:
RNA was extracted with the standard TRIzol method or with the TRaPR isolation method.
Libraries were prepared with from TRIzol or TRaPR isolated RNA with the TRUseq or Lexogen sRNA library preparation kits or with a custom library preparation protocol.

value: plasma

tag: library preparation

value: Lexogen

tag: rna isolation

value: TraPR

tag: molecule subtype

value: small RNA


title: WT rep2

tag: strain


title: Mkx-ko rep3

tag: genotype


title: Mm.plasma.TraPR.Lexo.R1


title: Mm.plasma.TraPR.Lexo.R2


title: Mm.plasma.TRIzol.Lexo.R4

value: TRIzol


title: Mm.plasma.TRIzol.Lexo.R2


title: Mm.plasma.TRIzol.Lexo.R3


title: m1_Young2_B3


title: WT rep1


title: m1_Young1_C5


title: m1_AY_Y3_N2


title: Mm.plasma.TRIzol.Lexo.R1


title: Mkx-ko rep1


title: Mut rep2

city: Baoding

first: Dong

last: Yang

state: Hebei

address: No. 180, Wusi Road

institute: Hebei university

data_processing:
The library preparations were sequenced on an Illumina Hiseq 2500/2000 platform and 50bp single-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw datas were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010): Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3). The P-values was adjusted using the Benjamini& Hochberg method. Corrected P-value of 0.05 was set as the threshold for significantly differential expression by default.
Genome_build: Mus_musculus.GRCm38.89
Supplementary_files_format_and_content: tab-delimited text files include readcount, log2Foldchange, pval, padj and  significant for each Sample ...

source_name: main olfactory epithelium

extract_protocol:
MOE were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Qiagen miRNeasy Mini Kit was used with 3 ug of total RNA for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, NEB 3' SR Adaptor was directly, and specifically ligated to 3' end of miRNA, siRNA and piRNA. After the 3' ligation reaction, the SR RT Primer hybridized to the excess of 3' SR Adaptor (that remained free after the 3' ligation reaction) and transformed the single-stranded DNA adaptor into a double-stranded DNA molecule. This step is important to prevent adaptor-dimer formation, besides, dsDNAs are not substrates for ligation mediated by T4 RNA Ligase 1 and therefore do not ligate to the 5´ SR Adaptor in the subsequent ligation step. 5´ends adapter was ligated to 5´ends of miRNAs, siRNA and piRNA. Then first strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H–). PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for illumina and index (X) primer. PCR products were purified on a 8% polyacrylamide gel (100V, 80 min). DNA fragments corresponding to 140~160 bp (the length of small noncoding RNA plus the 3' and 5' adaptors) were recovered and dissolved in 8 μL elution buffer. At last, library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.

value: main olfactory epithelium

value: 3 month old

tag: gender

value: male


title: m1_AY_Y3_G4


title: m1_Young2_A9


title: Mut rep1


title: Mm.plasma.TraPR.Lexo.R3


title: WT rep2

value: wild type


title: WT rep1


title: m1_Young1_H13


title: m1_Young2_M3


city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

description:
FACS-ed feto-placental endothelial cells Sample 8 Mutant
sample name in processed data file:
Sample 8

data_processing:
The reads were aligned onto the mouse GRCm38 genome using TopHat 2.0.11
Gene abundance and differential expression were determined with Cufflinks 2.2.1 and expressed in fragments per kilobase per million mapped reads (FPKM). The cut off for expression was set at ≥1 FPKM.
Genes with a linear fold expression change greater than 1.5 and a Benjamini–Hochberg false discovery rate (FDR) <5% were considered differentially expressed.
FPKM values are included in this submission
Genome_build: GRCm38
Supplementary_files_format_and_content: FPKM values are included in this submission as tab-delimited text

growth_protocol: Feto-placental endothelial cells (FPEC - defined as CD31+/CD41- cells) were isolated by FACS from E16 labyrinthine zone placentae, using an Aria-Fusion cell sorter (BD Bioscience), with exclusion of cell duplets and dying cells (7AAD+).

extract_protocol:
Total RNA was extracted from sorted FPEC using RNeasy Plus Micro Kits (Qiagen – 74034). Quantity and quality were verified using the RNA 6000 Pico Kit (Agilent – 5067-1513) and an Agilent 2100 Bioanalyzer. Only RNA samples with RNA integrity numbers (RIN) >9.0 were used.
Total RNA (2 ng) was whole-transcriptome amplified using the Ovation RNA–Seq System V2 (NuGEN). To prepare the RNA–seq libraries the amplified cDNA (2μg per sample) was fragmented to 200bp using a Bioruptor Sonicator (Diagenode), end repaired and barcoded using the Ovation Rapid DR Library System (NuGEN).

value: feto-placental endothelial

tag: developmental stage

tag: Sex

value: Male

value: Mutant


description:
FACS-ed feto-placental endothelial cells Sample 6 Mutant
sample name in processed data file:
Sample 6


description:
FACS-ed feto-placental endothelial cells Sample 7 Mutant
sample name in processed data file:
Sample 7


description:
FACS-ed feto-placental endothelial cells Sample 5 Mutant
sample name in processed data file:
Sample 5


title: m1_AY_Y3_D8


title: 51-t22-c_S6_L001

city: Seattle

first: Richard

middle: G

last: James

state: WA

address: 1900 9th ave

institute: Seattle Children's Research Institute

description:
transfection 22, region 8-exon 4, RNA
51-t22-c_S6
processed data file: TableS3_RNA.xlsx

data_processing:
Library strategy: Amplicon
Illumina bcl2fastq v2.16 for base calling and demultiplex.
Paired-End read to mergeR algorithm to align read 1 and read 2 (https://www.h-its.org/downloads/pear-academic/).
Custom python scripts were used to keep sequences from homology directed repair and to trim to the editing region. Briefly, we kept entries that contained both the silent sgRNA blocking changes that we introduced for each sgRNA and a single additional NNK substitution within a single codon in the repair region associated with the ssODN library. Note that sequences containing the silent sgRNA blocking change without additional changes were also preserved. All remaining sequences were then trimmed so that they only contained the repair region associated with the ssODN library. Finally, we reverse complemented some fastq files so that all of the individual sequences corresponded with the coding strand, regardless of sequencing orientation.
To filter sequence by quality (minimum single base quality 25, average read quality 30) and extract counts for each variant present in fastq files from sequencing of gDNA from samples at day 2 and day 14, as well as in RNA at day 2, we used the Enrich2 software package (https://github.com/FowlerLab/Enrich2).
We used custom python scripts to scale, normalize and log transform the data from the growth and ibrutinib screens. For each variant in each replicate, we calculated fold-change by dividing the number of counts at day 14 by those at day 2. Next, the data generated from each replicate in each library was scaled (min-max) based on the average of the highest and lowest 2.5% of the measurements. For each replicate in each library, we then normalized each individual measurement to the scaled fold-change calculation of the silent guide blocking HDR sequence (‘_wt’). At this point, we log2-transformed each replicate. To calculate the “functional score” cited in the text and tables, we took the mean of the log2-transformed replicates. Lastly, for each variant, the lower bound of the 90% confidence interval was calculated by multiplying the standard error by the critical t-value (based on the number of degrees of freedom for each measurement) and subtracting this from the “functional score”. Likewise, the upper bound of the 90% confidence interval was calculated by multiplying the standard error by the critical t-value and adding this to the “functional score”.
Genome_build: GRCh38
Supplementary_files_format_and_content: *xlsx: Excel files include counts, normalized variant frequencies, scores for all variants.

organism: Homo sapiens

growth_protocol: TMD8 lymphoma cells were cultured at 37C in Iscove’s modified Dulbecco’s medium (IMDM) (Thermo Fisher Scientific) supplemented with 10% FBS and 55 mM beta-mercaptoethanol.

extract_protocol:
Zymo Research Genomic DNA Clean and Concentrator and Quick DNA/RNA kits.
Each sample was first amplified for 18 cycles with primers (see Table S6 for sequences) that generated 700-980bp amplicons using GXL PrimSTAR Polymerase (TaKaRa). Samples were then purified with Agencourt AMPure XP reagent (Beckman Coulter) at 0.8x beads to sample volume ratio according to manufacturer’s protocol and amplified for another 7 cycles with locus-specific primers containing Illumina adaptor sequences. The amplicons were purified with 1X AMPure beads, and reamplified for 7 cycles using primers containing Illumina p5 and p7 sequences and a unique sample index.

treatment_protocol: For each region, 2 x 10e6 human TMD8 cells were electroporated using a Neon (Invitrogen) with 2.5uM Cas9-gRNA complex (2.1:1.2 ratio) and 100pmol of ssODNs (equimolar mix of oligonucleotides). Exons 3-5 of CARD11 were divided into 9 regions to be targeted with a single gRNA (sgRNA). For each sgRNA, libraries of ssODNs for each amino acid position were ordered from IDT with mixed bases NNK (N= A, C, G, or T; K = G or T), or NNM for non target strands (M = A or C) to generate HDR templates with each of the 20 possible amino acids and one of the STOP codons. Each ssODN introduced (i) two synonymous substitutions at and near the PAM site to prevent Cas9-mediated cleavage of repaired DNA and (ii) a single NNK/NNM amino acid variant. Two days post transfection, a portion of the cells were lysed and their genomic DNA (gDNA) and mRNA isolated using Quick DNA Kit (Zymo Research) or AllPrep DNA/RNA Micro Kit (QIAGEN). The remainder of the cells were cultured in either IMDM with 50nM Ibrutinib or IMDM with vehicle (DMSO). On day 16 post transfection, gDNA from the cells was harvested again.

tag: cell line

value: lymphoma

value: untreated

tag: guide rna


title: 51-t22-g_S5_L001

description:
transfection 22, region 8-exon 4, gDNA
51-t22-g_S5
processed data file: TableS3_RNA.xlsx

tag: cell type


title: 51-t20-c_S4_L001

description:
transfection 20, region 8-exon 4, RNA
51-t20-c_S4
processed data file: TableS3_RNA.xlsx


title: 51-t20-g_S2_L001

description:
transfection 20, region 8-exon 4, gDNA
51-t20-g_S2
processed data file: TableS3_RNA.xlsx


description:
FACS-ed feto-placental endothelial cells Sample 3 Control
sample name in processed data file:
Sample 3

tag: tissue

value: Control


title: 34-t20-g_S1_L001

description:
transfection 20, region 5-exon 2, gDNA
34-t20-g_S1
processed data file: TableS3_RNA.xlsx


description:
FACS-ed feto-placental endothelial cells Sample 2 Control
sample name in processed data file:
Sample 2


title: 34-t20-c_S3_L001

description:
transfection 20, region 5-exon 2, RNA
34-t20-c_S3
processed data file: TableS3_RNA.xlsx


title: m1_Young1_M9

value: primary murine brain endothelial cells


title: C_P7

city: Barcelona

first: Ana

middle: Gámez

last: Valero

state: Barcelona

address: Universitat de Barcelona, Casanova 143, 4th Floor-Nord

country: Spain

institute: University of Barcelona (Neuroscience Institute)

description:
small RNA
RNA purification: miRVana Kit

data_processing:
Adapter trimming  Trimmomatic was used to remove the adapter sequences from the reads.
Read alignment  Reads were mapped to miRNA sequences using the efficient Bowtie2 algorithm
Quantification. For each sample, the number of reads that mapped to a particular miRNA sequence was counted.
Normalization. The count matrix was normalized through the weighted trimmed means of M-values (TMM)
Variables selection for biomarkers identification
Genome_build: mirBase version v20 (June 2013)
Supplementary_files_format_and_content: raw and normalized counts

source_name: Whole blood

growth_protocol: Platelets were isolated form fresh whole blood samples and mainteined at -80ºC until RNA isolation

extract_protocol:
Platelets were obtained by several centrifugation steps and final platelet-rich pellet was characterized by flow cytometry in order to check for the presence of leukocyte contamination. Platelet-rich pellets were thawed on ice. miRNA isolation was performed using the mirVana Paris Kit (Invitrogen). Briefly, 600 µL of lysis buffer and 1/10 of miRNA Homogenate Additive Mix were added to each pellet and incubated for 10 minutes on ice after vortexing. One volume of phenol-chloroform was added, mixed and centrifuged at 10,000 x g for 5 minutes. One-third and two-thirds volume of ethanol was added in 2 consecutive steps to the miRNA containing aqueous phase and passed through a filter column. After the recommended washing steps, miRNAs were obtained with 100 µL of elution buffer and stored at -80ºC until later analysis.
NEBNext Multiplex Small RNA Sample Preparation Set for Illumina (New England Biolabs)

tag: diagnosis

value: Healthy individual

value: M

value: Platelets


title: C_P6

description:
small RNA
RNA purification: miRVana Kit


title: m1_Young1_C1


title: TCF4-wt-2

city: Amsterdam

first: Marten

middle: Piet

last: Smidt

state: NH

address: Sciencepark 904

department: SILS

country: Netherlands

institute: UVA

data_processing:
adapter trimming and quality filtering
aligments (tophat 1.0.14/Bowtie 2.1.0)
mRNAseq readcounting (Htseq-count 0.6.1p1)
differential expression analysis WT vs Mut
Deseq 1.10.1 (R) for selection of differential expressed genes (137)
Genome_build: Mus musculus (GRCm38p4 Fasta and GFT format)
Supplementary_files_format_and_content: txt file, DESeq significant differential genes

source_name: Cortical dissected material E14.5

extract_protocol:
Dissected cortical material dfrom E14.5 mouse embryo’s, total RNA extraction (trizol)
RNAseq library construction from Total RNA samples (1-6) (Illumina “preparing samples for sequencing of mRNA” Rev. A ,September 2008)

treatment_protocol: WT vs KO

tag: sample type

value: neuronal material

tag: genotype/variation


title: TCF4-wt-3


title: TCF4-ko-3


title: C_P5

description:
small RNA
RNA purification: miRVana Kit

value: F


title: C_P4

description:
small RNA
RNA purification: miRVana Kit


title: TCF4-ko-2


description:
FACS-ed feto-placental endothelial cells Sample 4 Control
sample name in processed data file:
Sample 4


title: m1_Young1_L3


title: TCF4-ko-1


title: WT_H3K27ac

data_processing:
Raw sequencing reads were mapped to the mm9 genome with Bowtie by allowing up to two mismatches and keeping only uniquely mapped reads. PCR duplicated reads were removed with SAMtools.
H3K27ac ChIPseq peaks were identified with MACS version 2.1.0.
Defined H3K27ac peaks were then annotated to the mm9 genome with the Homer
Genome_build: mm9

source_name: tail tendon

growth_protocol: Tail tendons were obtained from WT and Mkx-/- mice and cut into small pieces, and washed  three times with PBS. The tissue fragments were digested with 0.2% collagenase (Life technologies) for 2hours at 37°C. The digest was centrifuged, and the pellet was suspended in Dulbecco’s modified Eagle’s medium (DMEM, low glucose; Gibco) with 10% (v/v) fetal bovine serum (FBS; Invitrogen) and 1% (v/v) penicillin-streptomycin (Gibco). At 100% confluence, cells were harvest for ChIP-seq experiments.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27ac antibody.
Libraries were constructed using NEBNext Ultra II DNA Library Prep Kit(E7645) following manufacture instructions.

value: tail tendon

value: WT

tag: age

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: m1_AY_Y3_J7


title: Mkx_KO_H3K27ac

value: Mkx-/-


title: C_P3

description:
small RNA
RNA purification: miRVana Kit


title: m1_Young1_M11


description:
FACS-ed feto-placental endothelial cells Sample 1 Control
sample name in processed data file:
Sample 1


title: m1_Young2_I15


title: m1_Young2_G15


title: m1_Young2_O11


title: DLB_P3

description:
small RNA
RNA purification: miRVana Kit

value: DLB patient


title: C_P2

description:
small RNA
RNA purification: miRVana Kit


title: TCF4-wt-1


title: C_P1

description:
small RNA
RNA purification: miRVana Kit


title: m1_AY_Y3_L6


title: JP38_VEH-untreated/SIV

type: RNA

city: San Antonio

first: Mahesh

last: Mohan

state: Texas

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

description: Test

data_processing:
QuantStudio run files representing all treatment groups and timepoints were analyzed using ExpressionSuite Software (Life Tech). The results from the ExpressionSuite software analysis containing five columns (well, sample, detector, task and CT values) were saved as a tab-delimited text file which was later imported and analyzed using the Omics Office StatMiner qPCR analysis software, TIBCO Spotfire, (Perkin Elmer, Waltham, MA). Omics Office StatMiner Software utilizes the comparative Cτ (ΔΔCτ) method to rapidly and accurately quantify relative gene expression across many genes and samples.
miRNA expression data was normalized to a combination of snoU6, RNU44 and RNU48
In all experiments, the CT upper limit was set to 28 meaning that all miRNA detectors with a CT value greater than or equal to 28 were excluded.
Due to the small sample size and exploratory nature of the study multiple comparisons correction was not applied.
ExpressionSuite v1.0.3 software automatically calculates all deltadeltaCT based fold-change calculations and provides p values from the uploaded QuantStudio data files.
Fold Change worksheet reports test/control (i.e., VEH-untreated/SIV vs Uninfected control) ratios.

label: FAM

organism: Macaca mulatta

source_name: VEH-untreated/SIV

label_protocol: microRNA profiling was performed using the TaqMan® OpenArray® Human microRNA panels (Life Tech) following the manufacturer’s instructions. Reverse transcription was first performed from 100 ng of total RNA using the microRNA reverse transcription kit. 2.5 µL of cDNA was preamplified using the TaqMan® PreAmp Master Mix kit. Preamplified products were first diluted and then loaded onto to TLDA plates. TLDA plates were run on the ABI 7900 HT Fast PCR system following the manufacturer’s recommended thermal cycling conditions.

extract_protocol: Total RNA (small and large) was extracted using the miRNeasy Mini kit (Qiagen). On-column DNase digestion was also performed to eliminate contaminating genomic DNA.

treatment_protocol: 7 animals were infected intravenously with 100 TCID50 SIVmac251 and 5 remained uninfected

value: male

tag: treatment

value: SIV Infected without Vehicle treatment

value: oropharyngeal mucosa


title: JR15_VEH-untreated/SIV

description: Test


title: DLB_P35

description:
small RNA
RNA purification: miRVana Kit


title: JR60_VEH-untreated/SIV

description: Test


title: KA05_VEH-untreated/SIV

description: Test


title: JJ71_VEH-untreated/SIV

description: Test


title: JD95_Uninfected Controls

description: Control

source_name: Uninfected Controls

value: none; untreated


title: P673_VEH-untreated/SIV

description: Test


title: m1_Young1_E12

extract_protocol:
Brain tissues were dissected using Miltenyi neural dissociation kit. Brain endothelial cells were isolated via FACS.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: DLB_P33

description:
small RNA
RNA purification: miRVana Kit


title: JD59_VEH-untreated/SIV

description: Test


title: GK22_Uninfected Controls

description: Control


title: GK11_Uninfected Controls

description: Control


title: DLB_P32

description:
small RNA
RNA purification: miRVana Kit


title: m1_Young2_F2


title: Whole seedlings, H2O2.bzip68.rep3

data_processing:
TopHat 2.1.0 software (Trapnell, Pachter and Salzberg, 2009) was used to map the reads to the Arabidopsis genome (TAIR10). RSEM 2.1.30 (Anders, Pyl and Huber, 2015) was used for statistical analysis of the read counts for each gene.
Genome_build: A. thaliana Ensemble 41 (TAIR10)
Supplementary_files_format_and_content: 20190704.bzip.counts.xlsx, Supplementary_Tables_S1_S2.BZIP68_CHIPSeq_peaks_v4.xlsx

growth_protocol: Arabidopsis seedlings were growth on 1/2 MS plates containing 3% sucrose and 0.8% agar for 14 days under 16h light/ 8h dark condition(with light 125 umoles/m2 seg )

extract_protocol: RNA was extracted using the Agilent Plant RNA Isolation Mini kit according to the manufacturer’s instructions. Bar-coded mRNA libraries were constructed by BGI (Shenzhen, China) using the Illumina’s reagents and protocols according to the manufacturer’s instruction. Samples were sequenced on Illumina HiSeq 2500 system.

treatment_protocol: Lowlight treatment: seedlings of wildtype and bzip68 mutant were grown on 1/2 MS plates in presence of white light (30 umoles/m2 seg). Mock: seedlings of wildtype and bzip68 mutant were grown on 1/2 MS plates in presence of white light (125 umoles/m2 seg) for 14 days then sparyed with water supplied with 0.01% triton X-100. H2O2 treatment: seedlings of wildtype and bzip68 mutant were grown on 1/2 MS plates in presence of white light (125 umoles/m2 seg) for 14 days then sparyed with 5 mM H2O2 supplied with 0.01% triton X-100.

value: whole seedlings


title: GJ01_Uninfected Controls

description: Control


title: JC65_Uninfected Controls

description: Control


title: DLB_P31

description:
small RNA
RNA purification: miRVana Kit


title: Whole seedlings, H2O2.bzip68.rep1


title: Whole seedlings, mock.bzip68.rep3

value: mock


title: Whole seedlings, H2O2.bzip68.rep2


title: Whole seedlings, mock.bzip68.rep2


title: m1_Young2_F7

value: primary murine brain endothelial cells


title: Whole seedlings, mock.bzip68.rep1


title: DLB_P1

description:
small RNA
RNA purification: miRVana Kit


title: m1_Young1_K17


title: m1_Young1_I12


title: Whole seedlings, H2O2.wt.rep3

value: wt


title: DLB_P34

description:
small RNA
RNA purification: miRVana Kit


title: Whole seedlings, H2O2.wt.rep2


title: m1_Young1_N16


title: Whole seedlings, H2O2.wt.rep1


title: m1_AY_Y3_B17


title: m1_Young1_F10


title: Whole seedlings, mock.wt.rep2


title: m1_AY_Y3_I1


title: Whole seedlings, LowLight.bzip68.rep3

growth_protocol: Arabidopsis seedlings were growth on 1/2 MS plates containing 3% sucrose and 0.8% agar for 14 days under 16h light/ 8h dark condition(with light 30 umoles/m2 seg )

value: LowLight


title: Whole seedlings, LowLight.bzip68.rep2


title: m1_Young2_C11


title: Whole seedlings, mock.wt.rep1


title: Whole seedlings, LowLight.bzip68.rep1


title: Whole seedlings, LowLight.wt.rep2


title: Whole seedlings, LowLight.wt.rep1


title: m1_Young2_M4


title: Cvi.ozone_II

city: Örebro

first: Luis

last: Morales

address: Fakultetsgatan 1

department: School of Science and Technology

country: Sweden

institute: Örebro University

data_processing:
The quality of raw reads was first inspected in Chipster using FastQC.
Removal of adapter sequences and trimming and cropping of the reads was done using Trimmomatic-0.33 (Bolgert et al., 2014) in single-end mode. The bases with a quality score less than 20 were trimmed from the beginning and the end of the sequences, and the reads shorter than 30 bases were removed from the analysis (-phred33, LEADING:20, TRAILING:20 and MINLEN:30).
Filtered reads were mapped to the Arabidopsis transcript reference database AtRTD2 (Zhang et al., 2017) using Kallisto V-0.43.0 (CMD:quant) (Bary et al., 2016) with 4000 bootstrap sets. The final count table for each biological replicate was obtained as the mean of the bootstrap runs.
Genome_build: Arabidopsis transcript reference database AtRTD2
Supplementary_files_format_and_content: Matrix-table including gene counts for each sample

source_name: Cvi.ozone_whole rosette

growth_protocol: Seeds were sown on 1:1 peat: vermiculite, stratified at 4°Cfor three days in the dark, and then grown at 22°C/19°C for a week. Subsequently four geminated seedlings were transplanted into 8 × 8 cm pots containing new 1:1 peat: vermiculite mixture. The pots were randomly placed into a controlled chamber (Weiss Bio1300; Weiss Gallenkamp), where plants were grown at 22°C/19°C, and relative humidity of 70%/90%, under a 12-h light/12-h dark cycle for two weeks.

extract_protocol:
Four rosettes per genotype from control and ozone treatment were pooled, frozen into liquid nitrogen and stored at -80°C. Three biological replicates of RNA were isolated with with GeneJet Plant RNA purification Mini Kit (Thermo Scientific). RNA quality and concentration were measured using Agilent 2100 Bioanalyzer and NanoDrop.
Libraries were prepared using 1µg total RNA following instructions from Illumina TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: Three weeks old plants were exposed with 350 nL L-1 ozone and control clean air for two hours.

value: 3 weeks old plants

value: 350 nL L-1 ozone for 2hrs

value: whole rosette


title: m1_Young1_I1


title: Cvi.ozone_III


title: Whole seedlings, LowLight.wt.rep3


title: Cvi.control_III

source_name: Cvi.control_whole rosette

value: control


title: Cvi.ozone_I


title: m1_Young2_P4


title: m1_Young1_I2


title: Whole seedlings, mock.wt.rep3


title: sham.3d.EC

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

description: cardiac endothelial cells, 3days sham

hyb_protocol: 100µl hyb-cocktail prepared from labeled low molecular weight RNA was hybridized for 16h at 48°C to GeneChip miRNA array. Microarrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 7G.

data_processing: Data were preprocessed in the R/Bioconductor environment using the affy package; background correction, normalization and probeset summary were performed with the „rma“ function using default parameter settings.

label: biotin

source_name: murine cardiac endothelial cells

label_protocol: 80µl of pooled total RNA were preprocessed with the Flash-Tag HSR kit (Genisphere, Hatfield, PA, USA) following the manufacturer's protocol, thereby labeling the low molecular weight RNA with biotin.

extract_protocol: Adult murine hearts were perfused with collagenase to get sigle cell suspension followed by gravitational centrifugation, cell pre-plating and magnetic cell sorting to obtain isolated cellular fractions. Total RNA was isolated using miRNeasy kits (Qiagen).

treatment_protocol: surgical procedure on mice- transaortic constriction or sham

tag: pool

tag: time point

value: sham

tag: fraction

value: endothelial cells


title: TAC.3d.AMCF

description: cardiac fibroblasts, 3days TAC

source_name: murine cardiacfibroblasts

value: Transaortic constiction

value: adult mouse cardiac fibroblasts


title: sham.3d.AMCF

description: cardiac fibroblasts, 3days sham


title: sham.3d.CMC

description: cardiomyocytes, 3days sham

source_name: murine cardiomyocytes

value: cardiomyocytes


title: Cvi.control_II


title: Cvi.control_I


title: m1_Young1_L11

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: raw count table


title: m1_Young1_B17


title: TAC.3d.EC

description: cardiac endothelial cells, 3days TAC


title: TAC.2w.EC

description: cardiac endothelial cells, 2weeks TAC


title: m1_AY_Y3_E11


title: TAC.3d.CMC

description: cardiomyocytes, 3days TAC


title: Mouse LSK [RPI10]

first: Luyi

last: Tian

state: MA

address: 415 main st Cambridge

institute: Broad institute

description:
RPI10
cellular barcode: 8bp as in barcode_annotation.csv
umi position: 6bp after the cell barcode
barcode position: R1 first eight base
Index sorted hematopoietic stem and progenitor cells from Dach1 reporter mice, FACS value in Naik.SCORE_NN168_SeqPrimer layout_Nov19.xlsx

data_processing:
Gene counting matrix generated using scPipe 1.4.0.
Reads were aligned using Rsubread 1.29.6.
Genome_build: ENSEMBL Homo_sapiens.GRCh38.88
Supplementary_files_format_and_content: Gene counting matrix, rows represent genes and each column is a well.

source_name: hematopoietic stem and progenitor cells with and without Bcor knockout

growth_protocol: All mice were bred and maintained under specific pathogen-free conditions at WEHI, according to institutional guidelines. C57BL/6 (CD45.2), C57BL/6 Pep3b (CD45.1), Cas9-Tg or Dach1-GFP mice aged between 8-16 weeks were used.

extract_protocol:
Bone marrow from C57BL/6-TG (UBC-GFP) was extracted and cells enriched for ckit (2B8 conjugated to APC) via magnetic activated cell sorting (MACS) positive selection using anti-APC beads (Miltenyi Biotec). The ckit-enriched fraction was subsequently stained for Sca-1 (E13 161-7 conjugated to Alexa Fluor 594 or Alexa Fluor 680), IL-7R (A7R34-2.2 conjugated to biotin with streptavidin-PECy7). C-kithi Sca1+IL-7R¬–CD11blo HSPCs were sorted using the single cell mode of a BD Influx, BD FacsARIA W or BD FacsAria L. Single cells, or 100-cell population controls, were sorted into 96 well round bottomed wells pre-seeded with 1.5 x 106 total C57BL/6 BM cells (filler cells) and cultured in Flt3L conditioned medium at 37 °C and 5% CO2 for 2.5 days.
For CEL-seq2, single cells were flow sorted into chilled 384-well PCR plates containing 1.2ul of primer/ERCC mix using a BD FACSAria III flow cytometer. Sorted plates were sealed and immediately frozen upside down at -80C. Then these plates, together with the mRNA mixture plates, were taken from -80C and processed using an adapted Cel-Seq2 protocol with the following variations. We pooled the samples after the first strand synthesis and the second strand synthesis was performed using NEBNext Second Strand Synthesis module. NucleoMag NGS Clean-up and Size select magnetic beads were used for all DNA purification and size selection steps.

treatment_protocol: Briefly, bone marrow cells were extracted from C57BL/6 mice and cultured at a density of 1.5 x 10e6 in 96-round bottom plates with DC culture medium and 200 ng/ml Flt3L obtained from Dr Jian-Guo Zhang (WEHI) for experiments in Figure 1, and from BioXcell (#BE0098) for experiments in Figures 2-4. To generate Flt3-conditioned medium that can sustain the growth and differentiation of isolated DC progenitors, medium derived from Flt3L cultures after 3.5 days was centrifuged to remove cells, then passed through a 0.22-μm filter, and frozen aliquots stored at –80°C, and supplemented with additional Flt3L when thawed, as described previously.

value: hematopoietic stem and progenitor cells


title: Mouse LSK [RPI8]

description:
RPI8
cellular barcode: 8bp as in barcode_annotation.csv
umi position: 6bp after the cell barcode
barcode position: R1 first eight base
Index sorted hematopoietic stem and progenitor cells from Dach1 reporter mice, FACS value in Naik.SCORE_NN168_SeqPrimer layout_Nov19.xlsx


title: Mouse LSK [RPI7]

description:
RPI7
cellular barcode: 8bp as in barcode_annotation.csv
umi position: 6bp after the cell barcode
barcode position: R1 first eight base
Index sorted hematopoietic stem and progenitor cells from Dach1 reporter mice, FACS value in Naik.SCORE_NN168_SeqPrimer layout_Nov19.xlsx


title: Mouse LSK [RPI6]

description:
RPI6
cellular barcode: 8bp as in barcode_annotation.csv
umi position: 6bp after the cell barcode
barcode position: R1 first eight base
Index sorted hematopoietic stem and progenitor cells from Dach1 reporter mice, FACS value in Naik.SCORE_NN168_SeqPrimer layout_Nov19.xlsx


title: m1_Young1_D15


title: Mouse LSK [RPI2]

description:
RPI2
cellular barcode: 8bp as in barcode_annotation.csv
umi position: 6bp after the cell barcode
barcode position: R1 first eight base
Index sorted hematopoietic stem and progenitor cells from Dach1 reporter mice, FACS value in Naik.SCORE_NN168_SeqPrimer layout_Nov19.xlsx


title: Mouse LSK [RPI4]

description:
RPI4
cellular barcode: 8bp as in barcode_annotation.csv
umi position: 6bp after the cell barcode
barcode position: R1 first eight base
Index sorted hematopoietic stem and progenitor cells from Dach1 reporter mice, FACS value in Naik.SCORE_NN168_SeqPrimer layout_Nov19.xlsx


title: m1_AY_Y3_H1


title: TAC.2w.CMC

description: cardiomyocytes, 2weeks TAC


title: m1_AY_Y3_E6


title: 2_KO_rep3

city: Pittsburgh

first: Amanda

middle: Catherine

last: Poholek

state: Pennsylvania

address: 4401 Penn Ave., Rangos Research Center 8129

department: Pediatrics

institute: University of Pittsburgh

data_processing:
Reads were aligned using TopHat and Bowtie2 following gene identification using Cufflinks.
Gene expression values (FPKM; fragments per kilobase exon per million mapped reads) were calculated using Cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: YFP+ T cells

extract_protocol:
CD4+YFP+ Th17 cells were sorted on a FACSAria II, directly into SmartSeq low-input RNA kit lysis bufferand mRNA prepared according to manufacturer's protocol.
Libraries were prepared using Nextera XT DNA library prep kits

treatment_protocol: Th17 WT (5 mice total, combined from two separate experiments) and Th17ΔSTAT3 (4 mice total combined from two separate experiments) were immunized with MOG(35-55) in CFA in flanks to induce EAE. On day 10 post-immunization dLN were harvested and stained for sorting.

tag: background strain

tag: genotype

value: IL17CrexROSAYFPxSTAT3fl/fl (KO)

tag: immunization

value: MOG(35-55) in CFA subcutaneously

value: YFP+ T cells


title: m1_AY_Y3_P4

first: Michelle

last: Chen

address: 318 Campus Drive

institute: Stanford

source_name: three-mo mouse BEC


title: TAC.4w.EC

description: cardiac endothelial cells, 4weeks TAC


title: 2_KO_rep1


title: 1_KO_rep2


title: 1_KO_rep1


title: TAC.4w.CMC

description: cardiomyocytes, 4Weeks TAC


title: 2_WT_rep2

value: IL17CrexROSAYFPxSTAT3fl/+ (WT)


title: 2_WT_rep1


title: TAC.4w.AMCF

description: cardiac fibroblasts, 4weeks TAC


title: TAC.2w.AMCF

description: cardiac fibroblasts, 2weeks TAC


title: 1_WT_rep3


title: m1_Young2_K12

value: primary murine brain endothelial cells


title: 1_WT_rep2


title: 1_WT_rep1


title: sham.2w.EC

description: cardiac endothelial cells, 2weeks sham


title: m1_Young2_D10


title: m1_AY_Y3_J12


title: sham.2w.AMCF

description: cardiac fibroblasts, 2weeks sham


title: m1_Young1_F14


title: sham.2w.CMC

description: cardiomyocytes, 2weeks sham


title: m1_Young2_L18


title: m1_Young1_D1


title: Placental labyrinthine zone_Igf2EpiKO [MeoxxJJ E19 51-6]

description: RNA from E19 Mus musculus Placental labyrinthine zone - Igf2EpiKO

hyb_protocol: The biotinylated ssDNA was hybridized onto Affymetrix GeneChip MouseGene 1.0 ST arrays, which screen the expression of 28,853 genes using 770,317 probes.

scan_protocol: Signals were detected using an Affymetrix GeneChip Scanner 3000 7G and analyzed using Partek Genomics Suite 6.4 software (St. Louis, MO, USA).

data_processing: Array profiling was performed using the Mouse Gene 1.0 ST Array (Affymetrix) and the analysis of the data was performed using GeneSpring GX 12.1 (Agilent, Santa Clara, CA, USA), with two algorithms: RMA (Robust Multiarray Average) and PLIER (Probe Logarithmic Intensity Error).

source_name: Placental labyrinthine zone

label_protocol: The total RNA was subjected to reverse transcription to cDNA using random hexamers tagged with T7 promoter and this was subsequently used as a template for cRNA amplification. The cRNA was then subjected to another round of reverse transcription followed by biotin labeling as described in the Affymetrix (Santa Clara, CA, USA) GeneChip whole transcript sense target labeling assay manual and labeled using the Affymetrix whole transcript kit according to the manufacturer's instructions

extract_protocol: Total RNA was extracted using RNeasy Midi Kits (Qiagen – 75144) and quantity and quality were verified using RNA 6000 Nano Kit (Agilent – 5067-1511) and an Agilent 2100 Bioanalyzer. Only RNA samples with RNA integrity numbers (RIN) >9.0 were used.

treatment_protocol: Conceptuses were isolated from the mother's uterus at the embryonic day 19 (E19). Labyrinthine zone were micro-dissected under microscope from each placenta and flash-frozen in liquid N2 and stored at -80C until RNA extraction.

tag: strain

value: Placental labyrinthine zone

tag: developmental stage

tag: Sex

value: male


title: m1_Young2_I4

tag: cell type


title: m1_Young1_H8


title: m1_AY_Y3_D9


title: m1_AY_Y3_J15


title: OMD_knockout1

city: London

first: Alex

last: Leung

state: London

address: 11-43 Bath Street

institute: UCL Institute Of Ophthalmology

data_processing:
Samples were sequenced on the NextSeq 500 instrument (Illumina, San Diego, US) using a 75bp single read run with a corresponding 16bp UMI read.
Run data were demultiplexed and converted to fastq files using Illumina’s bcl2fastq Conversion Software v2.19.
Fastq files were then aligned to the human genome Mus musculus GRCm38 using RNA-STAR 2.5.2b then UMI deduplicated using Je-suite (1.2.1).
Reads per transcript were counted using FeatureCounts and differential expression was estimated using the BioConductor package SARTools, a DESeq2 wrapper.
Genome_build: hg38
Supplementary_files_format_and_content: comma-separated text file, with columns of gene names, baseMean, log2FoldChange, lfcSE (standard error or the log2FoldChange), stat (Wald statistic), pvalue and padj

source_name: bladder tissue

extract_protocol:
Bladder tissue samples were excised and homogenised using a rotor-stator homogeniser. After centrifugation at 8,000 x g for 15 seconds and subsequent binding and washing steps, the samples were treated with DNase digestion for 20 minutes and eluted. RNA was quantified and qualified by Agilent’s 2200 Tapestation, measuring RNA concentration and agarose gel electrophoresis.
Samples were processed using the KAPA mRNA HyperPrep Kit (p/n KK8580) according to manufacturer’s instructions. Briefly, mRNA was isolated from total RNA using Oligo dT beads to pull down poly-adenylated transcripts. The purified mRNA was fragmented using chemical hydrolysis (heat and divalent metal cation) and primed with random hexamers.  Strand-specific first strand cDNA was generated using Reverse Transcriptase in the presence of Actinomycin D.  This allows for RNA dependent synthesis while preventing spurious DNA-dependent synthesis.  The second cDNA strand was synthesised using dUTP in place of dTTP, to mark the second strand. The resultant cDNA is then “A-tailed” at the 3’ end to prevent self-ligation and adapter dimerisation. Full length xGen adaptors (IDT), containing two unique 8bp sample specific indexes, a unique molecular identifier (N8) and a T overhang are ligated to the A-Tailed cDNA.  Successfully ligated cDNA molecules were then enriched with limited cycle PCR (50ng of starting material, 15 PCR cycles). The high fidelity polymerase employed in the PCR is unable to extend through uracil. This means only the first strand cDNA is amplified for sequencing, making the library strand specific (first-strand). Libraries to be multiplexed in the same run are pooled in equimolar quantities, calculated from Qubit and Bioanalyser fragment analysis.

tag: tissue

value: bladder tissue

value: OMD-/-


title: OMD_knockout2


title: PRELP_knockout3

value: PRLEP-/-


title: WT capture Hi-C

city: Baltimore

first: Xiang

last: Qiu

address: 251 Bayview Blvd.

institute: National Institutes of Health

data_processing:
The raw capture Hi-C data in FASTQ files were processed by HiCUP (version=0.7.2) with the settings of ‘Arima’ (genome digest file generated with hiccup_digester --arima) to mm10, with mapping tool Bowtie2 (version=2.3.5) . The processed reads in BAM files from HiCUP were further process in to HIC file through Juicer (version=1.6.0) for visualization of Juicebox  for raw interaction data, with the contact matrix resolution settings 200,1000,5000,25000,50000.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data files are in HIC format, which were generated by Juicer and can be visualized by Juicebox or other furthur analysis.

source_name: Pro-B cell line

growth_protocol: Pro-B cell lines were grown with complete 1640 RPMI medium (10% fetal bovine serum and 0.05mM 2-Mercaptoethanol)

extract_protocol:
The Hi-C preparation was performed using the Arima-HiC Kit (Arima Genomics, Inc. Cat# A510008). Briefly, D345 cells with  (106 cells per mutant or WT) were crosslinked using 37% formaldehyde. Fixed cells were lysed, digested with two restriction enzymes provided in Arima Kit and then ligated and de-crosslinked. Re-ligated fragments were sheared using a Covaris sonicator. DNA fragments of 200-600 bp were selected using the SPRI beads (Beckman Coulter, Inc. Cat#: B23318) and then enriched using the Enrichment Beads provided in Arima-HiC Kit.
Enriched DNA fragments were processed into Illumina compatible sequencing libraries with TruSeq unique dual (UD) index adapters (Cat# 20020590) using KAPA Hyper Prep reagents (Roche Molecular Systems, Inc. Cat# KK8500).   The customize SureSelect Target Enrichment probes were designed over the genomic interval (mm10, chr12: 113,201,001-116,030,000) by the SureDesign tool and manufactured by Agilent (Agilent Technologies, Inc.). Hi-C Libraries were hybridized to the probes according to Agilent protocol. Libraries were pooled and loaded onto Illumina NextSeq sequencer for paired-end 150 bp sequencing.
Capture Hi-C

treatment_protocol: We performed capture Hi-C to explore chromatin struture in pro-B cells at the WT or IGCR1 deficient IgH alleles without any treatment.

value: Pro-B cell line

value: Bone marrow

value: Wild type


title: WT duplicate capture Hi-C


title: D345/IGCR1-/-(1) duplicate capture Hi-C


title: OMD_knockout3


title: Placental labyrinthine zone_Igf2EpiKO [MeoxxJJ E19 51-5]


title: PRELP_knockout2


title: m1_Young1_F12

city: Stanford


title: PRELP_knockout1


title: Placental labyrinthine zone_Igf2EpiKO [MeoxxJJ E19 42-2]


title: Placental labyrinthine zone_Igf2EpiKO [MeoxxJJ E19 43-2]


title: Placental labyrinthine zone_Igf2EpiKO [MeoxxJJ E19 42-1]


title: D345/IGCR1-/-(1) capture Hi-C


title: WildType3

value: wild type


title: WildType2


title: WildType1


title: Placental labyrinthine zone_Igf2EpiKO [MeoxxJJ E19 43-8]


title: Placental labyrinthine zone_control [MeoxxJJ E19 52-2]

description: RNA from E19 Mus musculus Placental labyrinthine zone - Control (Igf2+/flox)

value: Control (Igf2+/flox)


title: Placental labyrinthine zone_control [MeoxxJJ E19 51-1]


title: m1_AY_Y3_K15


title: m1_Young2_K1


title: Placental labyrinthine zone_control [MeoxxJJ E19 43-7]


title: Placental labyrinthine zone_control [MeoxxJJ E19 43-9_2]


title: m1_Young1_D7


title: m1_Young2_D17


title: Placental labyrinthine zone_control [MeoxxJJ E19 43-6]


title: m1_AY_Y3_O3


title: m1_AY_Y3_L2


title: m1_Young1_J5


title: WildType4


title: m1_AY_Y3_G2


title: m1_Young1_F11


title: m1_Young1_O8


title: Mm.plasma.TraPR.TRUseq.R3

description: processed data file: Mm_plasma_miRNA_counts.csv

data_processing:
Illumina Casava1.8 software used for basecalling.
Trimming of reads with Trimmomatic 0.36
Mapping to the Arabidopsis thaliana genome (TAIR10) with Bowtie 1.2.1.1
Mapping to the Drosophila melanogaster genome (BDGP6) with Bowtie 1.2.1.1
Mapping to the Mus musculus genome (GRCm38) with Bowtie 1.2.1.1
Read counting to miRBase annotation with Rsubread 1.26.1
Read normalization with DEseq2.
Genome_build: TAIR10
Genome_build: BDGP6
Genome_build: GRCm38
Supplementary_files_format_and_content: comma separated text files of library and log2 normalized miRNA read counts

extract_protocol:
RNA was extracted with the standard TRIzol method or with the TRaPR isolation method.
Libraries were prepared with from TRIzol or TRaPR isolated RNA with the TRUseq or Lexogen sRNA library preparation kits or with a custom library preparation protocol.

value: plasma

tag: library preparation

value: TruSeq

tag: rna isolation

value: TraPR

tag: molecule subtype

value: small RNA


title: m1_Young2_O18


title: Mm.plasma.TraPR.TRUseq.R2


title: Mm.plasma.TraPR.TRUseq.R1


title: m1_Young1_L5


title: Mm.plasma.TRIzol.TRUseq.R3

value: TRIzol


title: NCH601 cell line-derived xenograft rep 2 [NCH601_X2]

city: Luxembourg

first: Anna

last: Golebiewska

state: Strassen

address: 84 Val Fleuri

department: Department of Oncology

country: Luxembourg

institute: Luxembourg Institute of Health

hyb_protocol: Upon hybridization, microarrays were washed, stained and scanned according to manufacturer’s standard procedures

scan_protocol: Microarrays were scanned with Affymetrix GeneChip Scanner GCS3000 system according to manufacturer standard procedures. Affymetrix GeneChip Command Console Scan Control 4.0.0.1567 was used for image processing

data_processing: Affymetrix CEL files containing hybridization raw signal intensities were processed to gene expression signals using the RMA (robust multichip average) algorithm implemented in the oligo package (version 1.44.0). hugene10sttranscriptcluster.db package version 8.7.0 was then used to map Affymetrix ID to entrez gene ID.

label: Biotin

source_name: Human GBM cell line-derived xenograft

label_protocol: the Affymetrix WT Terminal & Labeling kit before being hybridized on Affymetrix arrays according to the manufacturer’s instructions (protocol P/N 702808 Rev.6)

extract_protocol: Total RNA was extracted using the QIAGEN® RNeasy Mini Kit according to the manufacturer’s protocol

tag: cell line source

tag: tissue/cell type

value: GBM  cell line grown in mouse brain

tag: sample type

value: FACS-sorted human tumor Cell culture


title: m1_AY_Y3_G18

value: primary murine brain endothelial cells


title: Mm.plasma.TRIzol.TRUseq.R2


title: Mm.plasma.TRIzol.TRUseq.R1


title: NCH601 cell line-derived xenograft rep 4 [NCH601_X4]


title: NCH601 cell line-derived xenograft rep 3 [NCH601_X3]


title: m1_AY_Y3_C7


title: NCH601 cell line-derived xenograft rep 1 [NCH601_X1]


title: NCH601 cell line rep 3 [NCH601_C3]

source_name: Human GBM derived stem-like cell line

value: GBM cells in serum-free culture

value: Cell culture


title: NCH601 cell line rep 1 [NCH601_C1]


title: NCH601 cell line rep 2 [NCH601_C2]


title: Placental labyrinthine zone_control [MeoxxJJ E19 43-4]

value: Placental labyrinthine zone

value: male


title: Mm.liver.RNaseT1.TraPR.R3

description: processed data file: Mm_liver_miRNA_counts.csv

value: liver

value: RNaseT1 & TraPR


title: m1_Young2_L16


title: Mm.liver.RNaseT1.TraPR.R1


title: NCH644 cell line-derived xenograft rep 2 [NCH644_X2]


title: NCH644 cell line-derived xenograft rep 1 [NCH644_X1]


title: NCH644 cell line-derived xenograft rep 3 [NCH644_X3]


title: Mm.liver.TraPR.R3


title: NCH644 cell line rep 3 [NCH644_C3]


title: m1_AY_Y3_M8


title: Mm.liver.TraPR.R2


title: m1_Young2_J5


title: Mm.liver.RNaseT1.TRIzol.R3

value: RNaseT1 & TRIzol


title: Mm.liver.RNaseT1.TRIzol.R2


title: m1_AY_Y3_I12


title: NCH644 cell line rep 2 [NCH644_C2]


title: Mm.liver.TRIzol.R3


title: Mm.liver.RNaseT1.TRIzol.R1


title: Mm.liver.RNaseT1.TraPR.R2


title: m1_Young1_J3


title: Mm.liver.TRIzol.R2


title: m1_AY_Y3_G15


title: NCH421k cell line-derived xenograft rep 4 [NCH421k_X4]


title: NCH421k cell line-derived xenograft rep 3 [NCH421k_X3]


title: m1_Young2_I18


title: NCH421k cell line-derived xenograft rep 2 [NCH421k_X2]


title: RK9: Prefrontal Pyramidal Cortex

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

data_processing:
Illumina RTA v1.12 was used for base calling, and Illumina bc12fastq v2.20 for demultiplexing and fastq file generation
Sequenced reads were pre-processed using Trimmomatic and Flexbar. Reads were aligned to GRCm38 genome using STAR aligner with parameters trimLeft=10, minTailQuality=15, minAverageQuality=20, and minReadLength=30.
Aligned reads were converted to gene counts using featureCounts. Outputs for different cells were merged into a single file (ENS_counts.tsv) using custom Python code
Ensembl names were converted to gene names using Ensembl's Mus_musculus.GRC38.86.gtf file (gene_counts.tsv)
Reads were normalized using scran, and normalized values are stored in normalized_gene_counts.tsv
Genome_build: GRCm38
Supplementary_files_format_and_content: tab delimited text files. ENS_counts.tsv contains raw counts, with genes labeled by their Ensembl ENS numbers. gene_counts.tsv contains raw counts, with genes labeled by their gene names. normalied_gene_counts.tsv contains normalized (scran) counts of cells that passed quality control

source_name: Prefrontal Pyramidal Cortex

extract_protocol:
single cell cytosol extraction via patch pipette
Nextera XT

tag: side

value: Knockout Prefrontal Cortex Pyramidal D2 Cell

tag: quality control

value: Passed

tag: age

value: 32 days


title: NCH644 cell line rep 1 [NCH644_C1]


title: RK8: Prefrontal Pyramidal Cortex


title: RK7: Prefrontal Pyramidal Cortex


title: m1_Young2_G13


title: Mm.liver.TraPR.R1

value: TruSeq


title: NCH421k cell line rep 6 [NCH421k_C6]


title: RK23: Prefrontal Pyramidal Cortex


title: m1_AY_Y3_C2


title: RK5: Prefrontal Pyramidal Cortex

value: Knockout Prefrontal Cortex Pyramidal D1 Cell


title: RK22: Prefrontal Pyramidal Cortex


title: RK21: Prefrontal Pyramidal Cortex


title: RK2: Prefrontal Pyramidal Cortex

value: 31 days


title: RK18: Prefrontal Pyramidal Cortex


title: m1_Young1_K12


title: RK15: Prefrontal Pyramidal Cortex


title: RK6: Prefrontal Pyramidal Cortex


title: Mm.liver.TRIzol.R1

value: TRIzol

value: small RNA


title: m1_Young2_N1


title: RK13: Prefrontal Pyramidal Cortex


title: RK10: Prefrontal Pyramidal Cortex


title: RK1: Prefrontal Pyramidal Cortex

value: Failed


title: m1_AY_Y3_O1

value: primary murine brain endothelial cells


title: R9: Prefrontal Pyramidal Cortex

value: No Knock Out

value: Prefrontal Cortex Pyramidal D2 Cell

value: 30 days


title: m1_Young2_P8


title: R77: Prefrontal Pyramidal Cortex

value: 35 days


title: R75: Prefrontal Pyramidal Cortex


title: NCH421k cell line-derived xenograft rep 1 [NCH421k_X1]

value: GBM  cell line grown in mouse brain

value: FACS-sorted human tumor Cell culture


title: NCH421k cell line rep 5 [NCH421k_C5]

value: GBM cells in serum-free culture

value: Cell culture


title: R74: Prefrontal Pyramidal Cortex

value: Passed


title: NCH421k cell line rep 3 [NCH421k_C3]


title: m1_Young1_M16


title: m1_AY_Y3_M16


title: R70: Prefrontal Pyramidal Cortex

value: 34 days


title: NCH421k cell line rep 1 [NCH421k_C1]


title: NCH421k cell line rep 2 [NCH421k_C2]


title: R7: Prefrontal Pyramidal Cortex


title: U251 cell line-derived xenograft rep 2 [U251_X2]


title: m1_Young2_K13


title: R68: Prefrontal Pyramidal Cortex

value: Prefrontal Cortex Pyramidal D1 Cell


title: U251 cell line-derived xenograft rep 1 [U251_X1]


title: R76: Prefrontal Pyramidal Cortex


title: R65: Prefrontal Pyramidal Cortex

value: 33 days


title: NCH421k cell line rep 4 [NCH421k_C4]


title: R67: Prefrontal Pyramidal Cortex


title: m1_Young2_A14


title: U251 cell line rep 3 [U251_C3]

source_name: Human GBM derived adherent cell line

value: GBM cells in adherent culture


title: R64: Prefrontal Pyramidal Cortex


title: m1_AY_Y3_A9


title: R61: Prefrontal Pyramidal Cortex


title: R71: Prefrontal Pyramidal Cortex


title: R58: Prefrontal Pyramidal Cortex

value: 29 days


title: m1_AY_Y3_B14


title: R57: Prefrontal Pyramidal Cortex


title: m1_Young2_E8


title: R56: Prefrontal Pyramidal Cortex


title: R50: Prefrontal Pyramidal Cortex

value: 31 days


title: R52: Prefrontal Pyramidal Cortex


title: m1_Young2_K16


title: R5: Prefrontal Pyramidal Cortex


title: R47: Prefrontal Pyramidal Cortex


title: R48: Prefrontal Pyramidal Cortex


title: m1_Young1_B7


title: U251 cell line rep 1 [U251_C1]


title: R46: Prefrontal Pyramidal Cortex


title: m1_AY_Y3_N1


title: R45: Prefrontal Pyramidal Cortex


title: R43: Prefrontal Pyramidal Cortex


title: R44: Prefrontal Pyramidal Cortex


title: m1_Young1_E9


title: U87 cell line-derived xenograft rep 2 [U87_X2]


title: U87 cell line-derived xenograft rep 3 [U87_X3]


title: R40: Prefrontal Pyramidal Cortex


title: U251 cell line rep 2 [U251_C2]


title: R41: Prefrontal Pyramidal Cortex


title: R38: Prefrontal Pyramidal Cortex


title: U87 cell line rep 3 [U87_C3]


title: U87 cell line-derived xenograft rep 1 [U87_X1]


title: m1_Young1_G14


title: U87 cell line rep 6 [U87_C6]


title: U87 cell line rep 4 [U87_C4]


title: R36: Prefrontal Pyramidal Cortex


title: m1_Young2_P17


title: R37: Prefrontal Pyramidal Cortex


title: m1_Young2_I11


title: R34: Prefrontal Pyramidal Cortex

value: 28 days


title: m1_Young1_I7

value: primary murine brain endothelial cells


title: m1_Young1_M5


title: R32: Prefrontal Pyramidal Cortex

value: No Knock Out


title: U87 cell line rep 5 [U87_C5]


title: R33: Prefrontal Pyramidal Cortex


title: R42: Prefrontal Pyramidal Cortex

value: Prefrontal Cortex Pyramidal D2 Cell


title: R25: Prefrontal Pyramidal Cortex

value: 32 days


title: R24: Prefrontal Pyramidal Cortex


title: m1_AY_Y3_L11


title: U87 cell line rep 2 [U87_C2]


title: R18: Prefrontal Pyramidal Cortex


title: R16: Prefrontal Pyramidal Cortex


title: m1_AY_Y3_E12


title: R17: Prefrontal Pyramidal Cortex


title: U87 cell line rep 1 [U87_C1]


title: R1: Prefrontal Pyramidal Cortex


title: m1_AY_Y3_P6


title: Baseline-KO-5

city: Leuven

first: Massimiliano

last: Mazzone

address: Herestraat 49

country: Belgium

institute: VIB

description: countData.txt

data_processing:
Single-end 75bp reads were quality checked using FastQC (0.11.7) and low quality base calls and adapter contaminations were trimmed using Cutadapt (1.18)
Reads were aligned to the mm10 genome build using HISAT2 (2.1.0)
After an aditional round of quality check with FastQC (0.11.7), read counts were summarized at the gene level using featureCounts of the subread suite (1.6.2)
Genome_build: mm10
Supplementary_files_format_and_content: txt file containing raw read counts summarized on the gene level

source_name: Muscle

extract_protocol:
Muscles were removed, and macrophages were sorted as F4/80+ , and RNA was harvested using Qiagen Rneasy Micro Kit (Cat#74004).
SMART-Seq V4

value: Muscle associated macrophages

value: Normal Muscle

value: GLUD1 KO


title: Baseline-KO-3

description: countData.txt


title: Patient P13-derived PDOX rep 2 [P13_X2]

source_name: Human GBM PDOX

value: GBM tumor cells grown in mouse brain

value: FACS-sorted human tumor Cell culture


title: Patient P13-derived PDOX rep 1 [P13_X1]


title: m1_AY_Y3_O4


title: AVLF_R5b: Aortic Insufficienty rep5b

city: Palo Alto

first: Kevin

middle: James

last: Jaatinen

state: CA

address: 870 Quarry Rd Ext

department: Cardiothoracic Surgery

institute: Stanford University

data_processing:
The raw sequencing reads were cleaned by removing low-quality reads, adapters, and reads with >10% N.
The reference genome and gene model annotation files were downloaded from human genome websites (http://www.ncbi.nlm.nih.gov, http://uswest.ensembl.org/Homo_sapiens, http://genome.ucsc.edu). Indexes of the reference genome were built using Bowtie v2.0.6
Paired-end clean reads were aligned to the reference genome using STAR.
HTSeq v0.6.1 was used to count the read numbers mapped to each gene.
Fragments per kilobases per million (FPKM) were calculated to estimate the level of gene expression.
Differential gene expression analysis was performed using the DESeq2 R package
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with FPKM for every gene and every sample

source_name: Tricuspid Aortic Valve Leaflets

extract_protocol:
Normal control aortic valves were collected from non-matched transplant donor hearts. AS and AI aortic valves were collected from patients undergoing elective aortic valve replacement at our hospital. Total RNA was extracted from the aortic valve leaflets using the PureLink™ RNA Minikit (Thermo Fisher Scientific, USA) with on-column DNAse digestion according to the manufacturer’s instructions. A 10-minute proteinase K digestion was added during the lysis step to further homogenize the tissue. RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent, USA). RNA integrity scores were between 7.4 and 9.2.
A complementary DNA (cDNA) strand-specific library was created in duplicate using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs Inc, USA). After library construction, samples were diluted and quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA). cDNA insert size was detected using an Agilent 2100 Bioanalyzer (Agilent, USA). Library quality was assessed by quantitative polymerase chain reaction (qPCR) ensuring effective concentration >2 nM.
cDNA libraries were sequenced using Illumina HiSeq 2500 (Illumina®, USA). 150-bp paired-ends reads were generated with approximately 30 million reads per sample. Sequencing was performed in duplicate for each sample.

value: Tricuspid Aortic Valve Leaflets

value: F

tag: bmi

tag: degree of aortic valve disease

value: Moderate AI

tag: left ventricle ejection fraction

tag: other medical history

value: Radiation-induced heart disease, severe mitral valve regurgitation, coronary disease


title: Baseline-KO-2

description: countData.txt

tag: genotype


title: Patient P13-derived PDOX rep 3 [P13_X3]


title: Patient P8-derived PDOX rep 3 [P8_X3]


title: Baseline-KO-1

description: countData.txt


title: AVLF_R5a: Aortic Insufficienty rep5a

tag: Sex


title: Patient P8-derived PDOX rep 2 [P8_X2]


title: R11: Prefrontal Pyramidal Cortex

tag: cell type

value: Passed

value: 30 days


title: Patient P8-derived PDOX rep 1 [P8_X1]


title: m1_AY_Y3_E1


title: m1_AY_Y3_C5


title: m1_AY_Y3_O13


title: m1_AY_Y3_I18


title: Baseline-WT-6

description: countData.txt

tag: tissue

value: WT


title: AVLF_R4b: Aortic Insufficienty rep4b

value: M

value: Severe AI

value: Hypertension, atrial fibrillation


title: Baseline-WT-5

description: countData.txt


title: AVLF_R4a: Aortic Insufficienty rep4a


title: Patient T185-derived PDOX [T185_X]

value: Tumor tissue


title: Patient P3-derived PDOX rep 2 [P3_X2]


title: m1_AY_Y3_O8

value: primary murine brain endothelial cells