title: mEB_scQer_scv2_oBC_rep2_S2

description: 10X Genomics (custom oBC library)

data_processing:
GEx libraries: Fastq files were generated using the makefastq command from cellranger (v6.0.1), and the gene expression count matrices were then generated with cellranger count command, with transcriptome reference mm10-3.0.0. Raw count matrices were then imported as a Seurat object (filtering gene expressed in less than 3 cells, and cell barcodes with less than 50 genes measured). Cell barcodes in the high total UMI mode with low mitochondrial RNA proportion were filtered as likely bona fide cells (fraction of mitochondrial UMI >1% and <12.5%, total gene expression UMI > 450). The filtered count matrices were then used to evaluate doublet scores using scrublet (scrub_doublets command, 30 principal components, mean_center=true, normalize_variance=true), and cell barcodes with doublet score > 0.3 (separating the two modes of the simulated doublet distribution from scrublet) were filtered out. Datasets from all replicates were then combined in a single Seurat object, dimensionally reduced and clustered (NormalizeData, normalization.method= “LogNormalize”, scale.factor=10000; FindVariableFeatures with selection.method = “vst”, nfeatures=1000; ScaleData with all genes as features; RunPCA with identified variable features and 100 principal components; FindNeighbors, dims=1:50; FindClusters, resolution=0.2; RunUMAP, dims=1:50, n.neighbors=50) without batch correction given the good correspondence between replicates. The following additional quality filtering steps were applied to retain high confidence singlet cells. Clusters comprising less than 1% of cells were considered likely doublets/artifacts, and corresponding cells were removed. Cells members of each cluster identified were separately sub-clustered with the same procedure as above (except resolution 0.5 in FindNeighbors). Any sub-cluster with a median doublet score above 0.15 was deemed composed of likely doublets, and corresponding cells were removed. Cells with anomalously high gene expression UMI counts (>8k) were removed. Finally, cells with an estimated MOI > 110 (roughly corresponding to the top 0.1% of the distribution, MOI estimated through oBC UMI > 10) were filtered out. In the end, n=43799 cells passed all these quality filters (6124 replicate 1, 6442 replicate 2, 6442 replicate 3).  mBC libraries: Data was converted to fastq using bcl2fastq, and fastqs were minimally processed (e.g., trimming read 1 to 28 cycles) to be compatible with cellranger (version 6.0.1, 10x Genomics), which was run to perform error correction on cell barcodes. The resulting position sorted bam files were then parsed for the mBC reads as follows using a custom python script. Reads aligning to the reference genome or without either corrected cell barcode or UMI (tags CB and UB in the bam file) were discarded. Only reads with the exact expected 7 nt sequence (TCGACAA) downstream of the mBC (positions 16 to 22) were retained. List of all UMIs corresponding to a cell barcode and mBC pair were stored, discarding chimeric UMIs (taken to be UMIs for which the proportion of reads associated to a given mBC vs all other mBC in the specified cell barcode falls below 0.2). mBC comprised of all Gs (empty read) were discarded. Finally, the UMI count was error corrected as follows. For each given mBC and cell barcode, the Hamming distance between all UMIs was calculated, a graph created by connecting UMIs that were a Hamming distance ≤ 1, and the resulting the number of connected components in the graph was taken as the error-corrected UMI count for a given cell barcode-mBC pair. These error corrected UMI counts were used for the per single-cell quantification of the reporter mRNA expression.  oBC libraries: processed in an entirely analogous way to the strategy for mBC, with the following modifications: two sequencing runs were combined in a single fastq prior to processing, read 2 were trimmed to 23 cycles, and only reads with the GCTTTAA (constant region after the oBC) at positions 17 to 23 were retained. The number of UMIs per oBC per cell barcode was also taken as the error corrected (1 Hamming distance) count and our measure of oBC expression in single cells (see below for a normalization strategy to correct for gene expression UMIs).  Given that cell barcodes derived from capture sequence vs. poly-dT reverse transcription primer are different (bases 8 and 9 reverse complemented) on the same bead (and not error corrected by cellranger in our application), we converted the CS1 cell barcode to its poly-dT counterpart to enable matching across the different libraries.   Only cell barcodes passing the QC filters from the GEx analysis were retained in the final count tables. Only mBC and oBC present in the subassembly librarie were retained.
Assembly: mm10
Supplementary files format and content: The four processed files are:   GEx_obj_sc_rep_mEB_series_v2: Seurat processed object containing transcriptome quantification and cell annotation metadata (combined for all replicates).   oBC_counts_sc_rep_mEB_v2: Raw oBC count table (per cellbarcode, restricted to oBC from the list determined in the subassembly and UMI counts > 1).  Column 1: cell barcode; column 2: replicate ID; column 3: oBC; column 4: read counts  mBC_poly_dT_counts_sc_rep_mEB_v2: Raw mBC count table (per cellbarcode, restricted to mBC from the list determined in the subassembly). Column 1: cell barcode; column 2: replicate ID; column 3: mBC; column 4: read counts; column 5: UMI counts; capture modality.   assigned_oBC_CRE_mBC_joined_counts_sc_rep_mEB_series_v2: Final assigned joined cell-oBC-CRE_mBC table. Restricting to oBC with >10 UMI counts, and to uniquely matchable oBC-CRE-mBC triplets. column 1: cell barcode; column 2:  replicate ID; column 3: oBC; column 4: mBC; column 5: CRE class (promoters [exogenous series]  or devCRE); column 6: CRE right identity, column 7: CRE right orientation, column 8: CRE left identity, column 9: CRE left orientation; column 10: read counts oBC; column 11: UMI counts oBC; column 12: read counts mBC; column 13: UMI counts mBC. Note: all but the pairwise CREs will have NA for columns 8 and 9 (CRE left).

growth_protocol: 7 scQer libraries were pooled with the following proportions (pluripotent up::endoderm down high 13%, pluripotent up::endoderm down low 13%, endoderm up::pluripotent down high 13%, endoderm up::pluripotent down low 13%, mutated CREs 33%, literature-selected CREs 12%, exogenous promoters 3%) prior to transfection in mESCs (biological triplicates, 2M cells per transfection, lipofectamine 2000). Puromycin selection (2 ug/mL) was applied following cell post-transfection recovery (day 3), and mEB induction (4 plates of EB per replicate, one set of mEB per transfection biological replicate) initiated on day 10 post-transfection after unintegrated plasmid dilution. On day 23 post mEB induction, 2 plate's worth of mEBs cells were processed and sequencing libraries constructed.  EB induction: exponentially growing mESCs are lifted from the plate (aspirate medium, wash with PBS, add 2.5 mL [for 10 cm plate] 0.05% trypsin , incubate 2 minutes at 37C, deactivate trypsin and triturate to a single-cell suspension with 10 mL pre-warmed SL medium). Cells are then counted and spun down (5 min at 300 g). Supernatant is aspirated and cells are resuspended to 2 M/mL in CA medium (medium for EB induction: DMEM, 10% FBS, 1x MEM non-essential amino-acids, 1x Glutamax , 10-5 beta-mercaptoethanol). Cells are counted again, and density adjusted to 1 M/mL with CA medium. 3 mL (3 M cells) are added to 12 mL of CA medium in 10 cm plates (non gelatinized, non adherent). One the next day, plates are gently agitated to promote cell aggregation. Following induction, embryoid bodies (mEBs) are passaged every two days (no daily medium change). mEBs are collected using a serological pipette and transferred to a 50 mL conical tube (typically three plates are pooled). Leftover mEBs on plates are recovered by a CA medium wash and pooled with in the conical tube. mEBs are left to settle (initially up to 15-20 min, faster as the mEBs grow in size). Once mEBs have settled, medium is aspirated from the top, carefully avoiding disturbing the loose pellet. Fresh, pre-warmed, CA medium is then added to 15 mL/plate and mEBs redistributed to plates.

extract_protocol:
mEBs were processed at the three weeks end point as follows (for each replicate): 2 plates of mEBs were pooled into a 50 mL conical left to settle. Medium was aspirated and mEBs were washed twice with PBS, resuspended in 3 mL PBS in the second wash, and split in two 1.5 mL aliquots in 2 mL tubes. PBS was aspirated from the tubes, and 500 uL of trypsin 0.25% was added per tube. Tubes were then mixed on a thermomixer at 37C and 650 rpm for 4 minutes. Cells were then gently dissociated by pipetting up and down 10 times, and placed back on the thermomixer for 2 min. 1 mL of SL medium was then added per sample and pipetted to obtain a single-cell suspensions, the two samples were combined in a 15 mL conical, and passed through a 100 um strainer. The strained single-cell suspension was counted, and cells were spun down (300 g, 5 min), resuspended to 4 M/mL, and taken to FACS. >600k cells were then FACS sorted (in <50 min) in pre-warmed SL medium to ensure the single-cell nature of the suspension (no gating on fluorescence proteins) prior to generating the emulsions for single-cell RNA-seq. Sorted cells were then spun down at 400 g at 4C for 5 min, the medium gently aspirated, and resuspended to an expected 2.5 M cells/mL (based on FACS sort event counts) in ice cold PBS + 0.04% BSA, cells were counted and volume adjusted to 1200 k/uL with ice cold PBS+BSA.  Single-cell suspensions in PBS+BSA were taken as the starting point for the 10x Genomics protocol (v3.1 with feature barcoding). Emulsion and reverse transcription were performed per the manufacturer’s instruction. Given prior empirical experience with mEBs processing, each 10x lane was slightly overloaded (by an additional 20%) to approach the expected recovery of 10k cells/lane. Each replicate was profiled with 1 lanes of 10x, for a total of 3 lanes.
For single-cell reporters, three libraries are generated: the standard 3’ gene expression library from 10x (GEx), and two custom derived libraries, one for each reporter RNA (oBC and mBC), obtained from nested PCRs from the amplified cDNA. Briefly, Single-cell library preparation proceeded following the manufacturer's protocol (v3.1 manual CG000205 Rev D, 10x Genomics), with some modifications.For cDNA amplification, primers specific to the mBC (oSR38) and oBC (o246) reporter transcripts were spiked-in the reaction (similar to TAP-seq) at final concentration of 0.5 uM to boost capture. Following cDNA amplification, both the bead and supernatant derived material (steps 2.3Ax and 2.3Bxiv respectively) were saved for downstream processing.  Gene expression libraries for all replicates were prepared following the manufacturer’s protocol from 25% of the bead fraction amplified cDNA.  oBC enriched libraries were prepared as follows. 25% of the supernatant fraction from the amplified cDNA was taken as input for semi-nested inner PCR was performedwithKapa Robust (50 uL 2x master mix, supernatant cDNA, 5 μL 10 μM NextP5_index1 primer, 5 μL 10 μM indexed primers [o501-o506, one per sample], 0.5 uL SYBr green, and water to 100 μL; run parameters: 3 min at 95C, and cycles 20 s at 95C, 20 s at 60C, 20 s at 72C) withtracking with qPCRand stopped before the inflection point. Libraries were purified by 1.5x ampure.To avoid loop-the-loop products in the oBC libraries, the lowest band in the circularized ladder amplicons was size selected on PAGE (6% TBE, 180V, 30 min) for each library and used for sequencing.  Only the poly-dT captured libraries were generated for the mBC for the mouse embryoid body experiment. 25% of the bead-fraction of the purified amplified cDNA was used as template for PCR withKapa Robust (50 uL 2x master mix, supernatant cDNA, 5 μL 10 μM o324 primer, 5 μL 10 μM o529, 0.5 uL SYBr green, and water to 100 μL; run parameters: 3 min at 95C, and cycles 20 s at 95C, 20 s at 65C, 50 s at 72C), with tracking by qPCR and purifying by 1x ampure. A final PCR (same condition as above) was performed to index amplicons with primers o076 and P7-indexed primers (o530-o533), and the resulting amplicons purified by 1x ampure.   Read structures:  Read structures: GEx: read 1, cell-barcode+UMI (28 cycles); index 1, library index (10 cycles); read 2, transcriptome (90 cycles)  oBC: read 1, cell-barcode+UMI (28 cycles, no custom primers); index 1, library index (10 cycles, primer o432); read 2, oBC (90 cycles, primer o433)  mBC: read 1, cell-barcode+UMI (28 cycles, no custom primers); index 1, library index (10 cycles, primer o534); read 2: mBC (90 cycles, primer o334)  GEX (reseq): read 1, cell-barcode+UMI (34 cycles); index 1, library index (15 cycles); read 2, transcriptome (79 cycles)
scRNA-seq (with custom reporter libraries)

value: Day 23


title: mEB_scQer_scv2_oBC_rep3_S3

status: Public on Oct 17 2023

type: SRA

city: Montreal

first: Jean-Benoit

last: Lalanne

state: QC

address: 5155 Chem. de la Rampe

department: Biochemistry and Molecular Medicine

country: Canada

institute: University of Montreal

description: 10X Genomics (custom oBC library)

library_source: transcriptomic single cell

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell line

value: WD44 (mouse embryonic stem cells)

tag: cell type

value: Mouse embryoid bodies

tag: genotype

value: monoclonal CRISPRi (dCAS9-KRAB) cell line, high MOI (polyclonal) single-cell reporter cassette (89% devCRE library + 10% promoter series + 1% EEF1A1-mCherry) delivered by piggyBac

tag: time


title: WT (ADT, HTO)

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

description:
protein
3 mice, hashtagged
WT_CITE

library_source: other

data_processing:
Raw data were processed using cellranger-3.1.0 with refdata-gex-mm10-2020-A and refdata-cellranger-vdj_GRCm38_alts_ensembl-mouse-2.2.0 as reference.   .Mkfastq, count and vdj were used in default parameter settings with 3000 expected cells for demultiplexing, detection of intact cells, quantification of gene expression, antibody capture as well as assembly and quantification of T cell receptor sequences.
Assembly: mm10
Supplementary files format and content: h5: aggregated gene count matrix in hdf5 format including antibody counts for CD127,  AntiAPC, CD279, CD197, CD39, CD185, CD31, KLRG1, CD183, CD49d, CD73, FQPQNGQFI, KAVYNFATC, SGVENPGGYCL, CSANNSHHYI, ISHNFCNL as well as hashtag counts for different biological replicates. feature_reference.csv: ADT/HTO reference file, fasta: high-confidence contig sequences of immune receptors with the corresponding cellular barcode and contig-id; csv: results from single cell immune profiling, comprising the annotation of the immune receptor, cellular barcode and contig-id.

molecule: protein

source_name: Spleen

extract_protocol:
Wildtype and Il1rl1-ExAB-/- mice (n = 3 per genotype) were infected intravenously with LCMV-WE (2x106 PFU). At day 7 post infection, splenocytes were isolated by mechanical disruption and erythrocytes were lysed by incubation in erythrocyte lysis buffer (10 mM KHCO3, 155 mM NH4Cl, 0.1 mM EDTA, pH 7.5). Obtained cell suspensions were passed through 70µm filters and T cells were enriched by depleting CD19+ B cells using magnetic activated cell sorting (MACS, Miltenyi Biotec). Subsequently, live CD90+ CD8+ CD44+ T cells were flowcytometrically sorted using a BD Aria II device, stained with Total-Seq antibodies (Biolegend) and LCMV dCODE dextramers (Immudex) according to manufacturer’s instructions and subjected to the 10x Genomics scRNA-Seq workflow.
See sorting strategy.
10x Genomics workflow for cell capturing. For the preparation of scRNA gene expression (GEX), TCR and CiteSeq libraries the Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1 as well as the Chromium Single Cell 5' Feature Barcode Library Kit (10x Genomics) were used for CD127 (GTGTGAGGCACTCTT), antiAPC (TTAACCGTCTCCCTT), CD279 (GAAAGTCAAAGCACT), CD197 (TTATTAACAGCCCAC), CD39 (GCGTATTTAACCCGT), CD185 (ACGTAGTCACCTAGT), CD31 (GCTGTAGTATCATGT), KLRG1 (GTAGTAGGCTAGACC), CD183 (GTTCACGCCGTGTTA), CD49d (CGCTTGGACGCTTAA), CD73 (ACACTTAACGTCTGG), FQPQNGQFI (GTGGTCGACCGTCTG), KAVYNFATC (CCTTAATATGTAGAA), SGVENPGGYCL (AGGAACCGCTGTTGA), CSANNSHHYI (TCATGTCAGACTTGG), ISHNFCNL (CGTGCAAGGCCGGAA) as well as , Hashtag1 (ACCCACCAGTAAGAC), Hashtag2 (GGTCGAGAGCATTCA), Hashtag3 (CTTGCCGCATGTCAT), Hashtag4 (AAAGCATTCTTCACG),Hashtag5 (CTTTGTCTTTGTGAG). After cDNA amplification the feature barcode libraries were prepared separately using the Single Index Kit N Set A (10x Genomics). TCR target enrichment was performed using the Chromium Single Cell V(D)J Enrichment Kit for murine T cells (10x Genomics). Final GEX and TCR libraries were obtained after fragmentation, adapter ligation and final Index PCR using the Single Index Kit T Set A (10x Genomics). The Qubit dsDNA HS assay kit (life technologies) was used for library quantification and fragment sizes were determined using the Fragment Analyzer with the NGS Fragment Kit (1-6000bp) (Agilent)
Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1 as well as the Chromium Single Cell 5' Feature Barcode Library Kit (10x Genomics) were used

tag: strain

value: C57BL/6J background

tag: genotypes

value: WT

tag: sorting strategy

value: live CD90+ CD8+ CD44+ T cells


title: DNA_techrep1_mEB_bulk_v2_repA1_d00_S13

description: Bulk MPRA

library_source: genomic

data_processing:
Sequencing data was demultiplexed using bcl2fastq. Raw fastq files were processed first by trimming unnecessary cycles from the 3’ end using seqtk (https://github.com/lh3/seqtk). Forward and reverse mBC reads were joined and error corrected with PEAR (options -v 15 -m 15 -n 15 -t 15). Using custom python and R scripts, successfully assembled barcode reads were combined with UMI reads, mBC/UMI pairs were counted, and the read counts and UMI count per mBC was determined.
Supplementary files format and content: bulk_MPRA_counts_mEB_v2_poolA and bulk_MPRA_counts_mEB_v2_poolB: summary count tables for bulk MPRA data.  column 1: originating library short identifier, column 2: reporter architecture identifier, column 3: position of CRE relative to reporter, column 4: reporter ORF, column 5: promoter id, column 6: logical boolean indicating whether U6/oBC cassette is present on construct, column 7: logical boolean indicating whether cHS4 insulators are present on construct, column 8: pool id, column 9: CRE class, column 10: CRE id, column 11: mBC, column 12: biological replicate, column 13: technical replicate identifier, column 14: harvest day, column 15-20: UMI and read counts for RNA, DNA as well as normalised UMI counts (UMI divided by total UMI count in sample [individual normalization pe rsample])
Library strategy: Bulk MPRA

molecule: genomic DNA

source_name: WD44 (mouse embryonic stem cells)

growth_protocol: The two respective library pools (A and B, see manuscript for details) were reverse transfected (lipofectamine 2000) in mESCs. Specifically, each pool was transfected in 6 separate reactions (2M cells transfected and plated in 6 cm plates) with 400 ng hyPBase plasmid, 8 ug of reporter pool. Following recovery of cells for 2 days, cells from pairs of transfection replicates from each pool were combined (from 6 to 3 plates of cells), and the resulting three set of cells were hereafter maintained separately, constituting our biological triplicates. Puromycin (2 ug/mL) selective pressure was applied 3 days post transfection and until induction of mEBs, which happened 11 days post transfection. mEB induction proceeded as described below, with 15M of cells split in 5 plates (3M/plate) for each biological replicate. 3M of cells per replicate were also sampled for the day 0 time point. Plates from the same replicates were mixed at each medium change (once every two days). One plate’s worth of mEB was harvested on days 4, 18, 20, and 22. At harvest, cells/mEBs were fixed in 80% methanol and placed at -80C until RNA/DNA extraction for library preparation.  EB induction: exponentially growing mESCs are lifted from the plate (aspirate medium, wash with PBS, add 2.5 mL [for 10 cm plate] 0.05% trypsin , incubate 2 minutes at 37C, deactivate trypsin and triturate to a single-cell suspension with 10 mL pre-warmed SL medium). Cells are then counted and spun down (5 min at 300 g). Supernatant is aspirated and cells are resuspended to 2 M/mL in CA medium (medium for EB induction: DMEM, 10% FBS, 1x MEM non-essential amino-acids, 1x Glutamax , 10-5 beta-mercaptoethanol). Cells are counted again, and density adjusted to 1 M/mL with CA medium. 3 mL (3 M cells) are added to 12 mL of CA medium in 10 cm plates (non gelatinized, non adherent). One the next day, plates are gently agitated to promote cell aggregation. Following induction, embryoid bodies (mEBs) are passaged every two days (no daily medium change). mEBs are collected using a serological pipette and transferred to a 50 mL conical tube (typically three plates are pooled). Leftover mEBs on plates are recovered by a CA medium wash and pooled with in the conical tube. mEBs are left to settle (initially up to 15-20 min, faster as the mEBs grow in size). Once mEBs have settled, medium is aspirated from the top, carefully avoiding disturbing the loose pellet. Fresh, pre-warmed, CA medium is then added to 15 mL/plate and mEBs redistributed to plates.

extract_protocol:
DNA and RNA were extracted from methanol fixed samples using the AllPrep kit (Qiagen) following manufacturer's instructions.
RNA and DNA was extracted from methanol fixed cells (AllPrep kit, Qiagen). MPRA libraries were constructed as follows: for RNA libraries, 5 ug of RNA was reverse transcribed with UMI containing primer oJBL753 using SuperScript IV (10 uL 500 ng/uL RNA mixed with 2 uL 1 uM oJBL753; 5 min at 65C, ice for >2 min; followed by addition of 4 uL 5x buffer, 1 uL 0.1M DTT, 1 uL 10 mM dNTPs, 1 uL water, 1 uL SSIV as a master mix for 20 uL total reaction; 55C for 60 min, 80C for 10 min). The cDNA was taken directly as template for PCR1 (25 uL reactions, 10 uL cDNA, primers oJBL039+Nextera v2 P7 indexed primers; 4 elongation cycles). Following the first PCR, reactions were cleaned up with 1x Ampure XP beads, eluted in 12 uL 10 mM Tris 8. 4 uL of PCR1 eluates were taken to PCR2 (10 uL reactions, primers oJBL077+oJBL359, tracked with qPCR and SYBr green, stopped at cycles 9-15 depending on reaction’s inflection point). Reactions were again purified with 1x Ampure XP and eluted in a final volume of 10 uL 10 mM Tris 8. For DNA, approximately 10 ug genomic DNA was amplified in 25 uL reactions (primers oJBL039+oJBL753; 4 cycles). Following 1x Ampure XP cleanup and elution in 12 uL 10 mM Tris 8, 4 uL of the eluate was amplified in a second round of PCR (10 uL reactions, 15 elongation cycles; primers oJBL360+Nextera v2 P7 indexed primers), cleaned up with 1x Ampure XP, and eluted in 10 uL 10 mM Tris 8. Each biological replicate was process in technical duplicate, for a total of 48 libraries (2 cell lines ⨉ 2 library types RNA/DNA ⨉ 3 bottlenecking factors ⨉ 2 biological replicates ⨉ 2 technical replicates). All reactions were performed in 96-well plates. To quantify final amplicon concentrations, a real-time qPCR experiment was performed using P5 and P7 primers (oJBL076, oJBL077 respectively).   Samples were pooled according to their concentration as determined by qPCR and sequenced on a Nextseq2000 using custom set of primers (read 1: oJBL369, 15 cycles to read mBC; index 1: oJBL335 [Nextera index 1], 10 cycles to read the sample index; read 2: oJBL494 [Nextera read 2], 10 cycles to read the pseudo-UMI; index 2: oJBL371, 15 cycles to read the reverse complement of the mBC).

tag: day

value: Day 00


title: Il1rl1-ExAB-/- (ADT, HTO)

description:
protein
3 mice, hashtagged
AB_CITE


title: Il1rl1-ExAB-/- (GEX)

description:
total RNA
3 mice, hashtagged
AB_GEX

library_source: transcriptomic


title: mEB_scQer_scv2_mBC_rep3_S6

description: 10X Genomics (custom mBC library)


title: mEB_scQer_scv2_oBC_rep1_S1

description: 10X Genomics (custom oBC library)


title: alt-splicing RNA-Seq - Hippocampus Aged Female Replicate 3

city: Los Angeles

first: Kelsey

last: Martin

state: CA

address: 615 Charles E Young Drive South

department: Biological Chemistry

country: USA

institute: UCLA

data_processing:
For differential splicing analysis, the analysis package rMATS version 4.0.2 (Shen et al., 2014) was used on fastq files.
Alternative splicing events were included for analysis if events had FDR-adjusted p-value < 0.05, total reads ≥ 50 and skipping/junction reads > 20.
Assembly: mm10
Supplementary files format and content: Excel table with alternative splicing events including skipped exon (SE), alternative 5’ splice site (A5SS), alternative 3’splice site (A3SS), mutually exclusive exons (MXE), and retained introns (RI). Listed are exon locations, exon inclusion levels and p-values.

molecule: polyA RNA

source_name: hippocampus

growth_protocol: Mice were housed in groups under a 12:12 hr light/dark cycle with food provided ad libitum until they reached the age of 10 weeks (young adult) and 80 weeks (aged).

extract_protocol:
RNA was extracted from Trizol using a Trizol/RNeasy hybrid protocol. Briefly, after phase separation, the aqueous phase was mixed with one volume of 70% ethanol and passed through an RNeasy spin column (QIAGEN RNeasy Mini Kit).
mRNA libraries were prepared with poly-A selection using the TruSeq Stranded mRNA Library Prep Kit (Illumina 20020594)

treatment_protocol: For sample collection, mice were deeply anesthetized with isoflurane and euthanized by cervical dislocation. The brain was quickly removed and cooled for one minute in ice-cold PBS before the hippocampus from each hemisphere was dissected on ice and processed immediately.

value: hippocampus

tag: age

value: Aged

tag: Sex

value: Female


title: RNA-Seq - Hippocampus Aged Female Replicate 4

data_processing:
RNA-seq reads were mapped to the mouse genome (mm10) using STAR with the two-pass option (Dobin et al., 2013). Only uniquely mapped reads were used for downstream analysis.
Lowly expressed genes were removed by retaining only genes with counts per million > 0.1 in at least four samples (17,821 genes).
Read counts were normalized via the trimmed mean method before differential expression analysis (DEA)(Robinson and Oshlack, 2010).
For DEA, the analysis package edgeR (Robinson et al., 2010) was used, with an FDR < 0.05 cutoff.
Assembly: mm10
Supplementary files format and content: Excel table with normalized counts, fold changes and DE p-values for all genes

extract_protocol:
RNA was extracted from Trizol using a Trizol/RNeasy hybrid protocol. Briefly, after phase separation, the aqueous phase was mixed with one volume of 70% ethanol and passed through an RNeasy spin column (QIAGEN RNeasy Mini Kit).
Total RNA libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero (Illumina 20020596).


title: RNA-Seq - Hippocampus Aged Female Replicate 2


title: RNA-Seq - Hippocampus Young Female Replicate 2

value: Young Adult


title: WT (GEX)

description:
total RNA
3 mice, hashtagged
WT_GEX


title: RNA-Seq - Hippocampus Aged Male Replicate 1

value: Male


title: RNA-Seq - Hippocampus Aged Male Replicate 2


title: RNA-Seq - Hippocampus Young Male Replicate 1


title: RNA-Seq - Hippocampus Aged Male Replicate 4


title: RNA-Seq - Hippocampus Young Female Replicate 4


title: RNA-Seq - Hippocampus Young Male Replicate 3


title: RNA-Seq - Hippocampus Aged Male Replicate 3


title: RNA-Seq - Hippocampus Aged Female Replicate 3


title: alt-splicing RNA-Seq - Hippocampus Aged Female Replicate 4


title: RNA-Seq - Hippocampus Young Male Replicate 2


title: RNA-Seq - Hippocampus Young Male Replicate 4


title: alt-splicing RNA-Seq - Hippocampus Young Female Replicate 2


title: alt-splicing RNA-Seq - Hippocampus Young Female Replicate 1


title: alt-splicing RNA-Seq - Hippocampus Young Female Replicate 4


title: alt-splicing RNA-Seq - Hippocampus Aged Male Replicate 4


title: alt-splicing RNA-Seq - Hippocampus Aged Female Replicate 1


title: alt-splicing RNA-Seq - Hippocampus Aged Female Replicate 2


title: alt-splicing RNA-Seq - Hippocampus Aged Male Replicate 2


title: alt-splicing RNA-Seq - Hippocampus Aged Male Replicate 3


title: alt-splicing RNA-Seq - Hippocampus Young Female Replicate 3


title: alt-splicing RNA-Seq - Hippocampus Aged Male Replicate 1


title: RNA-Seq - Hippocampus Young Female Replicate 3


title: alt-splicing RNA-Seq - Hippocampus Young Male Replicate 4


title: RNA-Seq - Hippocampus Young Female Replicate 1


title: alt-splicing RNA-Seq - Hippocampus Young Male Replicate 3


title: alt-splicing RNA-Seq - Hippocampus Young Male Replicate 1


title: alt-splicing RNA-Seq - Hippocampus Young Male Replicate 2


title: Old, replicate 2, scRNAseq

city: La Jolla

first: Jingting

last: Yu

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

description: 10x Genomics

data_processing:
CellRanger (v.6.0.1) was used to perform sample-demultiplexing, barcode processing and single-nuclei gene-UMI counting, which resulted in an expression matrix for each experiment by aligning to the reference GRCH38 using CellRanger with default parameters
Assembly: GRCH38
Supplementary files format and content: Tab-separated values files and matrix files

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol:
Peripheral blood was obtained from normoglycemic Y adults who were lean (Y; avg: 31.81 yrs; BMI 22.20 kg/m2) or normoglycemic O adults who were lean (O; avg: 68.11 yrs; BMI 23.46 kg/m2). CD4+ T cells were isolated according to our established protocol. Briefly, fifty milliliters of peripheral blood was collected into acid/citrate/dextrose containing tubes by venous puncture. PBMCs were purified by histopaque. CD4+ T cells were isolated from the PBMCs by negative selection using MACS columns (Miltenyi Biotech).
Libarary was prepared according to manufacter's instructions (single cell 3' v3 protocol, 10x Genomics).

value: Peripheral blood

value: CD4+ T cells

value: Old


title: Young, replicate 1, scRNAseq

description: 10x Genomics

value: Young


title: Old, replicate 3, scRNAseq

description: 10x Genomics


title: H3K27ac_ctrl rep 1

city: Wauwatosa

first: John

middle: Anto

last: Pulikkan

state: WI

address: 8727 W Watertown Plank Rd

institute: Versiti

data_processing:
library strategy: CUT&Tag
Reads were aligned to the hg38 Human genome using Bowtie2  and peaks were called using SEACR v1.3  from each sample using IgG controls in stringent peak calling mode. Visualization was created using deeptools. Peaks were tested for differential expression between controls and samples with DESeq2 v1.24.0. DESeq2 Wald tests were used to determine whether fold changes were significantly different from zero. Pre-ranked gene set enrichment analysis was conducted using shrunken fold-changes and clusterProfiler v3.12.0. Gene ontology database was used for GSEA. The Benjamini-Hochberg method was used to adjust p-values for false discovery in both differential expression and GSEA analyses.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: Hematopoietic

growth_protocol: ME-1 cells were cultured in RPMI media supplemented with 20% FBS 1% P/S

extract_protocol:
CUT&Tag was perfomed according to Bench Top CUT&Tag v3 (protocols.io, Hatice S Kaya-Okur,Steven Henikoff).
Libraries were contructed according to Bench Top CUT&Tag v3 (protocols.io, Hatice S Kaya-Okur,Steven Henikoff) using indexed primers described by Buenrostro, J.D. et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523:486 (2015).

treatment_protocol: ME-1 cells without any treatment

value: Hematopoietic

value: leukemic cell line

tag: antibody


title: N-MYC_1 rep3

value: N-Myc


title: Young, replicate 3, scRNAseq

description: 10x Genomics


title: IgG control rep2

value: IgG


title: N-MYC_1 rep2


title: IgG control rep1


title: Old, replicate 1, scRNAseq

description: 10x Genomics


title: Young, replicate 2, scRNAseq

description: 10x Genomics


title: IgG control rep3


title: WT_MNP_D18_Rep3

city: San Francisco

first: Deepak

last: Srivastava

address: 1650 Owens St

department: GICD

institute: J David Gladstone Institutes

description: scRNA-seq of total RNA in cell type

data_processing:
Illumina Casava v1.8 was used for base-calling.
Reads were demultiplexed, aligned, read normalized and quantified with the Cellranger Suite v3.1.0 from 10X genomics
Additional filtering, quality control and doublet removal was done using Seurat v3 according to specifications in the tutorials (https://satijalab.org/seurat/pbmc3k_tutorial.html)
Assembly: hg19
Supplementary files format and content: normalized gene-cellbarcode expression matrix in csv format

source_name: Motor neuron progenitor cells

growth_protocol: Cardiac progenitors cells were differentiated from WTC11 hiPSC lines by the WNT modulation protocol.  In brief,  6 uM CHIR were added for 48hours, followed by 5 uM IWP4 for 48 hours. Cells were then grown RPMI with B27 supplement minus insulin until day 10, then with RPMI with B27 plus insulin

extract_protocol:
Single cell suspensions were loaded into the Chromium controller (10X genomics) microfluidic chip for single cell droplet library preparation.
Libraries were prepared according to the manufacturer’s instructions (10X Genomics) using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (PN- 1000121) and Chromium i7 Multiplex Kit (PN-120262).

treatment_protocol: Detailed in "characteristics: Treatment" to specify different treatments on samples.

value: d18 hiPSC-derived motor neuron progenitor cells

tag: treatment

value: untreated


title: siRNA_ISL1_CP_D8

description: scRNA-seq of total RNA in cell type

source_name: Cardiac progenitor cells

value: d8 hiPSC-derived cardiac progenitor cells

value: siRNA:D5 CP cells were transfected with fluorescently labeled MISSION® Predesigned ISL1 siRNA (MilliporeSigma, Cat#SASI_Hs01_00109412)-lipofectamine complexes then harvested 3 days later (D8) after transfection confirmation with fluorescent label.


title: H3K27ac_ctrl rep 3


title: IKO_MNP_D18_Rep2

description: scRNA-seq of total RNA in cell type


title: Cord blood fresh, EPCR+

city: Seattle

first: Brandon

last: Hadland

state: WA

address: 1100 Fairview Avenue N., D2-115, P.O. Box 19024

institute: Fred Hutchinson Cancer Center

description:
10x Genomics
Day0

data_processing:
The Cell Ranger 2.1.1 pipeline (10X Genomics) was used to align reads to the GRCh38 reference genome and generate feature barcode matrix, filtering low-quality cells using default parameters.
The Monocle (v.3.2.3.0) platform was used for downstream analysis, combining read-depth normalized data across samples where applicable.
Assembly: GRCh38
Supplementary files format and content: 10X Cell Ranger output files in filtered feature-barcode matrix: "genes.tsv" contains gene information, "barcodes.tsv" contains cellular barcodes, and "matrix.mtx" contains a sparse matrix of UMIs.

source_name: Cord Blood

extract_protocol:
FACS-isolated primary cells or lentiviral transduced and cultured cells harvested by pipetting were washed with PBS/0.04% ultrapure BSA, and resuspended in PBS/BSA for loading into the 10X Genomics Chromium Single Cell B Chip, and processed in the Chromium single cell controller.
The 10X Genomics Version 3.1 single cell 3’ kit was used to prepare single cell mRNA libraries for freshly isolated primary cells or cultured according to manufacturer protocols with the Index Kit T Set A. Sequencing was performed for pooled libraries from each sample on an Illumina NextSeq 500 using the 100 cycle, high output kit.

value: Hematopoietic cells, primary

value: Cord Blood

tag: cell fraction


title: siRNA_Control_CP_D8

description: scRNA-seq of total RNA in cell type

value: siRNA:D5 CP cells were transfected with fluorescently labeled MISSION® Universal Negative Control #1 siRNA (MilliporeSigma, Cat#SIC001-5X1NMOL)-lipofectamine complexes then harvested 3 days later (D8) after transfection confirmation with fluorescent label.


title: IKO_MNP_D18_Rep3

description: scRNA-seq of total RNA in cell type


title: NKO_CP_D8_Rep2

description: scRNA-seq of total RNA in cell type


title: NKO_CP_D8_Rep3

description: scRNA-seq of total RNA in cell type


title: WT_MNP_D18_Rep2

description: scRNA-seq of total RNA in cell type


title: Cord blood cultured, Scramble control

description:
10x Genomics
Day4

value: Hematopoietic cells, cocultured


title: NKO_CP_D8_Rep1

description: scRNA-seq of total RNA in cell type


title: H3K27ac_ctrl rep 2


title: N-MYC_1 rep1


title: RNA-Seq - Hippocampus Aged Female Replicate 1

value: hippocampus

value: Aged

value: Female


title: WT_CP_D8_Rep3

description: scRNA-seq of total RNA in cell type


title: IKO_CP_D8_Rep1

description: scRNA-seq of total RNA in cell type


title: WT_CP_D8_Rep2

description: scRNA-seq of total RNA in cell type


title: IKO_CP_D8_Rep2

description: scRNA-seq of total RNA in cell type


title: IKO_CP_D8_Rep3

description: scRNA-seq of total RNA in cell type


title: WT_CP_D8_Rep1

description: scRNA-seq of total RNA in cell type


title: PDFP_3-T

city: daejeon

first: Seung-Jin

last: Park

address: gwahakro

country: South Korea

institute: KRIBB

data_processing:
Base calling was performed by Illumina Genome Studio(V2010.1).
Reference genome sequence data from Homo sapiens were obtained from the University of California Santa Cruz Genome Browser Gateway (assembly ID: hg38). The reference genome index and reads mapping of tissue samples were performed using the STAR software (ver. 2.5.3a).
Assembly: hg38
Supplementary files format and content: tab-delimited text format with raw counts of transcripts

source_name: Thyroid

extract_protocol:
Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.
Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.

value: Thyroid

value: Tumor

tag: cell subtype

value: PTC


title: PDFP_11T


title: PDFP_2-T1


title: PDFP_7T


title: PDFP_1-T

value: PD


title: PDFP_6T1


title: FP39_T


title: FP4_T


title: FP38_T


title: FP6_T


title: PDFP_5T


title: FP8_T


title: FP36_T


title: PDFP_8T


title: FP35_T


title: FP34_T


title: FP5_T


title: PDFP_10T


title: FP33_T


title: FP7_T


title: FP31_T


title: FP32_T


title: FP28_T


title: FP26_T


title: FP9_T


title: FP23_T


title: FP22_T


title: FP21_T


title: FP20_T


title: FP19_T


title: FP15_T


title: FP1_T


title: ATCFP_8-T

value: ATC


title: ATCFP_10T1


title: ATCFP_9T2


title: ATCFP_5-T


title: FP11_T


title: ATCFP_4-T


title: ATCFP_7-T1


title: FP13_T


title: 518T1


title: 523T


title: 499T


title: 492T


title: 497B


title: 494T


title: ATCFP_2-T


title: 493T


title: 475T


title: 409T


title: 405T1


title: FP18_T


title: FP12_T


title: ATCFP_1-T


title: 403T


title: 498T


title: 402T


title: 401T


title: 399T


title: 398T


title: 394T


title: 393T


title: 396T


title: 386T


title: 389T1


title: 384T1


title: 383T


title: 382T


title: 484T


title: 385T


title: 395T1


title: 381T


title: 408T


title: 407T


title: 404T


title: 379T2


title: 378T1


title: 377T1


title: 375T


title: 374T


title: 373T


title: 397T


title: 370T1


title: 368T1


title: 400T


title: 388T


title: 367T


title: 366T


title: 364T


title: 365T


title: 362T


title: 363T


title: 361T


title: 359T


title: 360T


title: 358T


title: 357T


title: 354T


title: 353T


title: 352T


title: 355T


title: 351T


title: 348T


title: 350T


title: 371T1


title: 369T1


title: 347T


title: 346T


title: 316T-P


title: 318T


title: 315T


title: 313T


title: 314T


title: 310T


title: 308T


title: 309T


title: 307T


title: 356T


title: 301T


title: 303T


title: 299T


title: 302T


title: 297T


title: 292T


title: 290T


title: 286-T-P


title: 284-T


title: 282T


title: 285-T-P


title: 281T


title: 283T


title: 279T


title: 277T


title: 274T


title: 278T


title: 273T


title: 305T


title: 270-T_P


title: 304T


title: 268T


title: 262-T-P


title: 258-T


title: 261-GD


title: 296T


title: 298T


title: 255-T


title: 256-T


title: 257-T


title: 300T


title: 253-T


title: 251-T


title: 248-T


title: 272T


title: 245-T


title: 246-T


title: 244-T


title: 243-T


title: 242-T


title: 240-T


title: 238-T


title: 259T


title: 237-T


title: 236-T


title: 235-T


title: 233-T


title: 230-T


title: 254-T5


title: 227-T_P


title: 229TR


title: 232-T


title: 225-T


title: 224-T


title: 247-T


title: 222-T


title: 220-T


title: 221-T


title: 223-T


title: 218-T


title: 241-T


title: 226-T_P


title: 216-T


title: 211T


title: 215-T


title: 213-T


title: 209-T-P


title: 219-T


title: 210-T


title: 207-T


title: 205T


title: 203-T


title: 204T


title: 202-T


title: 206-T


title: 201-T


title: 200T-P


title: 195T


title: 186-T_P


title: 185-T_P


title: 183-T_P


title: 198-T


title: 182-T_P


title: 184-T_P


title: 180-T_P


title: 178-T_P


title: 177-T_P


title: 175T


title: 208T


title: 176-TR


title: 173-T


title: 171-T


title: 172-T


title: 169-T_P


title: 174-T


title: 181-T-P


title: 167-T_P


title: 168T


title: 165-T_P


title: 164-T-P


title: 179-T_P


title: 162-T_P


title: 163-T


title: 159-T-P


title: 160-T_P


title: 161-T_P


title: 157-T_P


title: 155T


title: 156-T-P


title: 158-T_P


title: 153-T_P


title: 154-T_P


title: 152-T_P


title: 149-T


title: 150-T


title: 151-T


title: 146-T


title: 141-T


title: 148-T_P


title: 145-T


title: 138-T


title: 147-T_P


title: 142-T


title: 137-T


title: 140-T-P


title: 143T


title: 144T


title: 139T


title: 130-T_P


title: 131-T_P


title: 127-T


title: 124-T


title: 134-T-P


title: 122-T


title: 132-T


title: 123-T


title: 128-T


title: 126-T


title: 121-T


title: 136-T


title: 129-T


title: 135-T


title: 119-T


title: 118-T


title: 125-T


title: 117-T


title: 113-T


title: 111T-P


title: 114-T


title: 116-T


title: 112-T


title: 110-T_P


title: 107-T-P


title: 115-T


title: 109T-P


title: 108-T_P


title: 120-T


title: 104-T_P


title: 103-T_P


title: 91-T


title: 93-T


title: 102-T_P


title: 92-T


title: 100T


title: 98-T


title: 96-T


title: 99-T


title: 97-T


title: 105T


title: 89-T


title: 101-T-P


title: 87T


title: 88-T


title: 106-T-P


title: 85-T


title: 80-T


title: 79-T


title: 76-T


title: 84-T


title: 77-T


title: 81-T


title: 78-T


title: 86-T


title: 82-T


title: 73-T


title: 75-T


title: 72-T


title: 68-T


title: 67-T_P


title: 66-T


title: 65-T-P


title: 69-T_P


title: 70-T


title: 62-T


title: 64-T


title: 61-T


title: 58-T


title: 59-T


title: 60-T


title: 56-T


title: 53-T


title: 55-T


title: 57-T


title: 52T


title: 54T


title: 49-T


title: 48-T


title: 46-T


title: 51-T


title: 43T


title: 41-T


title: 42-T


title: 40-T


title: 45-T


title: 50-T


title: 39-T


title: 38-T


title: 32-T


title: 37-T


title: 35-T


title: 36-T


title: 29-T


title: 33-T


title: 27-T


title: 28-T


title: 31-T


title: 30-T


title: 25-T


title: 26-T


title: 22-T


title: 24-T


title: 21-T


title: 20-T


title: 47-T


title: 19-T


title: 18-T


title: 17-T


title: 16-T


title: 14T


title: 15-T


title: 13T


title: 12-T


title: 11-B


title: 9-B


title: 10-T


title: 8-T


title: 6-T


title: 3-T


title: PDFP_4N

value: Normal


title: 1-T


title: PDFP_11N


title: PDFP_9N

value: Follicular neoplasm


title: FP4_N


title: FP8_N


title: PDFP_1N


title: FP39_N


title: FP37_N


title: FP36_N


title: FP32_N


title: PDFP_8N


title: FP22_N


title: FP31_N


title: FP21_N


title: FP20_N


title: FP18_N


title: FP17_N


title: FP13_N


title: 7-T


title: 2-T


title: PDFP_3-N


title: ATCFP_9N


title: FP7_N


title: ATCFP_6-N


title: ATCFP_3-N


title: ATCFP_1N


title: ATCFP_11N


title: 516N

value: Nodular hyperplasia


title: 510N


title: FP25_N


title: 499N


title: FP23_N


title: 498N


title: 496N


title: 497N


title: 494N


title: 493N


title: 409N


title: FP15_N


title: 492N


title: FP10_N


title: 475N


title: 404N


title: 402N


title: ATCFP_8-N


title: 401N


title: ATCFP_13N


title: 397N


title: 398N


title: 399N


title: 394N


title: 381N


title: 385N


title: 386N


title: 396N


title: 390N


title: 393N


title: 382N


title: 366N


title: 374N


title: 408N


title: 375N


title: 373N


title: 380N


title: 363N


title: 361N


title: 407N


title: 360N


title: 362N


title: 358N


title: 359N


title: 357N


title: 403N


title: 355N


title: 356N


title: 353N


title: 354N


title: 352N


title: 351N


title: 364N


title: 348N


title: 346N


title: 308N


title: 318N


title: 311N


title: 306N


title: 309N


title: 307N


title: 304N


title: 303N


title: 299N


title: 302N


title: 301N


title: 300N


title: 298N


title: 289N


title: 290-N


title: 286-N


title: 287-N


title: 349T


title: 284N


title: 285N


title: 349N


title: 347N


title: 283N


title: 312N


title: 282N


title: 280N


title: 277N


title: 297N


title: 291-N


title: 273N


title: 281N


title: 274N


title: 266-N-P


title: 268N


title: 264-N-P


title: 272N


title: 263-N-P


title: 260-N


title: 259N


title: 257N


title: 258-N


title: 256-N


title: 255-N


title: 254-N2


title: 253-N


title: 249-N


title: 251-N


title: 247-N


title: 248-N


title: 246-N


title: 279N


title: 275N


title: 245-N


title: 244-N


title: 267-N-P


title: 262-N


title: 241-N


title: 238-N


title: 239-N


title: 240-N


title: 237-N


title: 235-N


title: 232-N


title: 230-N


title: 233-N


title: 234-N


title: 229-N


title: 226-N


title: 227-N


title: 223-N


title: 225-N


title: 224-N


title: 222-N


title: 221-N


title: 220-N


title: 219-N


title: 218-N


title: 217-N-P


title: 213-N


title: 215-N


title: 212N


title: 243-N


title: 211N


title: 208N


title: 207-N


title: 205N


title: 206-N


title: 204N


title: 203N


title: 202N-P


title: 198-N


title: 191-N_P


title: 189N-P


title: 187-N_P


title: 190N


title: 200-N


title: 188N-P


title: 186N


title: 185N


title: 184N-P


title: 179-N-P


title: 182N


title: 210N


title: 173N


title: 176N


title: 171N


title: 166-N-P


title: 169N


title: 158N


title: 161N


title: 157N-P


title: 163N


title: 160N-P


title: 154-N-P


title: 143N


title: 137N


title: 148N


title: 121N


title: 110N


title: 118N


title: 108N


title: 88N


title: 93N


title: 68N-P


title: 100N


title: 77N


title: 67N-P


title: 66N


title: 65N


title: ALL sample at diagnosis [ALL_Validation_20]

city: Uppsala

first: Olga

last: Krali

address: Husargatan 3

country: Sweden

institute: Uppsala University

description:
MiSeq
RNAseq_read_counts.txt

data_processing:
The raw sequencing data were processed together using the nextflow-based (21.02.0.edge) nf-core/rnaseq (3.0) pipeline
The sequencing paired-end reads were trimmed by trimgalore (0.6.6)
Alignment to GRCh38 reference genome with ENSEMBL gene annotation (GRCh38.103) was conducted with STAR
Quantification of the aligned reads at transcript level took place with the help of Salmon (1.4.0)
Transcript level expression values were summarized to gene level with the bioconductor package tximeta (1.8.0)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including raw count values for each Sample

source_name: Bone Marrow/Peripheral Blood

extract_protocol:
The RNA was extracted using the AllPrep kit (Qiagen).
RNA sequencing libraries were prepared using the Illumina TruSeq stranded Total RNA (RiboZero human/mouse/rat) kit, Illumina TruSeq RNA Access library preparation kit or Script-Seq kit (EpiCentre), as indicated in each sample information.

value: Bone Marrow/Peripheral Blood

tag: disease

value: childhood B acute lymphoblastic leukemia

tag: disease state

value: diagnosis

value: Unclassified BCP-ALL

tag: revised (predicted)_genotype

value: female

tag: library protocol

value: ScriptSeq


title: 63-N

tag: tissue

tag: cell type


title: HMF

city: Pittsburgh

first: Oleg

last: Akilov

state: PA

address: 3601 Fifth Avenue, 5th Floor

department: Department of Dermatology

institute: University of Pittsburgh

data_processing: RNA sequencing and TCR sequencing files were preprocessed using the BD Targeted Multiplex Rhapsody Analysis Pipeline (v. 1.9-beta). Sequencing reads were demultiplexed and mapped onto the reference genome (GRCh38) using the Seven Bridges Genomic Platform (BD Rhapsody Bioinformatics), and a gene expression matrix was output. Supplementary files format and content: RSEC_MolPerCell contains the counts of molecules per gene in each cell with cell barcode. Supplementary files format and content: VDJ_perCell contains the TCR and BCR sequences in each cell associated by cell barcode.  Supplementary files format and content: Custom_panel contains transcript information for the custom panel of 61 malignancy-associated genes. Supplementary files format and content: Human_Immunology_Targeted_Panel contains transcript information for the commercial BD Rhapsody Human Immune Response Panel.

source_name: Skin Punch Biopsy

extract_protocol: Whole skin dissociation was performed using the Miltenyi Biotec Human Whole Skin Dissociation Kit on the same day as biopsy.

treatment_protocol: Three 1 cm punch biopsies were performed on the HMF patient during screening, treatment week 1, and treatment week 4.

value: Patch-stage hypopigmented mycosis fungoides

value: Skin cells


title: 61-N

tag: genotype


title: HEK293 cells, βarrestin1/2 KO, isoproterenol, biol rep 3

first: Valeria

last: Burghi

address: 3855 Health Sciences Drive, Room 2345

department: Pharmacology

institute: University of California San Diego

description: beta arrestin1/2 KO cells iso 3

data_processing:
The quantification of transcripts was calculated using Salmon (version 1.7.0), which provides accurate expression estimates.
The differential gene expression analysis including quality control, model fitting, and hypothesis testing was conducted using DESeq2.
Assembly: Homo sapiens (human) genome assembly GRCh38 (hg38) from Genome Reference Consortium
Supplementary files format and content: CSV file containing merged count values from all quant.sf files generated by Salmon. NOTE: Aligned against spliced transcripts

source_name: βarrestin1/2 knock out

growth_protocol: HEK293 wild type, β-arrestin1/2 KO and Gαs KO cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (D6429, Sigma) supplemented with 10% fetal bovine serum (FBS) (F2442, Sigma) and 1% penicillin/streptomycin (A5955, Sigma) and maintained in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
After stimulus, the cells were washed with PBS, total RNA was isolated with a RNeasy Mini Kit (74104, Qiagen) including an on-column DNase I digestion and quantified using a Nanodrop ND-1000 (Thermo Scientific).
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina Novaseq 6000 platform, according to effective library concentration and data amount.

treatment_protocol: Cells were seeded in poly-D-lysine coated 6 well-plates and transfected with wild type β2AR plasmid. The following day, the cells were serum starved overnight. After 48 hours of transfection, the cells were incubated with 1 μM isoproterenol or vehicle for 1 h.

tag: cell line

value: embryonic

value: {beta}arrestin1/2 knock out

value: incubation with isoproterenol

tag: time

value: 1 h


title: HEK293 cells, βarrestin1/2 KO, isoproterenol, biol rep 2

description: beta arrestin1/2 KO cells iso 2


title: 62N

value: Thyroid

value: PTC


title: HEK293 cells, βarrestin1/2 KO, basal, biol rep 3

description: beta arrestin1/2 KO cells basal 3

value: incubation with vehicle


title: HEK293 cells, βarrestin1/2 KO, isoproterenol, biol rep 1

description: beta arrestin1/2 KO cells iso 1


title: 59-N

value: Normal


title: 58-N


title: 101N


title: HEK293 cells, βarrestin1/2 KO, basal, biol rep 2

description: beta arrestin1/2 KO cells basal 2


title: 57-N


title: HEK293 cells, βarrestin1/2 KO, basal, biol rep 1

description: beta arrestin1/2 KO cells basal 1


title: HEK293 cells, Gαs KO, isoproterenol, biol rep 3

description: Gas KO cells iso 3

source_name: Gαs knock out

value: G{alpha}s knock out


title: 56-N


title: HEK293 cells, Gαs KO, isoproterenol, biol rep 1

description: Gas KO cells iso 1


title: 50-N


title: HEK293 cells, Gαs KO, isoproterenol, biol rep 2

description: Gas KO cells iso 2


title: HEK293 cells, Gαs KO, basal, biol rep 3

description: Gas KO cells basal 3


title: 60-N


title: 53-N


title: HEK293 cells, Gαs KO, basal, biol rep 2

description: Gas KO cells basal 2


title: 49-N


title: 48-N


title: 47-N


title: HEK293 cells, wild type, isoproterenol, biol rep 3

description: Wild type cells iso 3

source_name: wild type

value: wild type


title: HEK293 cells, Gαs KO, basal, biol rep 1

description: Gas KO cells basal 1


title: 45-N


title: HEK293 cells, wild type, isoproterenol, biol rep 2

description: Wild type cells iso 2


title: 46-N


title: 54-N


title: HEK293 cells, wild type, isoproterenol, biol rep 1

description: Wild type cells iso 1


title: HEK293 cells, wild type, basal, biol rep 3

description: Wild type cells basal 3


title: 43-N


title: HEK293 cells, wild type, basal, biol rep 2

description: Wild type cells basal 2


title: 42-N


title: 41-N


title: HEK293 cells, wild type, basal, biol rep 1

description: Wild type cells basal 1


title: 40-N


title: JIH5_CellLine_ATAC

city: Memphis

first: Daniel

last: Savic

state: Tennessee

address: 262 Danny Thomas Pl

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

data_processing:
Reads were mapped to the human genome using bowtie2
Peak calling was performed using MACS2 using the default q value of 0.05
Assembly: hg19
Supplementary files format and content: narrowPeak files for each experimental sample

extract_protocol:
Cells were transposed following to the Fast-ATAC protocol from the Greenleaf Lab
Libraries were prepared for sequencing using standard Illumina protocols for Nextera adapters

value: ALL


title: 39-N


title: PCapHiC_sample_136

data_processing:
Analysis of Promoter capture HiC data was performed using the Arima CHiC pipeline (v1.5, https://github.com/ArimaGenomics/CHiC). Briefly, this pipeline uses HiCUP v0.8.0 for mapping and quality assessment of promoter capture HiC data and CHiCAGO to identify significant looping interactions in the promoter capture HiC data using 5kb resolution (patient samples) or 3kb resolution (cell lines) and adj. p < 0.05.
Assembly: HG19
Supplementary files format and content: bedpe of significant loops restricted to only intrachromasomal loops with a loop interval less than 2 megabases

source_name: ALL

extract_protocol: Patient Samples: Arima promoter capture HiC (Arima: A510008, A303010, A302010) was performed according to the manufacturers provided instructions using unspecified proprietary buffers, solutions, enzymes, and reagents. Briefly, 1.5 to 5 million cells were fixed in 1% formaldehyde for 10 minutes. The amount of fixed cell suspension equal to 5mg of cell DNA was used for HiC. Cells were lysed with Lysis Buffer and conditioned with Conditioning Solution before their DNA was digested in a cocktail consisting of Buffer A, Enzyme 1, and Enzyme 2. The digested, fixed chromatin was biotinylated using using Buffer B and Enzyme B before being ligated using Buffer C and Enzyme C. The fixed, biotinylated, ligated DNA was then subjected to reversal of crosslinking and digestion of proteins before being purified. 100ul containing 1500ug of purified large proximally ligated DNA was fragmented for 24 cycles (30s on/ 30s off) using a Diagenode Bioruptor Plus bath sonicator. The fragmented DNA was then subjected to two-sided size selection targeting fragments between 200-600bp using AMPure XP DNA purification beads. Size selected DNA was then subjected to biotin enrichment using T1 streptavidin beads. Bead bound, enriched HiC DNA was then subjected to Arima library prep. Briefly, the sample underwent end repair followed by adapter ligation, at which point the sample was then subjected to 10 cycles of PCR amplification. The library DNA was then purified using AMPure XP DNA purification beads. The HiC library was then subjected to Arima promoter capture enrichment. The library was precleared of biotinylated DNA using T1 streptavidin beads before being subjected to promoter enrichment with biotinylated RNA probes. After washing, the captured fragments were then amplified an additional 13 PCR cycles. These libraries were submitted for deep sequencing on an Illumina Nova-seq where >100M 150bp paired-end reads were obtained.      Cell Lines: Arima promoter capture HiC (Arima: A510008, A303010, A302010) was performed according to the manufacturers provided instructions using unspecified proprietary buffers, solutions, enzymes, and reagents. Briefly, 10 million ALL cells were harvested, suspended in 5ml RT PBS which was brought to 2% formaldehyde by adding 37% methanol-stabilized paraformaldehyde for a 10-minute fixation. The amount of fixed cell suspension equal to 5mg of cell DNA was used for HiC. Cells were lysed with Lysis Buffer and conditioned with Conditioning Solution before their DNA was digested in a cocktail consisting of Buffer A, Enzyme 1, and Enzyme 2. The digested, fixed chromatin was biotinylated using using Buffer B and Enzyme B before being ligated using Buffer C and Enzyme C. The fixed, biotinylated, ligated DNA was then subjected to reversal of crosslinking and digestion of proteins before being purified. 100ul containing 1500ug of purified large proximally ligated DNA was fragmented for 24 cycles (30s on/ 30s off) using a Diagenode Bioruptor Plus bath sonicator. The fragmented DNA was then subjected to two-sided size selection targeting fragments between 200-600bp using AMPure XP DNA purification beads. Size selected DNA was then subjected to biotin enrichment using T1 streptavidin beads. Bead bound, enriched HiC DNA was then subjected to Arima library prep. Briefly, the sample underwent end repair followed by adapter ligation, at which point the sample was then subjected to 10 cycles of PCR amplification. The library DNA was then purified using AMPure XP DNA purification beads. The HiC library was then subjected to Arima promoter capture enrichment. The library was precleared of biotinylated DNA using T1 streptavidin beads before being subjected to promoter enrichment with biotinylated RNA probes. After washing, the captured fragments were then amplified an additional 13 PCR cycles. These libraries were submitted for deep sequencing on an Illumina Nova-seq where >100M 150bp paired-end reads were obtained.

tag: read length


title: PCapHiC_sample_95


title: PCapHiC_sample_99


title: 38-N


title: PCapHiC_sample_138


title: 34-N


title: 35-N


title: PCapHiC_sample_93


title: 36-N


title: PCapHiC_sample_124


title: 30-N


title: 32-N


title: PCapHiC_sample_19


title: PCapHiC_sample_151


title: PCapHiC_sample_101


title: 33-N


title: 29-N


title: 27-N


title: BALL1_PCap_HiC


title: 23-N


title: SEM_PCap_HiC

source_name: SEM

value: SEM


title: 24-N


title: 25-N


title: SUPB15_PCap_HiC


title: PCapHiC_sample_97


title: REH_PCap_HiC

source_name: REH

value: REH


title: 21N


title: 20-N


title: RS411_PCap_HiC


title: Nalm6_PCap_HiC


title: 17-N


title: 19-N


title: 697_PCap_HiC


title: 15-N


title: NK92 cells,DMSO, day3

city: Tianjin

first: Fengqi

last: Li

state: Tianjin

address: No. 92, Weijin Road, Xuefu Street, Nankai District

department: School of Pharmaceutical Science and Technology

country: China

institute: Tianjin university

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Assembly: hg18
Supplementary files format and content: txt，NK92_all.fpkm.txt. includes three sets of control and three sets of FPKM values of treatment
Supplementary files format and content: txt，PBNK_all.fpkm.txt. includes three sets of control and three sets of FPKM values of treatment

growth_protocol: PB-NK cells were expanded from peripheral blood mononuclear cells (PBMCs) using a commercial NK cell culture reagents (ALySTM 505UNK),NK92 cell line were cultured in α-MEM containing 0.2 mM Inositol, 0.1 mM β-mercaptoethanol, 0.02 mM Folic Acid, 200 U/mL recombinant IL-2 , 12.5% horse serum (HS) , 12.5% FBS , and 1% PS

extract_protocol:
the total RNA was isolated from cells by using  total RNA purification kit (Tiangen, Cat# DP419)
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

treatment_protocol: Incubate all cells in 5% CO2 at 37 °C, and when cells have grown to a certain density, add 50 nM dasatinib and DMSO for 3 d, and then extract the total RNA.

value: Natural killer cells in human patients with malignant non-Hodgkin lymphoma

value: DMSO treatment for 3 days


title: PB-NK cells，Dasatinib, day3

source_name: PB-NK

value: PB-NK

value: peripheral blood (PB)-NK cells

value: 50 nM Dasatinib treatment for 3 days


title: NK92 cells,Dasatinib, day3


title: PB-NK cells，DMSO, day3


title: 14-N


title: 13-N


title: 11-N


title: 12-N


title: 16-N


title: KMC7001_NPCs_2

city: Ann Arbor

first: Elizabeth

middle: Anne

last: Werren

state: MI

address: 1137 Catherine St.

institute: University of Michigan

description:
human_gene_counts.txt
human_ercc_counts.txt

data_processing:
FASTQ files were trimmed with Cutadapt v4.1 using default parameters. Read quality was assessed by FASTQC v0.11.9. MultiQC v1.7 was used to visualize FASTQC outputs and compare samples. ERCC spike-in FASTA and GTF annotation files were merged with human GRCh38.p13 reference genome FASTA with GTF release 39 or mouse GRCm39 reference genome FASTA with GTF release M28. FASTQ reads were then mapped to merged files using STAR alignment with parameter ‘--outSAMtype BAM SortedByCoordinate’.
Count analysis was performed on sorted BAM files using RSEM with paired-end alignment specified.
Differential expression analysis was carried out using DESeq2 v1.34.0 in R v4.1.2. ERCC spike-in counts were used to estimate size factors for each sample for DESEq2 analysis.
Alternative splicing analysis was performed on sorted BAM files using rMATS v4.1.2 with the following parameters: ‘-t paired --readLength 150 --variable-read-length --nthread 4’
Assembly: GRCh38/GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes ERCC spike-in counts for each sample

growth_protocol: Human ESC and iPSC lines were cultured using feeder free conditions on Matrigel (Corning) with mTeSR-1 (STEMCELL Technologies). Passaging was performed using mTeSR-1 supplemented 1 nM ROCK inhibitor (BD Biosciences 562822) to prevent differentiation. Both manual and chemical dissociation with Versene (Gibco 15040066) were performed for splitting. All mice were maintained according with the National Institutes of Health Guidelines for the Care and Use of Laboratory Animals and were approved by the Case Western Reserve Institutional Animal Care and Use Committee. CRISPR genome editing was performed in the University of California, San Diego Transgenic and Knockout Mouse Core. C57BL/6JN hybrid mice (Jackson Laboratory, 005304) were used for CRISPR editing of the Thoc6 locus. Founder mice with the Thoc6fs/+ allele were intercrossed with C57BL/6JN mice (Jackson Laboratory, 005304) for line maintenance. All ex vivo analyses were performed on tissue collected from mice of both sexes at embryonic day (E) 8.5-10.5. Sex-dependent differences were not assessed.

extract_protocol:
Total RNA was extracted from cultured hNPCs (two biological replicates per genotype) using TRIzol Reagent (Invitrogen 15596026) followed by DNAse column treatment using PureLink RNA extraction kit (Invitrogen 12183018A). Total RNA from dissected E9.5 mouse forebrain tissue (three biological replicates per genotype) was extracted using Picopure RNA isolation kit (Applied Biosystems KIT0204) according to manufacturer’s recommendations. hNPC and E9.5 mouse forebrain RNA samples were ribo-depleted followed by 151 bp paired-end sequencing on the Illumina NovaSeq 300 cycle, ~20-30 million reads per sample.
Library preparation and sequencing was conducted by the Advanced Genomics Core (AGC) at the University of Michigan using Illumina Total RNA library prep kit following manufacturer's instructions. ERCC spike-ins (Invitrogen 4456740) were added for sequencing controls at starting concentrations according to the manufacturer’s instructions.

treatment_protocol: human ESCs/iPSCs were passaged into 96-well V-shaped bottom ultra-low attachment cell culture plates (PrimeSurface® 3D culture, MS-9096VZ) to achieve a starting cell density of 600-1,000 cells per well in 30 µl of mTesRTM1 with 1 nM ROCK inhibitor. After 36 hours, 150 µl of N-2/SMAD inhibition media (cocktail of 1X N-2 supplement (Invitrogen 17502048), 2 μM A-83-01 inhibitor (Tocris Bioscience 2939), and 1 mM dorsomorphin (Tocris Bioscience 309350) in DMEM-F12 (Gibco 11330032)) was added for neural induction. On day 7, EBs were transferred to Matrigel-coated plates to enrich for neural rosettes at a density of 20-30 EBs per well of a 6-well plate, and media was changed to neural differentiation media (0.5X N-2 supplement, 0.5X B-27 supplement (Invitrogen 17504044) with 20 pg/μl bFGF and 1mM dorsomorphin inhibitor in DMEM/F-12). For monolayer NPC differentiation, neural rosettes were scored and uplifted on day 14, dissociated in Accutase (Gibco A1110501), and re-plated on poly-L-ornithine (PLO)/Laminin-coated plates for NPC expansion, selection, and passaging. 15 μg/mL PLO (Sigma-Aldrich P4957) diluted in DPBS (Gibco 14040-133); 10 μg/mL laminin (Sigma-Aldrich L2020) diluted in DMEM/F-12.

value: neural progenitor cells differentiated from induced pluripotent stem cells (iPSCs)

value: neural differentiation


title: 9-N


title: 10-N


title: KMC7002_NPCs_2


title: KMC7002_NPCs_1


title: KMC6003_NPCs_1

value: THOC6 E188K/E188K


title: KMC6003_NPCs_2


title: 18-N

value: Thyroid


title: 8-N

value: PTC


title: KMC6002_NPCs_2

value: THOC6 E188K/+


title: 6-N

value: Normal


title: KMC7001_NPCs_1


title: 5-N

value: Follicular neoplasm


title: KMC6002_NPCs_1


title: AS0041_NPCs_2

value: AS0041 New York Stem Cell Foundation (NYSCF) Diabetes iPSC Panel

value: wildtype


title: 4-N


title: 3-N


title: AS0041_NPCs_1


title: 1-N


title: AS0035_NPCs_1

value: AS0035 New York Stem Cell Foundation (NYSCF) Diabetes iPSC Panel


title: input_IKO_d18MNP_Rep1

description: ChIP of TF-bound DNA in cell type

data_processing:
Reads were demultiplexed for each sample
Reads were aligned to human hg19 genome with BWA-MEM
The BWA-aligned data was filtered with Filter Sam or Bam, output to BAM
The filtered BAM files were processed into BigWig files using BamCoverage for visualization on the UCSC genome browser
Peaks were determined from the BAM files with MACS2 Callpeak algorithm
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files are peak files in .bed format.

growth_protocol: Motor neuron progenitor cells (d18MNPs) were differentiated from hiPSC lines by modulation of growth factors in a 3-step process (NeuroLINCS Consortium et al., 2021).

extract_protocol:
In brief, progenitor cells were collected from plates and fixed and frozen. Thawed cells were then subjected to a nuclear extraction protocol involving shearing of chromatin. They rotated O/N with primary antibody (input saved prior) then antibody-TF complexes were captured via protein G Dynabeads. After washes, sample was eluted and then treated with proteinase and RNAse, leaving DNA to be further processed for ChIP-seq.
In brief, samples were prepared for library sequencing using the NEBNExt Ultra II DNA Library Kit for Illumina, and following manufacturer instructions. Sample integrity was confirmed via Bioanalyzer (Agilent) and then samples were run on an Illumina NextSeq 500 or an Illumina HiSeq 4000.

value: d18 hiPSC-derived motor neuron progenitor cells (d18MNP)

tag: ChIP

value: input

value: untreated

tag: molecule subtype

value: TF-bound DNA

tag: molecule

value: genomic DNA


title: AS0035_NPCs_2


title: H9_NPCs_2

value: H9 WiCell WA09

value: neural progenitor cells differentiated from embryonic stem cells (ESCs)


title: H9_NPCs_1

value: neural differentiation


title: ISL1_WT_d18MNP_Rep1

description: ChIP of TF-bound DNA in cell type

value: ChIP with anti-human-ISLET-1 antibody (Cat. AF1837, R&D Systems)


title: input_NKO_d6CP_Rep1

description: input sample of TF-bound DNA in cell type

growth_protocol: Cardiac progenitors cells (d6CPs) were differentiated from hiPSC lines by the WNT modulation protocol (Lian et al., 2013).

value: d6 hiPSC-derived cardiac progenitor cells (d6CP)


title: NKX25_NKO_d6CP_Rep1

description: ChIP of TF-bound DNA in cell type

value: ChIP with anti-NKX-2.5 Antibody (N-19) (Cat. sc-8697, Santa Cruz Technologies)


title: ISL1_NKO_d6CP_Rep1

description: ChIP of TF-bound DNA in cell type


title: Sample21_gastric epithelial cells, Lpp20-HA_delta_lnt_6

city: NASHVILLE

first: Mark

last: McClain

address: 1161 21st Ave South, A2321 Medical Center North

institute: Vanderbilt University Medical Cente

data_processing:
Trimmomatic
HiSat2
StringTie
edgeR
Assembly: human b37: hg19
Supplementary files format and content: Normalized_Counts.csv

source_name: stomach

growth_protocol: Deidentiified primary human gastric epithelial cells were cultured in Complete Human Epithelial Cell Medium (Cell Biologics)

extract_protocol:
Direct-zol RNA MiniPrep Plus (Zymo Research) including on-column DNAse treatment
RNA libraries were prepared for sequencing using standard Illumina protocols
Libraries were sequenced on a NovaSeq 6000 with paired reads of 150-bp length

value: stomach

value: primary

value: epithelial

value: WT

value: 300 ng per ml Lpp20-HA delta lnt, 4 hours


title: Sample18_gastric epithelial cells, Lpp20-HA_delta_lnt_3


title: Sample16_gastric epithelial cells, Lpp20-HA_delta_lnt_1


title: input_WT_d18MNP_Rep1


title: ISL1_IKO_d6CP_Rep1

description:
ChIP of TF-bound DNA in cell type
Peak calling on this sample resulted in no called peaks. File not included on the records.


title: input_WT_d6CP_Rep3


title: Sample14_gastric epithelial cells, Lpp20-HA_5

value: 300 ng per ml Lpp20-HA, 4 hours


title: Sample17_gastric epithelial cells, Lpp20-HA_delta_lnt_2


title: input_WT_d6CP_Rep2

description: ChIP of TF-bound DNA in cell type


title: Sample12_gastric epithelial cells, Lpp20-HA_3


title: input_WT_d6CP_Rep1

description: ChIP of TF-bound DNA in cell type


title: ISL1_WT_d6CP_Rep3

description: ChIP of TF-bound DNA in cell type


title: Sample13_gastric epithelial cells, Lpp20-HA_4


title: 2-N

value: Thyroid

value: Normal

value: PTC


title: Sample20_gastric epithelial cells, Lpp20-HA_delta_lnt_5


title: Sample11_gastric epithelial cells, Lpp20-HA_2


title: Sample19_gastric epithelial cells, Lpp20-HA_delta_lnt_4


title: ISL1_WT_d6CP_Rep1

description: ChIP of TF-bound DNA in cell type

value: untreated

value: TF-bound DNA


title: input_IKO_d6CP_Rep1

description: ChIP of TF-bound DNA in cell type

value: input

value: genomic DNA


title: Sample8_gastric epithelial cells, Pam2-CSK4_2

value: 100 ng per ml Pam2-CSK4, 4 hours


title: Sample9_gastric epithelial cells, Pam2-CSK4_3


title: Sample15_gastric epithelial cells, Lpp20-HA_6


title: Sample7_gastric epithelial cells, Pam2-CSK4_1


title: Sample4_gastric epithelial cells, Pam3-CSK4_1

value: 100 ng per ml Pam3-CSK4, 4 hours


title: S100A8 Healthy2

city: birmingham

first: lin

last: jin

state: alabama

address: 1824 6th ave s

department: Dermatology

institute: university of alabama at birmingham

data_processing:
FASTQ files were generated through BaseSpace using Illumina's bcl2fastq software.
CUT-RUNTools-2.0 (https://github.com/fl-yu/CUT-RUNTools-2.0) was used to trim, align, and call peaks. Used default settings, EXCEPT set "frag_120" to "FALSE".
bigWig files were generated using deepTools bamCoverage version 3.5.1 with parameters -of bigwig --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --ignoreForNormalization chrX chrM --binSize 10
Assembly: Gencode GRCh38 p13 Release 36
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&RUN

source_name: skin epidermis

extract_protocol:
HS and healthy skin tissues were cut into small pieces and were digested with 2.5U/ml Dispase-II (Millipores Sigma, Cat#4942078001) in Hanks’ Balanced Salt Solution (HBSS, Corning, Cat#21-022-CM) overnight at 4°C. After digestion, the epidermis was peeled off and minced. The minced epidermis was incubated with 0.05% trypsin-EDTA at 37°C for 40 mins for further digestion. The suspension was then filtered through a 40um cell strainer and spun down at 300g at 4°C for 5 mins.  Cells were then subjected to remove apoptotic and dead cells by using the Annexin Dead Cell Removal Kit (StemCell Technologies, 17899) and EasySep™ Magnet (StemCell Technologies, 18000). Enriched living cells were  were  for the application of CUT&RUN sequence.
CUT&RUN experiments were carried out following the protocol of Epicypher CUTANA CUT&RUN kit (version 1.8). Briefly,  epidermal cells (1X10^4) were isolated with Wash Buffer (20 mM HEPES, 150 mM NaCl, 0.5 mM Spermidine, 1X Roche cOmplete, protease inhibitor). The nuclei were captured with Concanavalin A (ConA) beads and incubated with 0.5 μg primary antibody for S100A8 (Abcam, cat#ab92331) in Antibody Buffer (Wash Buffer, 0.01% Digitonin, 2 mM EDTA) overnight at 4 °C. Then CUTANA pAG-MNase was added and incubated for 10 min at RT. CaCl2 was next added at a final concentration of 100 mM to activate the enzyme. The reaction was carried out for 2 hours at 4 °C and stopped by STOP buffer (340 mM NaCl, 20 mM EDTA, 4 nM EGTA, 50 μg/mL RNase A, and 50 μg/mL glycogen). Samples were incubated for 10 min at 37 °C in a thermocycler and quick spin down. DNA was purified using the CUANA DNA Purification Kit as the provided instructions. Purified CUT&RUN-enriched DNA was prepared sequencing libraries using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, Cat# E7645s).

value: skin epidermis

tag: Sex

value: male

value: healthy skin

tag: antibody


title: S100A8 HS3

value: HS, Hurley III


title: Sample3_gastric epithelial cells, control_3

value: stomach

value: primary

value: epithelial

tag: treatment


title: Sample2_gastric epithelial cells, control_2

value: WT


title: TO_2999

city: Kyoto

first: Yasuhiro

last: Takashima

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Kyoto University

data_processing:
The sequenced data were preprocessed and quantified for gene expression using STAR aligner (v2.5.1b) and RSEM (v1.3.1) tool.
Assembly: GRCh38-3.0.0
Supplementary files format and content: text file includes TPM values for each sample.

source_name: Bilaminoid D6 (CER1-GFP+/PDGFRA+)

extract_protocol:
Bilaminoids (D6) were manually picked. Each bilaminoid was transferred in a drop of Accutase and incubated at 37℃ for 15-20 min, then dissociated into single cells by repeated pipetting using glass capillaries. Each single cell was transferred into individual PCR tubes and immediately frozen in Smart-seq HT lysis buffer. To collect amnion-like cells(AMLCs), PGC-like cells(PGCLCs), and hematoendothelial progenitor-like cells(HEPLCs), CER1-GFP+ anterior visceral endoderm-like cells(AVELCs) were sorted as single-cells and immediately frozen in Smart-seq HT lysis buffer.
The libraries for scRNA-seq were prepared using the SMART-seq HT kit (Z4436N, Takara), following the manufacture’s instruction. The libraries were then sequenced on an NovaSeq 6000 or NextSeq 2000 with paired-end sequencing.

tag: analysis method

value: scRNA-seq

value: H9 ESCs

value: Bilaminoid Day6

tag: transgenes

tag: protocol

value: FACS:CER1-GFP and PDGFRA+


title: TO_2993


title: ISL1_WT_d6CP_Rep2

description: ChIP of TF-bound DNA in cell type

value: d6 hiPSC-derived cardiac progenitor cells (d6CP)

value: ChIP with anti-human-ISLET-1 antibody (Cat. AF1837, R&D Systems)

value: untreated

value: TF-bound DNA


title: TO_2971


title: TO_2981


title: TO_2970


title: S100A8 HS2

tag: disease state


title: S100A8 Healthy1

value: female


title: TO_2965


title: TO_2968


title: TO_2962


title: Sample5_gastric epithelial cells, Pam3-CSK4_2

value: 100 ng per ml Pam3-CSK4, 4 hours


title: TO_2957


title: Sample6_gastric epithelial cells, Pam3-CSK4_3


title: TO_2762

source_name: Bilaminoid D9 (CD34+)

value: Bilaminoid Day9


title: TO_2761


title: TO_2757


title: TO_2753


title: TO_2752


title: Sample1_gastric epithelial cells, control_1


title: TO_2751


title: TO_2749


title: TO_2731

source_name: Bilaminoid D6 (VTCN1+)


title: TO_2736


title: S100A8 HS1

value: skin epidermis

value: male

value: HS, Hurley II


title: TO_2746


title: TO_2723


title: VK8 Nasal Epithelial Cells, Non-Frequent Exacerbator

city: Cincinnati

first: Kieran

middle: J

last: Phelan

state: Ohio

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Computational Suite for Bioinformatitions and Biologists (CSBB)
Quality trimmed reads were mapped to the human hg19 genome, quantified using RSEM2 and mapped with Bowtie 23 using default thresholds
Assembly: hg19
Supplementary files format and content: comma-separated files include raw count values for each Sample

source_name: Primary Human Cells

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen) following manufactuer's instructions.
NEBNext Ultra II Direction RNA Library Prep Kit was used for library preparation.

tag: phenotype

value: Non-Frequent Exacerbator

value: Primary Human Cells

value: Nasal Epithelial Cells

tag: sample id


title: VK6 Nasal Epithelial Cells, Frequent Exacerbator

value: Frequent Exacerbator

tag: cell type


title: VK7 Nasal Epithelial Cells, Frequent Exacerbator


title: Sample10_gastric epithelial cells, Lpp20-HA_1

tag: tissue

value: stomach

value: primary

value: epithelial

tag: genotype

value: WT

value: 300 ng per ml Lpp20-HA, 4 hours


title: TO_2719

value: scRNA-seq

tag: cell line

value: H9 ESCs

value: Bilaminoid Day6


title: VK56 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2721


title: TO_2720


title: VK54 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: ISL1_IKO_d18MNP_Rep1

description: ChIP of TF-bound DNA in cell type

source_name: Motor neuron progenitor cells

value: d18 hiPSC-derived motor neuron progenitor cells (d18MNP)

value: ChIP with anti-human-ISLET-1 antibody (Cat. AF1837, R&D Systems)

value: untreated

value: TF-bound DNA

value: genomic DNA


title: TO_2692

source_name: Bilaminoid D9 (VTCN1+)

value: Bilaminoid Day9


title: VK53 Nasal Epithelial Cells, Non-Frequent Exacerbator

value: Non-Frequent Exacerbator

value: Primary Human Cells


title: TO_2717


title: TO_2750


title: VK51 Nasal Epithelial Cells, Non-Frequent Exacerbator

value: Nasal Epithelial Cells


title: TO_2684


title: VK52 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2686


title: VK50 Nasal Epithelial Cells, Frequent Exacerbator

value: Frequent Exacerbator


title: TO_2676


title: VK5 Nasal Epithelial Cells, Frequent Exacerbator


title: VK49 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: VK55 Nasal Epithelial Cells, Frequent Exacerbator


title: TO_2672


title: VK46 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: VK47 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2690


title: TO_2661


title: TO_2653


title: TO_2667


title: VK42 Nasal Epithelial Cells, Frequent Exacerbator


title: TO_2651


title: TO_2663


title: VK41 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2648


title: TO_2647


title: VK39 Nasal Epithelial Cells, Frequent Exacerbator


title: VK40 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2646


title: TO_2670


title: TO_2644


title: VK4 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: VK48 Nasal Epithelial Cells, Frequent Exacerbator


title: VK37 Nasal Epithelial Cells, Frequent Exacerbator


title: TO_2641


title: VK45 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: VK36 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: VK44 Nasal Epithelial Cells, Frequent Exacerbator


title: TO_2639


title: TO_2640


title: TO_2658


title: VK34 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2564


title: TO_2543


title: TO_2548


title: TO_2649


title: VK31 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: VK32 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: VK30 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: VK43 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2469


title: VK3 Nasal Epithelial Cells, Frequent Exacerbator


title: VK38 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: VK29 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2464


title: TO_2452


title: TO_2461


title: TO_2459


title: VK28 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: VK27 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2405

source_name: Bilaminoid D6

value: manual cell picking


title: VK25 Nasal Epithelial Cells, Frequent Exacerbator


title: TO_2400


title: VK35 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: VK24 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2399


title: TO_2398


title: VK33 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: VK22 Nasal Epithelial Cells, Frequent Exacerbator


title: TO_2396


title: TO_2542


title: VK23 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2397


title: TO_2390


title: VK21 Nasal Epithelial Cells, Frequent Exacerbator


title: VK20 Nasal Epithelial Cells, Frequent Exacerbator


title: TO_2387


title: VK2 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: VK19 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2386


title: VK18 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: VK26 Nasal Epithelial Cells, Frequent Exacerbator


title: VK15 Nasal Epithelial Cells, Frequent Exacerbator


title: VK17 Nasal Epithelial Cells, Frequent Exacerbator


title: TO_2383


title: TO_2381


title: TO_2384


title: TO_2385


title: VK14 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: VK11 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2380


title: TO_2379


title: TO_2378


title: VK13 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2377


title: VK1 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2374


title: TO_2388


title: JBM95 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2376


title: JBM94 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: JBM93 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2373


title: TO_2372


title: VK16 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2370


title: JBM92 Nasal Epithelial Cells, Frequent Exacerbator


title: JBM90 Nasal Epithelial Cells, Frequent Exacerbator


title: JBM91 Nasal Epithelial Cells, Frequent Exacerbator


title: TO_2368


title: TO_2367


title: TO_2366


title: JBM89 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: JBM87 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2365


title: JBM86 Nasal Epithelial Cells, Frequent Exacerbator


title: VK10 Nasal Epithelial Cells, Frequent Exacerbator


title: TO_2364


title: JBM85 Nasal Epithelial Cells, Frequent Exacerbator


title: JBM83 Nasal Epithelial Cells, Frequent Exacerbator


title: TO_2360


title: JBM82 Nasal Epithelial Cells, Frequent Exacerbator


title: TO_2363


title: TO_2361


title: TO_2357


title: JBM81 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: JBM80 Nasal Epithelial Cells, Frequent Exacerbator


title: JBM79 Nasal Epithelial Cells, Frequent Exacerbator


title: TO_2354


title: TO_2355


title: JBM76 Nasal Epithelial Cells, Frequent Exacerbator


title: JBM77 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: JBM75 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2351


title: JBM74 Nasal Epithelial Cells, Frequent Exacerbator


title: TO_2350


title: TO_2352


title: TO_2349


title: JBM72 Nasal Epithelial Cells, Frequent Exacerbator


title: JBM70 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2348


title: JBM69 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2347


title: JBM67 Nasal Epithelial Cells, Frequent Exacerbator


title: JBM68 Nasal Epithelial Cells, Frequent Exacerbator


title: TO_2345


title: JBM66 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: JBM65 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: JBM64 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: JBM63 Nasal Epithelial Cells, Frequent Exacerbator


title: TO_2340


title: TO_2339


title: TO_2312


title: TO_2353


title: JBM61 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2311


title: TO_2309


title: JBM60 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2308


title: JBM58 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2341


title: TO_2310


title: TO_2346


title: TO_2306


title: TO_2305


title: JBM55 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: JBM54 Nasal Epithelial Cells, Frequent Exacerbator


title: JBM53 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: JBM59 Nasal Epithelial Cells, Frequent Exacerbator


title: JBM52 Nasal Epithelial Cells, Frequent Exacerbator


title: TO_2300


title: JBM62 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2295


title: TO_2298


title: TO_2291


title: JBM46 Nasal Epithelial Cells, Frequent Exacerbator


title: JBM56 Nasal Epithelial Cells, Frequent Exacerbator


title: TO_2297


title: TO_2290


title: JBM50 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: JBM49 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: JBM45 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: JBM44 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2293


title: TO_2292


title: JBM47 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2285


title: TO_2280


title: TO_2289


title: JBM43 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2286


title: JBM42 Nasal Epithelial Cells, Frequent Exacerbator


title: TO_2304


title: JBM40 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2263


title: JBM38 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: JBM39 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2259


title: JBM37 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2264


title: JBM35 Nasal Epithelial Cells, Frequent Exacerbator


title: JBM41 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: JBM34 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2085


title: TO_2084


title: JBM33 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: JBM48 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: JBM32 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2260


title: TO_2074

value: FACS:CER1-GFP and PDGFRA+


title: JBM31 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: JBM30 Nasal Epithelial Cells, Frequent Exacerbator


title: TO_2094


title: TO_2013


title: JBM28 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2011


title: TO_2010


title: JBM27 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2012


title: JBM25 Nasal Epithelial Cells, Frequent Exacerbator


title: JBM24 Nasal Epithelial Cells, Frequent Exacerbator


title: JBM26 Nasal Epithelial Cells, Frequent Exacerbator


title: JBM29 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_2000


title: TO_2006


title: TO_2009


title: JBM23 Nasal Epithelial Cells, Frequent Exacerbator


title: JBM22 Nasal Epithelial Cells, Frequent Exacerbator


title: TO_1997


title: TO_1998


title: TO_2014


title: CD19+ from blood donor [867_B]

description:
HiSeq 2500
RNAseq_read_counts.txt

source_name: Peripheral blood

value: Peripheral blood

tag: disease

value: non-leukemic

value: no disease

value: Control

tag: revised (predicted)_genotype

tag: library protocol

value: ScriptSeq


title: TO_1996

value: scRNA-seq

value: H9 ESCs

value: Bilaminoid Day6


title: TO_1999


title: JBM21 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_1995


title: CD19+ from blood donor [858_B]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: CD3+ from blood donor [858_T]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: JBM20 Nasal Epithelial Cells, Frequent Exacerbator


title: TO_2092


title: TO_1990


title: TO_1994


title: CD3+ from blood donor [845_T]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: TO_1984


title: TO_1983


title: JBM18 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_1982


title: JBM19 Nasal Epithelial Cells, Frequent Exacerbator


title: JBM17 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: CD19+ from blood donor [845_B]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: TO_2005


title: CD3+ from blood donor [867_T]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: TO_1980


title: JBM16 Nasal Epithelial Cells, Frequent Exacerbator


title: TO_1972


title: CD19+ from blood donor [817_B]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: TO_1989


title: JBM15 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_1958


title: TO_1960


title: ALL sample at relapse [ALL_368_r]

description:
HiSeq 2500
RNAseq_read_counts.txt

source_name: Bone Marrow/Peripheral Blood

value: Bone Marrow/Peripheral Blood

value: childhood B acute lymphoblastic leukemia

value: relapse

value: Unclassified BCP-ALL

value: male

value: RNAaccess


title: JBM14 Nasal Epithelial Cells, Non-Frequent Exacerbator

value: Non-Frequent Exacerbator

value: Primary Human Cells

value: Nasal Epithelial Cells


title: TO_1956

value: manual cell picking


title: TO_1954


title: TO_1948


title: TO_1947


title: ALL sample at relapse [ALL_1026_r]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: TO_1926


title: TO_1981


title: ALL sample at diagnosis [KSALL34]

description:
HiSeq 2500
RNAseq_read_counts.txt

value: diagnosis

value: female


title: ALL sample at diagnosis [ALL_1097]

description:
HiSeq 2500
RNAseq_read_counts.txt

value: TruSeq


title: JBM11 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_1923


title: JBM12 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_1921


title: JBM10 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_1922


title: TO_1968


title: TO_1894


title: TO_1892


title: ALL sample at diagnosis [ALL_1135]

description:
HiSeq 2500
RNAseq_read_counts.txt

value: PAX5 P80R


title: JBM09 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: CD3+ from blood donor [817_T]

description:
HiSeq 2500
RNAseq_read_counts.txt

value: Peripheral blood

value: non-leukemic

value: no disease

value: Control

value: ScriptSeq


title: TO_1887

value: scRNA-seq

value: H9 ESCs

value: Bilaminoid Day6


title: ALL sample at diagnosis - technical replicate 3 [ALL_317_3]

description:
HiSeq 2500
RNAseq_read_counts.txt

value: Bone Marrow/Peripheral Blood

value: childhood B acute lymphoblastic leukemia

value: male

value: RNAaccess


title: TO_1888

value: manual cell picking


title: JBM13 Nasal Epithelial Cells, Non-Frequent Exacerbator

value: Non-Frequent Exacerbator

value: Primary Human Cells

value: Nasal Epithelial Cells


title: ALL sample at diagnosis [ALL_1128]

description:
HiSeq 2500
RNAseq_read_counts.txt

value: diagnosis

value: Unclassified BCP-ALL

value: TruSeq


title: ALL sample at diagnosis [ALL_1110]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: TO_1884


title: JBM07 Nasal Epithelial Cells, Frequent Exacerbator

value: Frequent Exacerbator


title: TO_1882


title: JBM06 Nasal Epithelial Cells, Frequent Exacerbator


title: ALL sample at diagnosis [ALL_1163]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_1154]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: TO_1883


title: JBM04 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: JBM03 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: ALL sample at diagnosis [ALL_1190]

description:
HiSeq 2500
RNAseq_read_counts.txt

value: female


title: TO_1872


title: TO_1873


title: TO_1852


title: ALL sample at diagnosis [ALL_1150]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: TO_1869


title: JBM02 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: TO_1846


title: JBM08 Nasal Epithelial Cells, Non-Frequent Exacerbator


title: ALL sample at diagnosis [ALL_1061]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: TO_1839


title: TO_1870


title: TO_1886


title: TO_1832


title: TO_1841


title: ALL sample at diagnosis [ALL_1072]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: TO_1834


title: CD3+ from blood donor [899_T]

description:
HiSeq 2000
RNAseq_read_counts.txt

value: Peripheral blood

value: non-leukemic

value: no disease

value: Control

value: ScriptSeq


title: CD19+ from blood donor [899_B]

description:
HiSeq 2000
RNAseq_read_counts.txt


title: TO_1827

value: scRNA-seq

value: H9 ESCs

value: Bilaminoid Day6


title: TO_1824

value: manual cell picking


title: TO_1877


title: ALL sample at relapse [ALL_380_r]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: Bone Marrow/Peripheral Blood

value: childhood B acute lymphoblastic leukemia

value: relapse

value: HeH

value: male


title: ALL sample at diagnosis [ALL_1060]

description:
HiSeq 2500
RNAseq_read_counts.txt

value: diagnosis

value: Unclassified BCP-ALL

value: TruSeq


title: TO_1822


title: ALL sample at diagnosis - technical replicate 2 [ALL_680_2]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: TO_1809


title: ALL sample at relapse [ALL_464_r]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_1047]

description:
HiSeq 2500
RNAseq_read_counts.txt

value: female


title: TO_1801


title: ALL sample at diagnosis - technical replicate 2 [ALL_555_2]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: TO_1806


title: ALL sample at relapse [ALL_680_r]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_869]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: ALL sample at relapse [ALL_257_r]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: TO_1775


title: ALL sample at diagnosis [ALL_1100]

description:
HiSeq 2500
RNAseq_read_counts.txt

value: PAX5 P80R


title: TO_1772


title: ALL sample at relapse [ALL_210_r]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: TO_1802


title: TO_1755


title: TO_1773


title: ALL sample at diagnosis [ALL_1092]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: TO_1823


title: TO_1742


title: TO_1750


title: ALL sample at diagnosis [ALL_851]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: ALL sample at relapse [ALL_358_r]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: childhood T acute lymphoblastic leukemia

value: T-ALL


title: TO_1728


title: ALL sample at diagnosis [ALL_1089]

description:
HiSeq 2500
RNAseq_read_counts.txt

value: RNAaccess


title: ALL sample at diagnosis [ALL_989]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: Sample at remission [Constitutional_559rep2]

description:
HiSeq 2000
RNAseq_read_counts.txt

value: remission

value: Control

value: ScriptSeq


title: TO_1720

value: scRNA-seq

value: H9 ESCs

value: Bilaminoid Day6

value: manual cell picking


title: TO_1796


title: ALL sample at diagnosis - technical replicate 2 [ALL_317_2]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: Bone Marrow/Peripheral Blood

value: childhood B acute lymphoblastic leukemia


title: TO_1771


title: TO_1693