title: NOD, Standard, Rep3, WGBS

value: liver


title: WT_msE9.5_forebrain_2

status: Public on Oct 17 2023

type: SRA

city: Ann Arbor

first: Elizabeth

middle: Anne

last: Werren

state: MI

address: 1137 Catherine St.

country: USA

institute: University of Michigan

description:
mouse_gene_counts.txt
mouse_ercc_counts.txt

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

source_name: E9.5 forebrain tissue

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.

tag: tissue

value: E9.5 forebrain tissue

tag: cell line

tag: cell type

tag: genotype

value: wildtype

tag: treatment


title: ATAC_sample_147

city: Memphis

first: Daniel

last: Savic

state: Tennessee

address: 262 Danny Thomas Pl

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

library_source: genomic

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 include Genomic Intervals

molecule: genomic DNA

organism: Homo sapiens

source_name: ALL

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: WT_msE9.5_forebrain_1


title: ATAC_sample_97


title: BMT2 SI Tumour Rep 1

city: Glasgow

first: Kathryn

last: Gilroy

address: Switchback Road

country: United Kingdom

institute: Cancer Research UK Scotland Institute

data_processing:
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences and low-quality base calls, defined as those with a Phred score of less than 20, using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.98 using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Assembly: GRCm38.98
Supplementary files format and content: matrix of raw counts

source_name: Small Intestine

extract_protocol:
RNA was isolated using the Rneasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
Libraries for cluster generation and DNA sequencing were prepared using an Illumina TruSeq RNA sample kit, then run on an Illumina NextSeq 500 (2x36 cycles, paired end, single index).

treatment_protocol: Induction of genetic recombination was performed by 1 x 80mg/kg intraperitoneal injection of Tamoxifen. Tissues were harvested at clinical endpoint.

tag: Sex

value: Female

value: Small Intestine

value: vilCreER BrafV600E/+ Mlh1fl/fl Tgfbr2fl/fl

tag: sample type

value: Primary Tumour


title: BL6, Standard, Rep2, RNA

city: Philadelphia

first: Phillip

last: Wulfridge

state: Pennsylvania

address: 3601 Spruce St

institute: The Wistar Institute

data_processing:
Alignment (WGBS): TrimGalore/Bismark/Bowtie2
Alignment (RNA-Seq): kallisto
Assembly: mm9
Supplementary files format and content: CpG reports containing methylation information of CpG dinucleotides; abundance files with estimated abundances of gene expression.

source_name: liver

growth_protocol:
Diet study: 4-week-old A/J, BL6, and NOD mice were acclimated for 2 weeks on a standard laboratory diet, then randomly assigned to  standard or American diet groups for 24 weeks.
Drug study: 9-week-old BL6 and NOD mice were obtained from The Jackson Laboratory and acclimated for 6 weeks on a standard laboratory diet, then randomly assigned to standard-vehicle, American-vehicle, or American-GW4064 treatment groups. Mice were fed their assigned diet for 6 weeks and treated with DMSO or 50 mg/kg GW4064 via intraperitoneal injection twice a week.

extract_protocol:
Genomic DNA was extracted from liver samples using the Qiagen DNEasy kit, with an additional RNase incubation step (50 μg/sample, 30 minutes) prior to column application to remove RNA.
RNA was isolated from mouse liver using a Maxwell 16 LEV simplyRNA kit.
Whole genome bisulfite sequencing single indexed libraries were generated using NEBNext Ultra DNA library Prep kit for Illumina. Input gDNA was fragmented by Covaris S220 or LE220 Focused-ultrasonicator to average insert size of 350bp. Size selection was performed using AMPure XP beads and insert sizes of 300-400bp was isolated. Samples were bisulfite converted after size selection using EZ DNA Methylation-Gold Kit or EZ DNA Methylation-Lightning Kit.
cDNA was generated using a Transcriptor First Strand cDNA Synthesis Kit (Roche). Strand specific mRNA libraries were generated using the TruSeq Stranded mRNA protocol.

tag: study

value: Diet study

tag: strain

tag: diet

value: Standard

value: untreated


title: HET_msE9.5_forebrain_3

value: Thoc6 +/fs


title: NOD, Standard, Rep2, WGBS

value: NOD


title: AKPN SI Tumour Rep 2

value: Male

value: vilCreER Apcfl/+ KrasG12D/+ p53fl/fl Notch1Tg/+


title: BL6, Standard, Rep1, RNA


title: AKPN SI Tumour Rep 3


title: ATAC_sample_57


title: Mixed spleen and lymph node Treg CD4 T cells (RNA), freshly isolated, untreated, rep3

city: Minneapolis

middle: L

last: Mueller

state: MN

address: 2101 6th Street SE

department: Medicine

institute: University of Minnesota Medical School

data_processing:
Hisat2/featureCounts
bigwigCompare/deepTools (3.5.1.0.1)
GRCm38/mm10
tab-delineated text matrix includes raw counts for each sample (n = 12) and 54,532 features
bigwigCompare output (bigWig) file that represents the "sum" of reads in all sample replicates with binSize=50

source_name: mixed spleen and lymph node

extract_protocol:
QIAGEN RNeasy Kit
Takara SMARTer Stranded Total RNA-seq Kit v2 Pico Input Mammalian

value: mixed spleen and lymph node

value: Treg CD4 T cell

value: wildtype C57BL/6 Foxp3-GFP polyclonal


title: NOD, Standard, Rep1, WGBS

value: liver


title: ATAC_sample_146


title: ATAC_sample_145


title: ATAC_sample_144


title: Mixed spleen and lymph node anergic CD4 T cells (RNA), freshly isolated, untreated, rep3

value: Anergic CD4 T cell


title: Mixed spleen and lymph node Teff CD4 T cells (RNA), freshly isolated, untreated, rep3

value: Teff CD4 T cell


title: AKPN SI Tumour Rep 1


title: AJ, American, Rep5, WGBS

value: A/J

value: American


title: mEB_scQer_scv2_mBC_rep2_S5

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 mBC library)

library_source: transcriptomic single cell

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: WD44 (mouse embryonic stem cells)

value: Mouse embryoid bodies

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

value: Day 23


title: ATAC_sample_138

value: ALL


title: mEB_scQer_scv2_mBC_rep1_S4

description: 10X Genomics (custom mBC library)


title: Mixed spleen and lymph node naiveCD4 T cells (RNA), freshly isolated, untreated, rep3

value: NaiveCD4 T cell


title: AJ, American, Rep3, WGBS

value: Diet study

value: untreated


title: AJ, American, Rep4, WGBS


title: Mixed spleen and lymph node Treg CD4 T cells (RNA), freshly isolated, untreated, rep2


title: ATAC_sample_135


title: ATAC_sample_136


title: AJ, American, Rep2, WGBS


title: mEB_scQer_GEX_rep3_reseq_S3

description: 10X Genomics (Gene expression, 3' end)


title: Mixed spleen and lymph node anergic CD4 T cells (RNA), freshly isolated, untreated, rep2


title: AJ, American, Rep1, WGBS


title: mEB_scQer_GEX_rep3_S3

description: 10X Genomics (Gene expression, 3' end)


title: ATAC_sample_112


title: Mixed spleen and lymph node Teff CD4 T cells (RNA), freshly isolated, untreated, rep2


title: ATAC_sample_111


title: mEB_scQer_GEX_rep2_reseq_S2

description: 10X Genomics (Gene expression, 3' end)


title: AJ, Standard, Rep5, WGBS

value: Standard


title: AJ, Standard, Rep4, WGBS


title: Mixed spleen and lymph node Treg CD4 T cells (RNA), freshly isolated, untreated, rep1

value: mixed spleen and lymph node


title: ATAC_sample_52


title: AJ, Standard, Rep3, WGBS


title: mEB_scQer_GEX_rep1_reseq_S1

description: 10X Genomics (Gene expression, 3' end)


title: ATAC_sample_51


title: mEB_scQer_GEX_rep1_S1

description: 10X Genomics (Gene expression, 3' end)


title: ATAC_sample_50


title: AU2124

city: Bellaterra (Cerdanyola del Vallès)

first: Sandra

middle: Alonso

last: Alonso

state: Barcelona

address: Carrer de la Val Moronta, Unitat de Biologia Cel·lular, Facultat de Biociències, UAB

department: Departament de Biologia Cel·lular, Fisiologia i Immunologia

country: Spain

institute: Universitat Autònoma de Barcelona

data_processing:
Libraries were sequenced in NovaSeq 6000 (Illumina) with a read lenght of 2x15bp.
RNA-seq reads were mapped against Mus musculus reference genome (GRCme39) using STAR sofftware version 2.7.8a with ENCODE parameters.
Annotated genes were quantified with RSEM v1.3.0 using the annotation file from GENCODE version M27 and default parameters.
Assembly: GRCm39

source_name: Embryo 3, mESC line 7 (3.7)

growth_protocol: Bm-mESCs cells were cultured on a feeder layer of mitomycin C-inactivated human foreskin fibroblast, and maintained in DMEM supplemented with 20% Knockout Serum Replacement, 100 uM 2-β mercaptoethanol, 1x non-essential amino acids, 1.000 U/ml leukemia inhibitory factor, 1 uM MEK inhibitor PD0325901, 10 uM TGFβ inhibitor SB431542, 50 U/ml penicilin and 50 ug/ml streptomicin, in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Feeders cells were removed and total RNA was extracted using the Maxwell RSC SimplyRNA Tissue Kit.
RNA libraries were prepared with KAPA Stranded mRNA-Seq Ilumina Platforms Kit following the manufacturer's recommendations.

treatment_protocol: Bm-mESCs cells were generated by culturing individual blastomeres of 8-cell mouse embryos obtained  by micromanipulation biopsy.

value: Embryo 3, mESC line 7 (3.7)

value: embryonic stem cells


title: AJ, Standard, Rep2, WGBS

value: liver


title: AJ, Standard, Rep1, WGBS


title: Mixed spleen and lymph node anergic CD4 T cells (RNA), freshly isolated, untreated, rep1

value: Anergic CD4 T cell

value: wildtype C57BL/6 Foxp3-GFP polyclonal


title: Mixed spleen and lymph node Teff CD4 T cells (RNA), freshly isolated, untreated, rep1

value: Teff CD4 T cell


title: Mixed spleen and lymph node naiveCD4 T cells (RNA), freshly isolated, untreated, rep1


title: AU2123

source_name: Embryo 3, mESC line 6 (3.6)

value: Embryo 3, mESC line 6 (3.6)


title: ATAC_sample_48


title: mEB_scQer_GEX_rep2_S2

description: 10X Genomics (Gene expression, 3' end)

value: WD44 (mouse embryonic stem cells)


title: ATAC_sample_49


title: Mixed spleen and lymph node naiveCD4 T cells (RNA), freshly isolated, untreated, rep2


title: AU2122

source_name: Embryo 3, mESC line 5 (3.5)

value: Embryo 3, mESC line 5 (3.5)


title: Mixed spleen and lymph node anergic CD4 T cells, freshly isolated, untreated, rep3

data_processing:
Bowtie2 (2.3.3.1)/Genrich (0.5)
bigwigCompare/deepTools (3.5.1.0.1)
GRCm38/mm10
tab-delineated text matrix includes raw counts for each sample (n = 11) and 38,509 called peaks
bigwigCompare output (bigWig) file that represents the "sum" of reads in all sample replicates with binSize=50

extract_protocol:
10mM Tris-Cl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Igepal CA-630
Nextera dual-indexed


title: ATAC_sample_47


title: Mixed spleen and lymph node Treg CD4 T cells, freshly isolated, untreated, rep3

value: Treg CD4 T cell


title: BL6, American, Rep4, WGBS

value: American


title: BL6, American, Rep5, WGBS


title: BL6, American, Rep3, WGBS


title: AU2121

source_name: Embryo 3, mESC line 4 (3.4)

value: Embryo 3, mESC line 4 (3.4)


title: Mixed spleen and lymph node Teff CD4 T cells, freshly isolated, untreated, rep3


title: ATAC_sample_46

value: ALL


title: BL6, American, Rep2, WGBS

value: Diet study


title: AU2119

source_name: Embryo 3, mESC line 2 (3.2)

value: Embryo 3, mESC line 2 (3.2)


title: Mixed spleen and lymph node Treg CD4 T cells, freshly isolated, untreated, rep2


title: BL6, American, Rep1, WGBS

value: untreated


title: ATAC_sample_45


title: AU2120

source_name: Embryo 3, mESC line 3 (3.3)

value: Embryo 3, mESC line 3 (3.3)


title: Mixed spleen and lymph node anergic CD4 T cells, freshly isolated, untreated, rep2

value: mixed spleen and lymph node


title: AU2118

source_name: Embryo 3, mESC line 1 (3.1)

value: Embryo 3, mESC line 1 (3.1)

value: embryonic stem cells


title: BL6, Standard, Rep5, WGBS

value: liver

value: Standard


title: ATAC_sample_44


title: Mixed spleen and lymph node Teff CD4 T cells, freshly isolated, untreated, rep2

value: Teff CD4 T cell

value: wildtype C57BL/6 Foxp3-GFP polyclonal


title: AU2117

source_name: Embryo 2, mESC line 7 (2.7)

value: Embryo 2, mESC line 7 (2.7)


title: ATAC_sample_43


title: BL6, Standard, Rep3, WGBS


title: ATAC_sample_41


title: AU2116

source_name: Embryo 2, mESC line 6 (2.6)

value: Embryo 2, mESC line 6 (2.6)


title: ATAC_sample_42


title: BL6, Standard, Rep2, WGBS


title: BL6, Standard, Rep4, WGBS


title: Mixed spleen and lymph node naiveCD4 T cells, freshly isolated, untreated, rep2

value: NaiveCD4 T cell


title: Mixed spleen and lymph node Treg CD4 T cells, freshly isolated, untreated, rep1

value: Treg CD4 T cell


title: KPNKF Tumour Organoid Rep 3

value: Female

value: Small Intestine

value: VilCreER KrasG12D/fl p53fl/fl Notch1Tg/+

value: Organoid from Primary Tumour


title: ATAC_sample_40

value: ALL


title: AU2115

source_name: Embryo 2, mESC line 5 (2.5)

value: Embryo 2, mESC line 5 (2.5)


title: Mixed spleen and lymph node anergic CD4 T cells, freshly isolated, untreated, rep1

value: mixed spleen and lymph node

value: Anergic CD4 T cell


title: BL6, Standard, Rep1, WGBS

value: Diet study

value: untreated


title: ATAC_sample_39


title: Mixed spleen and lymph node Teff CD4 T cells, freshly isolated, untreated, rep1


title: AU2113

source_name: Embryo 2, mESC line 3 (2.3)

value: Embryo 2, mESC line 3 (2.3)

value: embryonic stem cells


title: AU2112

source_name: Embryo 2, mESC line 2 (2.2)

value: Embryo 2, mESC line 2 (2.2)


title: ATAC_sample_38


title: AU2126

source_name: Embryo 2, mESC line 4 (2.4)

value: Embryo 2, mESC line 4 (2.4)


title: Mixed spleen and lymph node naiveCD4 T cells, freshly isolated, untreated, rep1

value: wildtype C57BL/6 Foxp3-GFP polyclonal


title: pre-diapause WGBS  repeat 2

city: Beijing

first: Pengfei

last: Lv

address: No. 2, Old Summer Palace West Road

country: China

institute: China agricultural university

data_processing:
Adaptor sequence trimming, mapping to the Ostrinia furnacalis reference genome using Bismark.
The methylation level of each CpG site was estimated using bismark_methylation_extractor
Assembly: Ostrinia furnacalis reference genome
Supplementary files format and content: txt

organism: Ostrinia furnacalis

source_name: heads

growth_protocol: The larvae of Ostrinia furnacalis (O. furnacalis) were collected in the corn field of the Shangzhuang experimental station of China Agricultural University. The collected larvae were reared in boxes (20 × 14 × 8 cm3) using an artificial diet (maize flour 150.0 g, soybean flour 150.0 g, glucose 75.0 g, vitamin C 4.0 g, agar 22.0 g, yeast power 90.0 g, sorbic acid 5.0 g, water 1400 mL), while adults were individually placed in ventilated boxes and laid eggs on waxed papers. All stages of O. furnacalis were kept at 27°C and 65% relative humidity under a photoperiod of 16 L: 8D. The newly molted fourth instar larvae were collected and maintained at 20 °C under a photoperiod of 12L: 12D for at least 30 days to achieve diapause (Guo et al, 2013). The newly molted fourth instar larvae maintained for 20 days at a photoperiod of 20 ° C and 12L: 12D were in a pre-diapause state.

extract_protocol:
Accel-NGS® Methyl-Seq DNA Library Kit
All steps of Illumina library preparation and sequencing were carried out at the Novogene’s (https://cn.novogene.com/) sequencing platform.

value: heads

tag: developmental stage

value: pre-diapause


title: diapause WGBS  repeat 2

value: diapause


title: ATAC_sample_37

source_name: ALL


title: AU2127

source_name: Embryo 1, mESC line 5 (1.5)

value: Embryo 1, mESC line 5 (1.5)


title: ATAC_sample_36


title: non-diapause WGBS  repeat 2

value: non-diapause


title: emphysema2

description: one sample from lung tissue

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

source_name: lung

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: lung

tag: disease state

value: emphysema


title: emphysema3

description: one sample from lung tissue


title: Con3

description: one sample from lung tissue

value: Con


title: diapause WGBS  repeat 1


title: AU2108

source_name: Embryo 1, mESC line 3 (1.3)

value: Embryo 1, mESC line 3 (1.3)


title: ATAC_sample_35

value: ALL


title: emphysema1

description: one sample from lung tissue


title: ATAC_sample_34


title: ATAC_sample_102


title: Con2

description: one sample from lung tissue


title: non-diapause WGBS repeat 1


title: AU2109

source_name: Embryo 1, mESC line 4 (1.4)

value: Embryo 1, mESC line 4 (1.4)


title: AU2106

source_name: Embryo 1, mESC line 1 (1.1)

value: Embryo 1, mESC line 1 (1.1)


title: ATAC_sample_143


title: diapause input

data_processing:
Adaptor sequence trimming, mapping to the Ostrinia furnacalis reference genome using Bowtie2.
PCR duplicate removal using Picard Tools (http://broadinstitute.github.io/picard/) were performed.
Broad peaks were called using MACS2.
annotated and analyzed by the R package CHIPseeker.
Deeptools bamCompare function was used to generate bigWig file format.
Assembly: Ostrinia furnacalis reference genome
Supplementary files format and content: bigWig
Supplementary files format and content: broadPeak

extract_protocol:
heads were lightly triturated in 450 µl 1×PBS, added 6.02 µl 37% formaldehyde for cross-linking before incubating at RT for 10 minutes. After de-crosslinking with 1×glutamate and washing the pellet three times with 1×PBS, added 250 µl SDS lysis buffer (containing protease inhibitor cocktail) and homogenize, centrifuged and the supernatant was taken.
All steps of Illumina library preparation and sequencing were carried out at the Novogene’s (https://cn.novogene.com/) sequencing platform.

tag: chip antibody

value: none (input)


title: pre-diapause WGBS  repeat 1


title: AU2107

source_name: Embryo 1, mESC line 2 (1.2)

value: Embryo 1, mESC line 2 (1.2)

value: embryonic stem cells


title: Con1

description: one sample from lung tissue


title: Acute3

description: one sample from lung tissue

value: Acute injury


title: AU2111

source_name: Embryo 2, mESC line 1 (2.1)

value: Embryo 2, mESC line 1 (2.1)


title: ATAC_sample_33


title: non-diapause input

value: heads


title: pre-diapause input

value: pre-diapause


title: RNA-Seq Th2 0h Replicate 2

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

data_processing:
Sequence reads were mapped to mouse GRCm38/mm10 genome with TopHat2 in very-sensitive settings for Bowtie2 and EnsEMBL annotation release 67.
Gene expression was quantified by feature featureCounts.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including raw counts for genes.

source_name: Spleen

extract_protocol:
Naive CD44- CD62L+ CD8+ P14 cells or CD44- CD62L+ CD4+ Smarta cells were flowcytometrically sorted from LCMV-TCRtg mice and differentiated in the presence of irradiated splenocytes from TCRbd-/- mice and cognate LCMV GP33-41 (P14) or GP64-80 peptide (Smarta) peptide (1µg/ml). T cells were cultivated in RPMI1640 + GlutaMax I (Thermo Scientific) supplemented with fetal calf serum (FCS) (10%), penicillin (100 U/ml), streptomycin (100 μg/ml), gentamycin (10 μg/ml) and b-mercaptoethanol (50 ng/ml). For CTL and Th1 differentiation, IL-12 (5 ng/ml), IL-2 (5 ng/ml), and anti-IL-4 antibody (11B11, 10 μg/ml) were added. For Th2 differentiation, IL-4 (5 ng/ml), IL-2 (5 ng/ml), anti-IL-12 (C18.2, 10 μg/ml) and anti-IFN-g antibody (XMG1.2, 10 μg/ml) were added. T cells were harvested at day 5 of culture using Histopaque density centrifugation and cultivated for additional 5 days in identical culture conditions.  At day 10 of culture, T cells were harvested and rested for 3 days in the presence of IL-2 (5 ng/ml) and IL-7 (5 ng/ml), without irradiated splenocytes or cognate peptide. At day 13, IL-12 (5 ng/ml) was added to CTLs and Th1 cells to induce ST2 expression. At day 14 of culture, dead cells were removed using Histopaque density centrifugation. Subsequently, 2,5x105 T cells were plated in 96 flat bottom well plates and stimulated with IL-33 (10ng/ul) or left untreated.
See Sorting strategy
RNA was purified using the Nucleospin RNA XS Micro kit (Macherey & Nagel) according to manufacturer’s instructions, without addition of carrier RNA.
Smart-Seq v4 mRNA Ultra Low Input RNA Kit (Clontech)

value: C57BL/6J background

tag: genotypes

tag: sorting strategy

value: CD44- CD62L+ CD4+ Smarta cells


title: Acute2

description: one sample from lung tissue


title: ATAC_sample_84


title: RNA-Seq Th2 0h Replicate 1


title: Acute1

description: one sample from lung tissue


title: ATAC_sample_31


title: pre-diapause H3K27me3


title: diapause H3K27me3

value: diapause


title: ATAC_sample_32


title: non-diapause H3K27me3

value: non-diapause


title: diapause H3K9me3


title: ATAC_sample_29


title: PPE-recovery

description: one sample from lung tissue

value: lung

value: PPE-recovery


title: ATAC_sample_30


title: Control

description: one sample from lung tissue

value: Control


title: ATAC_sample_28

value: ALL


title: RNA-Seq Th1 0h Replicate 2


title: RNA-Seq Th2 0h Replicate 3


title: Asthma

description: one sample from lung tissue

value: Asthma


title: ATAC_sample_27


title: RNA-Seq CD8 0h Replicate 3

value: CD44- CD62L+ CD8+ P14 cells


title: pre-diapause H3K9me3


title: RNA-Seq CD8 0h Replicate 2


title: ATAC_sample_26


title: NOD, AmericanGW4064, Rep2, WGBS

source_name: liver

value: Drug study

value: liver

value: NOD

value: American


title: oBC_CRE_pair_PluriUp_EndoDown_lo

description: mapping CRE pairs and mBC (scQer in mEBs, v2)

data_processing:
See library construction above and manuscript for details of data processing.
Supplementary files format and content: final_subassembly_bulk_MPRA_mEB_v2_poolA.txt.gz & final_subassembly_bulk_MPRA_mEB_v2_poolB.txt.gz: mBC map for bulk MPRA in mEBs (testing for different architectures): 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  final_subassembly_bulk_MPRA_promoter_architecture_positional_effects.txt.gz: list of mBC associated with libraries of promoters with different reporter architecturs. column 1: originating library short identifier, column 2: reporter architecture identifier, column 3: reporter ORF, column 4: promoter id, column 5: logical boolean indicating whether U6/oBC cassette is present on construct, column 6: logical boolean indicating whether cHS4 insulators are present on construct, column 7: mBC  final_subassembly_scQer_mEB_v2.txt.gz: list of oBC-CRE-mBC triplet for scQer (second round) in mEBs. column 1: library identifier, column 2: mBC, column 3: oBC, column 4: CRE class,  column 5: identity CRE downstream (right, promoter proximal), column 6: orientation CRE right, column 7: identity CRE upstream (left, promoter distal), column 8: orientation CRE upstream. Note: only for the pairwise CREs are fields 7 and 8 not NA, reflecting the fact that only one CRE is present for those constructs in contrast to the CRE pairs libraries.

organism: Escherichia coli

source_name: Bacteria (Escherichia coli)

extract_protocol:
Plasmids were purified with Zymo MidiPrep kit.
Promoter series (to assess positional effects):To obtain the list of mBC corresponding to each library, we prepared libraries for sequencing similarly to the DNA arm of bulk MPRA, as described before. Starting from 5 ng of each plasmid library, two rounds of PCR were performed (4 cycles PCR1 with primers oJBL039+oJBL753 to append a pseudo 10 bp UMI, followed by 8 cycles with oJBL361 and Nextera v2 P7 indexed primers). Amplicons were cleaned up with Ampure XP beads (1x), and pooled for sequencing. Sequencing was performed 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). The data was processed to a piled up file (counting number of reads and UMI per barcode per library). The count distributions per barcode per library were inspected and found to be bimodal. The bona fide barcodes present in the libraries were taken to be those in the high count mode (count threshold the minimum of the bimodal distribution), leading to 153.9k barcodes across the 20 libraries. To ensure no inter-library barcode collision (given that the libraries were pooled for the experiment), the final list of barcodes used was filtered to only have barcodes present in a single library out of the 20 pooled for the experiment, leading to a final set of 134.1k barcodes (13% multiply represented barcodes removed). Barcode complexity per library spanned 588 to 22.1k with interquartile range 3.6k to 11.3k.  Libraries p058 & p059: the connection between mBC and CRE was obtained using a similar strategy as that connecting oBC to CREs. Briefly, the plasmid library was tagmented as described before (section 2.4.4). Instead of using primers upstream of the oBC, primers downstream of the mBC were used. Following 13 cycles of semi-specific PCR (primers: indexed Nextera P5 + oJBL358). Fragments in the range 350-700 bp were size selected on PAGE, and paired-end sequenced on a Nextseq500 (read1 32 cycles Nextera_read1 primer: tagmented CRE; read 2 32 cycles primer oJBL371: mBC; index 2 10 cycles Nextera_index2 primer: sample index). Bioinformatic processing of the data was similar as for oBC-CRE subassembly, yielding 15.5k mBC with median 65 mBC/CRE for p058 and 27.8k mBCs with median 117 mBC/CRE for p059 passing the individual library controls (see below for additional filter to avoid inter-library collisions in the pool).   Library p092: given the architecture of the reporter was similar to the original p055 (except without the minimal promoter), we used the exact same strategy as previously described obtaining 49.4k valid mBCs and a median of 207 mBCs/CRE.   Libraries p091 & p096: since the CREs were inserted downstream of the GFP reporter, the CREs could be directly subassembled to the mBCs in this context. To do so, we again used tagmentation followed by 13 cycles of semi-specific PCR (primers: indexed Nextera P7 + oJBL708) and a PAGE size selection (600 bp to 900 bp). The library was paired-end sequenced on a Nextseq500 (read1 32 cycles oJBL707 primer: start of inserted CRE; index1 18 cycles Nextera_index1 primer: sample index, read 2 32 cycles primer oJBL371: mBC). Data processing for subassembly was similar as for the oBC-CRE mapping in p055, and leading to identification of 32.0k and 47.3k valid mBCs, and a median of 162 and 241 mBCs/CRE for libraries pJBL091 and pJBL096 respectively.   Promoters series (p033_v2 series) was performed by obtaining the list of mBC (PCR amplification and sequencing of the product) from sequencing of PCR products (two steps: PCR1 with Kapa HiFi in 20 uL, 4 cycles, primers oJBL039+oJBL358, Ampure 1x cleanup, PCR2 with Kapa HiFi in 20 uL, primers oJBL077+oJBL362-o366 indexed series for 10 cycles). The product was sequenced as a spike-in on Nextseq 2000 with custom primers  (read 1: 148 cycles, primer oJBL369; index 1: 10 cycles, empty [blank read]; index2: 10 cycles, primer oJBL370). Read 1 was sufficiently long to cover both the mBC and the pseudo-UMI installed by PCR1 of the library preparation. Read1 fastq was then trimmed to separate fastqs for the two pieces of information for downstream processing. mBC and UMI where the piled-up as for MPRA amplicons. The bona fide set of mBC present in each respective libraries was then determined from the high-count mode of the bimodal distribution of UMI count per mBC, yielding a median of 2.8k mBCs per promoter (span of 0.3k to 4.3k mBC for the different promoter, with UBCp being less well represented).   See manuscript for details of other subassemblies (e.g., processing of the Nanopore data).
Custom amplicons for reporter constructs subassemblies

value: Bacteria (Escherichia coli)


title: ATAC_sample_25


title: PPE-emphysema

description: one sample from lung tissue

value: PPE-emphysema


title: RNA-Seq Th1 0h Replicate 3


title: NOD, AmericanGW4064, Rep1, WGBS


title: oBC_CRE_pair_EndoUp_PluriDown_lo


title: NOD, AmericanVehicle, Rep1, WGBS

value: DMSO


title: NOD, AmericanVehicle, Rep2, WGBS


title: ATAC_sample_23


title: oBC_CRE_pair_PluriUp_EndoDown_hi


title: RNA-Seq CD8 0h Replicate 1

value: C57BL/6J background


title: oBC_CRE_pair_EndoUp_PluriDown_hi


title: BMDMs LPS rep 1

city: New York

first: Isabella

last: Kong

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
The single-end 75 bp were demultiplexed using Casavav1.8.2 and Cutadapt (v1.9) was used for read trimming.
The trimmed reads were subsequently mapped to the mouse genome (mm10) using HISAT2.
FeatureCounts was used for read counting after which differential gene expression analysis was performed using Voom-LIMMA packages.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: BMDM

growth_protocol: BMDMs were derived from the bone marrow of hips, femur and tibae of C57/Bl6J mice using L929 medium in DMEM+9%FCS. After differentiation, cells were seeded into 24-well plates at 600,000 cell/well and cultured at 10% CO2.

extract_protocol:
Total RNA was extracted using the ISOLATE II RNA Mini Kit (Meridian Bioscience).
3’mRNA-sequencing libraries were prepared using 100 ng of total RNA using the QuantSeq 3’mRNA-Seq Library Prep (Lexogen) according to the manufacturer’s instructions and sequenced on the NextSeq 500 (Illumina).

treatment_protocol: Cells were treated with ultrapure LPS-EB ultrapure at 50 ng/ml for 7 hours. Medium was washed off and cells were lysed in lysis buffer supplied by the rna-isolation kit (BioLine)

value: LPS

value: BMDM


title: NOD, StandardVehicle, Rep1, WGBS

value: Standard


title: BMDMs Untreated rep 3

value: Untreated


title: BMDMs LPS rep 3


title: p106_mBC_S20

description: mBC mapping for promoter series library (testing positional effects)


title: ATAC_sample_22


title: ATAC_sample_21


title: BMDMs Untreated rep 2


title: oBC_CRE_mutated_TFBS_series

description: oBC to CRE mapping for plasmid library mutated CREs (scQers in mEBs, v2)


title: BMDMs LPS rep 2


title: ATAC_sample_20


title: NOD, StandardVehicle, Rep2, WGBS


title: non-diapause H3K9me3

value: heads

value: non-diapause


title: BL6, AmericanGW4064, Rep2, WGBS


title: BMDMs Untreated rep 1


title: ATAC_sample_24

value: ALL


title: RNA-Seq Th1 0h Replicate 1

value: CD44- CD62L+ CD4+ Smarta cells


title: RNA-Seq Th2 2h -IL-33 Replicate 3


title: ATAC_sample_19


title: BL6, AmericanGW4064, Rep1, WGBS


title: ATAC_sample_18


title: BL6, AmericanVehicle, Rep2, WGBS


title: ATAC_sample_65


title: ATAC_sample_17


title: p105_mBC_S19


title: RNA-Seq Th2 2h -IL-33 Replicate 2


title: RNA-Seq Th2 2h -IL-33 Replicate 1


title: BL6, AmericanVehicle, Rep1, WGBS


title: p101_mBC_S15


title: p100_mBC_S14


title: RNA-Seq Th2 2h +IL-33 Replicate 2


title: RNA-Seq Th2 2h +IL-33 Replicate 3


title: p102_mBC_S16


title: ATAC_sample_15


title: ATAC_seq_BCAS_4

city: Shanghai

first: Zengyu

last: Zhang

state: Shanghai

address: Dong'an Road

department: Neurology

institute: Fudan University

data_processing:
ATAC-seq: Raw data was first processed by FastQC for quality control, and cleaned using Trim-galore. Clean data were then aligned to the Mouse (mm10) reference genome using default settings of Bowtie2 v2.3.4.3. After removing duplications, Samtools v1.9 was used to sort and build the alignment file index. MACS2 was used for peak calling. Parameters were used as follows: --keep-dup 1 --shift -100 --extsize 200 –nomodel. Diffbind was used for differential analysis.
Assembly: mm10
Supplementary files format and content: ATAC-seq: ATAC_peak text files

source_name: the right cerebral cortex

growth_protocol: The mice were housed at 25°C and fed standard rodent chow and tap water

extract_protocol:
Nuclei was extracted from isolated cerebral cortex in 5 ml of lysis buffer (0.32M sucrose, 5 mM CaCl2, MgAce2, EDTA, Tris-HCl pH=8, w/o 0.1% NP-40), followed by washing in a sucrose buffer, and collected by centrifugation.
ATAC-seq library was generated using reagents from TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501) according to the manuscript’s instruction with modifications.

treatment_protocol: The control group was exposed to sham operation. The experimental group was exposed to bilateral carotid artery stenosis (BCAS) operation

value: the right cerebral cortex


title: ATAC_sample_16


title: ATAC_sample_14


title: p099_mBC_S13


title: ATAC_sample_13


title: RNA-Seq Th2 2h +IL-33 Replicate 1


title: RNA-Seq Th1 2h -IL-33 Replicate 3


title: p098_mBC_S12


title: p103_mBC_S17


title: BL6, StandardVehicle, Rep2, WGBS

value: Drug study


title: ATAC_sample_9


title: BL6, StandardVehicle, Rep1, WGBS

value: liver


title: p104_mBC_S18


title: RNA-Seq Th1 2h -IL-33 Replicate 2


title: ATAC_sample_8


title: ATAC_seq_Sham_4

value: Sham operation


title: p097_mBC_S11


title: p042_mBC_S5


title: RNA-Seq Th1 2h -IL-33 Replicate 1


title: ATAC_seq_BCAS_2

value: bilateral carotid artery stenosis (BCAS) operation


title: p041_mBC_S4

value: Bacteria (Escherichia coli)


title: RNA-Seq Th1 2h +IL-33 Replicate 3


title: ATAC_sample_83


title: ATAC_seq_BCAS_3


title: ATAC_seq_Sham_3


title: ATAC_sample_139


title: ATAC_seq_Sham_2


title: RNA-Seq Th1 2h +IL-33 Replicate 1


title: ATAC_seq_Sham_1


title: RNA-Seq Th1 2h +IL-33 Replicate 2


title: ATAC_sample_133


title: p040_mBC_S10


title: RNA-Seq CD8 2h -IL-33 Replicate 3

value: CD44- CD62L+ CD8+ P14 cells


title: Nic-Mor-rep3

city: Wuhan

first: Jing-Jing

state: Hubei

address: 1 Lion Rock Street

department: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction

institute: Huazhong Agricultural University

data_processing:
All RNA-seq data were aligned to the mouse reference genome mm10 using STAR
Gene FPKM (Fragments per kilobase of transcript per million mapped reads) values were quantified using Stringtie (version 2.1.4)
Gene differential expression analysis using DESeq2 (version 1.30.1) based on the reads count file obtained by featureCounts (version 1.6.2)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene

source_name: embryo

extract_protocol:
The RNA-seq libraries were generated using the Smart-seq2 protocol as previously described with some modifications. Briefly, 15 embryos from nicotine treated and control groups were harvested at the  morula，ICM and TE stages. After zona pellucidae removal in 0.5% pronase E and three washes in 0.05% PVA, embryos were transferred into lysis buffer containing Triton X-100, oligo-dT primer, dNTP (Thermo Fisher Scientific) and RNase inhibitor (Takara). After 72℃ incubation for 3 min, reverse transcription mix (100 U SuperScript II reverse transcriptase, 10 U RNase inhibitor, 1× Superscript II first-strand buffer, 5 mM DTT, 1 M betaine, 6 mM MgCl2, 1 μM TSO) was added into sample lysis buffer, followed by 42℃ incubation for 90 min to obtain cDNA.
cDNA was preamplification for 16-18 cycles by using KAPA HiFi HotStart ReadyMix (KK2601, Roche) and IS PCR primers, followed by PCR purification by AMPure XP beads (A63881, Beckman). Finally, amplified cDNA was fragmented and RNA-seq library was constructed by using TruePrep DNA Library Prep Kit (TD502, Vazyme) according to the manufacturer’s instructions. Paired-end 150-bp sequencing was performed on the Illumina HiSeq X-Ten or NovaSeq 6000 system.

treatment_protocol: The fertilized embryos were cultured in G1-Plus medium at 37.5°C, 5% CO2 and saturated humidity ultimately. For Nicotine treatment, nicotine was prepared into 5 M concentrated storage and diluted by corresponding embryo culture media to 1 mM or 1.5 mM.

value: Morula

value: ICR

value: nicotine treated


title: p035_mBC_S8


title: ATAC_sample_121


title: p034_mBC_S7


title: p033_mBC_S6


title: Nic-Mor-rep2


title: ATAC_sample_11


title: RNA-Seq CD8 2h -IL-33 Replicate 1

value: C57BL/6J background


title: p029_mBC_S3


title: p039_mBC_S9


title: p028_mBC_S2


title: ATAC_seq_BCAS_1


title: RNA-Seq CD8 2h +IL-33 Replicate 2


title: ATAC_sample_10


title: p027_mBC_S1

source_name: Escherichia coli (for plasmid amplification)


title: ATAC_sample_7


title: Ctr-Mor-rep1

value: control


title: Nic-Mor-rep1


title: Nic-TE-rep2

value: TE


title: RNA-Seq CD8 2h +IL-33 Replicate 3


title: ATAC_sample_93


title: RNA-Seq CD8 2h +IL-33 Replicate 1


title: Nic-TE-rep1


title: WT (TCR profile)

description:
enriched TCR targets
3 mice, hashtagged
WT_TCRSeq

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.

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

value: WT

value: live CD90+ CD8+ CD44+ T cells


title: NKX2.5_adEGFP_d18MNP

city: San Francisco

first: Deepak

last: Srivastava

state: CA

address: 1650 Owens St

department: GICD

institute: J David Gladstone Institutes

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.

source_name: Motor neuron progenitor cells

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

value: Infected with virus (adCMV::EGFP)

tag: molecule subtype

value: TF-bound DNA

tag: molecule

value: genomic DNA


title: RNA-Seq CD8 2h -IL-33 Replicate 2


title: Il1rl1-ExAB-/- (TCR profile)

description:
enriched TCR targets
3 mice, hashtagged
AB_TCRSeq


title: input_adNKX25_d18MNP

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

tag: cell type

value: input

value: Infected with virus (adCMV::NKX2.5)


title: Nic-ICM-rep2

value: ICM


title: Ctr-Mor-rep2


title: ATAC_sample_4

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 include Genomic Intervals

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: ATAC_sample_12


title: RNA-Seq ST2+ Th2 Replicate 3

description: MR3 Th2

extract_protocol:
Naive CD44- CD62L+ CD8+ P14 cells or CD44- CD62L+ CD4+ Smarta cells were flowcytometrically sorted from LCMV-TCRtg mice and differentiated in the presence of irradiated splenocytes from TCRbd-/- mice and cognate LCMV GP33-41 (P14) or GP64-80 peptide (Smarta) peptide (1µg/ml). T cells were cultivated in RPMI1640 + GlutaMax I (Thermo Scientific) supplemented with fetal calf serum (FCS) (10%), penicillin (100 U/ml), streptomycin (100 μg/ml), gentamycin (10 μg/ml) and b-mercaptoethanol (50 ng/ml). For CTL or Th1 differentiation, IL-12 (5 ng/ml), IL-2 (5 ng/ml), and anti-IL-4 antibody (11B11, 10 μg/ml) were added. For Th2 differentiation, IL-4 (5 ng/ml), IL-2 (5 ng/ml), anti-IL-12 (C18.2, 10 μg/ml) and anti-IFN-g antibody (XMG1.2, 10 μg/ml) were added. T cells were harvested at day 5 of culture using Histopaque density centrifugation and cultivated for additional 5 days in identical culture conditions. At day 10 of culture, live ST2+ CTLs, Th1 and Th2 cells were flowcytometrically sorted and subjected to RNA isolation.
See Sorting strategy
RNA was purified using the Nucleospin RNA XS Micro kit (Macherey & Nagel) according to manufacturer’s instructions, without addition of carrier RNA.
TrueSeq stranded total RNA library kit (Illumina)

tag: genotype

value: Before Culture:Live CD44- CD62L+ CD4+ Smarta cells. After Culture:live ST2+ Th2s


title: ATAC_sample_3


title: NKX2.5_adNKX25_d18MNP

description: ChIP of TF-bound DNA in cell type

tag: treatment


title: Ctr-TE-rep2

value: ICR


title: input_adEGFP_d18MNP


title: ISL1_adNKX25_d18MNP

description: ChIP of TF-bound DNA in cell type

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


title: ATAC_sample_6


title: RNA-Seq ST2+ Th2 Replicate 2

description: MR3 Th1

value: C57BL/6J background


title: Ctr-ICM-rep2

value: control


title: Ctr-TE-rep1

value: TE


title: input_IKO_d18MNP_Rep3

description: ChIP of TF-bound DNA in cell type

value: untreated


title: ATAC_sample_142


title: ATAC_sample_140


title: RNA-Seq ST2+ Th1 Replicate 2

description: MR2 Th1

value: Before Culture:Live CD44- CD62L+ CD4+ Smarta cells. After Culture:live ST2+ Th1s


title: ATAC_sample_5


title: Ctr-ICM-rep1


title: RNA-Seq ST2+ Th2 Replicate 1

description: MR3 CD8


title: input_IKO_d18MNP_Rep2

description: ChIP of TF-bound DNA in cell type

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


title: ISL1_IKO_d18MNP_Rep3

description: ChIP of TF-bound DNA in cell type


title: ATAC_sample_98


title: RNA-Seq ST2+ Th1 Replicate 1

description: MR2 CD8


title: oBC_CRE_literature_selected

description: oBC to CRE mapping for plasmid library literature-selected CREs (scQers in mEBs, v2)

value: Bacteria (Escherichia coli)


title: ISL1_IKO_d18MNP_Rep2

description: ChIP of TF-bound DNA in cell type


title: input_WT_d18MNP_Rep3


title: ATAC_sample_92


title: ATAC_sample_2


title: p40_v2_mBC_S5

description: mBC mapping for promoter series library (bulk MPRA in mEBs, v2, pool A & B)


title: ATAC_sample_87


title: Nic-ICM-rep1

value: nicotine treated


title: p35_v2_mBC_S3


title: ATAC_sample_1


title: RNA-Seq ST2+ CD8 Replicate 3

description: MR1 Th2

value: Before Culture:Live CD44- CD62L+ CD8+ P14 cells. After Culture:live ST2+ CTLs


title: RNA-Seq ST2+ CD8 Replicate 2

description: MR1 Th1


title: p39_v2_mBC_S4


title: ATAC_sample_137


title: ISL1_WT_d18MNP_Rep3

description: ChIP of TF-bound DNA in cell type

value: TF-bound DNA

value: genomic DNA


title: p34_v2_mBC_S2


title: ISL1_WT_d18MNP_Rep2

description: ChIP of TF-bound DNA in cell type


title: p33_v2_mBC_S1


title: mBC_CRE_p96_20percent_S10

description: mBC to CRE mapping for plasmid library p096 (bulk MPRA in mEBs, v2, pool B)


title: NKX25_NKO_d6CP_Rep2

description: ChIP of TF-bound DNA in cell type

source_name: Cardiac progenitor cells

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)

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


title: AT16, scRNAseq

city: DAEJEON

first: SEONG EUN

last: LEE

address: 282 MUNHWA-RO

country: South Korea

institute: CHUNGNAM NATIONAL UNIVERSITY

description: 10x Genomics

data_processing:
The single-cell RNA sequencing data were mapped, and the number of molecules per barcode was quantified using the 10× software package Cellranger (version 3.0.2).
Assembly: GRCh38
Supplementary files format and content: tsv files of read count of each samples

source_name: anaplastic thyroid cancer

extract_protocol:
Freshly collected thyroid cancer tissues and mechanical digestion by chopping of the tissue and transferring it to a transfer container. And then, chemical digestion by reacting with a mixed solution of trypsin and collagenase type 4 and removal of red blood cells and deat cells.
Following the manufacturer's instructions, cells from thyroid samples were loaded according to the standard protocol of the Chromium Single Cell 3’ Reagent Kit (v3 chemistry, 10× Genomics) or Chromium Single Cell 5' Reagent Kit (v1.1 chemistry).

tag: tissue

value: anaplastic thyroid cancer

value: thyroid cells


title: ATAC_sample_132

source_name: ALL

value: ALL


title: AT13, scRNAseq

description: 10x Genomics


title: RNA-Seq ST2+ Th1 Replicate 3

description: MR2 Th2


title: mBC_CRE_p91_20percent_S8

description: mBC to CRE mapping for plasmid library p091 (bulk MPRA in mEBs, v2, pool B)


title: ISL1_NKO_d6CP_Rep3

description: ChIP of TF-bound DNA in cell type

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


title: input_WT_d18MNP_Rep2

value: input


title: ATAC_sample_129


title: ISL1_NKO_d6CP_Rep2

description: ChIP of TF-bound DNA in cell type


title: ATAC_sample_128


title: ISL1_IKO_d6CP_Rep2

description: ChIP of TF-bound DNA in cell type


title: ATAC_sample_126


title: oBC_CRE_p92_S1

description: oBC to CRE mapping for plasmid library p092 (bulk MPRA in mEBs, v2, pool A)


title: AT20, scRNAseq

description: 10x Genomics


title: PT9, scRNAseq

description: 10x Genomics

source_name: papillary thyroid cancer

value: papillary thyroid cancer


title: oBC_CRE_p57_S3

description: oBC to CRE mapping for plasmid library p057 (bulk MPRA in mEBs, v2, pool A)


title: NKX25_WT_d6CP_Rep3


title: ATAC_sample_120


title: AT17, scRNAseq

description: 10x Genomics


title: NKX25_NKO_d6CP_Rep3

description: ChIP of TF-bound DNA in cell type


title: CRE_mBC_p57_S4

description: CRE to mBC mapping for plasmid library p057 (bulk MPRA in mEBs, v2, pool A)


title: PT7, scRNAseq

description: 10x Genomics


title: oBC_CRE_p59_S2

description: oBC to CRE mapping for plasmid library p059 (bulk MPRA in mEBs, v2, pool A)


title: NKX25_WT_d6CP_Rep2


title: AT9, scRNAseq

description: 10x Genomics


title: ATAC_sample_119


title: ATAC_sample_148


title: PT8, scRNAseq

description: 10x Genomics


title: CRE_mBC_p56_S3

description: CRE to mBC mapping for plasmid library p056 (bulk MPRA in mEBs, v2, pool A)


title: NKX25_WT_d6CP_Rep1


title: RNA-Seq ST2+ CD8 Replicate 1

description: MR1 CD8

value: C57BL/6J background


title: PT5, scRNAseq

description: 10x Genomics


title: PT3, scRNAseq

description: 10x Genomics


title: ATAC_sample_116


title: PT12, scRNAseq

description: 10x Genomics


title: midgut_bl

city: columbia

first: Alexander

last: Franz

state: MO

address: 303 Connaway Hall

department: Department of Veterinary Pathology

institute: University of Missouri

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The analysis was performed with R package Seurat 3.1
Three data sets were integrated in to one, the single nuclei with over 500 & less than 6,500 genes were used for analysis, cells were clustered at resolution of 1. Uniform manifold approximation and projection (UMAP) was used to reduce the data dimensionality to visualize single-nucleus data.
Assembly: AaegL5.2_pre_mRNA
Supplementary files format and content: Tab-separated values files and matrix files

organism: Aedes aegypti

source_name: midgut

extract_protocol:
Around 30 midguts were dissected from 7-day old blood-fed femaleAe. aegyptiat 24h (h) post-blood meal (pbm) or from sugar-fed females.Single nuclei were extracted from dissected midguts  using the Nuclei PURE Prep nuclei isolation kit (Sigma-Aldrich, St. Louis, MO, USA).
Library was performed according to the manufacter’s instructions (single cell 3’  protocol, 10x Genomics).
single cell 3’  protocol, 10x Genomics

value: midgut

value: Higg's White Eye

tag: age


title: midgut

description: 10x Genomics


title: ATAC_sample_113


title: Rad6-1,Rad6 gene disruption mutant of Beauveria bassiana ARSEF2860

city: Hangzhou

first: Xin-Cheng

last: Luo

address: Yuhangtang Road

department: college of life science

institute: Zhejiang University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Beauveria bassiana ARSEF 2860

source_name: hyphal

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: hyphal

value: ARSEF 2860

value: Rad6 mutant


title: nanopore_CRE_pair_PluriUp_EndoDown_lo

value: Bacteria (Escherichia coli)


title: PT10, scRNAseq

description: 10x Genomics


title: Rad6-2,Rad6 gene disruption mutant of Beauveria bassiana ARSEF2861


title: Rad6-3,Rad6 gene disruption mutant of Beauveria bassiana ARSEF2862


title: ATAC_sample_107


title: nanopore_CRE_pair_PluriUp_EndoDown_hi


title: HeLa_shRbm6_2nd_rep

first: Dong

last: Chen

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
We discarded raw reads containing more than 2-N bases. Then, FASTX-Toolkit (Version 0.0.13) was used to trim the adaptors and low-quality bases from the raw sequencing reads. We deleted short reads less than 16 bp
Tophat2 was used to align the clean reads with the GRch38 genome allowing four mismatches, Next, we counted the gene reads and calculated the FPKM (fragments per kilobase of transcript per million fragments mapped)18 using the uniquely mapped reads.
The edgeR package in the R software was used for differential expression analysis, using cutoffs of P < 0.05 and fold change > 2 or < 0.5.
The ABLas pipeline was used to define and quantify AS events. The ratio of altered of AS events was calculated using Students t-test, with p < 0.05 indicating statistical significance.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: RBM6  knockdown in HeLa  cell

growth_protocol: HeLa cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum in 5% CO2 at 37 C.

extract_protocol:
The phenol-chloroform method was used to purify the total RNA. Genomic DNA contamination was removed by digestion using RQ1 DNase (Promega, Madison, WI, USA). RNA concentrations were determined by measuring the absorbance ratio at 260/280 nm (A260/A280). Electrophoresis through a 1.5% agarose gel was used to assess the RNA integrity.
A VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme, Nanjing, China) was used to prepare the RNA-Seq library from 1 μg of purified RNA from each sample. Polyadenylated RNAs from the total RNA were purified, randomly fragmented using heat treatment, and converted into double strand cDNA. Ligation products of 200_x001F_–500 bps were purified and digested using heat-labile uracil-DNA glycosylase (UDG). The cDNA was amplified, purified, and quantified, and then stored at 80 ℃ until sequencing. The Illumina HiSeq X Ten system (Illumina, San Diego, CA, USA) was used to perform RNA-Seq to produce 150 bp paired end sequences.

treatment_protocol: Lipofectamine 2000 (Invitrogen, Waltham, MA, USA) was used to transform the RBM6 short hairpin RNA ( shRNA) plasmid(ABlife, Wuhan, China) into Hela cells.

value: HeLa

value: RBM6  knockdown


title: ATAC_sample_134


title: nanopore_CRE_pair_EndoUp_PluriDown_lo


title: HeLa_shRbm6_1st_rep


title: ATAC_sample_103


title: WT-2,wild strain of Beauveria bassiana ARSEF2861

value: wild type


title: WT-3,wild strain of Beauveria bassiana ARSEF2862


title: ATAC_sample_118


title: HeLa_shCtrl_2nd_rep

source_name: HeLa  cell (control plasmid)

value: control plasmid


title: nanopore_CRE_pair_EndoUp_PluriDown_hi


title: HeLa_shCtrl_1st_rep


title: WT-1,wild strain of Beauveria bassiana ARSEF2860


title: mxaF Nd2O3 1

status: Public on Oct 16 2023

city: Berkeley

first: Norma

middle: Cecilia

last: Martinez-Gomez

address: 111 Koshland Hall

department: Plant and Microbial Biology

institute: University of California, Berkeley

data_processing:
All processing occurred using Kbase
Reads aligned using HISTAT2
Aligned reads assemebeled using StringTie
Differential expression matrix generated using DeSeq2
Assembly: NC_012808.1
Supplementary files format and content: comma deliminated file includes raw gene counts for each sample
Supplementary files format and content: comma deliminated file includes FPKM values for each sample

organism: Methylorubrum extorquens AM1

source_name: strain

growth_protocol: Cells were grown in Half Hypho Medium with 50 mM methanol and 2 uM Nd at 30C and 250rpm. WT without Nd was used as a reference.

extract_protocol:
RNA was harvested at mid-exponential phase using Rneasy kit (Qiagen).
RNA libraries for RNA-seq were prepared using Illumina DNA prep kit according to manufacturer's protocol

value: strain

value: dmxaF


title: mxaF Nd2O3 3


title: mxaF Nd2O3 2


title: mxaF NdCl3 3


title: mxaF NdCl3 2


title: WT 3

value: WT


title: mxaF NdCl3 1


title: WT 2


title: ATAC_sample_101

address: 262 Danny Thomas Pl

institute: St. Jude Children's Research Hospital

value: ALL


title: WT 1


title: ATAC_sample_100


title: Leaves, pair 2, indoors, biol rep 3

city: Vairao

first: Mariana

last: Sottomayor

state: Select:

address: Rua Padre Armando Quintas, No. 7

department: PLANTBIO

country: Portugal

institute: CIBIO, Research Centre in Biodiversity and Genetic Resources

data_processing:
Basecalling and demultiplexing was performed using Guppy v4.0.14, all reads were oriented based on barcode sequences using Pychopper (version 2.4), barcode sequences were trimmed, low-quality reads were removed and reads with < 50 bp were discarded.
Data quality and statistics was verified using the FastQC tool (version 0.19.11).
Quantification was obtained by mapping to IDIO+ using minimap2 (parameters: -uf -ax map-ont -p 0.99 -N 100 --for-only) and subsequent use of Salmon (version 1.4.0, parameters: --noErrorModel).
Assembly: IDIO+ (supplementary file Catharanthus_transcriptome_IDIOplus.fasta ; accession number GKIJ00000000)
Supplementary files format and content: Tab-delimited text files include count values for each Sample

organism: Catharanthus roseus

source_name: leaf

growth_protocol: growth chamber, 25 ºC,  16/8 photoperiod, fluorescent light, medium intensity 70 μmol m-2s-7

extract_protocol:
RNeasy Plant Mini Kit (Qiagen)
Nanopore SQK-PCB109 kit

value: leaf

value: second leaf pair from apex of fowering plants

value: whole leaves

tag: cultivar

value: Little Bright Eye

tag: protoplasts

value: not applicable


title: Leaves, pair 3, outdoors, biol rep 2

growth_protocol: outdoors, south oriented location

value: third leaf pair from apex of fowering plants


title: Leaves, pair 3, indoors, biol rep 1


title: Leaves, pair 2, indoors, biol rep 2


title: Leaves, pair 2, indoors, biol rep 1


title: Leaves, pair 3, outdoors, biol rep 3


title: Leaves, pair 3, outdoors, biol rep 1


title: Leaves, pair 3, indoors, biol rep 2


title: Leaves, pair 2, outdoors, biol rep 2


title: Leaves, pair 3, indoors, biol rep 3


title: Leaves, pair 2, outdoors, biol rep 1


title: Leaves, pair 2, outdoors, biol rep 3


title: DamKDM5_rep4

city: Bronx

first: Michael

middle: Francis

last: Rogers

state: NY

address: 1300 Morris Park Ave, Ullmann 809

department: Genetics

institute: Albert Einstein College of Medicine

description:
DamKDM5_average.bedgraph
DamKDM5_FDR0.01_processed.xlsx

data_processing:
Libraries were sequenced on a DNBSEQ platform with 50 bp read length and 20 M clean reads.
For Targeted DamID analyses, sequencing data were aligned to release 6 of the Drosophila melanogaster genome and processed using damidseq_pipeline as previously described (Marshall et al., 2016; Marshall & Brand, 2017).
Peaks were called using find_peaks (using the parameters fdr=0.01, min_quant=0.9) (Marshall et al., 2016) on the averaged replicates, and genes overlapping peaks identified using peaks2genes (Marshall et al., 2016).
Assembly: dm6
Supplementary files format and content: bedgraph profile of average DamKDM5 across 4 replicates normalized to 4 Dam alone replicates
Supplementary files format and content: excel file with called genes, binding score, FBgns, and gff coordinates for FDR cutoff < 0.01

organism: Drosophila melanogaster

source_name: Prothoracic gland

growth_protocol: UAS-LT3-dam or UAS-LT3-dam-kdm5 flies were crossed with tubulin-Gal80[ts]; spok-Gal4 flies and allowed to lay eggs for 24 hrs at 18ºC. Animals were incubated at 18ºC for 5 days and subsequently moved to 29ºC for 2 days.

extract_protocol:
Tissue processing was performed as previously described in Marshall et al., 2016 with the following modifications. A total of 100 wandering third instar larvae of each genotype were homogenized in 500 mM EDTA followed by DNA extraction using the Zymo Quick-DNA Miniprep Plus Kit. DpnI digestion, PCR adaptor ligation, DpnII digestion, and PCR amplification were performed as described. DNA was sonicated using a Diagenode Bioruptor Pico for 6 cycles (30-sec on/90-sec off, 4ºC) and analyzed using an Agilent Bioanalyzer. DamID adaptor removal and DNA cleanup were performed as described and samples were submitted to BGI Genomics for library construction and sequencing.
Libraries were prepared at BGI Genomics following a ChIP-seq workflow. DNA fragments were first end-repaired and dA-tailed using End Repair and A-Tailing (ERAT) enzyme. Adaptors were then ligated for sequencing and ligated DNA purified using AMPure beads. DNA was then PCR amplified with BGI primers for 8 cycles and PCR purified with AMPure beads. DNA was then homogenized, circularized, digested, and again purified. DNA was then prepared into proprietary DNA nanoballs (DNB™) for sequencing.

treatment_protocol: No treatment

value: wandering third instar larva

value: Prothoracic gland

value: tub-Gal80[ts] ; spok-Gal4 / UAS-LT3-damkdm5


title: Dam_rep2

value: tub-Gal80[ts] ; spok-Gal4 / UAS-LT3-dam


title: Dam_rep3


title: DamKDM5_rep3


title: Dam_rep4


title: Dam_rep1


title: DamKDM5_rep1


title: DamKDM5_rep2


title: Old-4HrZT

city: Chicago

last: Sharma

state: Illinois

address: 1653 W Congress Pkwy #12

institute: Rush University Medical Center

description:
FB21-007
featurecounts_mice_aging.xlsx

data_processing:
Reads from the RNA-Sequencing data were aligned to the Mus musculus genome assembly GRCm38 (mm10) using the STAR software [29]. Duplicated aligned reads were marked and removed using the Picardtools software. The gene expression count data were extracted using the HTseq software. The raw count data were normalized, followed by log2 transformation. We filtered out genes with mean read counts < 6. All data preprocessing was performed using R software.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Feature counts (Gene names in rows; samples in columns)

source_name: Pancreas

growth_protocol: C57BL/6J mice, born and raised at the University of Wisconsin-Parkside animal facility. The parental generation was obtained from the Jackson laboratory and the described procedures approved by the institutional animal care and use committee of the University of Wisconsin-Parkside. Breeding and housing colonies were housed under standard 12 hours of light followed by 12 hours of darkness (12L:12D) in light and temperature-controlled chambers and had continuous access to regular chow (ad-libitum) and fresh water. Mice were entered to our protocol at 4 months or 24 months of age. Both groups were singly housed and entrained for 4 weeks in LD chambers. Mice were sacrificed at 5 months or 25 months of age. Animal tissues following euthanasia were collected in 4-hour intervals under dark to allow for circadian analysis. Collected samples were partly persevered in RNA later for RNA processing, while a portion was used for flow cytometry as described below.

extract_protocol:
RNA was isolated from the pancreas using TRIzol extraction procedure. Briefly, frozen tissues were lightly ground in a mortar and pestle constantly submerged in liquid nitrogen. Frozen tissue between 10-100 mg was placed into RNase-free tubes containing TRIzol and RNase-free stainless-steel beads (NextAdvance, USA). Tissues were homogenized using a bullet blender at 4° C. Chloroform was used to separate the phases, and the RNA-containing aqueous phase was subjected to a column purification kit using RNeasy Mini RNA extraction kit (Qiagen, USA). RNA was DNase treated, and purified RNA was checked for integrity using an Agilent Bioanalyzer, all samples had an RNA integrity number above 8.0.
RNAseq libraries were prepared using Illumina mRNA Prep kit (Illumina, USA). Libraries were pooled to equal molarity and sequenced on an Illumina NovaSeq (2 × 100bp) to achieve a minimum of 40M reads per sample. FastQ files were downloaded to the Rush University computing cluster for further data processing.

tag: strain

value: Pancreas

value: Old

tag: Sex

value: male


title: Old-20HrZT

description:
FB21-011
featurecounts_mice_aging.xlsx

tag: time


title: Old-8HrZT

description:
FB21-008
featurecounts_mice_aging.xlsx


title: Old-24HrZT

description:
FB21-012
featurecounts_mice_aging.xlsx


title: Old-16HrZT

description:
FB21-010
featurecounts_mice_aging.xlsx


title: Old-12HrZT

description:
FB21-009
featurecounts_mice_aging.xlsx


title: Young-20HrZT

description:
FB21-005
featurecounts_mice_aging.xlsx

value: Young


title: Young-16HrZT

description:
FB21-004
featurecounts_mice_aging.xlsx


title: Young-12HrZT

description:
FB21-003
featurecounts_mice_aging.xlsx


title: Young-24HrZT

description:
FB21-006
featurecounts_mice_aging.xlsx


title: Young-8HrZT

description:
FB21-002
featurecounts_mice_aging.xlsx


title: Young-4HrZT

description:
FB21-001
featurecounts_mice_aging.xlsx


title: heart, Male TGSUR2A-55, s488476

city: Madison

first: Mohun

last: Ramratnam

state: WI

address: 600 HIGHLAND AVE

institute: University of Wisconsin

description:
s488476
TGSUR2A55_raw_counts.txt

data_processing:
Images were analyzed using bcl2fastq v2.20.0.422
The trimming software skewer was used to preprocess raw fastq files
R version 3.6.2 (2019-12-12)
Low abundance genes defined as those with an average read count below a threshold of 1.0 in two or more samples were then filtered out of the dataset
The RNAseq data was then normalized by the method of trimmed mean of M-values (TMM). Alignment was performed by using STAR (Spliced Transcripts Alignment to a Reference) against Mus musculus. Mapped paired-end reads for both genes and transcripts (isoforms) are counted in each sample using RSEM
Assembly: mm10
Supplementary files format and content: text file showing raw counts for each sample

source_name: heart

extract_protocol:
Total RNA was extracted from frozen tissue samples using Qiagen RNeasy Plus Universal Mini Kit (Qiagen, Hilden, Germany) with an on-column DNA digest
RNA library for RNA seq was prepared according the TruSeq® Stranded mRNA Sample Preparation Guide

tag: gender

value: Male

value: heart

value: SUR2A55 UP


title: heart, Female WT, s499045

description:
s499045
TGSUR2A55_raw_counts.txt

value: Female

value: WT


title: heart, Female WT, s488471

description:
s488471
TGSUR2A55_raw_counts.txt


title: heart, Female WT, s493823

description:
s493823
TGSUR2A55_raw_counts.txt


title: OB548, Ctrl, scRNAseq

first: Edward

last: Hsiao

address: 505 Parnassus Ave

institute: UCSF

description:
10x Genomics
genes.tsv
Rs1-tTA_GTF.xlsx
Rs1-tTA_FASTA.txt

data_processing:
A custom reference was created by incorpororating the ColI(2.3)-tTA and TetO-Rs1 sequences into the mm10 reference using the 'cellranger mkref' command (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references).
The demultiplexing, barcoded processing, and gene counting were made using the Cell Ranger software v2.2.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: mm10 (https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build#mm10_1.2.0)
Supplementary files format and content: Tab-separated values files and matrix files are output generated by the 'cellranger count' command (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count).
Supplementary files format and content: Xlsx and text files are GTF and FASTA formatted files used to make a custom mm10 reference using the 'cellranger mkref' command (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references).

extract_protocol:
Long bones (hip, femur, tibia, fibula, humerus, radius, and ulnar bones) were collected from two littermate control (control) and two ColI(2.3)+/Rs1+ 9-week-old male mice and were gently crushed using a mortar and pestle to release the cells. The bone fragments were washed with 1x PBS (Gibco) to separate the hematopoietic cells from the bone chips, which contain the stromal and osteoblastic lineages of interest. The bone chips were incubated in collagenase type I (Worthington Biochemical Corporation, Cat# LS004197, Lot#: 46E16633A), reconstituted in 1x PBS (Gibco) for 60 min at 37°C on an orbital shaker at 110 rpm. The collagenase was neutralized by adding 5 mL of fetal bovine serum (FBS; Seradigm, Lot# 290B14), centrifuged at 1200 rpm for 5 min, and resuspended in 2 mL of 2% FBS in PBS. A magnetic-activated cell sorting (MACS) dead cell removal kit (Miltenyi Biotec,130-090-101) was used per the manufacturer’s instructions to remove the dead cells from the isolated stromal cell population.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: FVB/N

value: 9 weeks old


title: OB776 Ctrl, scRNAseq

source_name: Long bones (hip, femur, tibia, fibula, humerus, radius, and ulnar bones)


title: heart, Male TGSUR2A-55, s488473

description:
s488473
TGSUR2A55_raw_counts.txt


title: OB774 Rs1, scRNAseq

value: Long bones (hip, femur, tibia, fibula, humerus, radius, and ulnar bones)


title: heart, Male WT, s479365

description:
s479365
TGSUR2A55_raw_counts.txt


title: heart, Male TGSUR2A-55, s488469

description:
s488469
TGSUR2A55_raw_counts.txt


title: heart, Female WT, s479369

description:
s479369
TGSUR2A55_raw_counts.txt


title: heart, Female TGSUR2A-55, s488470

description:
s488470
TGSUR2A55_raw_counts.txt


title: heart, Female TGSUR2A-55, s479367

description:
s479367
TGSUR2A55_raw_counts.txt


title: heart, Male WT, s488472

description:
s488472
TGSUR2A55_raw_counts.txt


title: OB549, Rs1, scRNAseq


title: heart, Male WT, s479366

description:
s479366
TGSUR2A55_raw_counts.txt


title: heart, Male WT, s479364

description:
s479364
TGSUR2A55_raw_counts.txt


title: heart, Male TGSUR2A-55, s479363

description:
s479363
TGSUR2A55_raw_counts.txt


title: heart, Female TGSUR2A-55, s477980

description:
s477980
TGSUR2A55_raw_counts.txt


title: HiC, embryonic stem cell, replicate 1

first: William

last: Chang

address: 1301 Morris Park Ave

department: Ophthalmology

data_processing:
Reads were aligned with bwa. HiC: bwa-mem with default settings. ChIP-seq: bwa aln/samse with default settings.
HiC: contact maps were created from reads with MAPQ > 30  with a maximum resolution of 5kb with the ENCODE HiC pipeline (https://github.com/ENCODE-DCC/hic-pipeline), based on Juicer.
HiC: loops and topologically-associated domains (TADs) were called within the ENCODE pipeline using the HiCCUPs and Arrowhead algorithms, respectively.
HiC: A/B compartment analysis was performed using dcHiC to calculate, select, and normalize principal components of the Pearson correlation of the contact matrix at 10kb resolution
ChIP-seq: peaks were called with MACS2 using default settings.
Assembly: mm10
Supplementary files format and content: .hic (contact maps)
Supplementary files format and content: .bedpe (chromatin loops)
Supplementary files format and content: .bed (TADs)
Supplementary files format and content: .bedGraph (A/B compartment scores)
Supplementary files format and content: .bw (ChIP-seq read density)
Supplementary files format and content: .narrowPeak (ChIP-seq peaks)

source_name: v6.5 mESC

growth_protocol: HiC: v6.5 mESCs derived by Dr. Rudolph Jaenisch (gifted by Dr. Meelad Dawlaty) were used. Cells were grown under feeder-free conditions on 0.2% gelatin and supplemented with LIF (24 ng/mL). Each replicate contained ~2.0 x 106 cells.

extract_protocol:
HiC: Lenses were dissected at P0.5 and then micro-dissected into lens epithelium and lens fiber under a dissection microscope. Each replicate of lens tissue was comprised of either 30 lens epithelium, or 30 lens fiber samples. Samples were kept on dry ice for the duration of the micro-dissection process. Samples were then homogenized using a disposable pestle tissue grinder. Homogenized tissues were fixed in 2.0% formaldehyde for 10 mins at room temperature. Formaldehyde was quenched with 0.125 M glycine to stop the reaction. The crosslinking method for mESCs was the same. ChIP-seq: 200 P0.5 lenses were obtained from CD-1 mice, microdissected into lens epithelium and lens fibers and stored in liquid nitrogen prior the use as we described earlier (Sun et al. 2015).
The Hi-C library was generated using the Arima-HiC kit according to the manufacturers protocols (A510008) and performed by the NYU Langone Health Genome Technology Center. The ChIP-seq library was generated by Active Motif: Immunoprecipitation was performed on 6 µg chromatin from microdissected lens cells with 5 µl anti-CTCF antibody (ActiveMotif cat. # 61311, lot #11219006).

tag: cell line

value: v6.5 mESC

value: embryonic stem cell


title: HiC, lens fiber, replicate 1

source_name: lens

value: lens

value: fiber


title: HiC, lens epithelium, replicate 2

value: epithelium


title: HiC, lens epithelium, replicate 1


title: HiC, embryonic stem cell, replicate 2


title: HiC, lens fiber, replicate 2


title: heart, Female TGSUR2A-55, s479368

description:
s479368
TGSUR2A55_raw_counts.txt