title: E14 DNMT1 KO single cells- Library 4

source_name: Embryonic stem cells

growth_protocol: Cells were grown on 0.1% gelatin in ES cell culture media; DMEM (1×) high glucose + glutamax (Gibco), supplemented with 10% FCS (Greiner) 100 µM β-mercaptoethanol (Sigma), 100 µM Non-essential amino acids (Gibco), 50 µg/mL Pen/Strep (Gibco) and 1000 U/mL ESGRO mLIF (Millipore).

extract_protocol:
Cells were isolated using hyaluronic acid (Sigma) and trypsin (Life Technologies) and sorted into 384-well plates containing lysis buffer and Vapor-lock.
Single cells were incubated at 50C for 15 hours, 75C for 20 minutes and 80C for 5 minutes. Glucosylation of 5hmC sites followed by dispensing 0.1 L of T4-BGT (NEB), 0.1 L of UDP-Glucose (NEB), 0.05 L of 10X NEB Buffer 4 and 0.25 L of nuclease-free water (final vol 0.5mL). After incubation at 37C for 16 hours, 0.5 L of the following reaction mixture is added: 0.1L of 25g/L Qiagen Protease, 0.05L of 10X NEB Buffer 4 and 0.35 L of nuclease-free water. The plate is then incubated at 50 o C for 5 hours, 75 o C for 20 minutes and 80 o C for 5 minutes. Thereafter, gDNA is digested by the restriction enzyme MspJI by the addition of 0.5 L of the following reaction mixture: 0.02 L of MspJI (NEB), 0.12 L of 30X enzyme activator solution (NEB), 0.05 L of 10X NEB Buffer 4 and 0.31 L of nuclease-free water. The digestion is performed at 37 o C for 5 hours followed by heat inactivation of MspJI at 65 o C for 20 minutes. Next, 0.2 L of cell-specific double-stranded adaptors are added to individual wells and these adapters are ligated to the fragmented gDNA molecules by adding 0.8 L of the following reaction mixture: 0.07 L of T4 DNA ligase (NEB), 0.1 L of T4 DNA ligase buffer (NEB), 0.3 L of 10 mM ATP (NEB) and 0.33 L of nuclease-free water. The ligation is performed at 16 o C for 16 hours. Next, wells containing unique cell-specific adapters are pooled using a multichannel pipette and incubated with 0.8X Agencourt Ampure (Beckman Coulter) beads for 30 minutes, washed twice with 80% ethanol and resuspended in 6.4 L of nuclease-free water. In vitro transcription and Illumina library preparation is performed as described previously in the scAba-seq protocol.

treatment_protocol: Six gRNA sequences targeting three exons of mouse Dnmt1 were used. Phosphorylated BbsI compatible restriction overhangs were added to gRNA top and bottom oligos and resuspended at 100 M in nuclease-free water. Annealing of the oligos was performed in 1x ligation buffer (NEB) using the following program: 97°C for 5 minutes, ramp down by 1°C per 1 minute to 20°C. The pX330 CRISPR-Cas9-GFP gRNA plasmid was mixed with 0.1 M gRNA oligo. The reaction was simultaneously digested with BbsI (NEB) and ligated with T4 DNA ligase (NEB) overnight at 16°C. Ligation reactions were transformed into DH5 competent cells and subsequently sequenced using Sanger dideoxy sequencing to confirm the correct insert. All six pX300-gRNA plasmids were pooled and 1 g was transfected into 2 million E14tg2a cells using Lipofectamine (Life Technologies). A separate pX300 empty vector was also transfected into E14tg2a to serve as a negative control. Two days later, single GFP positive cells were sorted into 384-well plates (BioRad) and subjected to scMspJI-seq.


title: LTHSC_TET2_272_C11_S35

status: Public on Feb 13 2020

type: SRA

city: New York

first: Franco

last: Izzo

state: NY

address: 1470 Madison Avenue

department: Oncological Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: Single cell RNA-seq from Smart-seq (from scRRBs + RNA protocol)

library_source: transcriptomic

data_processing:
Single cell RNA sequencing data generated with Chromium 10x v2 was processed using Cell Ranger (v2.1.0) with default parameters, and data generated with Chromium v3 was processed using the updated version of Cell Ranger (v3.1). For both chemistry versions, samples were sequenced at an average of 50,000 reads per cell. Raw sequencing data was de-multiplexed and post-processed following the custom pipelines provided by 10x Genomics. Briefly, raw base calls were de-multiplexed into fastq files using the cellranger mkfastq command, followed by alignment to the selected reference mm10 genome for mouse samples or hg19 genome for the human subject data, respectively. Barcode and UMI counting was performed using the cellranger count command with default parameters. Cell barcodes with UMI < 1,000 or mitochondrial gene percentage > 20% were filtered out.
For Drop-seq data, samples were prepared for sequencing using the Illumina Nextera XT kit, and sequenced on a NextSeq 500 (Illumina, San Diego, CA) at an average of 70,000 reads per cell. Libraries with large numbers of cells were divided into technical replicates, which were processed independently. Raw reads were processed and aligned (STAR aligner106) using the standard Drop-seq pipeline, and according to the ‘Drop-seq Alignment Cookbook’, both found at http://mccarrolllab.com/dropseq/.Reads were aligned to the mm10 transcriptome. For each read, a single optimal mapping position was retained. Unique transcripts mapping to alternative splice variants were combined for subsequent analysis. Single-cell expression matrices were generated using cellular barcodes and unique molecular identifiers (UMIs). Cells with UMI < 200 or mitochondrial gene percentage > 20% were filtered out.
For the dual protocol experiments, each pool of 96 cells was first demultiplexed by Illumina i7 barcodes, resulting in four pools of 24 cells. Each pool of 24 cells was further demultiplexed by unique cell barcodes. Reads were assigned to a given cell if they matched 80% of the template adapters. Adapters and adapter reverse complements (6 bp) were trimmed from the raw sequence reads. After adapter removal, reads were trimmed from their 3’ end for read quality by applying a 4 bp sliding window and removing bases until the mean base quality of the window had a Phred quality score greater than 15. We aligned trimmed reads in single-end mode to the mm10 mouse genome assembly using Bismark (v.0.14.5; parameters: -multicore 4 -X 1000 --un –ambiguous) running on bowtie2-2.2.8 aligner. Bismark methylation extractor (--bedgraph --comprehensive) was used to determine the methylation state of each individual CpG. For the single cell RNA, the sequenced paired-end read fragments were mapped against the mm10 mouse genome assembly using the 2pass default mode of STAR (version 2.5.2a) with the annotation of GENCODE (version 19). The number of read counts overlapping with annotated genes was quantified applying the ‘GeneCounts’ option in the STAR alignment.
ATAC-Bseq data was aligned to mm10 genome and methylation calling was performed through Bismark (version 0.14.4; parameters: --q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --maxins 500 Option '--directional' specified) running on bowtie2-2.2.8 aligner112. Accessibility peaks for each individual replicate were defined using MACS2 (v2.1.1.2); parameters: -f BAMPE --broad --broad-cutoff 0.1 -m 2 100).
Genome_build: mm10 for Mus musculus samples,  hg19 for Homo sapiens sample.
Supplementary_files_format_and_content: csv; Single-cell expression matrices were generated using cellular barcodes and unique molecular identifiers (UMIs). UMItabs contain the UMI count for each specified gene (rows) for each cell (columns). Cell barcodes are provided in the ".CellBarcodes" file for each sample.

molecule: polyA RNA

organism: Mus musculus

source_name: Long-term hematopoietic stem cells from bone marrow

extract_protocol: Bone marrow (BM) cells were isolated into cold phosphate-buffered saline (PBS), without Ca2+ and Mg2+, and supplemented with 2% bovine serum albumin (BSA) to generate single cell suspensions. Red blood cells (RBCs) were removed using ammonium chloride-potassium bicarbonate (ACK) lysis buffer, resuspended in PBS/2% BSA, and filtered through a 40μm cell strainer. Cells were sorted and inmediately underwent the indicated protocol.

treatment_protocol: Recombination was induced by 3 doses of polyinosinic:polycytidylic acid (pIpC; 12mg/kg/day; GE Healthcare) every other day via intra-peritoneal injection.

tag: tissue

tag: weeks after recombination

tag: sorting strategy

tag: genotype/variation

value: Mx1-Cre Tet2 fl/fl


title: XY_17GW_p0_PF328

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

description: Whole organ

data_processing:
Base calling. Image analysis and base calling were performed using RTA 1.17.20 and CASAVA 1.8.2.
Assembly of a unique set of human reference transcripts. Ensembl (Cunningham, et al., 2015) and RefSeq (Brown, et al., 2015; Pruitt, et al., 2014) transcript annotations of the hg19 release of the human genome were downloaded from the University of California Santa Cruz (UCSC) genome browser website (Rosenbloom, et al., 2015) in June 30th, 2015. Both transcript annotation files (GTF format) were subsequently merged into a combined set of non-redundant human reference transcripts (HRT) using Cuffcompare (Pollier, et al., 2013). We also defined a non-redundant dataset of human splice junctions (HSJ) extracted from alignments of human transcripts and expressed sequence tags (ESTs) provided by UCSC.
Mapping reads. RNA-seq-derived reads from each sample replicate were aligned independently to the the hg19 release of the human genome sequence with TopHat (version 2.0.10) (Trapnell, et al., 2009) using previously published approaches (Chalmel, et al., 2014; Pauli, et al., 2012; Trapnell, et al., 2012; Zimmermann, et al., 2015). Briefly TopHat program was run a first time for each RNA-seq fastq file using the HRT and HSJ datasets to improve read mapping. The resulting junction outputs produced by all TopHat runs were pooled and added to the HSJ dataset. TopHat was rerun a second time for each sample using the new HSJ dataset. The output of this second run comprised the final alignment (BAM format). Finally, BAM files corresponding to the same testis or ovary time of development were subsequently merged and sorted with the samtools suite (Li, et al., 2009).
Transcriptome assembly and quantification. The transcriptome of each gonad was subsequently assembled, compared to known transcript annotation and quantified  with the Cufflinks suite using default settings (Pollier, et al., 2013). Briefly, the assembly step that was performed by Cufflinks using the merged alignment files yielded a set of ~93000-192000 transcript fragments (transfrags) for each gonad. The Cuffcompare program was then used: (i) to define a non-redundant set of 180,242 assembled transcripts by tracking Cufflinks transfrags across all experiments; and, (ii) to compare the resulting transcripts to the HRT dataset (i.e. known transcript annotation). Finally, the abundance of each transcript in each experiment was assessed using Cuffdiff in fragments per kilobase of exon model per million reads mapped (FPKM). Abundance values were normalized using Cuffnorm to reduce systematic effects and to allow direct comparison between the individual samples.
Refinement of assembled transcripts. As suggested by (Chalmel, et al., 2014; Prensner, et al., 2011), we sequentially applied four filtering steps to eliminate poor-quality quantifications and identify the most robust transfrags from background signal. First, we selected 60,437 “detectable” or “expressed” transfrags defined as those for which abundance levels were above 1 FPKM in at least one sample. We next selected 60,136 transcripts with a cumulative exon length ≥200 nt. Third, all transfrags that were not automatically annotated by Cuffcompare as complete match (Cuffcompare class “=”), potentially novel isoform (“j”), unknown intronic (“i”, i.e. loci falling entirely within a reference intron and without exon-exon overlap with another known locus), intergenic (“u”) or antisense (“x”) isoforms were discarded. Finally, all transcript fragments that were annotated as either novel isoforms or novel genes (class codes “j”, “i”, “u” or “x”) and that did not harbor at least two exons (multi-exonic) were filtered out. Together, this strategy produced a high-confidence set of 35,194 transcripts fulfilling these refinement conditions and supporting total RNA molecules expressed testis or ovary development.
Genome_build: hg19
Supplementary_files_format_and_content: .bedgraph files contain genome-wide read coverage statistics, in bedGraph format, obtained with the "genomeCoverageBed" utility in BEDTools (release 2.12.0); .gtf file contains the reconstructed transcripts obtained with cufflinks and subsequently classified with cuffcompare in the cufflinks suite of tools (release 2.2.1); .txt file contains the FPKM expression levels quantified with Cufflinks for each transfrag and each sample; the columns are tab-separated.

molecule: total RNA

organism: Homo sapiens

source_name: Testis

extract_protocol:
Total RNA were extracted from tissues  using the RNeasy mini Kit (Qiagen), quantified using a NanoDrop™ 8000 spectrophotometer (Thermo Scientific) and quality controlled using a 2100 Electrophoresis Bioanalyzer (Agilent).
Libraries of template molecules suitable for strand specific high throughput DNA sequencing were created using “TruSeq Stranded Total RNA with Ribo-Zero Gold Prep Kit” (catalog # RS-122-2301, Illumina Inc.). Briefly, the removal of cytoplasmic and mitochondrial ribosomal RNA (rRNA) was performed from 500 ng of total RNA using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, the RNA was fragmented using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 12 cycles; 5 min at 72°C). Excess of PCR primers was removed by purification using AMPure XP beads (Agencourt Biosciences Corporation). Final cDNA libraries were quality-checked and quantified using a 2100 Electrophoresis Bioanalyzer (Agilent). The libraries were loaded in the flow cell at 7pM concentration and clusters were generated in the Cbot and sequenced in the Illumina Hiseq 2500 as paired-end 2x50 base reads following Illumina's instructions. Image analysis and base calling were performed using RTA 1.17.20 and CASAVA 1.8.2.

tag: sexe

value: Male

value: Testis

tag: age


title: LTHSC_TET2_272_C10_S34

value: Long-term hematopoietic stem cells from bone marrow


title: E14 DNMT1 KO- Library 1

city: Utrecht

first: Maya

last: Sen

address: 8 Uppsalalaan

country: Netherlands

institute: Hubrecht Institute

library_source: genomic

data_processing:
Library strategy: scMspJ1-seq
Fastq files are parsed for library barcodes. Read 1 was mapped to the mm10 or hg19 build using the Bowtie2, filtered for unique mapping full-length reads and demultiplexed. 5mCG positions are obtained from the sequencing data using custom scripts in R and Perl identifying CG dinucleotides in the mm10 or hg19 genome at the expected distance from the mapped read position. Finally, all PCR duplicates are removed. Computer codes will be made available upon request.
Hairpin bisulfite sequencing was performed on bulk mouse embryos samples ( 2-cell to 64 cell stage). The bulk embryos were treated with protease treatment (1 uL of 25 ug/uL Qiagen Protease, 1 uL of 10X NEB Buffer 4, and 8 uL of nuclease free water). Then, 0.5 ng of genomic DNA was digested with 20 mL of MspI master mix (1 uL of MspI R0104L, 2 mL 10X NEB Cutsmart buffer in a total volume of 20 uL) and incubated at 37 C for an hour. After digestion, the digested genomic DNA was ligated with 1 uL of 10 uM phosphorylated hairpin oligo and ligation master mix (1 mL of NEB T4 ligase M0202M, 1 uL of 10X NEB T4 Ligase buffer, 2 uL of 10mM ATP, 5 uL of nuclease free water) and incubated overnight at 16 C. For purification of the ligation mixture, we used Dynabeads? M-280 Streptavidin and followed the recommended protocol with the following exceptions: the bead-ligation mixture was incubated for at least an hour at RT on a rotator and cold 10 mM Tris-HCl wash step was included. Subsequently, we performed BS-seq on the sample using the protocol Clark, et al. 2017. After sequencing the libraries on a Miseq 300x300 or NextSeq 75x75 pair-end kit, we used HBS-tools (Sun, MA et al. 2015) and custom perl scripts were used to analyze the methylated CpG dyads. Hairpin oligo (G/iMe-dC/iMe-dC/G/iMe-dC/iMe-dC/GG/iMe-dC/GG/iMe-dC/AAG/iBiodT/GAAG/iMe-dC/iMe-dC/G/iMe-dC/iMe-dC/GG/iMe-dC/G) was resuspended in 100 uM of Low-TE. The hairpin oligo was phosphorylated (1 uL of 100 uM hairpin oligo, 3 uL of 10X T4 Ligase Buffer, 1 uL T4 PNK and 5 uL of nuclease free water) and incubated at 37 C for an hour. Subsequently the phosphorylated oligo heated at 94 C and placed in ice water to generate the loop.
Published scNMT libraries (GSE109262) analyzed for the bisulfite results were processed as described previously. The first nine bases of the raw reads were trimmed using Trim Galore (v0.5.0) and mapped using Bismark to the mouse genome (mm10) with the 129/CAST background. SNPs specific to 129/CAST mouse genome were prepared using SNPsplit (v0.3.2) and a list of known variant call files from the Mouse Genomes Project (http://www.sanger.ac.uk/resources/mouse/genomes/). After mapping with Bismark, duplicate sequences were removed and CpG methylation calls were extracted with strand-specific information. Further data analysis and visualization of the methylation calls used custom scripts that will be made available upon request.
Genome_build: mm10, hg19
Supplementary_files_format_and_content: mText files with 4 columns: Single Cell ID, chromosome, coordinate, strand, CNNR motif and strain [mouse only])

molecule: genomic DNA

tag: cell line

tag: strain


title: LTHSC_TET2_272_B8_S20


title: E14 DNMT1 KO single cells- Library 3


title: E14 DNMT1 KO single cells- Library 2


title: XY_17GW_p0_PF318

description: Whole organ


title: LTHSC_TET2_272_B9_S21


title: Colorectal cancer lymph node no1

type: RNA

city: Umeå

first: Marie-Louise

last: Hammarström

address: Peter Lestadius väg

department: Clinical Microbiology

country: Sweden

institute: Umeå universitet

hyb_protocol: cRNA hybridized on Sentrix HumanRef-8_V2streptavidin-Cy3

scan_protocol: Illumina Beadstation GX

data_processing: Illumina Beadstudio software version 3.3

label: biotin

source_name: Lymph node

label_protocol: Illumina Totalprep RNA Amplification Kit

extract_protocol: Acid guanidine-phenol-cholorform method according to Chomczynski P and Sacchi N (Nat Protoc. 2006: 1, 581–585).

tag: disease state

value: stage III


title: LTHSC_TET2_272_B7_S19


title: 24h UCB_Control_A [3_Control_1]

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

description:
3_Control_1.FCC66DFACXX_L3_R*_IACTTGA
CD34+ Hematopoietic stem and progenitor cells from donor A at t=24hr without addition of sEV

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 2.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

source_name: CD34+ UC-HSPCs_24h Control

growth_protocol: UCB was collected in Erasmus University Medical Center using Stemcare®/CB collection blood bag system (Fresenius Kabi Norge AS. Halden. Norway). Within 48 hours after collection, mononuclear cells were isolated using ficoll (Lymphoprep™, Fresenius Kabi Norge AS). CD34+ cells and viable DAPI-Lin-CD34+CD38lowCD45RAlowCD90+ cells were isolated. CD34+ cells and CD34+CD90+ cells were cultured in either serum-free Cellgenix GMP SCGM (Cellgenix, Freiburg, Germany) or Glycostem Basic Growth Medium (Glycostem, Oss, the Netherlands) supplemented with SCF (50 ng/ mL, Cellgenix) and Flt3L (50 ng/ mL, Cellgenix) at 37°C in a humidified atmosphere of 5% CO2. Cells were refreshed every 2-3 days.

extract_protocol:
RNA from CD34+ UC-HSPCs was isolated using NucleoSpin RNA XS kit (Macherey-Nagel, Duren, Germany)
mRNA version 2 library prep kit (Illumina)

treatment_protocol: UCB were treatemed with or without EVs isolated from 20 mL conditioned medium (from svHFOs) by low speed centrifugation (1500 rpm, 5 minutes; 4500 rpm, 10 minutes) followed by ultracentrifugation (20,000g, 30 minutes; 100,000g, 1 hour at 4°C) of the supernatant using the SW32Ti rotor (Beckman Coulter, Fullerton, CA, USA).

value: Umbillical cord blood (UCB)

tag: cell type

value: CD34+ Hematopoietic stem and progenitor cells (CD34+ UC-HSPCs)


title: Blastocyst Day 7 Library 4

source_name: Embryos

growth_protocol: Cleavage stage embryos, cryopreserved on day 2 or 3 of development, were warmed using EmbryoThaw™ media (Fertipro, Belgium), as outlined by the manufacturer. Blastocyst stage embryos, vitrified on day 5 or 6 of development, were warmed using the Vitrification Thaw kit (Irvine Scientific, Netherlands), as described (Van Landuyt et al., 2011). Embryos were transferred to either Cook Cleavage or Cook Blastocyst Medium (COOK, Ireland) depending on their developmental stage, and cultured in 20 μL medium droplets under mineral oil (Irvine Scientific, Netherlands) at 37 °C, 6% CO 2  and 5% O 2 .

extract_protocol:
When required, embryos were briefly treated with Acidic Tyrode’s Solution (Sigma-Aldrich, Belgium) for removal of the zona pellucida. All embryos were washed and subsequently dissociated by gentle trituration in TrypLE Express Enzyme (Life Technologies, Belgium) using glass capillaries. Single blastomeres were washed and manually deposited into 384-well plates containing lysis buffer and Vapor-lock. Plates were subsequently centrifuged at 1,000 rpm for 1 minute and stored at -80 °C until further processing.
Single cells were incubated at 50C for 15 hours, 75C for 20 minutes and 80C for 5 minutes. Glucosylation of 5hmC sites followed by dispensing 0.1 L of T4-BGT (NEB), 0.1 L of UDP-Glucose (NEB), 0.05 L of 10X NEB Buffer 4 and 0.25 L of nuclease-free water (final vol 0.5mL). After incubation at 37C for 16 hours, 0.5 L of the following reaction mixture is added: 0.1L of 25g/L Qiagen Protease, 0.05L of 10X NEB Buffer 4 and 0.35 L of nuclease-free water. The plate is then incubated at 50 o C for 5 hours, 75 o C for 20 minutes and 80 o C for 5 minutes. Thereafter, gDNA is digested by the restriction enzyme MspJI by the addition of 0.5 L of the following reaction mixture: 0.02 L of MspJI (NEB), 0.12 L of 30X enzyme activator solution (NEB), 0.05 L of 10X NEB Buffer 4 and 0.31 L of nuclease-free water. The digestion is performed at 37 o C for 5 hours followed by heat inactivation of MspJI at 65 o C for 20 minutes. Next, 0.2 L of cell-specific double-stranded adaptors are added to individual wells and these adapters are ligated to the fragmented gDNA molecules by adding 0.8 L of the following reaction mixture: 0.07 L of T4 DNA ligase (NEB), 0.1 L of T4 DNA ligase buffer (NEB), 0.3 L of 10 mM ATP (NEB) and 0.33 L of nuclease-free water. The ligation is performed at 16 o C for 16 hours. Next, wells containing unique cell-specific adapters are pooled using a multichannel pipette and incubated with 0.8X Agencourt Ampure (Beckman Coulter) beads for 30 minutes, washed twice with 80% ethanol and resuspended in 6.4 L of nuclease-free water. In vitro transcription and Illumina library preparation is performed as described previously in the scAba-seq protocol.

tag: developmental stage

value: Blastocyst embryos


title: LTHSC_TET2_272_B5_S17


title: XX_17GW_p0_PF315

description: Whole organ

source_name: Ovary

value: Female

value: Ovary


title: LTHSC_TET2_272_B6_S18


title: 0h UCB_A [1_0h_1A]

description:
1_0h_1A.FCC66DFACXX_L3_R*_IATCACG
CD34+ Hematopoietic stem and progenitor cells from donor A at t=0

source_name: CD34+ UC-HSPCs_0h


title: XX_17GW_p0_PF236

description: Whole organ


title: Blastocyst Day 7 Library 3


title: LTHSC_TET2_272_B4_S16


title: LTHSC_TET2_272_B3_S15


title: Blastocyst Day 7 Library 2


title: LTHSC_TET2_272_B12_S24


title: LTHSC_TET2_272_B1_S13


title: LTHSC_TET2_272_B2_S14


title: XY_13.14GW_p0_PF308

description: Whole organ


title: Blastocyst Day 7 Library 1


title: Blastocyst Day 6 Library 12


title: LTHSC_TET2_272_B10_S22


title: LTHSC_TET2_272_A9_S9


title: XY_13.14GW_p0_PF251

description: Whole organ


title: LTHSC_TET2_272_B11_S23


title: LTHSC_TET2_272_A7_S7


title: LTHSC_TET2_272_A8_S8


title: LTHSC_TET2_272_A6_S6


title: XX_13.14GW_p0_PF299

description: Whole organ


title: Blastocyst Day 6 Library 10


title: Blastocyst Day 6 Library 11


title: XX_13.14GW_p0_PF313

description: Whole organ


title: XY_12GW_p0_EH1299

description: Whole organ


title: LTHSC_TET2_272_A5_S5


title: XY_12GW_p0_EH1282

description: Whole organ


title: LTHSC_TET2_272_A4_S4


title: Blastocyst Day 6 Library 9


title: Blastocyst Day 6 Library 8


title: XY_12GW_m1_EH1152

description: Whole organ


title: LTHSC_TET2_272_A3_S3


title: LTHSC_TET2_272_A2_S2


title: LTHSC_TET2_272_A1_S1


title: LTHSC_TET2_272_A11_S11


title: LTHSC_TET2_272_A12_S12


title: LTHSC_TET2_272_A10_S10


title: Blastocyst Day 6 Library 7


title: XX_12GW_p0_EH1114

description: Whole organ


title: Blastocyst Day 6 Library 6


title: XY_12GW_m3_EH885

description: Whole organ


title: LTHSC_WT476_scRRBs_Pool4

description: Single cell RRBS (from scRRBs + RNA protocol)


title: Blastocyst Day 6 Library 5


title: LTHSC_WT476_scRRBs_Pool3


title: XX_12GW_p0_EH846

description: Whole organ


title: LTHSC_WT476_scRRBs_Pool1


title: LTHSC_WT476_scRRBs_Pool2


title: Blastocyst Day 6 Library 4


title: XX_12GW_p0_EH844

description: Whole organ


title: Blastocyst Day 6 Library 3


title: XX_12GW_m1_pEH412

description: Whole organ


title: LTHSC_WT_476_H7_S91


title: LTHSC_WT_476_H8_S92


title: LTHSC_WT_476_H6_S90


title: Blastocyst Day 6 Library 2


title: LTHSC_WT_476_H5_S89


title: Blastocyst Day 6 Library 1


title: LTHSC_WT_476_H3_S87


title: XY_9GW_p4_EH650

description: Whole organ


title: Blastocyst Day 5 Library 9


title: LTHSC_WT_476_H4_S88


title: XY_9GW_p3_EH319

description: Whole organ


title: LTHSC_WT_476_H2_S86


title: LTHSC_WT_476_H1_S85


title: Blastocyst Day 5 Library 8


title: Blastocyst Day 5 Library 7


title: LTHSC_WT_476_H12_S96


title: XY_9GW_p2_EH1287

description: Whole organ


title: LTHSC_WT_476_H9_S93


title: XX_9GW_p5_EH1031

description: Whole organ


title: Blastocyst Day 5 Library 4


title: XX_9GW_p5_EH727

description: Whole organ


title: XX_9GW_p4_EH986

description: Whole organ


title: LTHSC_WT_476_G8_S80


title: Blastocyst Day 5 Library 3


title: LTHSC_WT_476_G7_S79


title: LTHSC_WT_476_G4_S76


title: LTHSC_WT_476_H10_S94


title: LTHSC_WT_476_G6_S78


title: XY_9GW_p6_EH896

description: Whole organ


title: LTHSC_WT_476_G3_S75


title: XX_9GW_p4_EH456

description: Whole organ


title: LTHSC_WT_476_G5_S77


title: LTHSC_WT_476_G2_S74


title: XY_l7GW_p5_EH868_bis

description: Whole organ


title: LTHSC_WT_476_G1_S73


title: LTHSC_WT_476_H11_S95


title: Blastocyst Day 5 Library 1


title: LTHSC_WT_476_G12_S84


title: XY_l7GW_p5_EH467

description: Whole organ


title: LTHSC_WT_476_G9_S81


title: Morula stage embryos Library 4

value: Morula embryos


title: XY_l7GW_p4_EH1219

description: Whole organ


title: LTHSC_WT_476_G10_S82


title: Morula stage embryos Library 3


title: LTHSC_WT_476_G11_S83


title: LTHSC_WT_476_F8_S68


title: Morula stage embryos Library 1


title: LTHSC_WT_476_F7_S67


title: Morula stage embryos Library 2


title: Blastocyst Day 5 Library 2


title: LTHSC_WT_476_F5_S65


title: 8-cell and morula embryos Library 4

value: 8-cell and morula embryos


title: XX_l7GW_p5_EH1293

description: Whole organ


title: XY_l7GW_p4_EH1140

description: Whole organ


title: LTHSC_WT_476_F4_S64


title: 8-cell and morula embryos Library 3


title: LTHSC_WT_476_F3_S63


title: LTHSC_WT_476_F2_S62


title: XX_l7GW_p5_EH1076

description: Whole organ


title: LTHSC_WT_476_F1_S61


title: LTHSC_WT_476_F12_S72


title: XY_e7GW_p2_EH262

description: Whole organ


title: XX_l7GW_p4_EH1367

description: Whole organ


title: LTHSC_WT_476_F9_S69


title: LTHSC_WT_476_E9_S57


title: LTHSC_WT_476_F11_S71


title: LTHSC_WT_476_E8_S56


title: LTHSC_WT_476_E7_S55


title: 8-cell and morula embryos Library 1


title: LTHSC_WT_476_F6_S66


title: 8-cell and morula embryos Library 2


title: XY_e7GW_p1_EH981

description: Whole organ


title: LTHSC_WT_476_E5_S53


title: LTHSC_WT_476_E6_S54


title: 4-cell embryos Library 5

value: 4-cell embryos


title: XY_e7GW_p1_EH979

description: Whole organ


title: LTHSC_WT_476_E4_S52


title: 4-cell embryos Library 6


title: XX_l7GW_p5_EH1210

description: Whole organ


title: 4-cell embryos Library 4


title: LTHSC_WT_476_E2_S50


title: 4-cell embryos Library 3


title: LTHSC_WT_476_E1_S49


title: LTHSC_WT_476_E12_S60


title: AN naïve hTSC 2

city: Saint Louis

first: Bo

last: Zhang

state: Missouri

address: 4515 McKinley Research Bldg 03212

department: Developmental Biology

institute: Washington University School of Medicine

data_processing:
Raw reads were trimmed with cutadapt to remove low quality bases
Trimmed reads were aligned to hg38 using bwa mem
Aligned reads were quantified using methylQA density to create a bedgraph file
bedGraphToBigWig was used to convert a bedGraph file to a bigWig file
Genome_build: hg38
Supplementary_files_format_and_content: bigWig track files

source_name: hTSC

extract_protocol:
Cells were harvested by TrypLE Express dissociation and centrifuged at 500 RCF for 5 minutes at 4°C. The supernatant was aspirated. Cells were washed once with cold PBS. Cell pellets were then lysed in 100 μL ATAC-seq RSB [10mM Tris pH 7.4, 10mM NaCl, 3mM MaCl2] containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin by pipetting up and down and incubating on ice for 3 minutes. 1 mL of ATAC-seq RSB containing 0.1% Tween-20 was added and mixed with the lysis reaction. Nuclei were then pelleted by centrifuging at 800 RCF for 5 minutes at 4°C. Supernatant was removed, and the nuclear pellets were resuspended in 20 μL 2x TD buffer [20mM Tris pH 7.6, 10mM MgCl2, 20% Dimethyl Formamide]. Nuclei were counted, and 50,000 counted nuclei were then transferred to a tube with 2x TD buffer filled up to 25 μL. 25 μL of transposition mix [2.5 μL Transposase (100nM final) (Illunina, 20034197, 16.5 μL PBS, 0.5 μL 1% Digitonin, 0.5 μL 10% Tween-20, 5 μL H2O) was then added. Transposition reactions were mixed and incubated at 37°C for 30 minutes with gentle tapping every 10 minutes. Reactions were cleaned up with the Zymo DNA Clean and Concentrator-5 kit (Zymo Research, D4014).
The ATAC-seq library was prepared by amplifying for 9 cycles on a PCR machine. The PCR reaction was purified with Ampure XP beads (Beckman Coulter, A63880) using double size selection following the manufacturer’s protocol, in which 27.5 μL beads (0.55X sample volume) and 50 μL beads (1.55X sample volume) were used based on 50 μL PCR reaction. The ATAC-seq libraries were quantitated by Qubit assays and sequenced on an Illumina NextSeq platform. QC and analysis on ATAC-seq libraries was performed using AIAP (Liu et al., 2019).

value: human trophoblast stem cell (hTSC)

tag: derived from

value: naive hPSCs (AN)

tag: passage


title: XX_e7GW_p2_EH1064

description: Whole organ


title: LTHSC_WT_476_F10_S70


title: XX_e7GW_p2_EH700

description: Whole organ


title: AN naïve hTSC 1


title: XX_e7GW_p1_EH1284

description: Whole organ


title: H9 naïve hTSC 2

value: naive hPSCs (H9)


title: LTHSC_WT_476_E11_S59


title: LTHSC_WT_476_E10_S58


title: LTHSC_WT_476_D9_S45


title: XX_e7GW_p1_EH871

description: Whole organ


title: XY_e7GW_p1_EH975

description: Whole organ


title: XY_6GW_p4_EH518

description: Whole organ


title: H9 naïve hTSC 1


title: LTHSC_WT_476_E3_S51


title: LTHSC_WT_476_D8_S44


title: XY_6GW_p3_EH214

description: Whole organ


title: BT5 hTSC 1

value: blastocyst (BT5)


title: LTHSC_WT_476_D7_S43


title: LTHSC_WT_476_D6_S42


title: BT5 hTSC 2


title: LTHSC_WT_476_D5_S41


title: XY_6GW_p0_EH641

description: Whole organ


title: LTHSC_WT_476_D4_S40


title: BT5 hTSC rep 2  Bulk RNA-seq

data_processing:
Raw reads were trimmed with cutadapt to remove low quality bases
Trimmed reads were aligned to hg38 using STAR_2.5.4b with gencode v27 annotation
Aligned reads were quantified using featureCounts 1.6.3 from the subreads package
Genome_build: hg38
Supplementary_files_format_and_content: gene counts text file

extract_protocol:
Total RNA was isolated using the E.Z.N.A. total RNA kit I.
Library construction was performed using the SMARTer Directional cDNA Library Construction Kit

value: hTSC

tag: iPSc source


title: LTHSC_WT_476_D3_S39


title: BT5 hTSC rep 1  Bulk RNA-seq


title: 1.TP53C238F

city: Houston

first: Moran

last: Amit

state: TX

address: 1515 Holcombe Blvd

department: Head & Neck Surgery - Research

institute: The University of Texas MD Anderson Cancer Center

data_processing:
mRNA: Paired-end sequenced reads were checked by FastQC and aligned to the reference genome, UCSC mouse mm10 or GENCODE human GRCh38, using TopHat2. HTSeq was then used to estimate the number of reads that are mapped to each gene. The R Bioconductor package edgeR was applied to normalize the data using the trimmed mean of M (TMM) method and to determine significant differentially expressed genes between groups.
miRNA: Single-end sequenced reads were checked by FastQC. The QIAseq miRNA Library specific 3′ adapter sequence was trimmed from the 3’ ends of sequenced reads using cutadapt. The trimmed reads were then aligned to the reference genome, human GRCh38, using BWA. FeatureCounts was used to estimate the number of reads that are mapped to each mature miRNA. The R Bioconductor package edgeR was applied to normalize the data using the trimmed mean of M (TMM) method and to determine significant differentially expressed miRNAs between groups.
Genome_build: UCSC mouse mm10 or GENCODE human GRCh38
Supplementary_files_format_and_content: tab-delimited files include raw read count values for each sample (output of HTSeq-count or FeatureCounts)

source_name: PCI13 head and neck squamous cell carcinoma cell line

growth_protocol: Primary culture ; in vivo innoculation

extract_protocol:
RNa and miRNA were extracted in vitro or ex vivo using qiagen kits per manufacturer's instruction
mRNA: Illumina Compatible low input RNA libraries were prepared using the Smart-Seq V4 Ultra Low Input RNA (Clontech) and KAPA HyperPlus Library Preparation kits. The libraries were then sequenced on the Illumina HiSeq4000 sequencer using the 76bp paired end format.
miRNA: Illumina compatible miRNA libraries were prepared using the QIAseq miRNA Library Kit (Qiagen). The libraries were then sequenced on the Illumina NextSeq500 Sequencer using the 76nt SR High-Output flow cell.

treatment_protocol: HNSCC cells derived exosome (in vitro)

value: exosomes


title: 3.TP53R273H


title: XY_6GW_p0_EH307

description: Whole organ

value: Male

value: Testis


title: AN naive TSC rep 2  Bulk RNA-seq

value: Renal epithelial cells


title: brain_PL_con_03

city: Xi'an

first: Guohong

last: Cai

address: NO.169 Changle West Road

country: China

institute: Fourth Military Medical University

description: Gene expression data from sham surgery SD rats 14 days after surgery (control group)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Multispecies miRNA-4 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: con

organism: Rattus norvegicus

source_name: brain_PL_SNI (control)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Spared nerve injury(SNI) surgery was performed in SNI group. Briefly, the sural common peroneal and tibial branches of the left sciatic nerve were exposed under isoflurane anesthesia. The tibial and common peroneal nerves were transected. The sural nerve was kept intact. For sham surgery, nerves were exposed but not transected.

value: Sprague Dawley

value: brain

tag: brain region

value: prelimbic cortex (PL)

tag: Sex

value: male


title: brain_PL_con_02


title: 3.TP53Null


title: XX_6GW_p6_EH519

description: Whole organ

value: Female

value: Ovary


title: XX_6GW_p5_EH300

description: Whole organ


title: brain_PL_SNI_02

description: Gene expression data from SNI SD rats 14 days after surgery

label: SNI


title: brain_PL_SNI_03


title: brain_PL_con_01


title: LTHSC_WT_476_D1_S37

value: Long-term hematopoietic stem cells from bone marrow


title: brain_PL_SNI_01


title: XX_6GW_p2_EH323_OK

description: Whole organ


title: LTHSC_WT_476_D12_S48


title: 1.TP53WT

value: WT


title: XX_6GW_p2_EH731

description: Whole organ


title: H9 naive TSC rep 2  Bulk RNA-seq


title: 2.TP53WT


title: AN STB Bulk RNA-seq

source_name: STB

value: STB


title: LTHSC_WT_476_D11_S47


title: 2.TP53Null


title: 1.TP53G245D


title: naive.chipseq

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

country: Canada

institute: University of Alberta

data_processing:
Reads were QC by trimmomatic following dwfault parameters for single end reads
Good qulaity reads mapped to mm10 genome by tophat2 using default parameters
BAM files were processed by samtools
Gene reads number were counted by htseq-count
Chip-Seq peaks were called by MACS2
Genome_build: mm10
Supplementary_files_format_and_content: genes reads number or bed file

source_name: splenic B cell

growth_protocol: cells from each mouse were treated with TAT-CRE in OptiMEM to delete the yy1 gene and then grown in RPMI medium along with LPS+IL4 and 20% FBS for 48 hours

extract_protocol:
Follicular B cells were purified from spleen by positive selection using anti-CD23 antibody and Streptavidin coated microbeads (Milteny Biotech) according to the manufacturer’s instructions
Following the protocal from Illumina Truseq-Stranded RNA library kit and TruSeq ChIP Library Preparation Kit

treatment_protocol: Treated with TAT-CRE in OptiMEM to delete the yy1 gene

tag: mouse strain

value: C57BL/6 yy1 f/f

value: splenic B cell


title: tatcre.chipseq

tag: tissue


title: H9 STB Bulk RNA-seq


title: LTHSC_WT_476_D10_S46

tag: weeks after recombination


title: LTHSC_WT_476_D2_S38

tag: sorting strategy


title: 4.TP53G245D


title: mock.chipseq


title: AN EVT Bulk RNA-seq

source_name: EVT

value: EVT


title: LTHSC_WT_476_C9_S33

tag: genotype/variation


title: 2. TP53C238F


title: tatcre3.rnaseq


title: H9 EVT Bulk RNA-seq


title: WIBR3 naïve TSC Bulk RNA-seq

value: hTSC


title: LTHSC_WT_476_C8_S32


title: 2.TP53R273H

value: exosomes


title: LTHSC_WT_476_C7_S31


title: 3.TP53G245D


title: tatcre2.rnaseq


title: tatcre1.rnaseq


title: AN naïve TSC Bulk RNA-seq


title: H9 naïve TSC Bulk RNA-seq


title: 1.TP53R273H


title: LTHSC_WT_476_C5_S29


title: AN naïve Bulk RNA-seq

source_name: hPSC

value: hPSC


title: 1.TP53Null


title: mock1.rnaseq


title: LTHSC_WT_476_C4_S28


title: H9 naïve Bulk RNA-seq


title: 3.TP53WT


title: LTHSC_WT_476_C3_S27


title: H9 capacitated 2 Bulk RNA-seq


title: Y6050_KirbyE_Control_single-cells

city: Columbus

first: Elizabeth

middle: Diana

last: Kirby

state: OH

address: 1835 Neil Ave, 55 Psycholgy

department: Psychology

institute: The Ohio State University

description: 3 separate primary cultures of neural stem cells isolated from adult C57/Bl6 mouse (aged 6-9 weeks). Cells from the three cultures were pooled before sequencing.

data_processing:
10X single-cell reads were demultiplexed using cellranger (v3.1.0) mkfastq using default parameters
Demultiplexed fastq files were then grouped by cellbarcode, UMI collapsed, aligned, and analyzed using cellranger (v3.1.0) count using default parameters
Basecalls performed using Casava 1.8.2
Reads were trimmed using AdapterRemoval v2.2.0 to remove sequencing adapters
Reads were aligned against the human decontaminome using HISAT2 v2.0.6 using default parameters
Unaligned deconaminome reads were aligned against the human genome using HISAT2 v2.0.6 using default parameters
Reads were quantified using Subread FeatureCounts using GENCODE release M14
Genome_build: GRCh38
Supplementary_files_format_and_content: TSV Counts tables generated using Subread FeatureCounts, Unfiltered
Supplementary_files_format_and_content: Seurat v3.1.0 was used to post-process 10X generated counts table using default workflow: Transcripts present in less than 5 cells were filtered out; Cells with less than 200 or greater than 2500 transcripts were filtered out; Cells with more than 5% mitochondrial counts were filtered out; The resulting counts table was log-normalized; Cells in resulting counts table were ordered by cluster according to Seurat's default clustering algorithm with parameters reduction = 'pca', dims=1:10, and resolution = 0.5

source_name: Cultured adult dentate gyrus NSPCs

growth_protocol:
Grown on poly-d-lysine laminin coated plates in neurobasal A media with 1x B27 (without vitamin A), 1 x glutaMAX, 20 ng/ml recombinant epidermal growth factor and 20 ng/ml basic fibroblast grwoth factor.
Mice were all housed in standard vivarium ventillated cages with ad libitum food and water, 12h light cycle

extract_protocol:
Cells from two female and one male adult NSPC cultures were harvested with accutase and resuspended and washed in HBSS before making a mixed sample with equal numbers from culture for input to 10x genomics chip as per manufacturer instructions.
10X Genomics 3’ RNA-seq library was sequenced using paired-end 150bp approach on an Illumina HiSeq 4000 sequencer. CellRanger v3.0.2 (Zheng et al., 2017) was used to  demultiplex, align, and deduplicate sequencing reads in BCL files. Single-cell data in feature-barcode matrices were then processed using Seurat v3.0.1’s default pipeline (Butler et al., 2018) to identify unsupervised cell clusters and generate a t-Distributed Stochastic Neighbor Embedding (t-SNE) plot. Seurat’s feature expression analysis was used to visualize genes markers known to be expressed in cell populations displayed in the t-SNE plot.

value: 6-9 weeks


title: 1. TP53C238F


title: LTHSC_WT_476_C6_S30


title: mock3.rnaseq


title: 5.TP53G245D


title: 2.TP53G245D


title: LTHSC_WT_476_C12_S36


title: H9 primed StemPro Bulk RNA-seq


title: LTHSC_WT_476_C1_S25


title: mock2.rnaseq


title: H9 primed Bulk RNA-seq


title: DMC-3

first: Yuan

last: Qi

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

data_processing:
alignment and gene count by STAR (version 2.6.0b)
gene annotation used GENCODE M19 (Ensembl 94)
differential expression analysis carried out in R (3.5.1) using Bioconductor package DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-deliminated data matrix of normalized gene counts

source_name: pancreas

extract_protocol:
Flash frozen tissue was pulverized and homogenized in TRIzol RNA isolation reagent (Invitrogen). RNA was then purified using an RNeasy Mini Kit (Qiagen).
Barcoded, Illumina compatible, strand-specific total RNA libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina).

treatment_protocol: Adult mice (6-10 weeks old) were admisistered 4 hourly intraperitoneal injections of caerulein (individual dose: 50 ug/kg), 3 times a week for 3 consecutive weeks. Mice were sacrificed and tissue collected 5 days following the final treatment.

tag: genotype

value: Daxxfl/flMen1fl/flPdx1-CreTg (DMC)


title: 4.TP53R273H


title: DMC-4


title: DMC-1


title: LTHSC_WT_476_C10_S34


title: LTHSC_WT_476_C11_S35


title: ATAC_D3_S5

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

data_processing:
Alignment was performed using bowtie2 v2.3.4.1.
Peak calling was performed using MACS2 v2.1.0.
Analysis of the data was performed using CGAT tools and pipelines (https://github.com/cgat-developers).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

growth_protocol: Briefly, naïve CD4+ CD45RA+ T cells were purified from PBMCs of healthy donors with T-cell enrichment kit (Miltenyi) and then cultured in the presence of anti-CD3/CD28 activation beads (1:20 bead to cell ratio) (Invitrogen) plus polarization condition medium of RPMI-1640 containing 10% knockout serum replacement (ThermoFisher) supplemented with the following cytokines at 37C for 6 days. Naïve T cells were cultured in the presence of IL-1b (20 ng/ml, Peprotech), IL-6 (20 ng/ml, Peprotech), recombinant TGF-b (3 ng/ml, Peprotech) and IL-23 (10 ng/ml) (R & D) for 7 days. For Th17 cell expansion

extract_protocol: ATAC-seq was performed as described in Buenrostro et al. 2013.

treatment_protocol: Cells were treated with either DMSO or GSK-J4 for 48 hours following differentiation.

tag: treatment

tag: donor

tag: day

value: Day 7


title: ATAC_D3_S4

value: DMSO


title: DMC-2


title: LTHSC_WT_476_B9_S21


title: MC-3

value: Men1fl/flPdx1-CreTg (MC)


title: AN primed TSC Bulk RNA-seq

source_name: hPSC cultured in hTSC medium

value: hPSC cultured in hTSC medium

value: Renal epithelial cells


title: ATAC_D3_S3


title: MC-4


title: LTHSC_WT_476_C2_S26

source_name: Long-term hematopoietic stem cells from bone marrow


title: H9 primed TSC Bulk RNA-seq


title: H9 capacitated 1 Bulk RNA-seq


title: LTHSC_WT_476_B8_S20


title: ATAC_D3_S2

value: Day 4


title: MC-2


title: AN primed Bulk RNA-seq


title: ATAC_D3_S1

value: Day 0


title: LTHSC_WT_476_B5_S17

value: Long-term hematopoietic stem cells from bone marrow


title: DC-3

value: Daxxfl/flPdx1-CreTg (DC)


title: ATAC_D2_S4


title: ATAC_D2_S3


title: MC-1


title: RACE-Rep1-WT-TCRD

city: Guangzhou

first: Hao

last: bingtao

address: ShataiNan Road, Baiyun District, Guangzhou, Guangdong Province

institute: Southern Medical University

data_processing:
1) ChIP-seq data process pipline.Clean reads  were obtained following quality filtering and adaptor trimming using trim_glore (cutadapt version 0.4.4_dev) with parameter ‘-paired -q 20’, and reads were mapped to the mm10 genome assembly using bowtie2 (version 2.20.8) with parameters (-X 2000, --sensitive);RPKM normalized BigWig files were generated by BEDtools (version 2.26.0).
2)4C-seq data process pipline. Clean reads  were obtained following quality filtering and adaptor trimming using trim_glore (cutadapt version 0.4.4_dev) with parameter ‘-paired -q 20; The first MboI enzyme fragment behind the viewpoint was extracted and mapped to mm10 by bowtie2 version 2.3.4.3 with parameter : --very-sensitive. Reads numbers were counted and normalized by the total mapped reads per sample after self-ligation remove, and then differential interactions were identified by 4C-ker.
3)5' RACE data process pipline. Reads were obtained following quality filtering and adaptor trimming using trim_glore (cutadapt version 0.4.4_dev) with parameter ‘-paired -q 20’. Individual reads were analyzed with MIXCR v2.1.10 to derive unique clonotypes based on CDR3 homology. Reads that comprise the clonotypes of interest (with matching VJ genes to Mus Musculus library antibody) were extracted for further analysis. The corresponding germline sequences were retrieved from IMGT, the international ImMunoGeneTics database.
4)HiC data process pipline. Reads were obtained following quality filtering and adaptor trimming using trim_glore (cutadapt version 0.4.4_dev) with parameter ‘-paired -q 20’. Hi-C mapping, filtering, correction, and binning were performed with the HiC-Pro software v2.11.1. The reads were mapped to the mm10 mouse reference genome. TADs analysis was performed with the “Insulation Method”. A publicly available script (matrix2insulation.pl) was used to detect the TAD boundaries, with the following options: “--is 2000000 --ids 800000 --nt 0.3”. The script can be accessed through GitHub (https://github.com/dekkerlab/cworld-dekker).Hic file were transfer from HiCPro result by using Juicertools (version 1.13.02).
Genome_build: mm10
Supplementary_files_format_and_content: csv(clonetype counts matrix); hic(generated by juicertools)

source_name: RACE-WT-TCRD

growth_protocol: Mice were housed in a specific-pathogen-free facility managed by the Southern Medical University Division of Laboratory animal center.  All mice were handled in accordance with protocols approved by the Southern Medical University Institutional Animal Care and Use Committee.

extract_protocol:
For Repertoire-seq, a mixture 107 cell equivalents of RNA and 1 μM oligo(dT) primer in 8μl nuclease-free water was heated to 65°C for 5 min and cooled down on ice for at least five minutes to snap-anneal the oligo(dT) primer. The reaction was then adjusted to 250 mM Tris-HCl (pH 8.3), 375 mM KCl, 15 mM MgCl2, 0.5 mM dNTPs and 5 mM dithiothreitol, before addition of 2μl Superscript II (ThermoFisher), add 1μl 25uM 5′RACE adapter sequence (5′-GTCGCACGGTCCATCGCAGCAGTCACArGrGrG-3′) and 1μl in a final volume of 20 μl. The reaction was incubated for two hours at 50°C to synthesize cDNA and add RACE adapter by template switching. Reverse transcriptase was then inactivated by incubation at 85°C for 2 minutes.
For ChIP-seq,  CD3-stimulated  thymus was removed,cells were filtered through nylon mech. Red cells were lysed in AcK buffer.Cells were perforated and dealed with MNase, chromatin were isolated by immunoprecipitation.
For Hi-C, libraries were prepared using in-situ HiC protocol described in (Rao et al., 2014) with small modification.
For 4C, 3C sample preparation followed a previously described protocol(Hagège et al., 2007) with small modification, 3C samples were digested overnight at 37°C with 10 U of NlaIII.After purification,ligation and PCR amplification,the library preparation followed the protocol described in ChIP libary construction.
For ChIP-seq, ChIP product through end repair, dA-tailing and linker ligation, barcodes and Illumina adapters were then added by PCR amplification. The libraries were purified with QiaQuick PCR purification reagents (Qiagen) and size selection by 0.7× and 0.2×Ampure XP beads (Beckman, A63880).
For Repertoire-seq, the library preparation followed the protocol described in ChIP libary preperation after PCR amplification.
For 4C, the library preparation followed the protocol described in ChIP libary construction after PCR amplification.
Hi-C libraries were prepared using in-situ HiC protocol described in (Rao et al., 2014) with small modification.

treatment_protocol: To isolate DP thymocytes from Rag1-/- or Rag2-/- mice, mice were injected i.p. with 150 μg of anti-CD3ε antibody (2C11; Biolegend) at 3 weeks of age and thymi were harvested ten days later.

tag: strain background

value: EACBE+/+

tag: age

value: 4-8 weeks

value: thymus

value: thymocytes


title: DP-CBE-P

source_name: DP-CBE-P

value: CD3-stimulated thymus

tag: cell type


title: ATAC_D2_S5


title: DP-CBE-N

source_name: DP-CBE-N


title: LTHSC_WT_476_B3_S15


title: LTHSC_WT_476_B4_S16


title: ATAC_D2_S2


title: RACE-Rep2-WT-TCRB

source_name: RACE-WT-TCRB


title: RACE-Rep1-WT-TCRB


title: DC-4


title: DC-2


title: WT-4

value: wild type (WT)


title: RACE-Rep2-WT-TCRA

source_name: RACE-WT-TCRA


title: DC-1


title: LTHSC_WT_476_B2_S14


title: ATAC_D1_S5


title: ATAC_D2_S1


title: LTHSC_WT_476_B7_S19


title: LTHSC_WT_476_B1_S13


title: ATAC_D1_S4


title: LTHSC_WT_476_B6_S18


title: LTHSC_WT_476_B12_S24


title: WT-3


title: RACE-Rep2-WT-TCRD


title: RACE-Rep1-WT-TCRA


title: WT-2


title: LTHSC_WT_476_B11_S23


title: WT-1


title: ATAC_D1_S2


title: LTHSC_WT_476_B10_S22


title: RACE-Rep1-KO-TCRD

source_name: RACE-KO-TCRD

value: EACBE-/-


title: WT replicate #1

city: Porto

first: Bruno

last: Pereira

address: Rua Alfredo Allen, 208

country: Portugal

data_processing:
Trimming_The analysis of the generated sequence raw data was carried out using CLC Genomics Workbench 12.0.3 (Qiagen). Bioinformatic analysis started with trimming of raw sequences to generate high quality data. For each original read, the regions of the sequence to be removed were determined independently for each type of trimming operation based on the following parameters: a) Ambiguous limit – 2 nucleotides; b) Quality limit – 0.01 (error probability); c) Minimum number of nucleotides in reads – 15 nucleotides; d) Discard short reads.
Mapping_The high-quality sequencing reads were mapped against the reference genome, Mus musculus, using length and similarity fractions of 0.8.
Gene expression_The result of mapping served to determine the gene expression levels based on the TPM (Trancripts per Million), which is a variation of the RPKM method. RPKM is defined as the Reads per Kilobase of exon model per Million mapped reads. In other words, and in this case, it is given by dividing the total number of reads from a particular gene by the number of total mapped reads of the transcriptome (in Millions), times the length (kb) of that gene (Mortazavi et al., 2008, Nat. Methods).
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: Tab-delimited excel files include annotated transcripts, transcript lenght, number of exons, total transcript reads and associated TPM and RPKM values for each sample.

source_name: Small intestine

growth_protocol: Mice at P16

extract_protocol:
Small intestine tissue fragments were incubated with crypt chelating buffer (2 mM EDTA pH 8.0 in PBS) for 1 hour at 4°C with gentle rotation. After incubation, the fragments were allowed to settle, the supernatant discarded, and 8 mL of ice-cold PBS added. Fragments were shaken by hand at 3 cycles/second for 1 minute to dissociate the epithelial crypts from the basement membrane. Cell suspensions were observed under a microscope to check for crypt enrichment and filtered through a 40 μm mesh into a 50 mL falcon tube on ice to collect the first crypt fraction. Previous steps were repeated to release remaining crypts still attached to the tissue, combining both fractions in the same tube. The crypt suspension was centrifuged for 10 minutes at 300 × g at 4°C. Tri reagent (1 mL) was added to freshly isolated crypts and total RNA extracted according to the manufacturer`s guidelines (Sigma).
The library construction of cDNA molecules was carried out using a Stranded mRNA Library Preparation Kit. ). The generated DNA fragments were sequenced in the illumina Novaseq platform (illumina), using 150bp paired-end sequencing reads.

value: Small intestine crypts

tag: strain

value: Small intestine

value: Postnatal day 16 (P16)

value: Wild-type


title: Mex3a KO replicate #1


title: ATAC_D1_S1


title: Donor3-Th17_K4me3_DMSO_3

data_processing:
Alignment was performed using bowtie2 v2.3.4.1
Peak calling was performed using MACS2 v2.1.0
Analysis of the data was performed using CGAT tools and pipelines (https://github.com/cgat-developers)
Genome_build: Hg19
Supplementary_files_format_and_content: Bigwig

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.

treatment_protocol: Cells were treated with either DMSO or GSK-J4 for 48 houurs following differentiation

value: DMSO

tag: chip antibody

value: Th17 cell


title: LTHSC_WT_476_A7_S7


title: Donor3-Th17_K4me3_J4_3


title: LTHSC_WT_476_A8_S8


title: X4977_KirbyE_DGM2R_V1N_1_S12_L001

description: Denninger NSPC-DG seq

data_processing:
Basecalls performed using Casava 1.8.2
Reads were trimmed using AdapterRemoval v2.2.0 to remove sequencing adapters
Reads were aligned against the human decontaminome using HISAT2 v2.0.6 using default parameters
Unaligned deconaminome reads were aligned against the human genome using HISAT2 v2.0.6 using default parameters
Reads were quantified using Subread FeatureCounts using GENCODE release M14
Genome_build: GRCh38
Supplementary_files_format_and_content: TSV Counts tables generated using Subread FeatureCounts, Unfiltered

source_name: Adult dentate gyrus

growth_protocol: Mice were all housed in standard vivarium ventillated cages with ad libitum food and water, 12h light cycle

extract_protocol:
Approximately 30,000 cells from two female and two male adult NSPCs cultures were harvested with accutase and washed with PBS before RNA isolation with the Clontech Nucleospin RNA XS Plus isolation kit (Takara 740990.10) per manufacturer protocol. RNA was also isolated from whole DGs isolated from one male and one female C57/Bl6 mouse with the same kit. RNA quality and quantity was assessed with a Qubit RNA HS assay kit (Invitrogen). All cultured samples used had a RIN value of 10 while whole DG samples had RIN values over 8. Libraries were generated with the NEBNext Ultra II Directional RNA Library prep kit (Illumina) for the whole DGs and the Clontech HT kit for cultured NSPCs. Purified library products were then used in HiSeq 4000 paired-end sequencing (Illumina) to a depth of 15 - 20 million 2x150 bp clusters.
Libraries were generated with the NEBNext Ultra II Directional RNA Library prep kit (New England Biolabs) for the whole DGs and the Clontech SMART/Seq HT kit (Takara) for cultured NSPCs. Purified library products were then used in HiSeq 4000 paired-end sequencing (Illumina) to a depth of 15 - 20 million 2x150 bp clusters.

value: 7-9 weeks


title: X4978_KirbyE_DGF1R_V1N_1_S13_L001

description: Denninger NSPC-DG seq


title: RACE-Rep2-KO-TCRA

source_name: RACE-KO-TCRA


title: RACE-Rep2-KO-TCRB

source_name: RACE-KO-TCRB


title: RACE-Rep1-KO-TCRB


title: LTHSC_WT_476_A6_S6

data_processing:
Single cell RNA sequencing data generated with Chromium 10x v2 was processed using Cell Ranger (v2.1.0) with default parameters, and data generated with Chromium v3 was processed using the updated version of Cell Ranger (v3.1). For both chemistry versions, samples were sequenced at an average of 50,000 reads per cell. Raw sequencing data was de-multiplexed and post-processed following the custom pipelines provided by 10x Genomics. Briefly, raw base calls were de-multiplexed into fastq files using the cellranger mkfastq command, followed by alignment to the selected reference mm10 genome for mouse samples or hg19 genome for the human subject data, respectively. Barcode and UMI counting was performed using the cellranger count command with default parameters. Cell barcodes with UMI < 1,000 or mitochondrial gene percentage > 20% were filtered out.
For Drop-seq data, samples were prepared for sequencing using the Illumina Nextera XT kit, and sequenced on a NextSeq 500 (Illumina, San Diego, CA) at an average of 70,000 reads per cell. Libraries with large numbers of cells were divided into technical replicates, which were processed independently. Raw reads were processed and aligned (STAR aligner106) using the standard Drop-seq pipeline, and according to the ‘Drop-seq Alignment Cookbook’, both found at http://mccarrolllab.com/dropseq/.Reads were aligned to the mm10 transcriptome. For each read, a single optimal mapping position was retained. Unique transcripts mapping to alternative splice variants were combined for subsequent analysis. Single-cell expression matrices were generated using cellular barcodes and unique molecular identifiers (UMIs). Cells with UMI < 200 or mitochondrial gene percentage > 20% were filtered out.
For the dual protocol experiments, each pool of 96 cells was first demultiplexed by Illumina i7 barcodes, resulting in four pools of 24 cells. Each pool of 24 cells was further demultiplexed by unique cell barcodes. Reads were assigned to a given cell if they matched 80% of the template adapters. Adapters and adapter reverse complements (6 bp) were trimmed from the raw sequence reads. After adapter removal, reads were trimmed from their 3’ end for read quality by applying a 4 bp sliding window and removing bases until the mean base quality of the window had a Phred quality score greater than 15. We aligned trimmed reads in single-end mode to the mm10 mouse genome assembly using Bismark (v.0.14.5; parameters: -multicore 4 -X 1000 --un –ambiguous) running on bowtie2-2.2.8 aligner. Bismark methylation extractor (--bedgraph --comprehensive) was used to determine the methylation state of each individual CpG. For the single cell RNA, the sequenced paired-end read fragments were mapped against the mm10 mouse genome assembly using the 2pass default mode of STAR (version 2.5.2a) with the annotation of GENCODE (version 19). The number of read counts overlapping with annotated genes was quantified applying the ‘GeneCounts’ option in the STAR alignment.
ATAC-Bseq data was aligned to mm10 genome and methylation calling was performed through Bismark (version 0.14.4; parameters: --q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --maxins 500 Option '--directional' specified) running on bowtie2-2.2.8 aligner112. Accessibility peaks for each individual replicate were defined using MACS2 (v2.1.1.2); parameters: -f BAMPE --broad --broad-cutoff 0.1 -m 2 100).
Genome_build: mm10 for Mus musculus samples,  hg19 for Homo sapiens sample.
Supplementary_files_format_and_content: csv; Single-cell expression matrices were generated using cellular barcodes and unique molecular identifiers (UMIs). UMItabs contain the UMI count for each specified gene (rows) for each cell (columns). Cell barcodes are provided in the ".CellBarcodes" file for each sample.

extract_protocol: Bone marrow (BM) cells were isolated into cold phosphate-buffered saline (PBS), without Ca2+ and Mg2+, and supplemented with 2% bovine serum albumin (BSA) to generate single cell suspensions. Red blood cells (RBCs) were removed using ammonium chloride-potassium bicarbonate (ACK) lysis buffer, resuspended in PBS/2% BSA, and filtered through a 40μm cell strainer. Cells were sorted and inmediately underwent the indicated protocol.


title: Donor3-Th17_input_DMSO_3


title: L4974_KirbyE_M2_V1C_1_S17_L001

description: Denninger NSPC-DG seq

growth_protocol:
Grown on poly-d-lysine laminin coated plates in neurobasal A media with 1x B27 (without vitamin A), 1 x glutaMAX, 20 ng/ml recombinant epidermal growth factor and 20 ng/ml basic fibroblastgrowth factor.
Mice were all housed in standard vivarium ventillated cages with ad libitum food and water, 12h light cycle

tag: passage

value: 6-8 weeks


title: DP-Rag2ko-CBEwt-TRAV17-4C-rep2

data_processing:
library strategy: 4C-seq
1) ChIP-seq data process pipline.Clean reads  were obtained following quality filtering and adaptor trimming using trim_glore (cutadapt version 0.4.4_dev) with parameter ‘-paired -q 20’, and reads were mapped to the mm10 genome assembly using bowtie2 (version 2.20.8) with parameters (-X 2000, --sensitive);RPKM normalized BigWig files were generated by BEDtools (version 2.26.0).
2)4C-seq data process pipline. Clean reads  were obtained following quality filtering and adaptor trimming using trim_glore (cutadapt version 0.4.4_dev) with parameter ‘-paired -q 20; The first MboI enzyme fragment behind the viewpoint was extracted and mapped to mm10 by bowtie2 version 2.3.4.3 with parameter : --very-sensitive. Reads numbers were counted and normalized by the total mapped reads per sample after self-ligation remove, and then differential interactions were identified by 4C-ker.
3)5' RACE data process pipline. Reads were obtained following quality filtering and adaptor trimming using trim_glore (cutadapt version 0.4.4_dev) with parameter ‘-paired -q 20’. Individual reads were analyzed with MIXCR v2.1.10 to derive unique clonotypes based on CDR3 homology. Reads that comprise the clonotypes of interest (with matching VJ genes to Mus Musculus library antibody) were extracted for further analysis. The corresponding germline sequences were retrieved from IMGT, the international ImMunoGeneTics database.
4)HiC data process pipline. Reads were obtained following quality filtering and adaptor trimming using trim_glore (cutadapt version 0.4.4_dev) with parameter ‘-paired -q 20’. Hi-C mapping, filtering, correction, and binning were performed with the HiC-Pro software v2.11.1. The reads were mapped to the mm10 mouse reference genome. TADs analysis was performed with the “Insulation Method”. A publicly available script (matrix2insulation.pl) was used to detect the TAD boundaries, with the following options: “--is 2000000 --ids 800000 --nt 0.3”. The script can be accessed through GitHub (https://github.com/dekkerlab/cworld-dekker).Hic file were transfer from HiCPro result by using Juicertools (version 1.13.02).
Genome_build: mm10
Supplementary_files_format_and_content: csv(clonetype counts matrix); hic(generated by juicertools)


title: Donor2-Th17_K4me3_J4_1


title: RACE-Rep1-KO-TCRA


title: RACE-Rep2-KO-TCRD


title: L4973_KirbyE_M1_V1C_1_S16_L001

description: Denninger NSPC-DG seq

growth_protocol:
Grown on poly-d-lysine laminin coated plates in neurobasal A media with 1x B27 (without vitamin A), 1 x glutaMAX, 20 ng/ml recombinant epidermal growth factor and 20 ng/ml basic fibroblast growth factor.
Mice were all housed in standard vivarium ventillated cages with ad libitum food and water, 12h light cycle


title: DP-Rag2ko-CBEwt-TRAV17-4C-rep1


title: Donor2-Th17_K4me3_DMSO_1


title: ATAC_D1_S3

value: Day 7


title: LTHSC_WT_476_A9_S9

value: Long-term hematopoietic stem cells from bone marrow


title: LTHSC_WT_476_A4_S4


title: L4976_KirbyE_F2_V1C_1_S19_L001

description: Denninger NSPC-DG seq


title: DP-Rag2ko-CBEko-TRAV17-4C-rep2


title: LTHSC_WT_476_A3_S3


title: DP-Rag2ko-CBEko-TRAV17-4C-rep1


title: LTHSC_WT_476_A2_S2


title: Mm PNC p53NULL_4

source_name: Primary neuron culture

value: Mouse TG neurons

tag: group

value: in vitro


title: L4975_KirbyE_F1_V1C_1_S18_L001

description: Denninger NSPC-DG seq


title: LTHSC_WT_476_A1_S1


title: Donor1-Th17_K4me3_DMSO


title: Mm PNC p53NULL_3


title: DP-Rag2ko-CBEwt-TEAp-4C-rep2

value: 4-8 weeks


title: LTHSC_WT_476_A12_S12


title: Donor1-Th17_input_DMSO


title: LTHSC_WT_476_A5_S5


title: Mm PNC p53NULL_2


title: Th17Quant_K27_J43_R1

data_processing:
Alignment was performed using bowtie2 v2.3.4.1
Peak calling was performed using MACS2 v2.1.0
Analysis of the data was performed using CGAT tools and pipelines (https://github.com/cgat-developers)
Genome_build: Hg19 containing an artificial contigs consisting of SF9 genome
Supplementary_files_format_and_content: Bigwig

tag: antibody


title: LTHSC_WT_476_A11_S11


title: DP-Rag2ko-CBEko-TEAp-4C-rep2

value: thymocytes


title: Mm PNC p53NULL_1


title: DP-Rag2ko-CBEwt-TEAp-4C-rep1

value: CD3-stimulated thymus


title: DP-Rag2ko-CBEko-TEAp-4C-rep1


title: Th17Quant_K27_J42_R1


title: LTHSC_WT_476_A10_S10


title: Mm PNC p53WT_3


title: DP-Rag2ko-CBEwt-INT-4C-rep2


title: Donor2-Th17_input_DMSO_1


title: Th17Quant_K27_J41_R1


title: Mm PNC p53WT_2


title: ATAC-Bseq_Dnmt3aKO_2

description: ATAC-seq plus bisulfite conversion

data_processing:
Library strategy: ATAC-seq plus bisulfite conversion
Single cell RNA sequencing data generated with Chromium 10x v2 was processed using Cell Ranger (v2.1.0) with default parameters, and data generated with Chromium v3 was processed using the updated version of Cell Ranger (v3.1). For both chemistry versions, samples were sequenced at an average of 50,000 reads per cell. Raw sequencing data was de-multiplexed and post-processed following the custom pipelines provided by 10x Genomics. Briefly, raw base calls were de-multiplexed into fastq files using the cellranger mkfastq command, followed by alignment to the selected reference mm10 genome for mouse samples or hg19 genome for the human subject data, respectively. Barcode and UMI counting was performed using the cellranger count command with default parameters. Cell barcodes with UMI < 1,000 or mitochondrial gene percentage > 20% were filtered out.
For Drop-seq data, samples were prepared for sequencing using the Illumina Nextera XT kit, and sequenced on a NextSeq 500 (Illumina, San Diego, CA) at an average of 70,000 reads per cell. Libraries with large numbers of cells were divided into technical replicates, which were processed independently. Raw reads were processed and aligned (STAR aligner106) using the standard Drop-seq pipeline, and according to the ‘Drop-seq Alignment Cookbook’, both found at http://mccarrolllab.com/dropseq/.Reads were aligned to the mm10 transcriptome. For each read, a single optimal mapping position was retained. Unique transcripts mapping to alternative splice variants were combined for subsequent analysis. Single-cell expression matrices were generated using cellular barcodes and unique molecular identifiers (UMIs). Cells with UMI < 200 or mitochondrial gene percentage > 20% were filtered out.
For the dual protocol experiments, each pool of 96 cells was first demultiplexed by Illumina i7 barcodes, resulting in four pools of 24 cells. Each pool of 24 cells was further demultiplexed by unique cell barcodes. Reads were assigned to a given cell if they matched 80% of the template adapters. Adapters and adapter reverse complements (6 bp) were trimmed from the raw sequence reads. After adapter removal, reads were trimmed from their 3’ end for read quality by applying a 4 bp sliding window and removing bases until the mean base quality of the window had a Phred quality score greater than 15. We aligned trimmed reads in single-end mode to the mm10 mouse genome assembly using Bismark (v.0.14.5; parameters: -multicore 4 -X 1000 --un –ambiguous) running on bowtie2-2.2.8 aligner. Bismark methylation extractor (--bedgraph --comprehensive) was used to determine the methylation state of each individual CpG. For the single cell RNA, the sequenced paired-end read fragments were mapped against the mm10 mouse genome assembly using the 2pass default mode of STAR (version 2.5.2a) with the annotation of GENCODE (version 19). The number of read counts overlapping with annotated genes was quantified applying the ‘GeneCounts’ option in the STAR alignment.
ATAC-Bseq data was aligned to mm10 genome and methylation calling was performed through Bismark (version 0.14.4; parameters: --q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --maxins 500 Option '--directional' specified) running on bowtie2-2.2.8 aligner112. Accessibility peaks for each individual replicate were defined using MACS2 (v2.1.1.2); parameters: -f BAMPE --broad --broad-cutoff 0.1 -m 2 100).
Genome_build: mm10 for Mus musculus samples,  hg19 for Homo sapiens sample.
Supplementary_files_format_and_content: csv; Single-cell expression matrices were generated using cellular barcodes and unique molecular identifiers (UMIs). UMItabs contain the UMI count for each specified gene (rows) for each cell (columns). Cell barcodes are provided in the ".CellBarcodes" file for each sample.

source_name: Lineage negative, Sca1 positive, c-Kit positive hematopoietic bone marrow progenitors

value: Mx1-Cre Dnmt3a fl/fl


title: DP-Rag2ko-CBEwt-INT-4C-rep1


title: Th17Quant_K27_DMSO3_R1


title: ATAC-Bseq_Dnmt3aKO_1

description: ATAC-seq plus bisulfite conversion

value: Lineage negative, Sca1 positive, c-Kit positive hematopoietic bone marrow progenitors


title: Donor1-Th17_K4me3_J4


title: Mm PNC p53WT_1


title: ATAC-Bseq_Tet2KO_2

description: ATAC-seq plus bisulfite conversion

value: Mx1-Cre Tet2 fl/fl


title: DP-Rag2ko-CBEko-INT-4C-rep1


title: Th17Quant_K27_DMSO2_R1


title: ATAC-Bseq_Tet2KO_1

description: ATAC-seq plus bisulfite conversion


title: Th17Quant_K27_DMSO1_R1


title: DP-Rag2ko-CBEwt-Ea2-4C-rep2


title: DP-Rag2ko-CBEwt-Ea2-4C-rep1


title: ATAC-Bseq_WT2

description: ATAC-seq plus bisulfite conversion


title: Bulk 32-cell and 64-cell embryos Library 1

data_processing:
Library strategy: Hairpin bisulfite sequencing
Fastq files are parsed for library barcodes. Read 1 was mapped to the mm10 or hg19 build using the Bowtie2, filtered for unique mapping full-length reads and demultiplexed. 5mCG positions are obtained from the sequencing data using custom scripts in R and Perl identifying CG dinucleotides in the mm10 or hg19 genome at the expected distance from the mapped read position. Finally, all PCR duplicates are removed. Computer codes will be made available upon request.
Hairpin bisulfite sequencing was performed on bulk mouse embryos samples ( 2-cell to 64 cell stage). The bulk embryos were treated with protease treatment (1 uL of 25 ug/uL Qiagen Protease, 1 uL of 10X NEB Buffer 4, and 8 uL of nuclease free water). Then, 0.5 ng of genomic DNA was digested with 20 mL of MspI master mix (1 uL of MspI R0104L, 2 mL 10X NEB Cutsmart buffer in a total volume of 20 uL) and incubated at 37 C for an hour. After digestion, the digested genomic DNA was ligated with 1 uL of 10 uM phosphorylated hairpin oligo and ligation master mix (1 mL of NEB T4 ligase M0202M, 1 uL of 10X NEB T4 Ligase buffer, 2 uL of 10mM ATP, 5 uL of nuclease free water) and incubated overnight at 16 C. For purification of the ligation mixture, we used Dynabeads? M-280 Streptavidin and followed the recommended protocol with the following exceptions: the bead-ligation mixture was incubated for at least an hour at RT on a rotator and cold 10 mM Tris-HCl wash step was included. Subsequently, we performed BS-seq on the sample using the protocol Clark, et al. 2017. After sequencing the libraries on a Miseq 300x300 or NextSeq 75x75 pair-end kit, we used HBS-tools (Sun, MA et al. 2015) and custom perl scripts were used to analyze the methylated CpG dyads. Hairpin oligo (G/iMe-dC/iMe-dC/G/iMe-dC/iMe-dC/GG/iMe-dC/GG/iMe-dC/AAG/iBiodT/GAAG/iMe-dC/iMe-dC/G/iMe-dC/iMe-dC/GG/iMe-dC/G) was resuspended in 100 uM of Low-TE. The hairpin oligo was phosphorylated (1 uL of 100 uM hairpin oligo, 3 uL of 10X T4 Ligase Buffer, 1 uL T4 PNK and 5 uL of nuclease free water) and incubated at 37 C for an hour. Subsequently the phosphorylated oligo heated at 94 C and placed in ice water to generate the loop.
Published scNMT libraries (GSE109262) analyzed for the bisulfite results were processed as described previously. The first nine bases of the raw reads were trimmed using Trim Galore (v0.5.0) and mapped using Bismark to the mouse genome (mm10) with the 129/CAST background. SNPs specific to 129/CAST mouse genome were prepared using SNPsplit (v0.3.2) and a list of known variant call files from the Mouse Genomes Project (http://www.sanger.ac.uk/resources/mouse/genomes/). After mapping with Bismark, duplicate sequences were removed and CpG methylation calls were extracted with strand-specific information. Further data analysis and visualization of the methylation calls used custom scripts that will be made available upon request.
Genome_build: mm10, hg19
Supplementary_files_format_and_content: mText files with 4 columns: Single Cell ID, chromosome, coordinate, strand, CNNR motif and strain [mouse only])

source_name: Embryos

growth_protocol: B6 mouse embryos were obtained from four 3-month-old superovulated B6 mothers (injected with pregnant mare serum gonadotropin (PMSG) and human chorionic gonadotropin (HCG) 22 h later) and incubated in M16 medium at 37°C and 5% CO2.

extract_protocol:
Embryos were picked manually and deposited into a 0.5 mL eppendorf with lysis buffer and Vapor-lock.
Hairpin bisulfite sequencing was performed on bulk mouse embryos samples ( 2-cell to 64 cell stage). The bulk embryos were treated with protease treatment (1 uL of 25 ug/uL Qiagen Protease, 1 uL of 10X NEB Buffer 4, and 8 uL of nuclease free water). Then, 0.5 ng of genomic DNA was digested with 20 mL of MspI master mix (1 uL of MspI R0104L, 2 mL 10X NEB Cutsmart buffer in a total volume of 20 uL) and incubated at 37 C for an hour. After digestion, the digested genomic DNA was ligated with 1 uL of 10 uM phosphorylated hairpin oligo and ligation master mix (1 mL of NEB T4 ligase M0202M, 1 uL of 10X NEB T4 Ligase buffer, 2 uL of 10mM ATP, 5 uL of nuclease free water) and incubated overnight at 16 C. For purification of the ligation mixture, we used Dynabeads™ M-280 Streptavidin and followed the recommended protocol with the following exceptions: the bead-ligation mixture was incubated for at least an hour at RT on a rotator and cold 10 mM Tris-HCl wash step was included. Subsequently, we performed BS-seq on the sample using the protocol Clark, et al. 2017. After sequencing the libraries on a Miseq 300x300 or NextSeq 75x75 pair-end kit, we used HBS-tools (Sun, MA et al. 2015) and custom perl scripts were used to analyze the methylated CpG dyads. Hairpin oligo (G/iMe-dC/iMe-dC/G/iMe-dC/iMe-dC/GG/iMe-dC/GG/iMe-dC/AAG/iBiodT/GAAG/iMe-dC/iMe-dC/G/iMe-dC/iMe-dC/GG/iMe-dC/G) was resuspended in 100 uM of Low-TE. The hairpin oligo was phosphorylated (1 uL of 100 uM hairpin oligo, 3 uL of 10X T4 Ligase Buffer, 1 uL T4 PNK and 5 uL of nuclease free water) and incubated at 37 C for an hour. Subsequently the phosphorylated oligo heated at 94 C and placed in ice water to generate the loop.

tag: developmental stage

value: 32-cell and 64-cell embryos


title: DP-Rag2ko-CBEko-INT-4C-rep2

tag: tissue


title: Th17Quant_input_DMSO1_R1

value: Input


title: Mm TG p53NULL_3

source_name: Murine TG neurons

value: in vivo


title: Mm TG p53NULL_2


title: Mm TG p53WT_3


title: Mm TG p53NULL_1


title: DP-Rag2ko-CBEko-Ea2-4C-rep2


title: Bulk HBS 32-cell embryos Library 3

value: 32-cell embryos


title: ATAC-Bseq_WT1

description: ATAC-seq plus bisulfite conversion

tag: weeks after recombination


title: Mm TG p53WT_2


title: DP-Rag2ko-CBEko-Ea2-4C-rep1


title: scATAC_Dnmt3aKO_1

description: Single cell ATAC-seq

tag: sorting strategy


title: Bulk HBS 32-cell embryos Library 2


title: Mm TG p53WT_1


title: Bulk HBS 32-cell embryos Library 1


title: scATAC_Dnmt3aKO_2

description: Single cell ATAC-seq

tag: genotype/variation


title: scATAC_Tet2KO_2

description: Single cell ATAC-seq


title: DP-Rag2ko-CBEwt-Ea1-4C-rep1


title: MT30DAS, biological rep3

city: Wuhan

first: Feng

last: Zhu

address: No.1,Shizishan Street

department: College of Horticulture & Forestry Sciences

institute: Huazhong Agricultural University

description: replicate 3 for the mutant type citrus  at 30 days after storage

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Solanum lycopersicum whole genome using Top Hat.
Assembles the matched reads to estimates their abundances using HTSeq.
Tests for differential expression in RNA-Seq samples using edgeR
Genome_build: Reference genome sequences and annotations were downloaded from the citrus genome websit (https://www.citrusgenomedb.org/)

organism: Citrus reticulata

source_name: Fruit

extract_protocol:
Total RNA was extracted by Trizol method
20 mg total RNA was prepared to enrich mRNA by using the oligo (dT) magnetic beads. After adding fragmentation buffer, the mRNA was interrupted to short fragments (approximately 200 bp). The first strand cDNA was then synthesized with random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. The double-strand cDNA was purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition. Finally, sequencing adaptors were ligated to the fragments.

treatment_protocol: No treatment

tag: cultivar

value: Citrus reticulata cv. Suavissima

value: flavode

tag: genotype

value: staygreen mutant

value: 30 days after flowering


title: DP-Rag2ko-CBEko-Ea1-4C-rep1


title: Bulk HBS 16-cell and 32-cell embryos Library 1

value: 16-cell and 32-cell embryos


title: scATAC_Tet2KO_1

description: Single cell ATAC-seq


title: MT30DAS, biological rep2

description: replicate 2 for the mutant type citrus  at 30 days after storage


title: Bulk 16-cell embryos Library 1

value: 16-cell embryos


title: scATAC_WT2

description: Single cell ATAC-seq


title: MT30DAS, biological rep1

description: replicate 1 for  the mutant type citrus  at 30 days after storage


title: DP-Rag2ko-CBEwt-H3K27ac-rep1

value: Rabbit polyclonal to Histone H3(acetyl K27)-ChIP Grade

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: scATAC_WT1

description: Single cell ATAC-seq


title: Bulk HBS 8-cell embryos Library 2

value: 8-cell embryos


title: DP-Rag2ko-CBEko-H3K27ac-rep2

tag: strain background

value: 4-8 weeks

value: CD3-stimulated thymus

value: thymocytes


title: Bulk HBS 8-cell embryos Library 1


title: DropSeq_Tet2KO_1_20wk

description: Single cell RNA sequencing

source_name: Lineage negative hematopoietic bone marrow progenitors

value: Lin-

value: Mx1-Cre Tet2 fl/fl


title: Bulk HBS 4-cell embryos Library 2

value: 4-cell embryos


title: WT30DAS, biological rep1

description: replicate 1 for  the wild type citrus  at 30 days after storage

value: wild type

tag: age


title: Bulk HBS 4-cell embryos Library 1


title: DP-Rag2ko-CBEwt-H3K4me3-rep2

tag: cell type

value: Anti-trimethyl-Histone H3(Lys4)

value: Merck-Millipore


title: DropSeq_Idh2R140Q_1_4wk

description: Single cell RNA sequencing

value: Lineage negative hematopoietic bone marrow progenitors

value: Mx1-Cre Idh2 R140Q/WT


title: MT210DAF, biological rep3

description: replicate 3 for the mutant type citrus  at 210 days after flowering

value: Citrus reticulata cv. Suavissima

value: flavode

value: staygreen mutant

value: 210 days after flowering


title: DropSeq_Tet2KO_4_4wk

description: Single cell RNA sequencing


title: Bulk HBS 2-cell embryos Library 3

tag: strain

value: 2-cell embryos


title: DP-Rag2ko-CBEko-H3K27ac-rep1

tag: chip antibody

value: Rabbit polyclonal to Histone H3(acetyl K27)-ChIP Grade

value: Abcam


title: DropSeq_WT1_20wk

description: Single cell RNA sequencing


title: DP-Rag2ko-CBEko-H3K4me3-rep2

value: 4-8 weeks

value: CD3-stimulated thymus


title: MT210DAF, biological rep2

description: replicate 2 for the mutant type citrus  at 210 days after flowering


title: DropSeq_Tet2KO_3_4wk

description: Single cell RNA sequencing

value: Lin-


title: Bulk HBS 2-cell embryos Library 2


title: DP-Rag2ko-CBEwt-H3K27ac-rep2

value: thymocytes


title: DP-Rag2ko-CBEko-H3K4me3-rep1


title: Bulk HBS 2-cell embryos Library 1


title: DropSeq_Tet2KO_2_4wk

description: Single cell RNA sequencing

value: Mx1-Cre Tet2 fl/fl


title: WT30DAS, biological rep3

description: replicate 3 for the wild type citrus  at 30 days after storage

value: wild type

value: 30 days after flowering


title: WT30DAS, biological rep2

description: replicate 2 for the wild type citrus  at 30 days after storage


title: WT210DAF, biological rep3

description: replicate 3 for the wild type citrus  at 210 days after flowering


title: WT210DAF, biological rep2

description: replicate 2 for the wild type citrus  at 210 days after flowering


title: DP-Rag2ko-CBEwt-H3K4me3-rep1

value: Anti-trimethyl-Histone H3(Lys4)

value: Merck-Millipore


title: DropSeq_Tet2KO_1_4wk

description: Single cell RNA sequencing

value: Lineage negative hematopoietic bone marrow progenitors


title: Krt13 KO tongue at P20, biological rep 3

city: Madison

last: Chang

state: WI

address: 1300 University Ave

department: Dermatology

institute: University of Wisconsin-Madison

description: Sample KO-B3

data_processing:
Illumina bcl2fastq v2.20
Read trimming with Skewer v0.2.2b -m pe -q 20 -k 15 -l 25
Read alignment with STAR v2.5.3a --runThreadN 10 --twopassMode Basic --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMattributes NH HI AS NM MD XS --outSAMunmapped Within --outFilterMultimapNmax 50
Expression estimation with RSEM rsem-calculare-expression v1.2.31 --alignments --paired-end --no-bam-output
Differential expression estimation with edgeR v3.28.0
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: MS Excel differential expression results

source_name: Krt13 KO tongue at P20

growth_protocol: P0 or P20 mice were euthanized and tongues were dissected in cold PBS

extract_protocol:
Trizol and Rneasy according to the manufacturer's instructions
Illumina TruSeq stranded
mRNA library for sequencing

treatment_protocol: P0 whole tongues and P20 ventral tongues were dissected and kept in Trizol

value: Krt13 KO

value: tongue


title: Krt13 KO tongue at P20, biological rep 2

description: Sample KO-B2


title: DropSeq_WT3_4wk

description: Single cell RNA sequencing


title: Krt13 KO tongue at P20, biological rep 4

description: Sample KO-B4


title: Krt13 KO tongue at P20, biological rep 1

description: Sample KO-B1


title: H3_H3LNLDMXX

city: Shanghai

first: Jun

last: Long

address: Xincun Road

department: Department of Hematology

institute: Tongji Hospital

data_processing:
Raw sequence reads were initially processed using FastQC (Babraham Institute) for quality control, and then adapter sequences and poor quality reads were removed using Cutadapt.
Quality-filtered reads were then mapped to human genome (hg38) using RNA-seq aligner STAR.
Uniquely mapped reads were calculated using HTSeq-count.
Differentially expressed genes were identified using R package DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: DESeq2 output

source_name: AML cells

growth_protocol: MV4-11 cells were grown in RPMI1640 containing 10% FBS,  2mM L-glutamine and antibiotics.

extract_protocol: RNA was isolated using RNeasy Mini Kit with genomic DNA depletion.  1 ug  total RNA was used to prepare  sequencing libraries by NEBNext Ultra RNA Library Prep Kit for Illumina (Cat# E7530L).

treatment_protocol: Culture medium was added with DMSO or 22d (10nM). MV4-11 cells were treated 18 hours before harvesting for RNA extraction.

tag: cell line

value: AML cell line

tag: treatment


title: 4foxm1

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Brain

extract_protocol:
Total RNA was harvested by Trizol reagent.2 ug of total RNA was used to construct sequencing libraries.
RNA libraries sequencing was performed using standard Illumina protocols

value: WT


title: WT210DAF, biological rep1

description: replicate 1 for  the wild type citrus  at 210 days after flowering

value: Citrus reticulata cv. Suavissima

value: flavode

value: 210 days after flowering


title: DropSeq_WT1_4wk

city: New York

first: Franco

last: Izzo

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

description: Single cell RNA sequencing


title: H2_H3LNLDMXX


title: control tongue at P20, biological rep 5

description: Sample WT-B5

source_name: control tongue at P20

value: control


title: H1_H3LNLDMXX


title: MT210DAF, biological rep1

description: replicate 1 for  the mutant type citrus  at 210 days after flowering

value: staygreen mutant


title: 3foxm1-nestin


title: 2nestin


title: DropSeq_Tet2KO_1_Lin_c-Kit_4wk

description: Single cell RNA sequencing

source_name: Lineage negative, c-Kit positive hematopoietic bone marrow progenitors

value: Lin-; c-Kit+


title: CON3_H3LNLDMXX

value: DMSO


title: control tongue at P20, biological rep 3

description: Sample WT-B3


title: control tongue at P20, biological rep 4

description: Sample WT-B4


title: DropSeq_Tet2KO_2_Lin_c-Kit_4wk

description: Single cell RNA sequencing

value: Lineage negative, c-Kit positive hematopoietic bone marrow progenitors

value: Mx1-Cre Tet2 fl/fl


title: DNMT3A-F755S

description: Single cell RNA sequencing

source_name: Lineage negative, CD34+ hematopoietic bone marrow progenitors

value: Lin-; CD34+


title: DropSeq_WT2_Lin_c-Kit_4wk

description: Single cell RNA sequencing


title: CON2_H3LNLDMXX


title: control tongue at P20, biological rep 2

description: Sample WT-B2


title: AAV_library_3

city: Heidelberg

first: Ana

last: Martin-Villalba

address: Im Neuenheimer Feld 280

department: Molecular Neurobiology

country: Germany

institute: German Cancer Research Center

description: 157 AAV serotypes

data_processing:
extracting reads that match the amplicon via regular expression (GNU grep)
counting 15bp barcodes (Python 3.5, GNU/unix tools)
matching barcodes to AAVs (R 3.6.0)
normalization by input and ranking by barcode proportion (R 3.6.0)
Genome_build: not applicable
Supplementary_files_format_and_content: standard CSV tables containing the observed barcode counts

source_name: subventricular zone

growth_protocol: The lateral v-SVZ was micro-dissected as whole mount as previously described 50. Tissue of single mice was digested with trypsin and DNase according to the guidelines of the Neural Tissue Dissociation Kit (T) (Miltenyi Biotec) using a Gentle MACS Dissociator (Miltenyi Biotec). Cells were cultured and expanded for 8-12 days in Neurobasal medium (Gibco) supplemented with B27 (Gibco), heparin (Sigma), glutamine (Gibco), Pen/Strep (Gibco), EGF (PromoKine) and FGF (PeloBiotech).

extract_protocol:
RNA was isolated by using the PicoPure RNA Isolation Kit (ThermoFisher). For RNA isolation of in vitro transduced cells, 1500 cultured NSCs per set were lysed in 100 µl extraction buffer. For isolation of FACS-sorted in vivo transduced cells, batches of 500 cells or less were generated and were lysed in 100 µl extraction buffer. Up to 6 batches (2500 cells) were obtained per set, depending on the cell type (Table S2, Table S3). The cell-containing extraction buffer was incubated for 30 min at 42°C and the lysate was frozen at -80°C to increase the amount of isolated RNA. The cell lysate was mixed 1:1 with 70% ethanol and RNA was extracted according to the guidelines of the PicoPure RNA Isolation Kit (ThermoFisher). RNA was dissolved in 11 µl nuclease-free H2O. The cDNA synthesis was performed as described in 52 by using Locked Nucleic Acid-TSO (Table S1) and by using either 14 cycles for in vitro cultured NSCs, 15 cycles ( >300 cells per batch) or 16 cycles (<300 cells per batch) for FACS-sorted in vivo transduced cells for the cDNA enrichment step. After purification 52 using AMPure XP beads (Beckman Coulter), cDNA was dissolved in 10µl H2O.
Barcodes were PCR-amplified by using 10 ng cDNA as input material. Phusion High-Fidelity DNA Polymerase (ThermoFisher) was used according to its manual in combination with 10 mM dNTPs (ThermoFisher) and the Bar_fwd and Bar_rev primers (Table S1). The PCR was performed on a T100 Thermal Cycler (Bio Rad) with the following conditions: initiation for 30 s at 98°C, followed by 35 cycles of denaturation for 10 s at 98°C, annealing/extension for 20 s at 72°C and a final step for 5 min at 72°C. The PCR amplicon was AMPure XP bead-purified (Beckman coulter) 52 with a bead:sample ratio of 0.8:1 in the first round and 1:1 in the second round. Next, 10 ng or 15 ng (library #1 or #3, respectively) of PCR amplicon was used for NGS library preparation with the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina (NEB) for samples from library #1 and the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) for samples from library #3. Multiplexed libraries were generated by following the manual and by using the NEBNext Multiplex Oligos for Illumina (NEB). All multiplexed samples for library #1 and library #3 are listed in Table S2 and Table S3. For sequencing, up to 50% of PhiX were spiked in.

treatment_protocol: For RNA sequencing, NSCs were seeded in 48-well plates (Greiner Bio-One) and incubated overnight. AAV library #1 or library #3 (multiplicity of infection (MOI): 10000) were added to the media and remained for the duration of seven days. For IHC, Labtek chambers (ThermoFisher) were coated with PDL (Sigma) / Laminin (Sigma) and NSCs were seeded at a density of 2x104 cells per cm2 overnight. AAVs were added (MOI: 10000) and remained in the media for 7 days.

value: brain

tag: Sex

value: male


title: AAV_library_1

description: 91 AAV serotypes


title: DropSeq_WT2_4wk

description: Single cell RNA sequencing

value: Lineage negative hematopoietic bone marrow progenitors

value: Lin-


title: 6foxm1-nestin

tag: developmental stage


title: FTO-sh2-2

city: DUARTE

first: Lei

last: Dong

state: CA

address: 1500 DUARTE RD

institute: City of Hope

description: shFTO rep2

data_processing:
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
the TPM were calculated using RSEM 1.2.31 with default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: RSEM output file containing the expression of genes

source_name: cervix squamous cell carcinoma SiHa cell line

growth_protocol: Human SiHa cell line was grown in MEM media supplemented with 10% FBS and 1% 100 Pen Strep .

extract_protocol:
Total mRNA was extracted using TRIZOL reagent
FastTrack MAG Maxi mRNA isolation kit

treatment_protocol: SiHa cells were havested at 48 h after virius infection.

tag: celll line

value: SiHa

tag: lentivirus

value: FTO shRNA


title: DropSeq_WT1_Lin_c-Kit_4wk

description: Single cell RNA sequencing

tag: tissue

tag: weeks after recombination

tag: sorting strategy


title: CON1_H3LNLDMXX

value: AML cell line


title: Chromium10X_Dnmt3aKO_3_4wk

description: Single cell RNA sequencing

tag: genotype/variation

value: Mx1-Cre Dnmt3a fl/fl


title: Chromium10X_Tet2KO_3_4wk

description: Single cell RNA sequencing


title: Hs PNC p53NULL_1

data_processing:
mRNA: Paired-end sequenced reads were checked by FastQC and aligned to the reference genome, UCSC mouse mm10 or GENCODE human GRCh38, using TopHat2. HTSeq was then used to estimate the number of reads that are mapped to each gene. The R Bioconductor package edgeR was applied to normalize the data using the trimmed mean of M (TMM) method and to determine significant differentially expressed genes between groups.
miRNA: Single-end sequenced reads were checked by FastQC. The QIAseq miRNA Library specific 3′ adapter sequence was trimmed from the 3’ ends of sequenced reads using cutadapt. The trimmed reads were then aligned to the reference genome, human GRCh38, using BWA. FeatureCounts was used to estimate the number of reads that are mapped to each mature miRNA. The R Bioconductor package edgeR was applied to normalize the data using the trimmed mean of M (TMM) method and to determine significant differentially expressed miRNAs between groups.
Genome_build: UCSC mouse mm10 or GENCODE human GRCh38
Supplementary_files_format_and_content: tab-delimited files include raw read count values for each sample (output of HTSeq-count or FeatureCounts)

extract_protocol:
RNa and miRNA were extracted in vitro or ex vivo using qiagen kits per manufacturer's instruction
mRNA: Illumina Compatible low input RNA libraries were prepared using the Smart-Seq V4 Ultra Low Input RNA (Clontech) and KAPA HyperPlus Library Preparation kits. The libraries were then sequenced on the Illumina HiSeq4000 sequencer using the 76bp paired end format.
miRNA: Illumina compatible miRNA libraries were prepared using the QIAseq miRNA Library Kit (Qiagen). The libraries were then sequenced on the Illumina NextSeq500 Sequencer using the 76nt SR High-Output flow cell.

value: Human DRG neurons


title: control tongue at P20, biological rep 1

description: Sample WT-B1

tag: genotype

value: tongue


title: Krt13 KO tongue at P0, biological rep 5

description: Sample KO-A5

source_name: Krt13 KO tongue at P0

value: Krt13 KO


title: Hs PNC p53NULL_3


title: Krt13 KO tongue at P0, biological rep 3

description: Sample KO-A3


title: FTO-shNC-2

description: shNC rep2

value: shRNA control


title: FTO-shNC-1

description: shNC rep1


title: Krt13 KO tongue at P0, biological rep 4

description: Sample KO-A4


title: Hs PNC p53NULL_2


title: Chromium10X_WT4_4wk

description: Single cell RNA sequencing