title: ZK_P_hmC_4

city: Atlanta

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

data_processing:
Paired end sequencing reads of MeDIP-seq library and 5hmC-Seal-seq library were firstly mapped to human genome (hg38) by Bowtie 2 (2.4.4) (2) with “--no-mixed --no-discordant”.
Aligned reads in bam file were sorted by genomic coordinate by samtools.
Peaks for were identified by MACS2 version 2.2.6 with their corresponding input bam file
Assembly: mm9
Supplementary files format and content: narrowPeak
Library strategy: 5hmC-Seal-seq

source_name: NeuN Positive

growth_protocol: NeuN positive and NeuN negative cells were isolated from P30 mouse cortex

extract_protocol:
DNA was extracted by adding equal volume of buffered phenol:chloroform:isoamyl alcohol (25:24:1 ratio) and centrifuged in Phase-Lock tubes at 15,000 RPM at room temperature. Supernatant was transferred to clean tubes. An equal volume of isopropanol was then added to the supernatant and mixed well at room temperature to precipitate the DNA. The DNA was then centrifuged at 10,000g for 10 minutes at room temperature, and then washed in 70% ethanol. After all ethanol was removed, the DNA pellet was eluted in nuclease-free water and incubated at 55 for 1 hour before storing at -20.
5mg of genomic DNA was sonicated to 300-400 base pairs and 5hmC containing fragments were glucosylated (T4 phage ß-glucosyltransferase enzyme and UDP-6-N3-glucose). The glucosylated fragments were purified and then biotinylated (disulfide biotin linker) and pulled down with Dynabeads MyOne Streptavidin C1 beads. The 5hmC fragments were released from the beads using dithiothreitol and purified for a final time. DNA fragments were eluted in nuclease-free water and quantified by Qubit.

treatment_protocol: Maternal mouse were treated by ZIKA virus or PBS as Mock control

value: treated with ZIKA virus

value: NeuN Positive


title: patient_5IgG_MBC_Low_affinity_TH media

status: Public on Oct 25 2023

type: SRA

city: Indianapolis

first: Prasida

last: Holla

state: IN

address: 1044 W walnut St

department: Pediatric Infectious Diseases

country: USA

institute: Indiana University School of Medicine

library_source: transcriptomic

data_processing:
Raw NGS reads were trimmed to remove adapters and low-quality regions using Trimmomatic v0.33
Trimmed reads were aligned to the human hg38 reference genome and Gencode release 26 annotation using STAR v2.5.2b
Read and alignment quality were assessed using MultiQCv1.1 to aggregate QC metrics from Picard (http://broadinstitute.github.io/picard/), FastQC v0.11.5, FastQ screen v0.9.3 and RseQC v1.1.8
Gene-level expression was quantified using RSEM v1.3.0
Assembly: Human - hg38 / Gencode Release 26
Supplementary files format and content: Text files generated using RSEM v1.3.0  containing raw counts

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood monouclear cell (PBMC)

growth_protocol: Peripheral blood draw was done, and mononuclear cells were isolated by ficoll gradient purification. B cells were further sorted into subsets by staining with fluorophore conjugated antibodies and FACS

extract_protocol:
Cells were lysed with RLT buffer (Qiagen) and RNA was isolated using the Qiagen AllPrep 96 kit as per manufacturer's instructions except treatment with 27 units DNAse I to removegenomic DNA contamination. cDAN was synthesized using SMART-Seq v4 Ultra Low Input RNA kit
600 pg sheared cDNA was used as input into the low Inout Library Prep kit v2 (Clonetech/Takara Bio) and prepared following manufacturer's protocol Final NGS libraries were assessed on a BioAnalyzer 2100 using High Sensitivity Chips. The libraries were normalized to 0.5 nM, pooled equally and prepared for sequencing on the NextSeq (illumina, San Diego) following manufacturer's guidelines  for two mid-output 2X76 cycles.

treatment_protocol: Sorted B cell subsets (Naïve, IgM MBC and IgG MBC) from each patient were stimulated under different conditions. Cells were incubated on a planar lipid bilayer embedded with either low affinity or high affinity antigens (Low_affinity and High_affinity respectively). As a control, cells were incubated with no antigen (Unstimulated). Cells were also stimulated with low- or high affinity antigens in the presence of a cocktail (IL-4+IL-21+anti-CD40 antibody) that mimics T cell help in vitro (labeled T cell or TH media). Cells were treated with T cell stimulation/ TH media only, or in addition to low- or high affinity antigens on PLB (Low_affinity+TH media and High_affinity+T cell respectively).

tag: tissue

value: peripheral blood monouclear cell (PBMC)

tag: cell type

value: B lymphocyte

tag: genotype

value: WT

tag: treatment

value: Low_affinity+TH media


title: HUVECs, VmiR-1 Input 3

city: New Haven

first: Asawari

last: Korde

state: CT

address: 300 Cedar street

institute: Yale University School of Medicine

data_processing:
The reads were trimmed using trimmomatic.
The reads were aligned to the reference genome hg19 using HiSat2.
The counts were generated using htseq.
Assembly: hg19
Supplementary files format and content: csv file with genes in the rows and samples in columns.

source_name: Human umbilical vein endothelial cells

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were purchased from the Yale Vascular Biology and Therapeutics tissue culture core facility, cultured in the M199 (Gibco) medium containing 20% FBS (Heat inactivated, Gibco), 1% ECGS, and 1% penicillin, and streptomycin.

extract_protocol:
The beads were directly added to TRIzol after washing three times (wash buffer: 0.1M NaP pH 8.0) and the RNA extracted with Phenol-chloroform extraction protocol.
RNA libraries were prepapred using low-input kit

treatment_protocol: Cells were transduced with lentiviruses containing vascular-specific miR-1 (V-miR-1) overexpression or empty (V-ctrl) vector for 36-48 hours. Cells were checked for fluorescence and then collected by scraping in cold PBS, spun down (300 g for 10 min at 4°C), and resuspended in 250 µl of cold lysis buffer (10 mM Hepes, pH 7.4, 150 mM KCl, 3 mM MgCl2, 0.2 mM DTT, 10% glycerol, 0.5% NP-40, and 1 mM PMSF). Part of this lysate was kept as “input fraction,” and the rest was immunoprecipitated with anti-Ago2 antibody (Clone 11A9, Cat # SAB4200085, Sigma-Aldrich) and dynabeads protein A (Cat# 10002D, Life Technologies).

value: Human umbilical vein endothelial cells

value: V-miR-1 overexpression

tag: rip antibody


title: Subcutaneous tumor treated with IL-27 vector [LCS9574_TIL27_1]

city: West Lafayette

first: Marxa

middle: Leao

last: Figueiredo

address: 625 Harrison St

department: Basic Medical Sciences

institute: Purdue University

data_processing:
Cutadaptand perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases, followed by sequence quality verification using FASTQC.
HISAT2 was used to map reads to the human genome.
The mapped reads of each sample were assembled using StringTie. All transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie and ballgown was used to estimate the expression levels of all transcripts.
StringTie was used to perform expression level for mRNAs by calculating FPKM. mRNAs differential expression analysis were performed by R package DESeq2.
Assembly: GRCh38 (Ensembl release-101)
Supplementary files format and content: Tab delimited text file containing raw counts for each sample

organism: Mus musculus

growth_protocol: Mouse adenocarcinoma cell line TC2Ras was cultured in Dulbecco’s modified Eagle’s medium–nutrient mixture F-12 (DMEM-F12) (Gibco, Waltham, Massachusetts) supplemented with 10% FBS (Hyclone, Cytiva, Marlborough, MA) and 1% antibiotic-antimycotic (Anti-Anti) (Gibco). Male C57/BL6 mice (8-10 weeks of age) were obtained from Envigo. Mice were handled in accordance with an approved study protocol by the Purdue Animal Care and Use Committee (PACUC). TC2ras cells were prepared for implantation by adding trypsin (0.25% Trypsin-EDTA, Gibco, Billings, MT) to the cells and washing with sterile 1x DPBS. The pellet was resuspended in 1x DPBS at an appropriate concentration. For the intratibial model, 105 TC2Ras-Luc cells were injected in each tibia in 10ul sterile 1xDPBS. For the subcutaneous model, 3x105 TC2Ras cells were injected in each flank in 50uL sterile 1xDPBS. Implantation was performed under 2% inhaled isoflurane anesthesia delivered by high-flow vaporizer (VetFlo, Kent Scientific, Torrington, CT). In the subcutaneous model, tumors were harvested one week post implantation for RNA-sequencing analysis. In the intratibial model, three mice per group were euthanized 14 days post implantation, whereas the rest of the mice (n=4) were allowed to progress to the ethical endpoint. Post-euthanasia, tumors were collected in RNAlater (Invitrogen, Waltham, MA) and preserved for further RNA isolation and analysis. In short, RNA was isolated using RNeasy kit (Qiagen) according to manufacturer's protocol. Poly(A) RNA sequencing library was prepared following Illumina's TruSeq-stranded-mRNA protocol and conducted by LC Sciences (Houston, TX, USA). Poly(A) tail-containing mRNAs were purified using oligo-dT Briefly, magnetic beads with two rounds of purification, and fragmented using divalent cation buffer at elevated temperature. Quality control analysis and quantification of the sequencing library were performed using an Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000. For transcript assembly and estimating transcript expression levels, software is described by Figueiredo et al. (2020) (21). For differential expression analysis of mRNAs, StringTie was used by calculating fragments per kilobase million (FPKM). The differentially expressed mRNAs were selected with log2 (fold change) > 1.5 or log2 (fold change) < -1.5 and with statistical significance (p < 0.05) by edgeR.

extract_protocol:
tumors were collected in RNAlater (Invitrogen, Waltham, MA) and preserved for further RNA isolation and analysis. In short, RNA was isolated using RNeasy kit (Qiagen) according to manufacturer's protocol.
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip.

value: tumor

tag: cell line

value: Prostate adenocarcinoma


title: NLS_Input_Mock_2

city: Cleveland

first: Soon Yeul

last: Yi

state: OH

address: CWRU Wood Research Building W127A, 2109 Adelbert Rd,

department: Biochemistry

institute: Case Western Reserve University

data_processing:
*library strategy: CLIP-seq
Raw fastq files were first treated with fastX collapser to remove duplicated reads. Then, using CTK stripBarcode.pl the 7nt unique molecular identifier sequence at the 5'end was removed. Next, fastX trimmer and clipper was used to remove the barcode, spacer (GGG), and L32 sequence. Processed reads were then mapped to GRCh38.p14 genome using Bowtie2 (seed length 15nt, allow no mismatch). Mapped output (.sam) files were further processed using samtools (view, sort, index) and bedtools (bamtobed). Lastly, PCR duplicates were collapsed using CTK tag2collapse.pl.
Processed final bed files from each library were all combined into a single bed file and HOMER program was used to call peaks using makeTagDirectory and findPeaks (options: -o auto -style factor -L 2 -localSize 10000 -strand separate -minDist 50 -size 20 -fragLength 25). Finally, read counts per peak were normalized by the respective mapped depth of each library to generate the final normalized peak matrix.
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text file containing peak coordinates, mapped-depth normalized read counts per peaks per libraries, peak annotation, and replicate counts.

growth_protocol: Huh-7.5 cell lines were grown and maintained at 37 °C and 5% CO2 in DMEM supplemented with 0.1 mM nonessential amino acids and 5% FBS.

extract_protocol:
Cell pellets were lysed with PBS lysis buffer (1x PBS, 0.1% SDS, 0.5% NaDoc, 0.5% NP-40, 1 protease inhibitor tablet (Roche)) for 10 minutes on ice. Lysate was then treated with RQ1 DNase (Promega) for 5 minutes at 37'C with shaking at 1100RPM.  The lysates were then briefly treated with RNase I at 1:100 or 1:5000 dilutions at the same condition as DNase treatment. Lysates were clarified by centrifuging on tabletop 4'C centrifuge for 10 minutes. HuR IP was performed overnight at 4'C with nutation, with an additional streptavidin capture step for coCLIP samples. Immunoprecipitated samples were labeled with radioactivity (gamma-32P-ATP (Revity)) and ran on SDS-PAGE. The gels were transferred to a nitrocellulose membrane, and bands 10-30kDa above the HuR (37kDa) were excised. The excised membranes were treated with proteinase K (Roche) to release the protein-bound RNAs from the membrane.
CLIP footprints were reverse-transcribed using the BrdU incorporation and bead-capture strategy described previously (PMID: 24613350).

treatment_protocol:
Cellular stress was induced by treating cells with 0.5mM sodium arsenite for 45 minutes. At 30 minutes prior to harvest, cells were prepared for proximity labeling  by incubating samples with 0.5mM biotin phenol for 30 minutes. Subsequently, the APEX reaction was initiated with 1mM hydrogen peroxide for 1 minute. After labeling, the reaction was stopped using ice cold quencher solution (10mM sodium ascorbate, 5mM Trolox in PBS). Quencher solution was replaced by ice-cold PBS for crosslinking using 254nm UV light, on ice, for a dose of 400mJ/cm^2 and a dose of 200mJ/cm^2. Samples were scraped into tubes, centrifuged and cell pellets stored at -80C until use.
Cellular fractions were acquired using a fractionation protocol described previously (PMID:26240403).

value: Hepatocellular Carcinoma

value: APEX-NLS

value: Mock

tag: apex-reaction

value: Yes

tag: hur antibody

value: HuR 3A2 (Santa Cruz, cat. #sc-5261)


title: Pronuclei 140min, +123nM CTCF, Smc3 ChIP-Seq

city: Vienna

first: Roman

middle: R

last: Stocsits

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

library_source: genomic

data_processing:
Basecalling software: Illumina RTA
ChIP-seq reads were mapped uniquely with 0 to 2 errors against the Xenopus laevis v9.2 genome as well as the Mus musculus mm9 genome assembly using  bowtie version 1.2.2.
Peaks were called using the intersection of the peaks called using MACS version 1.4.2 with an assumed mappable genome size of 2.5e9 and a p-value threshold of 1e-10, and MACS v2.2.5 with default parameters.
TDF files for IGV and Juicebox browsers were generated from wig files using igvtools toTDF
bedGraph files (*.bedGraph) have been built using MACS v2.2.5 with -B option
Assembly: Xenopus laevis v9.2, mm9
Supplementary files format and content: bedGraph files for ChIP-Seq signal distributions represent genomic distribution of the factors as described in the paper, they can be used for visualization in IGV and Juicebox browsers
Supplementary files format and content: bed files describe genomic location and can be used as coordinates and for visualization in IGV and Juicebox browsers

molecule: genomic DNA

organism: Xenopus laevis

source_name: pronuclei generated by incubating de-membranated Xenopus laevis sperm in Xenopus egg extract for 140 min, with addition of recombinant CTCF protein

growth_protocol: Xenopus laevis XL177 cells were cultured at 16-20º C in medium containing 65% Leibovitz’s L-15 (Thermo Fisher Scientific, #11415064), 15% FBS (Gibco, 10270106), 20% H2O, 100 U/ml Penicillin and 100 µg/ml Streptomycin (Sigma, P0781). Pronuclei were generated by incubating de-membranated Xenopus laevis sperm in Xenopus egg extract.

extract_protocol:
Samples were crosslinked with 1% formaldehyde for 10 minutes at room temperature. After quenching with glycine and cell lysis with SDS, chromatin was sonicated using a Bioruptor sonication device.
ChIP was performed as previously described (Wendt et al., Nature 2008), and the following antibodies were used: anti-Smc3 (Bethyl, A300-060A), anti-CTCF (Millipore, 07-729). The DNA samples were submitted for library preparation and Illumina deep sequencing on HiSeq 2500 SR50 to the Next Generation Sequencing Facility at Vienna BioCenter Core Facilities (VBCF), member of the Vienna BioCenter (VBC), Austria.

treatment_protocol: No treatment was applied to XL177 cells. Some of the pronuclei samples were treated by adding recombinant CTCF protein.

tag: antibody

value: anti-Smc3 (Bethyl, A300-060A)


title: patient_5IgM_MBC_Low_affinity_TH media


title: Mouse sperm swim-up

data_processing:
Basecalling software: Illumina RTA
Hi-C preprocessing of PE fastq files using hicup version 0.7.1
bowtie2 version 2.2.5 mapping against hg19, mm9 and Xenopus laevis v9.2 reference assemblies
truncating, mapping, filtering and deduplicating of Hi-C raw data through hicup process, conversion to input files for HOMER software and juicer tools.
Analyzing Hi-C data with Homer for TAD detection and insulation scores.
juicer tools pre version 1.22.01 to derive .hic files (Aiden Lab) containing Hi-C matrices for usage with Juicebox and juicer tools for further Hi-C processing like loop a.k. corner peak calling using hiccups subroutine.
Assembly: hg19, mm9 and Xenopus laevis v9.2
Supplementary files format and content: hic files: contain Hi-C matrices for usage with Juicebox, made with  juicer tools pre command.

source_name: mouse sperm isolated from cauda epididymides by swim-up

growth_protocol: Xenopus laevis XL177 cells were cultured at 16-20º C in medium containing 65% Leibovitz’s L-15 (Thermo Fisher Scientific, #11415064), 15% FBS (Gibco, 10270106), 20% H2O, 100 U/ml Penicillin and 100 µg/ml Streptomycin (Sigma, P0781). Pronuclei were generated by incubating de-membranated Xenopus laevis sperm in Xenopus egg extract. Human, mouse and frog sperm cells were isolated by density gradient centrifugation or swim-up.

extract_protocol:
Samples were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Hi-C was performed according to the previously described in situ Hi-C protocol (Rao et al., Cell 2014).
Hi-C libraries were prepared according to the previously described in situ Hi-C protocol (Rao et al., Cell 2014).

treatment_protocol: Some of the frog sperm samples were de-membranated. Two of the XL177 samples were crosslinked in either PBS or Xenopus egg extract (ULSS). Some of the pronuclei samples were treated by adding recombinant CTCF protein.

value: mouse sperm


title: Pooled GEX library for 9 brain organoids replicate#2

first: Catarina

last: Martins-Costa

address: Dr.-Bohr-Gasse 3

institute: IMBA - Institute of Molecular Biotechnology of the OeAW

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Two CellPlex 10X libraries (named "40k" and "50k" in the metadata table) with the same CMOs were sequenced. ScRNA-seq reads were processed with cellranger multi v6.0.1 using the prebuild 10X GRCh38 reference refdata-gex-GRCh38-2020-A and setting include-introns to true. Further processing such as dimensionality reduction, clustering, and visualization of the scRNA-seq data was performed in R v4.2.2 with Seurat v4.2.0. Cells identified as stressed using Gruffi (Vertesy et al., 2022) were removed, cells with 800 to 6000 detected genes, less than 6% mitochondrial and 30% ribosomal content were retained.
Assembly: hg38
Supplementary files format and content: Seurat object containing counts and metadata of the filtered object (removal of non-telencephalic clusters, Gruffi, and quality filter), in .rds format
Supplementary files format and content: Tab-separated CMO, count, and metadata files

source_name: Brain organoid

growth_protocol: Human telencephalic brain organoids.

extract_protocol:
Multiplexing was performed using the 10x Genomics 3’ CellPlex Kit.
Library preparation was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

treatment_protocol: Modes of exogenous ECM addition: droplet embedding ("drop"), liquid embedding ("liq"), and no exogenous addition ("no").

value: Brain organoid

value: H9 ESCs

value: Neural progenitors and neurons

tag: age

value: 120 days


title: ZK_P_hmC_1

value: treated with ZIKA virus

value: NeuN Positive


title: HUVECs, VmiR-1 Ago 1

value: Human umbilical vein endothelial cells

value: anti-Ago2 antibody (Clone 11A9, Cat # SAB4200085, Sigma-Aldrich)


title: NLS_Enrich_Arsenite_4

value: Sodium Arsenite


title: patient_5IgG_MBC_Low_affinity

value: peripheral blood monouclear cell (PBMC)

value: B lymphocyte

value: WT


title: mouse embryonic fibroblasts, Smc3 ChIP-Seq, replicate 3

source_name: mouse embryonic fibroblasts

value: mouse embryonic fibroblasts


title: HUVECs, Vctrl Ago 3

value: control


title: HUVECs, Vctrl Input 3


title: patient_5IgG_MBC_High_affinity


title: NLS_Enrich_Mock_4

value: Hepatocellular Carcinoma

value: APEX-NLS

value: Mock

value: Yes

value: HuR 3A2 (Santa Cruz, cat. #sc-5261)


title: NES_Input_Mock_2

value: APEX-NES


title: patient_5Naive_Low_affinity_TH media

value: Low_affinity+TH media


title: NLS_Enrich_Mock_3


title: patient_5Naive_Low_affinity


title: NLS_Enrich_Arsenite_3


title: NLS_Input_Arsenite_2


title: patient_5IgG_MBC_High_affinity_TH media

value: High_affinity+ T cell


title: ZK_N_hmC_3

source_name: NeuN Negative

value: treated with ZIKA virus

value: NeuN Negative


title: MWIK_1

city: San Francisco

first: Jun Hyung

last: Sin

state: CA

address: 513 Parnassus Ave S-1076

department: Pediatrics

institute: University of California, San Francisco

data_processing:
FASTQ files were converted into single cell matrices using 10X Cell Ranger and were transformed into a Seurat object using the Seurat package in R
Initial exclusion criteria included features that were present in less than 100 cells and cells where less than 1000 features were detected

source_name: Thymus

extract_protocol:
Freshly sorted EPCAM+Ly51- mTECs were collected in 0.04% BSA in PBS, then sent to the UCSF Genomics core for processing
Per UCSF Genomics Core
Single cells were captured using the 10X Chromium microfluidics system and cells were encapsulated and barcoded cDNA libraries were prepared using the single-cell 3'mRNA kit (10X Genomics). Single cell libraries were sequenced using a NovaSeq 6000 (lllumina)

value: Thymus

value: medullary thymic epithelial cell

value: Foxn1-Cre(+) Ikaros+/fl


title: HUVECs, Vctrl Input 1

value: Human umbilical vein endothelial cells


title: patient_5IgM_MBC_High_affinity_TH media

value: peripheral blood monouclear cell (PBMC)

value: B lymphocyte

value: WT


title: ZK_P_hmC_3

value: NeuN Positive


title: ZK_P_hmC_2


title: HUVECs, VmiR-1 Input 1

value: V-miR-1 overexpression


title: patient_5IgG_MBC_TH media

value: T cell help


title: Human sperm DGC biol. rep. 2

source_name: human sperm isolated from ejaculate by discontinuous density gradient centrifugation (DGC)

value: human sperm


title: ZK_N_hmC_1


title: Mock_P_hmC_4

value: mock


title: patient_5Naive_TH media


title: mouse embryonic fibroblasts, Smc3 ChIP-Seq, replicate 2

value: mouse embryonic fibroblasts

value: anti-Smc3 (Bethyl, A300-060A)


title: ZK_N_hmC_4


title: patient_5Naive_High_affinity_TH media

value: High_affinity+ T cell


title: patient_5IgM_MBC_High_affinity


title: HUVECs, Vctrl Input 2

value: control


title: patient_5Naive_High_affinity


title: patient_5IgG_MBC_Unstim

value: Unstimulated


title: ATAC_Wt4R

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

data_processing:
ATAC-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to mouse assembly mm10 using bowtie2 (v2.2.2) with default parameters.
To create density files, read overlap density was calculated with an extension of 0 bp and the signal was then normalized to the size factor calculation in DESeq2 and created using the BEDTools suite.
Assembly: mm10
Supplementary files format and content: BigWig files containing normalized read density.

source_name: cerebellum

extract_protocol:
SmoM2 animals between 6-16 weeks and SmoM2-Kmt2dCf/Cf animals between 5-8 weeks were used for sequencing experiments. The tumor tissue of the brain was macro-dissected from the surrounding normal brain tissue, dissociated and processed using the Papain Kit (Worthington Biochemical Corporation) and the manufacturer’s protocol. The GFP+ tumor cells were isolated by fluorescence activated cell sorting in the MSKCC Flow Cytometry Core. From each sample 70,000 cells were processed for ATAC-seq, and 1-5 million cells were frozen at -80°C for RNA-seq. Frozen cell pellets of 100,000-3 million cells from spinal cord metastatic tumors and 1-5 million cells from the primary brain tumors prepared as described above were used for RNA sequencing.
Samples were eluted in 20uL of elution buffer and PCR-amplified using the NEBNext 2X Master Mix (NEB) for 10 cycles and sequenced on a HiSeq 2500 (Illumina).

tag: disease state

value: primary medulloblastoma

value: cerebellum

tag: anatomic location

value: right hemisphere

value: granule cell precursors

value: SmoM2 overexpression


title: ATAC_Wt7L

value: left hemisphere


title: HUVECs, VmiR-1 Input 2

value: Human umbilical vein endothelial cells


title: ATAC_Wt6R


title: ZK_N_hmC_2

value: treated with ZIKA virus

value: NeuN Negative


title: Mock_P_hmC_2

value: NeuN Positive


title: Human sperm DGC biol. rep. 4

value: human sperm isolated from ejaculate by discontinuous density gradient centrifugation (DGC)

value: human sperm


title: HPMEC cells treated with TNF replicate 2

city: West Haven

first: Francesc

last: Lopez

department: Department of Genetics

institute: Yale University

description: total RNA

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. For each read, we trimmed the first 6 nucleotides and the last nucleotides at the point where the Phred score of an examined base fell below 20 using in-house scripts. If, after trimming, the read was shorter than 45-bp, the whole read was discarded.
Trimmed reads were mapped to the human reference genome (hg19) with a known transcriptome index (UCSC Known Gene annotation) with Tophat v2.1.1 using the very-sensitive preset, first strand library type, and providing the corresponding gene model annotation. Only the reads that mapped to a single unique location within the genome, with a maximum of two mismatches in the anchor region of the spliced alignment, were reported in these results.
We tallied reads aligning to exons of genes with the program HTSeq v0.6.1p1.
Tophat alignments were then processed by Cuffdiff to obtain differential gene expression using first strand library type, providing gene model annotation and the genome sequence file for detection and correction of sequence-specific bias that random hexamer can cause during library preparation.
Assembly: hg19
Supplementary files format and content: Tab-delimited file including raw read counts produced with HTSeq v0.6.1p1

source_name: TNF treated HPMEC

growth_protocol: Primary isolated from human lung surgical pathology sampled, cultured in EGM2MV (Lonza), CD31 bead selected, passage 5 grown to 2 days post confluence and stimulated with 0.6 ng/mL TNF for 6 hours

extract_protocol:
Cell monolayers were washed with sterile phosphate buffered saline (PBS, Invitrogen) and total RNA was purified using the RNeasy Mini Kit (Qiagen) with an on-column DNase treatment.
Poly-A, strand-specific RNA library construction was performed by the Yale Center for Genomic Analysis utilizing the TruSeq Library Prep Kit 2.0 per the manufacturers specifications. . Following first-strand synthesis with random primers, second strand synthesis was performed with dUTP for generating strand-specific sequencing libraries.

treatment_protocol: Replicate cultures of HPMECs were maintained for 2 days post-confluence in a 12 well plate (Falcon) and stimulated with 0.5 ng/mL TNF (Invitrogen) for 6 hours or left untreated.

value: Capillary

value: Human pulmonary microvascular endothelial cells, primary isolates

value: Endothelial cell

value: Tumor Necrosis factor


title: Mock_P_hmC_1

value: mock


title: ATAC_Wt5R

value: primary medulloblastoma


title: patient_5IgM_MBC_Unstim

value: peripheral blood monouclear cell (PBMC)

value: B lymphocyte

value: WT

value: Unstimulated


title: patient_5Naive_Unstim


title: Human sperm swim-up replicate 1

source_name: human sperm isolated from ejaculate by swim-up


title: patient_5IgM_MBC_TH media

value: T cell help


title: Mock_N_hmC_4


title: Mock_P_hmC_3


title: Patient_4IgG_MBC_Low_affinity_TH media

value: Low_affinity+TH media


title: ATAC_Wt2R

value: cerebellum

value: right hemisphere

value: granule cell precursors

value: SmoM2 overexpression


title: mouse embryonic fibroblasts, Smc3 ChIP-Seq, replicate 1

value: mouse embryonic fibroblasts

value: anti-Smc3 (Bethyl, A300-060A)


title: HPMEC cells treated with TNF replicate 1

description: total RNA

value: Capillary

value: Human pulmonary microvascular endothelial cells, primary isolates


title: Mock_N_hmC_3

value: NeuN Negative


title: 3D +dTAG rep2

description: 5% MEF (mouse embryonic fibroblast) cells added for calibration purposes

data_processing:
Basecalling software: Illumina RTA
Aligment against hg19 reference assembly: bowtie version 1.2.2 , reads are trimmed and mapped uniquely to genome with 0 to 2 errors
ChIP-Seq  peak calling using MACS version 1.4.2 and version 2.2.5
TDF files for IGV and Juicebox browsers were generated from wig files using igvtools toTDF
Assembly: hg19
Supplementary files format and content: wig files for ChIP-Seq signal distributions represent genomic distribution of the factors as described in the paper.
Supplementary files format and content: tdf files for visualization in IGV and Juicebox browsers

source_name: HeLa Kyoto

growth_protocol: HeLa Kyoto (RRID:CVCL_1922) were got from Narumiya S (Kyoto University; Kyoto; Japan). MEFs were generated in the lab by 3T3 methods.

extract_protocol:
ChIP-Seq: Cells were cross-linked and scrapped of the plate. The DNA was fragmented and the protein of interest was immunoprecipitated with Flag antibody (cell signaling 14793S); Adaptors were ligated to the 5' and 3' ends and the library was prepared for Illumina sequencing by a qPCR amplification step.
Libraries were prepared for sequencing using standard Illumina protocols.

value: HeLa Kyoto

value: human cervical cancer cells

value: doxycycline (+)/Auxin (+)/dTAG(+)


title: HPMEC cells treated with TNF replicate 3

description: total RNA

value: Endothelial cell

value: Tumor Necrosis factor


title: ATAC_Wt1R

value: primary medulloblastoma


title: ATAC_Hm7R

value: SmoM2 overexpression, Kmt2d KO


title: Patient_4IgM_MBC_Low_affinity_TH media

value: peripheral blood monouclear cell (PBMC)

value: B lymphocyte

value: WT

value: Low_affinity+TH media


title: ATAC_Wt3L

value: cerebellum

value: left hemisphere

value: granule cell precursors

value: SmoM2 overexpression


title: ATAC_Hm7M

source_name: spinal cord

value: medulloblastoma spinal metastasis

value: spinal cord

value: spine

value: spinal metastasis


title: 3D -dTAG rep2

value: HeLa Kyoto

value: human cervical cancer cells

value: doxycycline (+)/Auxin (+)


title: Patient_4Naive_Low_affinity_TH media


title: Patient_4IgG_MBC_Low_affinity


title: Mock_N_hmC_2

value: mock

value: NeuN Negative


title: Mock_N_hmC_1


title: WT +dTAG rep2

value: doxycycline (+)/Auxin (+)/dTAG(+)


title: WT -dTAG rep2


title: Patient_4IgM_MBC_Low_affinity

value: peripheral blood monouclear cell (PBMC)

value: B lymphocyte


title: ATAC_Hm6R

value: primary medulloblastoma

value: right hemisphere

value: SmoM2 overexpression, Kmt2d KO


title: dox- rep2

value: doxycycline (-)


title: ZK_P_mC_3

description: Illumina Novaseq X plus

data_processing:
Paired end sequencing reads of MeDIP-seq library and 5hmC-seal-seq library were firstly mapped to human genome (hg38) by Bowtie 2 (2.4.4) (2) with “--no-mixed --no-discordant”.
Aligned reads in bam file were sorted by genomic coordinate by samtools.
Peaks for were identified by MACS2 version 2.2.6 with their corresponding input bam file
Assembly: mm9
Supplementary files format and content: narrowPeak

extract_protocol:
DNA was extracted by adding equal volume of buffered phenol:chloroform:isoamyl alcohol (25:24:1 ratio) and centrifuged in Phase-Lock tubes at 15,000 RPM at room temperature. Supernatant was transferred to clean tubes. An equal volume of isopropanol was then added to the supernatant and mixed well at room temperature to precipitate the DNA. The DNA was then centrifuged at 10,000g for 10 minutes at room temperature, and then washed in 70% ethanol. After all ethanol was removed, the DNA pellet was eluted in nuclease-free water and incubated at 55 for 1 hour before storing at -20.
3mg of genomic DNA was sonicated to 300-400 base pairs using a Covaris focused ultrasonicator. The DNA fragments were then subjected to end repair, A-tailing, adaptor ligation and USER digestion using the NEBNext Ultra II DNA Library Prep kit for Illumina (New England BioLabs, E7645S) according to the manufacturer’s protocol. Following USER digestion and purification, DNA was denatured for 10 minutes at 95°C and immunoprecipitated overnight at 4°C with 4mL of either 5mC antibody (Active Motif, 39649) or IgG antibody (Sigma 12-371) in IP buffer (500mM Tris-HCl, pH 7.4, 750mM NaCl and 0.25% TritonX). The mixture was then incubated with Protein G coated Dynabeads for at least 2 hours at 4°C, washed with ice cold IP buffer and finally washed in ice cold high salt (300mM NaCl) IP buffer. After the final washing, the beads were treated with 200mL digest buffer (1X TE Buffer, pH 7.4, 0.25% SDS, 0.25% Proteinase K (2.5mg/mL)) and shaken at 1000rpm for 2 hours at 55°C. The methylated DNA was recovered by phenol:chloform:isoamyl alcohol (25:24:1) extraction followed by precipitation in 3X volume of 100% ethanol supplemented with 3mL glycogen(5mg/mL) and 15mL NaAC pH 5.2 overnight at -20°C. The next day, the DNA was pelleted and washed with 75% ethanol and dissolved in nuclease-free water. Illumina indexes were added, PCR enriched and purified using the NEBNext Ultra II DNA Library Prep kit for Illumina following the manufacturer’s protocol.

value: treated by ZIKA virus

value: NeuN Positive

tag: chip antibody

value: Anti 5mC


title: ATAC_Hm6M

value: medulloblastoma spinal metastasis

value: spinal cord

value: spine


title: ATAC_Hm7L

value: cerebellum

value: left hemisphere

value: granule cell precursors


title: 3D +dTAG rep1

value: HeLa Kyoto

value: human cervical cancer cells


title: ATAC_Hm6L


title: WT +dTAG rep1

value: doxycycline (+)/Auxin (+)/dTAG(+)


title: ZK_P_mC_1

description: Illumina Novaseq X plus


title: ZK_N_mC_4

description: Illumina Novaseq X plus

value: NeuN Negative


title: ZK_P_mC_2

description: Illumina Novaseq X plus


title: Patient_4IgM_MBC_High_affinity_TH media

value: peripheral blood monouclear cell (PBMC)

value: B lymphocyte

value: WT

value: High_affinity+ T cell


title: 3D -dTAG rep1

value: doxycycline (+)/Auxin (+)


title: Patient_4Naive_High_affinity_TH media


title: WT -dTAG rep1


title: Patient_4IgG_MBC_High_affinity


title: dox- rep1

value: doxycycline (-)


title: Patient_4IgM_MBC_High_affinity


title: ZK_P_mC_4

description: Illumina Novaseq X plus

value: treated by ZIKA virus

value: NeuN Positive

value: Anti 5mC


title: ATAC_Hm4M

value: medulloblastoma spinal metastasis

value: spinal cord

value: spine

value: spinal metastasis

value: SmoM2 overexpression, Kmt2d KO


title: ZK_N_mC_2

description: Illumina Novaseq X plus


title: Patient_4Naive_Low_affinity


title: ZK_N_mC_3

description: Illumina Novaseq X plus


title: ZK_N_mC_1

description: Illumina Novaseq X plus


title: ATAC_Hm3R

value: primary medulloblastoma

value: cerebellum

value: right hemisphere

value: granule cell precursors


title: Patient_4Naive_High_affinity

value: peripheral blood monouclear cell (PBMC)

value: B lymphocyte


title: Patient_4IgG_MBC_High_affinity_TH media

value: WT

value: High_affinity+ T cell


title: ATAC_Hm3M


title: Mock_P_mC_4

description: Illumina Novaseq X plus

value: mock


title: ATAC_Hm2R


title: ATAC_Hm3L

value: left hemisphere


title: ATAC_Hm4R


title: Patient_4IgM_MBC_TH media

value: T cell help


title: Mock_P_mC_2

description: Illumina Novaseq X plus

value: NeuN Positive

value: Anti 5mC


title: Mock_P_mC_3

description: Illumina Novaseq X plus


title: ATAC_Hm2M

value: medulloblastoma spinal metastasis

value: spinal cord


title: Patient_4Naive_TH media


title: Patient_4IgG_MBC_Unstim

value: Unstimulated


title: ATAC_Hm4L

value: SmoM2 overexpression, Kmt2d KO


title: Mock_P_mC_1

description: Illumina Novaseq X plus


title: Mock_N_mC_4

description: Illumina Novaseq X plus

value: NeuN Negative


title: ATAC_Hm2L

value: primary medulloblastoma

value: cerebellum


title: ATAC_Hm1R

value: right hemisphere

value: granule cell precursors


title: Patient_4IgM_MBC_Unstim

value: peripheral blood monouclear cell (PBMC)

value: B lymphocyte


title: Mock_N_mC_3

description: Illumina Novaseq X plus


title: Patient_4Naive_Unstim

value: WT


title: Patient_4IgG_MBC_TH media


title: Patient_3IgM_MBC_Low_affinity_TH media

value: Low_affinity+TH media


title: ATAC_Hm1L

value: left hemisphere


title: Patient_3IgG_MBC_Low_affinity_TH media


title: Mock_N_mC_2

description: Illumina Novaseq X plus

value: mock


title: Mock_N_mC_1

description: Illumina Novaseq X plus


title: mTO, differentiation condition, scRNAseq

city: Shanghai

first: Qinying

last: Ye

address: Haike Road #230

country: China

institute: ShanghaiTech University

description: 10x Genomics

data_processing:
Data were aligned and quantiﬁed using Cell Ranger from the 10X Genomics pipeline with default parameters against the mm10 reference genome.
Contaminating cell doublets were removed using the Scrublet (Wolock et al.) and Doubletdetection (Gayoso et al.) package.
Quality control and filtering.
Assembly: mm10
Supplementary files format and content: h5 file

source_name: blastocyte

growth_protocol: E8.5 mouse placentae were digested with collagenase IV，cell aggregations were resuspended in growth factor-reduced Matrigel, and cultured with maintenance condition medium for 13 days. mTS cells were digested by Accutase ~7min, re-suspended n growth-factor-reduced Matrigel on ice, 25µL drops were plated per well into a 48-well culture plate , 5000-8000 cells/drop, and  cultured with maintenance condition medium for 7 days.

extract_protocol:
Organoids in the maintenance condition were dissociated by accutase incubation for 30-45 min with gentle pipetting every 10 min. Organoids in the differentiation condition were dissociated by the Papain Dissociation System for 30-45 min with gentle shaking/mixing every 10 min. Cell suspensions were passaged through 40 μm cell strainers to remove cell clumps.
Library was used the 10X Genomics with Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 according to manufacturer’s instructions.

treatment_protocol: Differentiate trophoblast organoids, mPO in maintenance condition were first passaged and cultured in maintenance medium without Y27632, FGF4 for 3 days, followed by culturing in the differentiation condition medium  for 16 days. mTO in maintenance condition were first passaged and cultured in maintenance medium without Y27632, FGF4 for 3 days, followed by culturing in the differentiation condition medium  for 17 days.

value: blastocyte

tag: stain

value: trophoblast stem cell

value: wild type


title: RNA_Wt_rep7L

data_processing:
RNA-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to mouse genome assembly mm10 using STAR (v2.4) with default parameters.
Read count tables were created using HTSeq v0.6.1.
Normalization and differential expression analysis were performed with DESeq2.
Assembly: mm10
Supplementary files format and content: Table_RNA_Wt_Hm_HmM_rawCounts.txt: Tab-delimited text file with un-normalized read counts over all genes.

extract_protocol:
SmoM2 animals between 6-16 weeks and SmoM2-Kmt2dCf/Cf animals between 5-8 weeks were used for sequencing experiments. The tumor tissue of the brain was macro-dissected from the surrounding normal brain tissue, dissociated and processed using the Papain Kit (Worthington Biochemical Corporation) and the manufacturer’s protocol. The GFP+ tumor cells were isolated by fluorescence activated cell sorting in the MSKCC Flow Cytometry Core. From each sample 70,000 cells were processed for ATAC-seq, and 1-5 million cells were frozen at -80°C for RNA-seq. Frozen cell pellets of 100,000-3 million cells from spinal cord metastatic tumors and 1-5 million cells from the primary brain tumors prepared as described above were used for RNA sequencing.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kit.

value: SmoM2 overexpression


title: Patient_3Naive_Low_affinity_TH media


title: Patient_3IgG_MBC_Low_affinity


title: mPO#2, differentiation condition, scRNAseq

description: 10x Genomics

source_name: placenta

value: placenta

value: trophoblast

tag: time


title: RNA_Wt_rep4R


title: RNA_Wt_rep5R


title: Patient_3IgM_MBC_Low_affinity


title: mPO#2, maintenance condition, scRNAseq

description: 10x Genomics


title: Patient_3Naive_Low_affinity


title: IKZF_2

data_processing:
Fragment files were created from FASTQ files using 10X Cell Ranger and were transformed into ArrowFiles in R using the ArchR package
Gene annotation was performed with the mm10 genome and doublets were removed using the filterDoublets function in ArchR
Iterative LSI-based dimensional reduction was performed with 4 iterations and after clustering and marker features analysis, clusters containing low number of variable features were removed from further analysis

extract_protocol:
Freshly sorted EPCAM+Ly51- mTECs were collected in 0.04% BSA in PBS, then lysed following the Chromium Single Cell ATAC Reagent Kit from 10X Genomics
Per UCSF Genomics Core
Using chromium single cell ATAC workflow (from 10X Genomics) nuclei were transposed and then encapsulated and barcoded. Libraries were sequenced using NovaSeq 6000 (Illumina)

value: Thymus

value: medullary thymic epithelial cell

value: Foxn1-Cre(+) Ikarosfl/fl


title: RNA_MetHm_rep7M

value: medulloblastoma spinal metastasis

value: spinal cord

value: spine

value: spinal metastasis

value: SmoM2 overexpression, Kmt2d KO


title: RNA_MetHm_rep6M


title: ATAC_Hm1M


title: Patient_3IgM_MBC_High_affinity_TH media

value: peripheral blood monouclear cell (PBMC)

value: B lymphocyte

value: WT

value: High_affinity+ T cell


title: Patient_3IgG_MBC_High_affinity_TH media


title: IKZF_1

value: Foxn1-Cre(+) Ikaros+/fl


title: Ppia knockout replicate 3

city: Houston

first: Andre

last: Catic

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Sequence reads were obtained from the Illumina Genome Analyzer Pipeline using Basespace.
Alignments: sequences were aligned to the mouse  reference genome mm9 with TopHat2  using default parameters
Assembly: mm9
Supplementary files format and content: Cufflinks output provided

source_name: bone marrow hematopoietic stem and progenitor cells

growth_protocol: see overall design above; biological triplicates of  Ppia heterozygous or knockout hematopoietic stem and progenitor sets were used.

extract_protocol:
Wild-type HSPCs were isolated from the hind limb long bones of 10-12 month-old female mice. c-Kit+ cells were stained and magnetically isolated from the lineage-depleted cell suspension using the EasySep mouse CD117 (c-Kit) positive selection kit (Stem Cell Technologies), following the manufacturer’s instructions. RNA extraction was carried out with the RNeasy Plus Mini kit with genomic DNA Eliminator columns (Qiagen) in combination with on-column DNaseI digestion (Qiagen), according to the vendor’s protocol.
Total RNA was quality-checked using Agilent RNA 6000 Pico kit (#5067-1513) and the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA). RNA with DV200 greater than 66% was used for library preparation. Total RNA-seq libraries were generated and prepared for multiplexing on the Illumina platform with the SMARTer Stranded Total RNA-Seq Kit v2 (#634418, Takara Bio, Japan) and the Unique Dual Index Kit (#634752, Takara Bio, Japan) following the manufacturer’s instructions. The libraries were sequenced on an Illumina NovaSeq 6000 System (Illumina, Inc., USA) with 150 nt paired-end sequencing.

treatment_protocol: see overall design above

tag: strain

value: 12 mo

value: Ppia full knockout


title: RNA_MetHm_rep4M


title: Ppia knockout replicate 2

value: bone marrow hematopoietic stem and progenitor cells


title: Patient_3Naive_High_affinity_TH media

source_name: peripheral blood monouclear cell (PBMC)


title: RNA_Wt_rep6R

value: primary medulloblastoma

value: cerebellum

value: right hemisphere

value: granule cell precursors

value: SmoM2 overexpression


title: RNA_MetHm_rep3M

value: medulloblastoma spinal metastasis

value: spinal cord


title: RNA_Hm_rep7L


title: Ppia heterozygous replicate 3

value: Ppia heterozygous


title: Ppia knockout replicate 1

value: 10 mo


title: RNA_Hm_rep6L

value: left hemisphere

value: SmoM2 overexpression, Kmt2d KO


title: Patient_3IgM_MBC_High_affinity

value: peripheral blood monouclear cell (PBMC)

value: B lymphocyte

value: WT


title: Patient_3Naive_High_affinity


title: RNA_Hm_rep4L


title: Ppia heterozygous replicate 2

value: 11 mo


title: RNA_Wt_rep3L


title: mTO, maintenance condition, scRNAseq

description: 10x Genomics

value: blastocyte

value: trophoblast stem cell

value: wild type


title: Dex 6850-XZ-9

city: Toledo

first: Rammohan

last: Shukla

address: 3000 Arlington Avenue

department: Department of Neurosciences

institute: University of Toledo

description:
Dex
paired-end next-generation RNA sequencing with a depth of 60 million reads per sample

data_processing:
Alignment Protocol: used HISAT2 version 2.1.0 to index mouse reference genomes and align RNAseq data. Notably, RPGs have about 2000 RP pseudogenes that are significantly homologous to the parent RPGs9, which impedes the ability of the standard alignment method to uniquely identify reads mapped to RPG and RP pseudogenes with high sequence homology. To circumvent this, we used a specialized alignment method. Briefly, we mapped all sequence reads to a “composite genome” that includes the entire mouse (GRCm38) genome sequence and spliced mRNA sequences of RPGs.
We then used subread version 1.5.0-p2 to quantify reads and map to genomic features.  We mapped RNA-seq reads to the composite genome without allowing mismatches and discarding reads mapped to more than one locus, thus ensuring that the reads mapped to RP pseudogenes are not from repetitive regions or normal RP genes.
Assembly: GRCm38
Supplementary files format and content: cData.csv - raw counts.

extract_protocol:
Using the RNeasy Mini Kit (Cat. 74104, Qiagen), we isolated the total RNA, according to the manufacturer’s instructions. DNase I treatment (Cat.79254, Qiagen) was performed during the RNA isolation procedure to remove genomic DNA, following the manufacturer’s recommendation. Total RNA was quantified using the NanoDrop One (Thermo Scientific, USA) and Agilent Tape Station.
Poly-A (standard) Library Prep.
NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) and xGen Broad-range RNA Library Prep (IDT, 1009813) with xGen Normalase UDI Primers (IDT, various)

tag: batch

tag: rin

value: Dissociated embryonic day 18 (E18) mouse cortical cells

value: Dexamethasone


title: Ppia heterozygous replicate 1

tag: tissue

value: bone marrow hematopoietic stem and progenitor cells


title: Patient_3IgG_MBC_TH media

data_processing:
Raw NGS reads were trimmed to remove adapters and low-quality regions using Trimmomatic v0.33
Trimmed reads were aligned to the human hg38 reference genome and Gencode release 26 annotation using STAR v2.5.2b
Read and alignment quality were assessed using MultiQCv1.1 to aggregate QC metrics from Picard (http://broadinstitute.github.io/picard/), FastQC v0.11.5, FastQ screen v0.9.3 and RseQC v1.1.8
Gene-level expression was quantified using RSEM v1.3.0
Assembly: Human - hg38 / Gencode Release 26
Supplementary files format and content: Text files generated using RSEM v1.3.0  containing raw counts

extract_protocol:
Cells were lysed with RLT buffer (Qiagen) and RNA was isolated using the Qiagen AllPrep 96 kit as per manufacturer's instructions except treatment with 27 units DNAse I to removegenomic DNA contamination. cDAN was synthesized using SMART-Seq v4 Ultra Low Input RNA kit
600 pg sheared cDNA was used as input into the low Inout Library Prep kit v2 (Clonetech/Takara Bio) and prepared following manufacturer's protocol Final NGS libraries were assessed on a BioAnalyzer 2100 using High Sensitivity Chips. The libraries were normalized to 0.5 nM, pooled equally and prepared for sequencing on the NextSeq (illumina, San Diego) following manufacturer's guidelines  for two mid-output 2X76 cycles.

tag: cell type

tag: genotype

value: T cell help


title: Patient_3IgM_MBC_TH media

tag: treatment


title: ZK498

data_processing:
RNAseq data were aligned to mm9 genome by tophat
Bam file were used by TEtranscripts for DE analysis of gene and repetitive element
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited file of DEseq2 result

molecule: polyA RNA

source_name: prefrontal cortex

extract_protocol:
Tissue was homogenized in TRIzol using a hand-held pestle homogenizer and incubated in TRIzol for at least 5 minutes. Chloroform (1:5 ratio) was added, the tubes shaken, and incubated at room temperature for 15 minutes. Samples were then centrifuged at 12,000g for 15 minutes at 4℃. The top aqueous layer was transferred to a clean tube, and the RNA was precipitated in 3M NaAc pH 5.2 (10:1 ratio), 4ul of glycogen (5mg/ml), 100% isopropanol (1:1 ratio) overnight at -80℃. The next day, the samples were centrifuged at 15,000 RPM for 20 minutes at 4℃. The resulting RNA pellet was washed once in 75% ethanol, centrifuged at 7,500g for 10 minutes at 4℃. The washed RNA pellet was dissolved in nuclease-free water.
RNAseq libraries were generated using TruSeq RNA Sample Prep V2 kit (New England BioLabs) with 1ug of RNA to first obtain poly-A-enriched RNA and synthesize cDNA, and then the same library construction protocol was followed using 5ng of cDNA.

treatment_protocol: Zika virus treatment; PBS treatment as control

value: zika virus affected


title: Patient_3Naive_TH media


title: Patient_3IgG_MBC_Unstim

value: Unstimulated


title: ZK418


title: Control 6850-XZ-6

description:
Control
paired-end next-generation RNA sequencing with a depth of 60 million reads per sample

tag: cell line


title: ZK254


title: Patient_3Naive_Unstim


title: PBS247

value: untreated


title: Patient_2IgG_MBC_Low_affinity_TH media

value: Low_affinity+TH media


title: Control 6850-XZ-4


title: PBS246


title: Patient_2IgM_MBC_Low_affinity_TH media


title: PBS237


title: Ru 6850-XZ-36

description:
Ru
paired-end next-generation RNA sequencing with a depth of 60 million reads per sample

value: Dexamethasone + mifepristone (RU-486)


title: Patient_2Naive_Low_affinity_TH media


title: PBS075


title: RNA_Hm_rep3R

value: primary medulloblastoma

value: cerebellum

value: right hemisphere

value: granule cell precursors

value: SmoM2 overexpression, Kmt2d KO


title: Patient_2IgG_MBC_Low_affinity

value: peripheral blood monouclear cell (PBMC)

value: B lymphocyte

value: WT


title: ZK469


title: Ru 6850-XZ-34

value: Dissociated embryonic day 18 (E18) mouse cortical cells


title: Patient_2IgM_MBC_Low_affinity


title: Dex 6850-XZ-7

value: Dexamethasone


title: Ru 6850-XZ-33


title: Patient_2Naive_Low_affinity


title: mZK_PFC_794

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2
Gonome was split into 500bp bin and reads count for each bin was calculated
Bins that have less than 20 reads in ZK group or PBS group were removed before downstream analysis
edgeR was used to call differential 5hmC level bins
Genome_build: mm9
Supplementary_files_format_and_content: edgeR result to compare 5hmC level for each bin in ZK and PBS group

extract_protocol:
DNA was extracted by adding equal volume of buffered phenol:chloroform:isoamyl alcohol (25:24:1 ratio) and centrifuged in Phase-Lock tubes at 15,000 RPM at room temperature. Supernatant was transferred to clean tubes. An equal volume of isopropanol was then added to the supernatant and mixed well at room temperature to precipitate the DNA. The DNA was then centrifuged at 10,000g for 10 minutes at room temperature, and then washed in 70% ethanol. After all ethanol was removed, the DNA pellet was eluted in nuclease-free water and incubated at 55C for 1 hour before storing at -20C.
Enriched DNA from 5hmC capture were subjected to library construction using the NEBNext Ultra II DNA Library Prep kit for Illumina (New England BioLabs) according to manufacturer’s protocol.


title: Patient_3IgM_MBC_Unstim


title: mZK_PFC_793


title: Ru 6850-XZ-32


title: Patient_2IgG_MBC_High_affinity_TH media

value: High_affinity+ T cell


title: Control 6850-XZ-5


title: crr -Pi #3

city: LAUSANNE

first: JOAQUIN

last: CLUA

address: BIOPHORE

department: DBMV

country: Switzerland

institute: UNIL

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011). Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1). Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013). Reads were aligned against Arabidopsis thaliana.TAIR10.39 genome using STAR (v. 2.5.3a, Dobin et al. 2013). The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1, Anders et al. 2014) using Arabidopsis thaliana.TAIR10.39 gene annotation. Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7, Wang et al. 2012)
Reads were also aligned to the Arabidopsis thaliana.TAIR10.39 transcriptome using STAR (v. 2.5.3a, Dobin et al. 2013) and the estimation of the isoforms abundance was computed using RSEM (v. 1.2.31, Li and Dewey 2011).
Supplementary files format and content: Normalized expression values all genes. Excel file showing the normalize expression values for each gene in each replicate
Supplementary files format and content: Statistical analysis was performed for genes in R (R version 3.5.3). Genes with low counts were filtered out according to the rule of 1 count per million (cpm) in at least 1 sample. Library sizes were scaled using TMM normalization and log-transformed into counts per million or CPM (EdgeR package version 3.24.3; Robinson et al. 2010). Differential expression was computed with limma-trend approach (Ritchie et al. 2015) by fitting all samples into one linear model. Moderated t-test was used for each contrast and F-test was used for interaction. For each group of comparisons, the adjusted p-value is computed by the Benjamini-Hochberg method, controlling for false discovery rate (FDR or adj.P.Val).
Supplementary files format and content: Differential expression testing. Excel file showing the normalized expression value for each gene and the differential expression testing between genotypes and conditions
Supplementary files format and content: Statistical analysis was performed for genes in R (R version 3.5.3). Genes with low counts were filtered out according to the rule of 1 count per million (cpm) in at least 1 sample. Library sizes were scaled using TMM normalization and log-transformed into counts per million or CPM (EdgeR package version 3.24.3; Robinson et al. 2010). Differential expression was computed with limma-trend approach (Ritchie et al. 2015) by fitting all samples into one linear model. Moderated t-test was used for each contrast and F-test was used for interaction. For each group of comparisons, the adjusted p-value is computed by the Benjamini-Hochberg method, controlling for false discovery rate (FDR or adj.P.Val).

organism: Arabidopsis thaliana

source_name: Root

growth_protocol: Arabidopsis seedlings were grown in 1/6MS agar plates for 7 days with or without phosphate

extract_protocol:
RNA from roots was extracted using Promega ReliaPrep™ RNA Tissue Miniprep System
Illumina Sequencing library preparation

treatment_protocol: The control condition was 1mM phosphate and the treated samples were grown without the addition of phosphate

value: Root

value: crr mutant

value: Minus Pi (-Pi)


title: Patient_2IgM_MBC_High_affinity_TH media


title: crr -Pi #2


title: mWT_PFC_560

value: untreated


title: Dex 6850-XZ-30


title: Ru 6850-XZ-35


title: Patient_3IgG_MBC_High_affinity


title: Patient_2Naive_High_affinity_TH media


title: mWT_PFC_559


title: crr -Pi #1


title: Patient_2IgG_MBC_High_affinity


title: mWT_PFC_558


title: Control 6850-XZ-3


title: crr +Pi #3

value: Control (+Pi)


title: Dex 6850-XZ-8


title: Dex 6850-XZ-29


title: crr +Pi #2


title: Dex 6850-XZ-28


title: Dex 6850-XZ-27


title: Patient_2IgM_MBC_High_affinity


title: Patient_2Naive_High_affinity


title: crr +Pi #1


title: young animal replicate 2

description:
young_2
total mRNA

data_processing:
Sequence reads were obtained from the Illumina Genome Analyzer Pipeline using Basespace.
Alignments: sequences were aligned to the mouse reference genome mm9 with TopHat2 using default parameters.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *_genes.fpkm_tracking: Cufflinks output provided.

extract_protocol:
Wild-type HSPCs were isolated from the hind limb long bones of 4- to 6-month-old and 31- to 33-month-old male mice. c-Kit+ cells were stained and magnetically isolated from the lineage-depleted cell suspension using the EasySep mouse CD117 (c-Kit) positive selection kit (Stem Cell Technologies), following manufacturer’s instructions. After overnight growth in serum-free medium (StemSpan SFEM, Stem Cell Technologies), supplemented with murine TPO (20 ng/ml, PeproTech), SCF (10 ng/ml, PeproTech), and the beta-Catenin agonist CHIR99021 (250 nM, Stemgent), HSPCs were harvested as cell pellets.
Immediately after, RNA extraction was carried out with the RNeasy Plus Mini kit with genomic DNA Eliminator columns (Qiagen) in combination with on-column DNaseI digestion (Qiagen), according to the vendor’s protocol.
Total RNA-seq libraries were generated and prepared for multiplexing on the Illumina platform with the TruSeq stranded total RNA library prep (Illumina) according to manufacturer’s protocol. Libraries included ERCC ExFold RNA spike-in mixes (Thermo Fisher Scientific) to assess the platform dynamic range. The resultant libraries were quality-checked on a Bioanalyzer 2100 instrument (Agilent) and quantified with a Qubit fluorometer (Thermo Fisher Scientific).
Paired-end

value: wild type

value: bone marrow hematopoietic stem and progenitor cells

tag: Sex

value: male


title: young animal replicate 1

description:
young_1
total mRNA


title: aged animal replicate 2

description:
old_2
total mRNA


title: Patient_2IgG_MBC_TH media

value: T cell help


title: Dex 6850-XZ-26


title: Ru 6850-XZ-31

value: Dexamethasone + mifepristone (RU-486)


title: Col-0 -Pi (crr mutant control) #3

value: Col-0 ecotype


title: mZK_PFC_795

value: zika virus affected


title: aged animal replicate 1

description:
old_1
total mRNA


title: Patient_2IgM_MBC_TH media

value: peripheral blood monouclear cell (PBMC)

value: B lymphocyte


title: Dex 6850-XZ-25

value: Dissociated embryonic day 18 (E18) mouse cortical cells


title: Col-0 -Pi (crr mutant control) #1


title: Col-0 -Pi (crr mutant control) #2


title: Patient_2Naive_TH media

value: WT


title: Patient_2IgG_MBC_Unstim

value: Unstimulated


title: Col-0 +Pi (crr mutant control) #3

value: Root


title: Control 6850-XZ-23


title: Ribo.4e-2

city: FuZhou

first: Jing

last: Zhang

state: Fujian Province

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

institute: Fujian Agriculture and Forestry University

description: Ribo.4e 3 repeats

data_processing:
In total, we yielded paired-end reads of 2x150bp for 24 libraries of RNA  sequencing (RNA-seq), which included wild type and mutation with three biological repeats from immunoprecipitated (IP) and input samples, respectively.
The fastx_clipper script from FASTXtoolkit (http://hannonlab.cshl.edu/fastx_toolkit) was used for adapter sequence trimming of FASTQ files from input and IP samples using following parameters: -l 20 -d 0 -n -v -M 6.
Then above clean reads were aligned to the Arabidopsis reference genome (TAIR10) using TopHat v2.0.11 with following parameters: -a 8 -m 0, which required the min anchor length and maximum number mismatches for junction reads was 8 and 0, respectively.
Reads aligned to multiple genome regions were discarded.
Assembly: TAIR10
Supplementary files format and content: The row data folder contains the raw sequencing data for each sample. Each sample has two FASTQ files with R1 or R2 in the file name
Supplementary files format and content: The row_counts compressed file contains the FPKM file of each sample, including gene, counts and FPKM data
Library strategy: Ribo-seq

source_name: seedling

growth_protocol: Plants were grown in growth chambers or growth room at 22°C under different long day conditions (16h light / 8h dark).

extract_protocol:
The immunopurification of ribosomes was performed as described previously (Zanetti et al., 2005, Branco-Price et al., 2008a).
TruSeq Stranded mRNA LT Sample Prep Kit - Set A

treatment_protocol: Whole seedlings were freezed in liquid nitrogen at ZT16, just before lights off.

value: seedling

value: 9-day-old, ZT16

tag: ecotype

value: Columbia

value: eif4e mutant

tag: sequencing type

value: translatome


title: Ribo.4e-3

description: Ribo.4e 3 repeats


title: Ribo.4e-1

description: Ribo.4e 3 repeats


title: Control 6850-XZ-24


title: Patient_2Naive_Unstim


title: Control 6850-XZ-22


title: Patient_1IgG_MBC_Low_affinity_TH media

value: Low_affinity+TH media


title: Ribo.WT-3

description: Ribo.WT 3 repeats

value: Wild type


title: Control 6850-XZ-20


title: Ribo.WT-2

description: Ribo.WT 3 repeats


title: Control 6850-XZ-21


title: Patient_1Naive_Low_affinity_TH media


title: halo_nac_r2

city: Paterna

first: José Tomás

last: Matus

state: Valencia

address: Carrer del Catedràtic Agustín Escardino Benlloch

country: Spain

institute: Institute for Integrative Systems Biology

data_processing:
Base calling was done with Illumina Offline Base Caller (OLB 1.9.4).
Raw reads were trimmed using fastp version 0.21.0 with the following parameters: " -w 16 --n_base_limit 5 cut_front_window_size 1 cut_front_mean_quality 30 --cut_front cut_tail_window_size 1 cut_tail_mean_quality 30 --cut_tail -l 20 -i "
Trimmed reads were aligned by bowtie2 version 2.0-beta7  against the Vitis vinifera genome assembly PN40024_12X.2 with default parameters, and additionally filter for alignments with MAPQ score of at least 30.
Peaks were called using GEM peak caller version 3.4 with the default version 3.4 read distribution, PN40024_12X.2 genome sequences, in multi-replicate mode and with the Pix-halo samples as control, and parameters “–q 1 –t 1 –k_min 6 –kmax 20 –k seqs 600 –k_neg_dinu_shuffle”, limited to nuclear chromosomes.
Peak summits called by GEM were associated with the closest gene model in the V1 transposed on the 12X.v2 assembly annotation file using the BioConductor package ChIPpeakAnno (16) with default parameters (i.e., NearestLocation).
Supplementary files format and content: Peak regions in narrowPeak format were created by GEM analysis.
Library strategy: DAP-Seq

organism: Vitis vinifera

source_name: young leaf

growth_protocol: Leaf material was collected and pooled from fruiting cuttings of cv. ‘Syrah’.

extract_protocol:
Genomic DNA was extracted from 1 g of ground young cv. ‘Syrah’ leaves and the Illumina libraries were prepared as previously described (Galli et al., 2018). The VviNAC61 sequence was transferred from the pENTR/D-TOPO to the Gateway-compatible destination vector pIX-HALO (Bartlett et al., 2017). The HALO-VviNAC61 and GST-HALO (used as negative control) fusion proteins were in vitro translated using the TNTR SP6 coupled reticulocyte lysate system (Promega). Two replicates were used for the TF and input libraries. The DAP-seq was performed according to previously described procedure (Galli et al., 2018)
The eluted DNA fragments are PCR amplified with a full-length indexed TruSeq primer and directly sequenced on the Illumina NextSeq 500.

treatment_protocol: Leaf material was collected and flash frozen with liquid nitrogen prior gDNA isolation.

tag: cultivar

value: Syrah

tag: protein

value: pIX-HALO

tag: protein affinity tag

value: HALO

tag: expression system

value: rabbit reticulocyte lysate

tag: dna source

tag: replicate


title: halo_nac_r1


title: Patient_1IgG_MBC_Low_affinity

value: peripheral blood monouclear cell (PBMC)


title: Control 6850-XZ-2


title: Total.4e-3

description: Total.4e 3 repeats

data_processing:
In total, we yielded paired-end reads of 2x150bp for 24 libraries of RNA  sequencing (RNA-seq), which included wild type and mutation with three biological repeats from immunoprecipitated (IP) and input samples, respectively.
The fastx_clipper script from FASTXtoolkit (http://hannonlab.cshl.edu/fastx_toolkit) was used for adapter sequence trimming of FASTQ files from input and IP samples using following parameters: -l 20 -d 0 -n -v -M 6.
Then above clean reads were aligned to the Arabidopsis reference genome (TAIR10) using TopHat v2.0.11 with following parameters: -a 8 -m 0, which required the min anchor length and maximum number mismatches for junction reads was 8 and 0, respectively.
Reads aligned to multiple genome regions were discarded.
Assembly: TAIR10
Supplementary files format and content: The row data folder contains the raw sequencing data for each sample. Each sample has two FASTQ files with R1 or R2 in the file name
Supplementary files format and content: The row_counts compressed file contains the FPKM file of each sample, including gene, counts and FPKM data

tag: time

value: transcriptome


title: Ribo.WT-1

description: Ribo.WT 3 repeats


title: NAC61_rep2

tag: gene id vcost

tag: gene id v1

tag: protein family

value: NAC

tag: protein source

value: Vitis vinifera


title: Control 6850-XZ-19

tag: batch

tag: rin

tag: cell type

value: Dissociated embryonic day 18 (E18) mouse cortical cells


title: Total.4e-2

description: Total.4e 3 repeats

tag: tissue

tag: genotype


title: Patient_1IgM_MBC_Low_affinity

value: B lymphocyte

value: WT

tag: treatment


title: NAC61_rep1

tag: cultivar


title: Total.4e-1

description: Total.4e 3 repeats

value: seedling

value: 9-day-old, ZT16

tag: ecotype

tag: sequencing type


title: Col-0 +Pi (crr mutant control) #2

value: Root

tag: cell line

value: Col-0 ecotype

value: Control (+Pi)


title: Ru 6850-XZ-17

value: Dexamethasone + mifepristone (RU-486)


title: Patient_1Naive_Low_affinity


title: Ru 6850-XZ-18


title: Patient_1IgG_MBC_High_affinity_TH media

value: High_affinity+ T cell


title: Total.WT-2

description: Total.WT 3 repeats

value: Columbia

value: Wild type


title: Patient_1IgM_MBC_Low_affinity_TH media

value: Low_affinity+TH media


title: Ru 6850-XZ-16


title: Patient_1Naive_High_affinity_TH media

value: peripheral blood monouclear cell (PBMC)


title: TAM PLC-PRF-5 donor9

type: RNA

city: Bangkok

first: Tanapat

last: Palaga

address: Payathai Road, Pathumwan

department: Microbiology

country: Thailand

institute: Chulalongkorn University

description: Human Myeloid Innate Immunity Panel consists of 770 genes which 730 genes are targeted genes and 40 genes are housekeeping genes.

hyb_protocol: RNA were mixed with capture probes and reporter probes and incubated at 65 °c overnight for hybridization.

scan_protocol: The hybridized RNA were immobilized on the slide through biotin-streptavidin interaction. Reporter probes were conjugated with unique barcode for each gene, which it was used to identify genes. The hybridization reactions were loaded and run the process into the nCounter SPRINT (NanoSting Technologies, WA). The hybridized RNA were purified and lay down the barcode in the same direction and captured image to count the barcodes.

data_processing: One barcode indicated one RNA molecule. The instrument counted and released into raw count gene expression data, which was normalized and analyzed using Advancced Analysis 2.0 plugin in NanoString’s software nSolver V.4.0.

label: Biotin

source_name: Infiltrating monocytes from PLC/PRF/5 spheroids

label_protocol: Two hundred nanograms of RNA were mixed with capture probes and color-coded reporter probes as target-specific sequences with 770 genes, including 730 targeted genes and 40 reference genes in human myeloid innate immunity panel.

extract_protocol: These monocytes were collected in Buffer RLT. The total RNA was isolated using Qiagen mini-RNeasy (Qiagen, Germany) according to the manufacturer’s protocol.

tag: donor

tag: donor status

value: Healthy donor


title: Ru 6850-XZ-15


title: Patient_1IgG_MBC_High_affinity


title: Ru 6850-XZ-14


title: iPSC-derived GD2-CARTs, ADT-derived cDNA

city: Bunkyo

first: Miki

last: Ando

state: Tokyo

address: Hongo 2-1-1

department: Hematology

country: Japan

institute: Juntendo University

description: Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

library_source: other

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT sequences were concatenated and treated as Custom library with default settings (v3.0.2) and aligning to the GRCh38 genome build.
Further processing was done with Seurat v3.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: Cultured T cells

extract_protocol:
1x10^6 sample cells were used 14 days after stimulation.
Library was prepared using Chromium Single Cell 3ʹ v3.1 protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell 3’ v3.1 protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp). For the mRNA derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions for Single Cell 3’ v3.1 protocol (10x Genomics). -CITE-seq library: amplification was performed at 95°C for 3’ followed by ten cycles at 95°C f¬¬or 20’’; 60°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3’ Small RNA RPI1 primer as i7 primer (Illumina).

value: iPSC-derived GD2-CARTs

tag: library type

value: ADT

tag: antibodies/tags

value: TotalSeqTM-B Human Universal Cocktail, V1.0


title: TAM PLC-PRF-5 donor8

value: Infiltrating monocytes from PLC/PRF/5 spheroids


title: iPSC-derived GD2-CARTs, mRNA-derived cDNA

description: 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: mRNA


title: Patient_1Naive_High_affinity

first: Prasida

last: Holla

institute: Indiana University School of Medicine

value: B lymphocyte

value: WT


title: TAM HepG2 donor9

source_name: Infiltrating monocytes from HepG2 spheroids


title: Patient_1IgM_MBC_High_affinity


title: TAM PLC-PRF-5 donor6


title: TAM PLC-PRF-5 donor7


title: Dex 6850-XZ-12

value: Dissociated embryonic day 18 (E18) mouse cortical cells

value: Dexamethasone


title: Col-0 +Pi (crr mutant control) #1

value: Root

value: Col-0 ecotype

value: Control (+Pi)


title: peripheral blood-derived GD2-CARTs, ADT-derived cDNA

value: peripheral blood-derived GD2-CARTs


title: TAM HepG2 donor8

value: Infiltrating monocytes from HepG2 spheroids


title: Patient_1IgG_MBC_TH media

value: T cell help


title: Total.WT-3

description: Total.WT 3 repeats

value: seedling

tag: time

value: 9-day-old, ZT16

value: Columbia

value: Wild type

value: transcriptome


title: Dex 6850-XZ-11


title: peripheral blood-derived GD2-CARTs, mRNA-derived cDNA


title: Dex 6850-XZ-10


title: Total.WT-1

description: Total.WT 3 repeats


title: Patient_1Naive_TH media

value: peripheral blood monouclear cell (PBMC)


title: Patient_1IgM_MBC_TH media


title: Patient_1IgG_MBC_Unstim

value: Unstimulated


title: Control 6850-XZ-1


title: mPO, differentiation condition, scRNAseq

description: 10x Genomics

data_processing:
Data were aligned and quantiﬁed using Cell Ranger from the 10X Genomics pipeline with default parameters against the mm10 reference genome.
Contaminating cell doublets were removed using the Scrublet (Wolock et al.) and Doubletdetection (Gayoso et al.) package.
Quality control and filtering.
Assembly: mm10
Supplementary files format and content: h5 file
Supplementary files format and content: Tab-separated metadata file

growth_protocol: E8.5 mouse placentae were digested with collagenase IV，cell aggregations were resuspended in growth factor-reduced Matrigel, and cultured with maintenance condition medium for 13 days

treatment_protocol: Differentiate trophoblast organoids, mPO in maintenance condition were first passaged and cultured in maintenance medium without Y27632, FGF4 for 3 days, followed by culturing in the differentiation condition medium  for 16 days

value: placenta

tag: strain

value: trophoblast

value: wild type

tag: age

value: differentiation condition


title: TAM HepG2 donor6

value: Healthy donor


title: TAM HepG2 donor7


title: MO donor9

source_name: Freshly isolated monocytes

value: Freshly isolated monocytes


title: Patient_1IgM_MBC_Unstim

value: B lymphocyte

value: WT


title: mGro_2

city: Hangzhou

first: Jianzhao

last: Liu

address: 866 Yuhangtang Rd, Hangzhou, Zhejiang Province, P.R. China

institute: Zhejiang University

description:
mGRO-seq
chromatin RNA

data_processing:
Library strategy: mGRO-Seq
The adapters and low quality bases were removed by using cutadapt (v1.15).
The fastq files were aligned to the human genome (hg38) using Hisat2 (v2.1.0).
The Picard (MarkDuplicates, http://broadinstitute.github.io/picard/) was used for removing PCR duplicates. Reads mapped to tRNA and rRNA were removed.
Data visualizationwas applied with the bedTools genomeCoverageBed function4 to get a BedGraph file with histogram of coverage values. BedGraph files were then converted to bigWig files were converted from BedGraph by using UCSC bedGraphToBigWig and visualized in the Integrative Genomics Viewer (IGV).
Mutations of the mapped reads were extracted by custom scripts. Only A-to-C mutations were chosen to reduce background noises: Fold-change = (The abundance of mutant A-to-C positions (mGRO-seq)) / (The abundance of mutant A-to-C positions(Control)) and Fold-change > 2.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: HeLa cells

growth_protocol: HeLa cells were grown in DMEM containing 10% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin until 80% confluency.

extract_protocol:
TRIzol (Invitrogen, 10296010) was added to terminate the reaction and extract RNA, followed by DNA depletion by DNase I digestion. RNA was resuspend in nuclease-free water and adjusted to 200~300 ng/μL.
rRNA was depleted by NEBNext® rRNA Depletion Kit (NEB, E0350), and RNA was resuspended in 30 μL nuclease-free water. The efficiency of rRNA depletion was measured by RT-qPCR using PrimeScript™ 1st Strand cDNA Synthesis Kit (TOYOBO, 6110A) and iTaq™ Universal SYBR® Green Supermix (Bio-Red, 1725124). A sequence library was constructed using NEBNext® Ultra II Directional RNA Library Prep Kit (NEB, E7760), with several modifications. Briefly, RNA was resuspended in 5 μL nuclease-free water, and fragmented with 4 μL NEBNext First Strand Synthesis Reaction Buffer and 1 μL Random Primers for 7 min at 94 °C. RT was performed by adding 8 μL NEBNext Strand Specificity Reagent, 5 μL 5× reaction buffer for RT, and 2 μL recombinant HIV-1 reverse transcriptase (Worthington Biochemical Corporation), for 10 min at 25°C, 1 h at 37°C, and then 15 min at 70°C, and finally held at 4°C. Then the following steps followed the manufacture’s protocol. The library sizes were validated using Agilent 2100 Bioanalyzer and sequenced on Illumina Hiseq X10 with paired-end 2×150 bp read length.

treatment_protocol: Cells were washed in PBS and resuspended in 4 mL of sucrose buffer I (0.32 M sucrose, 5 mM CaCl2, 2 mM magnesium acetate, 0.1 mM EDTA, 10 mM Tris-HCl pH 8.0, 1 mM DTT and 0.5% (v/v) CA-630) at the cell density no more than 5×107 cells/mL. Cells were incubated for 5 min and homogenized by 15 mL Tissue Grinder (WHEATON, 357544) using a tight fitting pestle until over 90% of nuclei were released. An equal volume of sucrose buffer Ⅱ (2 M sucrose, 5 mM magnesium acetate, 0.1 mM EDTA, 10 mM Tris-HCl pH 8.0 and 1 mM DTT) was added, and the mix was gently pipetted up and down. Nuclei were isolated by using Optima L-90K ultra centrifuge supplied with SW40Ti swing rotor. 4.4 mL sucrose buffer Ⅱ, 8 mL cell lysis, and 1 mL sucrose buffer Ⅰ was added at bottom, medium and top of the gradient in a SW tube, respectively. Nuclei were centrifuged for 45 min at 30,000 g, and resuspended in glycerol storage buffer (40% (v/v) glycerol, 5 mM magnesium acetate, 0.1 mM EDTA and 50 mM Tris-HCl, pH 8.3) at the nuclei density of 5 x 107 nuclei/mL. 100 μL HeLa nuclei (~5×106) was added with 10 μL 5 M NaCl and mixed gently until the solution became clear. An equal volume of nuclease-free water was added, and chromatin was pelleted by centrifugation at 12,000 rpm for 30 s. The chromatin pellet was washed three times with 500 μL 50 mM Tris-HCl (pH 7.5), and resuspended in 100 μL glycerol storage buffer. An equal volume of 2× chromatin run-on buffer (10 mM Tris-HCl, pH 7.4, 5 mM MgCl2, 1 mM DTT, 300 mM KCl, 100 μM ATP, 500 μM UTP, 500 μM CTP, 500 μM GTP, 400 μM a6ATP, 4 units/μL RRI, and 1% (w/v) Sarkosyl) was added, and the reaction lasted for 5 min at 37 °C with gentle mixing. The ratio of a6ATP and ATP was optimized, and the total concentration of a6ATP and ATP was 500 μM in accordance with the concentrations of other nucleoside triphosphates.

value: HeLa


title: mGro_Ctrl_2

description:
mGRO-seq
chromatin RNA


title: mGro_Ctrl_1

description:
mGRO-seq
chromatin RNA


title: Ru 6850-XZ-13

tag: batch

value: Dissociated embryonic day 18 (E18) mouse cortical cells

value: Dexamethasone + mifepristone (RU-486)


title: MO donor8


title: mPO, maintenance condition, scRNAseq

description: 10x Genomics

value: maintenance condition


title: Patient_1Naive_Unstim

city: Indianapolis


title: Control_ImmStim_2

status: Public on Oct 24 2023

city: Newcastle upon Tyne

first: Rebekah-Louise

last: Scanlan

address: Westgate Rd

country: United Kingdom

institute: Newcastle University

description: Biological replicate 2

data_processing:
Paired end sequencing files for each sample and sequencing run were aligned to the human genome (HG38) using HISAT
Differential expression analysis were performed using the DESeq2 package
Assembly: HG38
Supplementary files format and content: Supplementary files format and content: *.csv, containing raw counts and normalised counts.

source_name: Brain

extract_protocol:
Total RNA was purified using RNeasy Mini Kit (Qiagen).
Complementary DNA was prepared using Maxima Reverse Transcriptase and Oligo dT (12–18) (Thermo Fisher Scientific- Life tech). qPCR was performed using a real-time PCR kit (Bio-Rad1725271) following the manufacturer’s protocol

value: Brain

value: Microglial

value: immune stimulation with dsDNA


title: APTX_KO_NonStim_1

description: Biological replicate 1

value: APTX knockout


title: APTX_KO_ImmStim_1

description: Biological replicate 1


title: APTX_KO_ImmStim_3

description: Biological replicate 3


title: APTX_KO_ImmStim_2

description: Biological replicate 2


title: APTX_KO_NonStim_3

description: Biological replicate 3


title: MO donor7


title: MO donor6


title: APTX_KO_NonStim_2

description: Biological replicate 2


title: Control_ImmStim_1

description: Biological replicate 1


title: mGro_1

description:
mGRO-seq
chromatin RNA


title: Control_ImmStim_3

description: Biological replicate 3


title: Control_NonStim_2

description: Biological replicate 2


title: Control_NonStim_1

description: Biological replicate 1


title: Multiome_ATAC_E13.5wt

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

data_processing:
Raw fastqs were aligned to mm10 genome build using the standard Cellranger multiomics settings and imported to ArchR (v.1.0.1). Doublets were identified and filtered, and cells were filtered for minimum 4 TSS enrichment, 2500 fragments per cell. Dimensionality reduction was performed using LSI based on the cell-by-fragment matrix and cell-by-gene matrix, and clusters were identified. Peaks were called based on original clustering, discarding reads from promoters (2500 bp ± TSS) and exons. Cluster assignments were confirmed using canonical marker genes based on gene expression, and gene ontology enrichment of marker genes identified using getMarkerFeatures function of ArchR. Statistical significance and strength of enrichments were determined using a t-test, grouping cells by cluster.
Assembly: mm10
Supplementary files format and content: matrix.mtx.gz: Tab-delimited text files containing genes by barcode counts CellRanger matrix
Supplementary files format and content: features.tsv.gz: CellRanger feature file containng list of transcripts used in matrix file
Supplementary files format and content: barcodes.tsv.gz: CellRanger barcode file containing list of cell barcodes used in matrix file
Supplementary files format and content: peaks.bed: BED file of peaks called in ATAC-Seq
Supplementary files format and content: cut_site.bigwig: BIGWIG profile of ATAC-Seq signal

source_name: secondary palate

extract_protocol:
Samples were mechanically broken into single-nuclei suspensions following the manufacturer’s instructions for Nuclei Isolation from Complex Tissues for Single Cell Multiome ATAC + Gene Expression Sequencing (10X Genomics—protocolCG000375). After isolation, the nuclei integrity was accessed under a microscope and counted using the CellDrop (Denovix) and acridine orange (AO) and propidium iodide (PI) as dye. Transposition and Gel Bead-in-Emulsion (GEM) generation, using a Chromium Single Cell Multiome ATAC + 3′ Gene Expression following the manufacturer’s instructions (10x Genomics—protocolCG000338Rev F) were performed, aiming for a total of 10,000 nuclei per sample. In brief, the nuclei were transposed in a bulk solution using Tn5 transposase with sequencing adapters that were pre-loaded. The transposed nuclei were loaded onto a microfluidic chip to create GEMs. The gel beads contained two types of oligos that were used for snRNA-seq and snATAC-seq.
The mRNA was reverse transcribed and underwent template switching and transcript extension to produce barcoded cDNA. The snATAC-seq oligo was formed of a partial Illumina primer sequence, a 10X barcode, and a spacer that allowed the barcode to attach to the adapter-tagged DNA fragments. The GEMs were broken using a recovery agent to produce a bulk pool of barcoded molecules. The pre-amplified product was then split into portions available for snRNA-seq and snATAC-seq library construction. P5, i7, and P7 sequences compatible with Illumina bridge amplification were added to the DNA fragments through PCR to produce snATAC-seq libraries. Additional amplification of the cDNA was performed on the snRNA-seq samples before proceeding to fragmentation, end repair, A-tailing, and ligation. A sample dual index PCR was used to add the P5, i5, i7, and P7 sequences to the final snRNA-seq library.
Multiome: RNA-Seq and ATAC-Seq

value: secondary palate

value: Wild-type

tag: developmental stage


title: Multiome_GEX_E13.5pax9KO


title: Multiome_ATAC_E15.5wt


title: Multiome_GEX_E13.5wt


title: Multiome_GEX_E15.5wt


title: ST6028

first: Alejandra

last: Borjabad

state: NY

address: 1468 Madison Ave

institute: Icahn School of Medicine

data_processing: Data processing was performed by Novogene Co.

source_name: Brain / striatum

extract_protocol:
RNA was extracted using Rneasy Kit from Qiagen.
Libraries were prepared by Novogene Co.

value: Brain / striatum


title: ST6020


title: ST6019


title: ST6011


title: ST6018


title: ST6013


title: Control_NonStim_3

description: Biological replicate 3

tag: cell type


title: Multiome_ATAC_E13.5pax9KO

tag: tissue


title: trNK, 72h, IL-21, ATACseq 1

city: Beijing

first: Chao

last: Zhong

address: 38 Xueyuan Rd , Haidian District

department: Institute of Systems Biomedicine

institute: Peking University

description: ATAC-seq

data_processing:
For bulk RNA-Seq, sequence reads were mapped to the mouse (mm10) genome with hisat2 (2.1.0) with default settings and we kept one hit if multiple reads were mapped to the same position for each RNA-Seq library.For each RNA-Seq sample, gene expression was quantified using featureCounts function in Subread package.
For single-cell RNA-Seq, the sequencing data were aligned and quantified using the BD Rhapsody WTA Local bioinformatics pipeline (version 1.9.1, BD) against the mouse mm10 reference genome
For ATAC-Seq, raw sequencing reads were trimmed with Trimmomatic. Trimmed reads were aligned to mm10 assembly of mouse genome using Bowtie2. Then, the aligned reads were sorted using samtools, and duplicates were removed using PICARD. Peak-calling for ATAC-Seq was performed with MACS on bam files, with a q-value threshold of 0.01. Consensus peaks from all NK samples were merged to create a raw peak universe. Peak annotation and motif analysis were performed with HOMER. ATAC-Seq tracks were visualized using Integrative Genomics Viewer.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read counts for each Sample
Supplementary files format and content: bigWig

source_name: uterus

growth_protocol: Wild-typre males co-habited with virgin females overnight and the detection time of a copulation plug was thought as gestation day(gd) 0.5. Then the males and females were separated into different cages. Uterine trNK or cNK were isolated at gd6.5. For the experiments in vitro, trNK were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using Single Cell Full Length mRNA-Amplification Kit (Vazyme) following manufacturer's protocols. 5ng total RNA was used for the construction of sequencing libraries. DNA was harvested using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme)  following manufacturer's protocols.
RNA libraries for RNA-seq or DNA libraries for ATAC-seq were prepared using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme)  following manufacturer's protocols.

treatment_protocol: 15ng/ml IL-15 with or without 20ng/mL IL-21 were added into the medium where sorted trNK were cultured in vitro.

value: uterus

value: trNK

tag: genotype


title: trNK, 72h, IL-21 2

description: bulk RNA-Seq

tag: treatment


title: cNK, gd6.5, ATACseq 2

description: ATAC-seq

value: cNK


title: trNK, 72h, ATACseq 2

description: ATAC-seq

value: 10ng/ml IL-15


title: trNK, 72h, IL-21 1

description: bulk RNA-Seq


title: trNK, 72h, ATACseq 1

description: ATAC-seq


title: trNK, 72h 2

description: bulk RNA-Seq


title: trNK, 72h, IL-21, ATACseq 2

description: ATAC-seq


title: trNK, 72h 1

description: bulk RNA-Seq


title: ST6006


title: ST6027


title: trNK, 24h 2

description: bulk RNA-Seq


title: trNK, 24h, IL-21 1

description: bulk RNA-Seq


title: ST6012


title: trNK, 24h 1

description: bulk RNA-Seq


title: trNK, 6h, IL-21 2

description: bulk RNA-Seq


title: ST6026


title: trNK, 24h, IL-21 2

description: bulk RNA-Seq


title: trNK, 0h, IL-21 2

description: bulk RNA-Seq


title: trNK, 6h 2

description: bulk RNA-Seq


title: trNK, 6h 1

description: bulk RNA-Seq


title: trNK, 0h 2

description: bulk RNA-Seq


title: Lymph_node_none_infect_Veh_rep4

city: Epalinges

first: Sanam

last: Peyvandi

address: Ch. Boveresses 155

institute: University of Lausanne

data_processing:
The resulting FASTQ files were sample-demultiplexed and aligned to the reference genome using STARsolo version 2.7.9a.
The differentially expressed gene analysis were performed using DESeq2 version 3.15 (Love et al. 2014)
Assembly: mm10
Supplementary files format and content: tab separated,  counts matrix

source_name: Lymph node

extract_protocol:
Draining lymph nodes were recovered in RLT plus buffer,homogenized using tissue lyzer. mRNA was extracted using Qiagen RNAeasy mini kit.
The reverse transcription was performed using barcoded oligo-dT primers. The resulting cDNA from each sample was pooled into a single tube before proceeding to cDNA second strand synthesis. To generate Illumina-compatible libraries, the Unique Dual Indexed (UDI) library preparation method was employed following the previously described protocol (Alpern et al., 2019).

value: Lymph node

tag: infection

value: non infected

value: Vehicle


title: Lymph_node_none_infect_Veh_rep3


title: Lymph_node_none_infect_Veh_rep2


title: trNK, gd6.5, ATACseq 1

description: ATAC-seq

value: WT


title: Lymph_node_none_infect_Veh_rep1


title: Lymph_node_none_infect_ACB_rep2


title: Lymph_node_none_infect_ACB_rep1


title: Lymph_node_none_infect_ACB_rep4


title: Lymph_node_infected_Veh_rep1

value: LmSd infected


title: Lymph_node_infected_Veh_rep2


title: Lymph_node_infected_ACB_rep4


title: Lymph_node_infected_ACB_rep2


title: Lymph_node_infected_ACB_rep3


title: Lymph_node_infected_ACB_rep1


title: control_cKIT_IgG

city: New Haven

first: Bluma

middle: J

last: Lesch

address: 333 Cedar Street

department: Genetics

description: 150bp PE CUT&Tag

data_processing:
Quality filtering was performed using FASTX-Toolkit. The adapter sequences (CTGTCTCTTATACACATCT) were trimmed for each filtered file using cutadapt and Seqkit was then used to match paired reads. Reads were then aligned to the mm10 mouse genome assembly using Bowtie2 with –end-to-end –very-sensitive settings enabled. The sequencing depth was equalized across all samples and the resultant .sam file was converted to bam files. After sorting and indexing using SAMtools the bam files were converted to bigwig format using bamCoverage. We generated metagene plots from the bigwig files using deepTools. Peak calling was performed using SEACR.
see data processing associated with each sample
Assembly: mm10
Supplementary files format and content: .bed files of peaks

source_name: testis

extract_protocol:
Dissociated germ cells were incubated in the dark for 30 mins with PE conjugated anti-cKIT at 1:800 (Thermo, 12-1171-82). Stained cells were then washed twice, resuspended to 10 million cells/ml and sorted on a two-laser (466 nm and 561 nm) cell sorter (Bio-Rad S3) as previously described (Vasiliauskaitė et al., 2018). 50,000 cells were pelleted for library prep.
CUT&Tag libraries were prepared using the Active Motif anti-Rabbit assay kit (Active Motif, 53160) with minor amendments to the manufacturer’s protocol. Briefly, cKIT+ cells were sorted from dissociated testis and centrifuged at 1,000 xg for 3 mins at room temperature before washing the cell pellet in the buffer provided. For each reaction, 50 µl of cell suspension (50,000 cKIT+ cells) was incubated with 6 µl of concanavalin A beads in a 0.5ml tube. After 10 minutes, the beads were captured using a magnetic stand and resuspended in 50 µl of antibody buffer containing PIC ,digitonin, and 1 µg of primary antibody. After overnight incubation at 4°C, the liquid was removed, and the beads were incubated at room temperature for 60 minutes with 50 µl of secondary antibody diluted in Dig-wash buffer. The beads were then washed once with 500 µl Dig-wash buffer before incubating with 50 µl of diluted transposomes for 60 minutes. After a single wash with 500 µl of Dig-300 buffer the beads were incubated with 125 µl of Tagmentation buffer for 60 minutes in a thermomixer set at 400rpm 37°C. The DNA was then extracted and PCR amplified according to the manufacturer’s instructions. Finally, SPRI bead clean-up was performed before eluting purified DNA into 16 µl elution buffer. An Agilent 2100 Bioanalyzer using a high sensitivity DNA assay kit was used to assess the quality of prepared libraries, which were then paired-end sequenced to achieve ~30 million reads.

value: testis

value: cKIT+ spermatogonia

value: Kdm6a fl/y; Cre- (control)

tag: antibody

value: Millipore NI01 IgG


title: trNK, 0h 1

description: bulk RNA-Seq


title: trNK, 0h, IL-21 1

description: bulk RNA-Seq


title: kdm6a_cKO_cKIT_K27me3_3

description: 150bp PE CUT&Tag

value: Kdm6a fl/y; Ddx4-Cre+ (cKO)

value: CST9733 anti-H3K27me3


title: kdm6a_cKO_cKIT_K27me3_2

description: 150bp PE CUT&Tag


title: kdm6a_cKO_cKIT_K27me3_1

description: 150bp PE CUT&Tag


title: control_cKIT_K27me3_1

description: 150bp PE CUT&Tag


title: Lymph_node_none_infect_ACB_rep3


title: Skin_Spleen_Pool, B6_WT_and_Hobit_KO_001 [LaneA_VDJ]

city: Parkville

first: Jan

last: Schroeder

state: Victoria

address: Peter Doherty Institute Melbourne

department: DMI

country: Australia

institute: University of Melbourne

description: dual index

data_processing:
library strategy: CITE-seq
Sequencing reads were aligned to the reference genome using cellranger (v 7.0.0)
We used the multi subcommand to align samples from two batches to the transcriptome, CITE-seq, and TCR references
The hashtag anitbodies are treated as CITE-seq antibodies as well and demultiplexed using HTODemux command in Seurat
Assembly: Cellranger 10x genome mm10-2020-A (transcriptome)
Supplementary files format and content: CSV file for CITE-seq antibodies and hashtag sequences for demultiplexing
Supplementary files format and content: Tar files of VDJ-seq contains CSV files from the cellranger multi command
Supplementary files format and content: Tar files of filtered feature barcode matrices from the cellranger multi command.

molecule: other

source_name: Naïve, B6 WT Skin, Hobit KO Skin, B6 WT Spleen, Hobit KO Spleen (match cell barcodes of batch1 lane A GEX/HTO for demultiplexing)

extract_protocol:
10x Genomics Chromium Next GEM Single Cell 5' Gene Expression Kit with Feature Barcoding technology for Cell Surface Protein and Immune Receptor Mapping (v2 Chemistry Dual Index)
Chromium Single Cell Mouse TCR Amplification Kit. Libraries were sequenced across two separate flow cells (Batch 1 and Batch 2 in the raw files correspond to these runs).

value: CD8+ T cell


title: Skin_Spleen_Pool, CD4cre_and_WT_cMaf_CD4cre_KO_001 [LaneB_VDJ]

description: dual index

source_name: Naïve, CD4-cre WT Skin, cMaf CD4cre KO Skin, CD4cre WT Spleen, cMaf CD4-cre KO Spleen (match cell barcodes of batch1 lane B GEX/HTO for demultiplexing)


title: Lymph_node_infected_Veh_rep4


title: Lymph_node_infected_Veh_rep3


title: Skin_Spleen_Pool, B6_WT_and_Hobit_KO_002 [LaneD_VDJ]

description: dual index

source_name: Naïve, B6 WT Skin, Hobit KO Skin, B6 WT Spleen, Hobit KO Spleen (match cell barcodes of batch1 lane D GEX/HTO for demultiplexing)


title: Microdissection_WT_External_3

city: Rennes

first: Luc

last: Paillard

state: Brittany

address: 2 Ave Leon Bernard

department: IGDR (UMR6290)

country: France

institute: Univ Rennes

description:
External
DEA_tab_Microdissection_3D_WT_Internal_vs_External.csv

data_processing:
Only sens reads are use for this analysis since the library correspond to 3’end RNA-seq
reads were trimmed following lexogene suggestion, the adaptator and the polyA tail, only read with a length superior to 20 nt were kept
Trimmed reads were map to the mouse genome (GRCm38.p6) with STAR software (2.7.8a)
Uniquely mapped reads were count by featureCount (v1.6.0)
Supplementary files format and content: GRCm38.p6
Supplementary files format and content: Differential expression analysis by edgr, with cpm (count per millions) normaliezd for each sample and statistical Gene Expression difference for each genes.

source_name: Lens epithelial cells

extract_protocol:
RNA from 2D and 3D sample have been extracted with the Nucleospin kit (Macherey-Nagel) and the RNA from the microdissection (internal and external part) were extracted with a specific kit, the Arcturus PicoPure (ThermoFisher)
3’ end seq library were prepared using the QuantSeq 3’ mRNA-Seq library Kit (Lexogen)

value: Lens epithelial cells

tag: protocol

value: External


title: Skin_Spleen_Pool, CD4cre_and_WT_cMaf_CD4cre_KO_002 [LaneC_VDJ]

description: dual index

source_name: Naïve, CD4-cre WT Skin, cMaf CD4cre KO Skin, CD4cre WT Spleen, cMaf CD4-cre KO Spleen (match cell barcodes of batch1 lane C GEX/HTO for demultiplexing)


title: Microdissection_WT_External_2

tag: cell line


title: Skin_Spleen_Pool, B6_WT_and_Hobit_KO_001 [LaneA_GEX_HTO]

description: dual index

source_name: Naïve (HT1), B6 WT Skin (HT2), Hobit KO Skin (HT3), B6 WT Spleen (HT4), Hobit KO Spleen (HT5)


title: Microdissection_WT_External_1