title: s2t4_S8_R1_001

status: Public on Feb 05 2024

city: Wuerzburg

first: Chase

last: Beisel

address: Josef-Schneider-Str. 2 / Bau D15

institute: Helmholtz Institute for RNA-based Infection Research

description:
essentiality_screen_counts.csv
essentiality_screen_logFC.csv

data_processing:
Sequence reads with perfect matches were assigned to the gRNA library using a Python script
After filtering by 1 count per million in minimal 2 samples, gRNAs were first filtered by 1 count per million in minimal 2 samples in the essentiality screen.  Read counts of each gRNA were normalized with non-targeting guides using the trimmed Mean of M method in edgeR (version 3.28.0). RUVs in RUVSeq (version 1.20.0) (Risso et al., 2014) was used to capture batch effects between the two replicate experiments. Differential abundance (log2FC) of gRNAs between time points was calculated using the quasi-likelihood F test after fitting in a generalized linear model.
Assembly: NC_000913.3
Supplementary files format and content: CSV, counts and normalized differential abundance of each gRNA in different time points
Library strategy: CRISPR screen

source_name: bacterial cells

extract_protocol:
Library plasmids were isolated by mini- or midiprep (Zymo Research kits)
The sequencing libraries were generated in two steps using the KAPA HiFi HotStart Library Amplification Kit for Illumina® platforms (Roche). With the first PCR the sequencing primer binding sites, with the second PCR the unique indices and flow cell-binding sequence were added. The amplicons of the first and second PCR reactions were purified using solid-phase reversible immobilization beads (AMPure XP, Beckman Coulter) following the manufacturer’s instructions to remove excess primers and possible primer dimers. For the library from the genome-wide essentiality screen, forward primers were used, with the terminal end staggered by one base pair so as to add to sequencing library complexity. Libraries from the dual-sgRNA screen were sequenced on a NovaSeq 6000 sequencer, libraries from the genome-wide essentiality screen were sequenced on a Illumina NextSeq system.

value: base edited, base editor version "s"

tag: time point

value: time point 4


title: SMC__Pat23

status: Public on Feb 14 2024

type: SRA

city: Daejeon

first: Jun Hyeong

last: Lee

address: 291 Daehak-ro, Yuseong-gu, Daejeon

country: South Korea

institute: KAIST

library_source: transcriptomic

data_processing:
The adapter sequences in the FASTQ file were trimmed out by Trimmomatic (v.0.39)
To filter out rRNA, SortMeRNA (v.2.1b) was used.
The filtered reads were aligned to the hg38 reference genome by the STAR aligner (v.2.7.6a) in two-pass basic mode with gencode annotation (v.35)
The aligned reads were then sorted by samtools (v.1.7) and the read counts were calculated by HTSeq
To quantify gene expression, the read counts were normalized in the TPM value.
Assembly: Hg38
Supplementary files format and content: tab-delimited text file includes TPM values for each sample (Protein-coding genes only)

molecule: total RNA

organism: Homo sapiens

source_name: Lung cancer tissue

extract_protocol:
The AllPrep DNA/RNA Mini Kit (Qiagen, USA) was used to purify RNA from formalin-fixed paraffin-embedded (FFPE) or fresh tumor samples.
Library preparation was performed with either the TruSeq RNA Library Prep Kit v2 (Illumina, USA) or the TruSeq RNA Access Library Prep Kit (Illumina, USA), following the manufacturer’s instructions.

tag: tissue

value: Lung cancer tissue

tag: ethnicity

value: Korean

tag: treatment outcome

value: Non-responder

tag: treatment

value: PD-1/PD-L1 inhibitor


title: s1t4_S4_R1_001

country: Germany

library_source: other

molecule: other

organism: Escherichia coli

tag: strain


title: s1t2_S2_R1_001

value: time point 2


title: s1t3_S3_R1_001

value: time point 3


title: s2t3_S7_R1_001


title: SMC__Pat19


title: s2t2_S6_R1_001


title: e2t4_S16_R1_001

value: base edited, base editor version "e"


title: s2t1_S5_R1_001

value: time point 1


title: SMC__Pat7

description: *** Raw data not provided for this sample due to patient privacy concerns ***

value: Responder


title: e2t2_S14_R1_001


title: e1t4_S12_R1_001


title: e1t2_S10_R1_001


title: e2t1_S13_R1_001


title: s1t1_S1_R1_001


title: e1t3_S11_R1_001


title: MOPS_2_S25_R1_001

description:
dual_sgRNA_screen_counts.csv
dual_sgRNA_screen_logFCs.csv

value: cultured in MOPS medium


title: e2t3_S15_R1_001


title: M9_1_S22_R1_001

value: cultured in M9 medium


title: M9_2_S23_R1_001


title: BE_2_S19_R1_001

value: base edited


title: killing_2_S21_R1_001

value: Cas9-induced killing of unedited cells


title: e1t1_S9_R1_001


title: BE_1_S18_R1_001


title: MOPS_1_S24_R1_001


title: killing_1_S20_R1_001


title: LB_2_S17_R1_001

value: cultured in LB medium


title: initial_library_S15_R1_001

value: initial library


title: Line#2, Tam-inducible, Day4, NEUROD1, rep6

status: Public on Jan 10 2024

city: Brookline

first: Ramesh

middle: A

last: Shivdasani

state: Massachusetts

address: SM1052, Smith10, 450 Brookline Ave

department: Medical Oncology

country: USA

institute: DFCI

library_source: genomic

data_processing:
library strategy: Cut&Run
Sequenced reads were aligned to the UCSC hg19 genome using CUT&RUNTools (https://bitbucket.org/qzhudfci/cutruntools/). Included files were from output folders for reads less than 120bp and peak calling with SEACR
Assembly: hg19
Supplementary files format and content: bigWig
Supplementary files format and content: text file includes the identified binding regions post-processing of the CUT&RUN dataset

molecule: genomic DNA

growth_protocol: DMEM, 20 % F12K, 20% FBS, 10% R-Spondin-2 conditioned medium, 10 mM nicotinamide, 100µg/ml Primocin, 1 μM A8301, 5 μg/ml  insulin, 10 μM Y-27632, 1 μM DMH1, 50 ng/ml EGF and 2 μM T3. Cells were cultured at 37oC at 7.5% CO2.

extract_protocol:
Nuclei were isolated, bound to concanavalin A coated magnetic beads and incubated with primary antibody, MNase  treated to extract antibody bound DNA fragments..
Cut&Run libraries were prepared using the NEBNext UltraII DNA Library Preparation Kit.

tag: cell line

tag: cell type

value: Neurog3 Tam-inducible Ileal intestinal stem cells

tag: chip antibody

value: anti-NEUROD1 (CST, #4373)


title: scATAC_WT [vivo WT PD1+Tim3+ CD8 T cell]

status: Public on Feb 01 2024

city: Shinjuku-ku

first: Taeko

last: Hayakawa

state: Tokyo

address: 35 Shinanomachi

department: Division of Tumor Immunology, Institute for Advanced Medical Research

country: Japan

institute: Keio University School of Medicine

description: vivo WT PD1+Tim3+ CD8 T cell

data_processing:
Fastq files were processed with cellranger-atac count pipeline, version 2.1.0.Assembly: mm10
(https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac)
Assembly: mm10
Supplementary files format and content: cut_sites(.bigwig)

organism: Mus musculus

source_name: B16-OVA tumor

extract_protocol:
On day 10, after adoptive transfer CD8+PD1+Tim3+ TILs of each implanted mouse were used as a single-cell ATAC-seq sample.
Library was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell ATAC Reagent Kits v2, 10x Genomics).

value: B16-OVA tumor

value: CD8+PD1+Tim3+ TIL

tag: genotype

value: WT & NR4aDKO


title: scATAC_KO [vivo Nr4a dKO PD1+Tim3+ CD8 T cell]

description: vivo Nr4a dKO PD1+Tim3+ CD8 T cell


title: Line#2, Tam-inducible, Day4, NEUROD1, rep1


title: Line#2, Tam-inducible, Day4, NEUROD1, rep2


title: LB_1_S16_R1_001


title: Line#2, Tam-inducible, Day4, NEUROD1, rep4


title: Line#2, Tam-inducible, Day4, NEUROD1, rep3


title: Line#2, Tam-inducible, Day4, ASCL1, rep2

value: anti-ASCL1 (Abcam, #ab74065)


title: Line#2, Tam-inducible, Day4, ASCL1, rep3


title: Line#2, Tam-inducible, Day4, NEUROD1, rep7


title: HCT116 cells, control, rep1

status: Public on Jan 08 2024

city: Berlin

first: IBRAHIM

middle: AVSAR

last: ILIK

state: Berlin

address: Ihnestraße 63-73

institute: Max-Planck-Institut für molekulare Genetik

data_processing:
Illumina base calling, demultiplexing and FASTQ conversion
Read alignment to the human genome (GRCh38 assembly) using STAR 2.7.9a
Reads counted on GENCODE release 29 gene models using STAR 2.7.9a
Read alignments (.bam files) converted to bigWigs using bamCoverage 3.5.1
Assembly: hg38
Supplementary files format and content: Two-column tab-delimited text file with gene identifier and raw read count columns
Supplementary files format and content: Raw RNA-seq coverage in bigWig format, separate files for plus and minus strands

molecule: polyA RNA

extract_protocol:
Total RNA was extracted from cells with Quick-RNA MicroPrep kit (Zymo). Polyadenylated RNA was then isolated using Dynabeads™ mRNA Purification Kit. Purification was done twice to increase purity.
Strand-specific libraries were generated using KAPA Stranded RNA-seq Library Preparation Kit (Roche)

tag: sirna

value: control


title: Line#2, Tam-inducible, Day4, ASCL1 rep1


title: Line#2, Tam-inducible, Day4, IgG, rep1

value: IgG (Millipore, 12-370)


title: HCT116 cells, control, rep3


title: 6986-SK-12  Whole_blood_HKSA

status: Public on Jan 01 2024

city: Nashville

first: Ryan

last: Stark

state: Tennessee

address: 2200 Children's Way, 5121 Doctors' Office Tower

institute: Vanderbilt University Medical Center

description: 6986-SK-12 / Whole_blood_HKSA

data_processing:
RNA sequencing reads were adapter-trimmed and quality-filtered using Trimgalore v0.5. An alignment reference was generated from the GRCh38 human genome and GENCODE comprehensive gene annotations (Release 26), to which trimmed reads were aligned and counted using Spliced Transcripts Alignment to a Reference (STAR) v2.7.9a with the –quantMode GeneCounts parameter. On average, 46 million uniquely mapped reads were acquired per sample. DESeq2 package v1.34.0 was used to perform sample-level quality control, low count filtering, normalization and downstream differential expression analysis
Assembly: GRCh38 human genome
Supplementary files format and content: raw_counts.txt file contains raw counts per genes. These counts are outputs from Spliced Transcripts Alignment to a Reference (STAR) v2.7.9a alignment with the –quantMode GeneCounts parameter.
Supplementary files format and content: normalized_counts.txt file contains normalized counts per gene in each sample. These normalized counts are absolute values after normalization performed by DESeq2.

source_name: whole blood

extract_protocol: Extracted RNA was treated for globin and rRNA depletion by NEB globin/ribo reduction kit and was sequenced at 150 basepair Paired End (PE) sequencing performed on the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA) to generate approximately 50 million reads per sample

treatment_protocol: Blood was drawn via venipuncture from each participant and immediately aliquoted into 3 equal volume EDTA tubes containing either 100 μl of either sterile water (control), 3x108 CFU/ml of heat-killed Escherichia coli (HKEC strain 0111:B4, Invivogen, San Diego, CA, USA) or 3x108 CFU/ml heat-killed Staphylococcus aureus (HKSA, Invivogen), each resuspended in equal volumes of endotoxin-free, sterile water. Blood was then incubated on an orbital shaker at 80 rpm at 37 °C for 6 hours. Afterwards, blood was transferred to PAXgene Blood RNA Tubes (QIAGEN, Hilden, Germany) and stored in the freezer at −80 °C until RNA extraction

value: whole blood

value: Heat killed Staphylococcus aureus


title: 6986-SK-03  Whole_blood_HKSA

description: 6986-SK-03 / Whole_blood_HKSA


title: 6986-SK-06  Whole_blood_HKSA

description: 6986-SK-06 / Whole_blood_HKSA


title: HCT116 cells, control, rep2


title: 6986-SK-08  Whole_blood_HKEC

description: 6986-SK-08 / Whole_blood_HKEC

value: Heat killed Escherichia coli


title: 6986-SK-11  Whole_blood_HKEC

description: 6986-SK-11 / Whole_blood_HKEC


title: Line#2, Tam-inducible, Day4, NEUROD1, rep5


title: 6986-SK-02  Whole_blood_HKEC

description: 6986-SK-02 / Whole_blood_HKEC


title: 6986-SK-01  Whole_blood_Control

description: 6986-SK-01 / Whole_blood_Control

value: Control


title: Outgrowth_Overnight_Nonselective_1_1000_Dilution [R3-v2]

data_processing:
The count for each barcode in the samples was determined using the command "zgrep -c “CTGCNNNN” *.fastq.gz" where NNNN represents each 4-nt barcode
Genome_build: not applicable
Supplementary_files_format_and_content: count for each barcode in the sample

organism: Bifidobacterium breve

source_name: plasmid DNA

extract_protocol:
Barcode portion of plasmid amplified with PCR (268 bp) and purified with column, then submitted for sequencing.
Sequencing adaptor added to amplicons, then high-throughput amplicon sequencing performed by Genewiz.

value: plasmid DNA transformed into B. breve UCC2003, 20 mg/L, recoveries grown overnight. 20 mg/L Tetracycline then added to transformation recoveries in 1:1000 dilution cultures that were grown for 48 hours. Plasmid DNA was then extracted from cultures.

tag: dilution

tag: molecule subtype

value: plasmid DNA amplified with PCR


title: 6986-SK-07  Whole_blood_Control

description: 6986-SK-07 / Whole_blood_Control


title: 6986-SK-04  Whole_blood_Control

description: 6986-SK-04 / Whole_blood_Control


title: Colonies_tetracycline_20 [C20]

value: plasmid DNA transformed into B. breve UCC2003, plated on agar plates supplemented with 20 mg/L tetracycline, grown for 48 hours. Plasmid DNA then extracted from pooled colonies.


title: Line#2, Tam-inducible, Day4, IgG, rep2


title: Outgrowth_Overnight_Nonselective_1_100_Dilution [R2-v2]

value: plasmid DNA transformed into B. breve UCC2003, 20 mg/L, recoveries grown overnight. 20 mg/L Tetracycline then added to transformation recoveries in 1:100 dilution cultures that were grown for 48 hours. Plasmid DNA was then extracted from cultures.


title: Outgrowth_Overnight_Nonselective_1_10,000_Dilution [R4-v2]

value: plasmid DNA transformed into B. breve UCC2003, 20 mg/L, recoveries grown overnight. 20 mg/L Tetracycline then added to transformation recoveries in 1:10,000 dilution cultures that were grown for 48 hours. Plasmid DNA was then extracted from cultures.


title: celLN stromal cell cLN_YP147

status: Public on Dec 31 2023

city: Nanjing

first: Mangge

last: Zou

address: No.6 Building, Life Science TechTown, 568 Longmian Avenue Jiangning District

country: China

institute: Legend Biotech

data_processing:
Data were demultiplexed using Cell Ranger software (version 2.0.0) based on 8 bp 10X sample indexes and paired-end FASTQ files generated. The cell barcodes and transcript UMIs were processed as previously described (Zheng et al., 2017). Subsequently, read 2, which contains the transcript insert sequence, was aligned to mouse UCSC mm10 reference genome using STAR aligner with default parameters (Dobin and Gingeras, 2015). The alignment results were used to quantify the expression level of mouse genes and generation of gene-barcode matrix, which were further processed with Seurat (version 3.0.0). All cells received an identifier which was used as common meta-data throughout the analysis including differentiation trajectories and dynamic gene regulatory networks (see below).
All cells with less than 500 or more than 5000 detected genes per cell were filtered out. Moreover, cells with more than 7.5 % of the total reads mapping to mitochondrial genes were removed. After quality control, in total 3034 cells were subjected to canonical correlation analysis and regressed against the variables, number of UMIs, percent of mitochondrial reads, percent of ribosomal reads. The first 30 principal components (PCs) were provided as an input for dimensionality reduction via t-SNE based on the JackStraw method. Cd31-expressing clusters (BECs and LECs) were excluded (resolution = 0.6) and only Cd31- clusters (NESs, 1166 cells) were re-embedded as described above.
For the subsequent analysis with NESs, The first 15 PCs were used as an input for t-SNE-mediated dimensionality reduction, and clusters were identified with graph-based clustering (FindClusters, resolution = 1.1). Markers significantly enriched in a cluster were identified via FindAllMarkers (Wilcoxon rank sum test, min.pct = 0.1, thresh.use = 0.1, only.pos = TRUE). DEGs in the comparison of PBS and infected group within each cluster were identified by the setting of “avg_logFC > 0.15 & p_val_adj < 0.05”.
Genome_build: mm10
Supplementary_files_format_and_content: CellRanger processed fastq output yielding RMCs and gene annotation

source_name: celiac lymph node

growth_protocol: Neonatal mice were orally infected with 104 CFU of Y. pseudotuberculosis YPIII derivative YP147 (ΔcnfY, KanamycinR). Twelve weeks post infection, LNs were harvested for stromal cell isolation.

extract_protocol:
Single CD45‑CD24‑ cells were sorted by FACS ARIA III (BD) and collected in PBS containing 0.04 % w/v BSA at a density of 400 cells/μl. Chromium™ Controller was used for partitioning single cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs)
Single Cell 3’ reagent kit v2 for reverse transcription, cDNA amplification and library construction (10xGenomics, Cat. #120236). The detailed protocol was provided by 10xGenomics. SimpliAmp Thermal Cycler was used for amplification and incubation steps (Applied Biosystems). Libraries were quantified by QubitTM 3.0 Fluometer (ThermoFisher) and quality checked using 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent).
Sequencing was performed in paired-end mode (2 x 75 cycles) using NextSeq 500 sequencer (Illumina) to attain approximately 170,000 reads per single cell.

treatment_protocol: For stromal cell isolation, celiac LN were resected and digested in RPMI 1640 medium (Gibco) containing 0.2 mg/ml collagenase D (Roche), 0.15 U/ml dispase (Roche) and 0.2 mg/ml DNase I (Roche). After digestion, cells were kept at 4°C in PBS containing 0.2 % BSA and 5 mM EDTA (Roth). In a first step, CD45- cells were enriched by autoMACS separation after direct magnetic labeling of CD45+ cells using CD45 Nanobeads (Biolegend). Subsequently, the CD45- fraction was stained using fluorescence-coupled antibodies and used to sort bulk CD45-CD24- non-hematopoietic cells (Aria III, 70 μm nozzle) for scRNA‑seq.

value: BALB/c

value: ex vivo isolated cells CD24-CD45-

tag: age

value: 12-week-old neonatally Yptb-infecteded mice


title: Outgrowth_Overnight_Nonselective_1_10_Dilution [R1-v2]

value: plasmid DNA transformed into B. breve UCC2003, 20 mg/L, recoveries grown overnight. 20 mg/L Tetracycline then added to transformation recoveries in 1:10 dilution cultures that were grown for 48 hours. Plasmid DNA was then extracted from cultures.


title: 6986-SK-05  Whole_blood_HKEC

description: 6986-SK-05 / Whole_blood_HKEC


title: Colonies_tetracycline_5 [C5]

value: plasmid DNA transformed into B. breve UCC2003, plated on agar plates supplemented with 5 mg/L tetracycline, grown for 48 hours. Plasmid DNA then extracted from pooled colonies.


title: Outgrowth_Antibiotics_Added_Immediately [R1-48]

value: plasmid DNA transformed into B. breve UCC2003, 20 mg/L tetracycline added to transformation recoveries in 1:10 dilution cultures that were grown for 48 hours. Plasmid DNA was then extracted from cultures.


title: SMC__Pat25

value: Lung cancer tissue

value: Korean

value: Responder

value: PD-1/PD-L1 inhibitor


title: Library_Pool [Pool]


title: Wing disc_AIDUb_replicate 3

city: Toulouse

first: muriel

last: BOUBE-TREY

address: 4bis av Hubert Curien

country: France

institute: CNRS INSERM

description: Control of ub driver effect (no Med19 degradation )

data_processing:
The quality control of fastq sequences was done with FastQC (v0.11.4), then reads were aligned using TopHat2 (v2.0) on the Drosophila melanogaster genome dm6.
Paired reads were counted by gene using htseq (v1.0).
These counts were used to perform differential gene expression analyses using DESeq2 (1.26.0) in R comparing UbAux with either Ub or AID control condition.
We selected differentially expressed genes (DEGs) by setting a significance determined by Benjamini-Hochberg adjusted P-values < 0.05 and -0.5<Log2(FoldChange)<0.5.
Genome_build: dm6
Supplementary_files_format_and_content: The excel file All_DEG_AID.xlsx, contains the matrix table of expressed genes in our samples obtained after the differential analysis  by DESeq2.
Supplementary_files_format_and_content: The excel file DEG_UbAuxvsUb_pad0.05_FC0.5.xlsx contains the matrix table obtained after the differential analysis AIDUbAux vs AIDUb by DESeq2 selecting differentially expressed genes with adjusted P-values < 0.05 and -0.5<Log2(FoldChange)<0.5.

organism: Drosophila melanogaster

source_name: Wing discs

growth_protocol: Flies were raised at 25°C on standard yeast agar cornmeal medium.

extract_protocol:
Wing discs were hand-dissected at 4°C RNA extraction was made using TRIzol reagent.
RNA Library was prepared using standard Illumina protocols for strand-specific  RNA-seq with PolyA selection.

treatment_protocol: Female  L3 larvae carrying ubiquitin gal4 driver and Med19AID were either fed with Auxin analog NAA (AIDUbAux) for 4h to induce M19 degradation, or not (AIDUb) as a control. A second control was performed to monitor Auxin effect with female Med19AID L3 larvae (without any driver)  that were fed with Auxin (AIDAux).There are 3 independant experiments A (samples 1,2,3), B (samples 4,5,6) and C (samples 7,8, 9).

value: ub> Med19AID

tag: auxin treatment

value: no

tag: developmental stage

value: L3 larvae


title: celLN stromal cell cLN_PBS

value: 12-week-old PBS-treated mice


title: Wing disc_AIDAux_replicate 3

description: Control of auxin effect (no Med19 degradation )

value: yes


title: Wing disc_AIDUbAux_replicate 3

description: Med19 degradation (drived by ub driver)


title: Wing disc_AIDUbAux_replicate 2

description: Med19 degradation (drived by ub driver)


title: 6986-SK-09  Whole_blood_HKSA

description: 6986-SK-09 / Whole_blood_HKSA

value: whole blood

value: Heat killed Staphylococcus aureus


title: Wing disc_AIDUb_replicate 2


title: Wing disc_AIDUbAux_replicate 1

description: Med19 degradation (drived by ub driver)


title: Wing disc_AIDAux_replicate 2


title: Wing disc_AIDAux_replicate 1


title: 6986-SK-10  Whole_blood_Control

description: 6986-SK-10 / Whole_blood_Control

value: Control


title: cLN2_PBS

data_processing:
Sequencing reads were mapped to mouse genome (mm10) using STAR and aligned reads to annotated genes were quantified with htseq-count
calculated read counts were further processed with DESeq2 for quantiﬁcation of differential gene expression. Raw read counts were converted to RPKM (reads per kilobase of exon length per million mapped reads) values.
Gene ontology analysis was performed using topGO
Genome_build: mm10
Supplementary_files_format_and_content: comma separated values (.csv) file of DESeq2 results

extract_protocol:
FSCs were FACS sorted into RLT+ lysis buffer (Qiagen) which contained 10 µl/ml β-mercaptoethanol (Roth). In the following, the total RNA was extracted with the RNeasy Plus Micro kit (Qiagen) according to manufacturer`s instructions
cDNA conversion was carried out using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Clontech Laboratories) according to manufacturer’s instructions, followed by PCR product purification with Agencourt AMPure XP magnetic beads (Beckman Coulter). Libraries were prepared with the Nextera XT DNA Library Prep Kit (Illumina) employing enzymatic tagmentation and simultaneous adapter ligation before subsequent indexing and fragment amplification. PCR product clean-up and size selection was performed with the Agencourt AMPure XP magnetic beads. RNA and cDNA quality and content as well as the correct sizing of cDNA library fragments was verified using the Agilent Technologies 2100 Bioanalyzer profiles and Qubit measurements after each step.
Sequencing of libraries was carried out at the sequencing facility on Illumina HiSeq2500 using 50 bp single-end reads and quality of sequenced libraries was verified with FastQC.

treatment_protocol: For stromal cell isolation, skin-draining pLNs (inguinal and axillary), mesenteric LNs and celiac LN were resected and digested in RPMI 1640 medium (Gibco) containing 0.2 mg/ml collagenase D (Roche), 0.15 U/ml dispase (Roche) and 0.2 mg/ml DNase I (Roche). After digestion, cells were kept at 4°C in PBS containing 0.2 % BSA and 5 mM EDTA (Roth). In a first step, CD45- cells were enriched by autoMACS separation after direct magnetic labeling of CD45+ cells using CD45 Nanobeads (Biolegend). Subsequently, the CD45- fraction was stained using fluorescence-coupled antibodies and used to sort CD45-CD24-CD31-PDPN+ FSCs by FACS (Aria II, 100 μm nozzle) for RNA‑seq analysis.

value: fibroblastic stromal cell

value: PBS

value: Balb/c


title: Wing disc_AIDUb_replicate 1


title: cLN3_YP147

value: Yersinia


title: cLN1_PBS


title: cLN2_YP147


title: mLN3_YP147

source_name: mesenteric lymph node


title: cLN3_PBS


title: mLN1_PBS


title: pLN3_YP147

source_name: skin-draining lymph node


title: mLN2_YP147


title: pLN1_PBS


title: mLN1_YP147


title: mLN2_PBS


title: mLN3_PBS


title: ResDC_cLN2_YP147

growth_protocol: Neonatal mice were orally infected with 104 CFU of Y. pseudotuberculosis YPIII derivative YP147 (ΔcnfY, KanamycinR). Twelve weeks post infection, LNs were harvested for dendritic cell isolation.

extract_protocol:
MigDCs and ResDCs were FACS sorted into RLT+ lysis buffer (Qiagen) which contained 10 µl/ml β-mercaptoethanol (Roth). In the following, the total RNA was extracted with the RNeasy Plus Micro kit (Qiagen) according to manufacturer`s instructions
cDNA conversion was carried out using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Clontech Laboratories) according to manufacturer’s instructions, followed by PCR product purification with Agencourt AMPure XP magnetic beads (Beckman Coulter). Libraries were prepared with the Nextera XT DNA Library Prep Kit (Illumina) employing enzymatic tagmentation and simultaneous adapter ligation before subsequent indexing and fragment amplification. PCR product clean-up and size selection was performed with the Agencourt AMPure XP magnetic beads. RNA and cDNA quality and content as well as the correct sizing of cDNA library fragments was verified using the Agilent Technologies 2100 Bioanalyzer profiles and Qubit measurements after each step.
Sequencing of libraries was carried out at the sequencing facility on Illumina NovaSeq6000 using 50 bp single-end reads and quality of sequenced libraries was verified with FastQC.

treatment_protocol: For dendritic cell isolation, skin-draining pLNs (inguinal and axillary), mesenteric LNs and celiac LN were resected and digested in RPMI 1640 medium (Gibco) containing 0.2 mg/ml collagenase P (Roche), 0.15 U/ml dispase (Roche) and 0.2 mg/ml DNase I (Roche). After digestion, cells were kept at 4°C in PBS containing 0.2 % BSA and 5 mM EDTA (Roth). In a first step, CD45+ cells were enriched by autoMACS separation after magnetic labeling of CD45+ cells using CD45 Nanobeads (Biolegend). Subsequently, the CD45+ fraction was stained using fluorescence-coupled antibodies and used to sort CD3-CD45R-Ly6G-CD11chiMHCII+ ResDCs and CD3-CD45R-Ly6G-CD11c+MHCIIhiMigDCs by FACS (Aria II, 70 μm nozzle) for RNA‑seq analysis.

value: resident dendritic cell


title: pLN2_YP147


title: ResDC_pLN3_YP147


title: ResDC_mLN2_YP147


title: ResDC_pLN1_YP147


title: pLN1_YP147


title: ResDC_pLN3_PBS


title: pLN3_PBS


title: cLN1_YP147


title: ResDC_pLN2_YP147


title: ResDC_pLN2_PBS


title: ResDC_cLN1_YP147


title: pLN2_PBS


title: ResDC_pLN1_PBS


title: MigDC_cLN3_YP147

value: migratory dendritic cell


title: ResDC_cLN3_PBS


title: ResDC_cLN3_YP147


title: ResDC_cLN1_PBS


title: MigDC_cLN1_PBS


title: ResDC_mLN3_YP147


title: ResDC_mLN1_YP147


title: ResDC_cLN2_PBS


title: ResDC_mLN3_PBS


title: ResDC_mLN2_PBS


title: ResDC_mLN1_PBS


title: MigDC_mLN2_PBS


title: MigDC_pLN2_YP147


title: MigDC_pLN3_YP147


title: MigDC_cLN2_YP147


title: MigDC_cLN1_YP147


title: MigDC_mLN2_YP147


title: MigDC_mLN1_YP147


title: MigDC_cLN2_PBS


title: 3xTxNK rep2

status: Public on Dec 21 2023

city: Madison

first: Zachary

middle: Scott

last: Morris

state: Wisconsin

address: 1111 Highland Ave., WIMR Tower 1, Room 3131

department: Human Oncology

institute: University of Wisconsin-Madison

data_processing:
The trimming software skewer was used to preprocess raw fastq files by trimming adaptor sequences from reads and clipping low quality bases (< 20 Phred)  from read 3' ends.
The trimmed paired-end reads were  aligned to GRCm39 using STAR
read alignments were processed by RSEM to estimate expected gene counts
Assembly: GRCm39
Supplementary files format and content: tab-delimited gene counts matrix plain text file

source_name: tumor

extract_protocol:
On day 12, distant tumors were collected. The tumor tissues were dissected and transferred to tubes containing 2.8 mm ceramic beads (Fisher Brand) with 1 ml of Trizol reagent (ThermoFisher). The samples were homogenized using a Bead Ruptor Elite (OMNI) for 45 s. RNA was isolated using Qiagen’s RNeasy Mini Kit according to the manufacturer’s instructions.
TrueSeq Stranded mRNA (Illumina) was used to construct libraries using 1ug of RNA as input.

value: tumor

value: Murin Head and Neck squmous cell carcinoma

value: primary tumor radiation therapy, intratumoral interleukin-2, intratumoral cetuximab, and anti-NK1.1 depletion antibody


title: IgG rep2

value: primary tumor intratumoral IgG


title: MigDC_mLN3_PBS


title: MigDC_pLN3_PBS


title: MigDC_mLN1_PBS


title: MigDC_pLN1_YP147


title: MigDC_pLN2_PBS


title: 3xTx rep1

value: Murine Head and Neck squmous cell carcinoma carcinoma

value: primary tumor radiation therapy, intratumoral interleukin-2, and intratumoral cetuximab


title: CD4+ TCRb+CD44+, wild type control, 3

status: Public on Nov 22 2023

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2, https://benthamopen.com/ ABSTRACT/TOBIOIJ-7-1) was used to remove any remaining adapter sequence.
Reads were aligned by STAR1 2.4.2a to GRCm38.91
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2)30, and HTSeq-count (v0.4.1).
Assembly: GRCm38.91
Supplementary files format and content: Processed data is in .csv format. Each row is a gene, each column is a sample.

source_name: spleen

extract_protocol:
cDNA was prepared with SMARTseq kit, Takara.
RNA libraries for RNA-seq were prepared using NexteraXT kit, Illumina.

treatment_protocol: 250 cells were sorted into SMARTseq buffer.

value: spleen

value: memory CD4+ T cells

value: WT

value: cell sorting

tag: time

value: ex-vivo

value: wildtype


title: MigDC_cLN3_PBS

value: PBS


title: CD4+ TCRb+CD44+, wild type control, 2


title: MigDC_mLN3_YP147

value: Balb/c


title: 3xTxNK rep3


title: CD4+ TCRb+CD44+, STAT1GOF/CMVCre, 3


title: IgG rep4


title: 3xTxNK rep1


title: 3xTx rep3


title: 3xTx rep4


title: IgG rep1


title: IgG rep3


title: HNRNPDL knockdown replicate 1

status: Public on Nov 21 2023

city: Marburg

first: Julia

middle: E.

last: Weigand

address: Marbacher Weg 6

department: Pharmacy

institute: University of Marburg

data_processing:
Reads were mapped to the human genome (GRCh38/hg38 assembly) using the splice-aware aligner STAR version 2.5.4b (Dobin et al. 2013).
The htseq-count script from the HTSeq python package version 0.6.1p1 (Anders et al. 2015) was used to count reads within genes annotated in GENCODE version 32.
Genome_build: Human genome GRCh38/hg38 assembly
Supplementary_files_format_and_content: Tab-delimited table of read counts per gene. Generated by running htseq-count with default parameters.

source_name: whole cell RNA extract

growth_protocol: HUVECs (Lonza, CC-2519) were cultured in T75 flasks in EBM medium (Lonza) supplemented with 10% FCS (Thermo Fisher Scientific) and EGM single quots [(hEGF, Hydrocortison, GA-1000, bovine brain extract (Lonza)]. HUVECs were split once a week and only passages 2 and 3 were used for experiments.

extract_protocol:
Total RNA from HUVECs was isolated 48 h later, using the miRNeasy Mini kit (Qiagen), including the optional on-column DNA digest with the RNase-Free DNase Set (Qiagen). After isolation, 500 ng RNA were quality checked on a 1% agarose gel.
For the HNRNPDL knockdown experiments (n = 2), total RNA from HUVECs transfected either with a non-silencing control siRNA (si_ctrl) or an siRNA targeting HNRNPDL (si_DL) was used to generate polyA-enriched strand-specific cDNA libraries. Libraries were sequenced on a HiSeq 2000 (Illumina), obtaining 76 nt paired-end reads.

treatment_protocol: For siRNA transfection, 3.5x10^5 cells were seeded in 60 mm cell culture dishes. 24 h later, transfection was performed using Lipofectamine RNAiMAX according to the manufacturer’s protocol with 60 pmol siRNA (nonsilencing control siRNA: 5´-UUCUCCGAACGUGUCACGU[dT][dT]-3´ or an siRNA targeting HNRNPDL [5´-GGGUAUAACUAUGGGAACU[dT][dT]-3´]) in OptiMEM medium. After 4 h the transfection mixes were removed, and fresh medium was added.

value: HUVEC

value: siRNA targeting HNRNPDL


title: 3xTx rep2


title: HNRNPDL knockdown replicate 2


title: 10xATAC_D018_13_hu_Lobe_atac_lib

status: Public on Nov 07 2023

city: Palo Alto

first: Lattice

last: Data Coordination

state: CA

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

library_source: genomic single cell

data_processing:
raw_matrix_normalized:False; raw_matrix_value_scale:linear; raw_matrix_background_barcodes_included:False
The snRNA-seq and snATAC-seq raw data were processed with cell ranger.
Assembly: raw_matrix_assembly:GRCh38
Supplementary files format and content: raw_matrix_file_format:hdf5

source_name: peripheral region of retina

extract_protocol:
Samples included in this study were retinal tissues of 20 donors from the Utah Lions Eye Bank. All donors were screened for medical history, and only the ones with no of retinal diseases were used in this study. Post-mortem phenotyping with OCT were performed to confirm that there were no drusen, atrophy, or any other disease phenotypes on retina. One eye was collected from each donor. All eye tissues were collected and dissected within 6 hours post-mortem. With 4mm and 6mm disposable biopsy punches, macula and peripheral retina were collected and flash frozen in liquid nitrogen, and stored at -80°C before nuclei isolation.   Nuclei for snRNA-seq were isolated by fresh-made pre-chilled RNase-free lysis buffer. The frozen tissue was resuspended and triturated in lysis buffer and homogenized with a WheatonTM Dounce Tissue Grinder.
Single cell Gene Expression Library was prepared according to Chromium Next GEM Single Cell  500 3' Reagent Kits v3.1 (10x Genomics).   Single cell ATAC Library was prepared according to Chromium Next GEM Single cell ATAC  511 Reagent kit v1.1 (10x Genomics).

value: peripheral region of retina

tag: assay

value: 10x scATAC-seq

tag: Sex

value: female

value: European

value: >89 years

value: FALSE

tag: donor id

tag: raw matrix_feature_keys

value: genomic coordinates

tag: raw matrix_value_units

value: fragment ends

tag: raw matrix_assays

value: snATAC-seq


title: AAEFMG, replicate1

status: Public on Nov 17 2023

city: Wuhan

first: Han

last: Xia

state: Hubei

department: Key Laboratory of pathogenic Viruses and Biosafety

institute: Wuhan Institute of Virology, CAS

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw reads were qualified, demultiplexed, mapped to the reference library of midgut cells of Aedes aegypti,  barcode counting, gene counting and data aggregation using with Cell Ranger.
Assembly: AaegL5.0
Supplementary files format and content: Tab-seperated value files and matrix files

organism: Aedes aegypti

source_name: midgut

extract_protocol:
Female adult mosquitoes at 7 days after eclosion were anesthetized on ice. Subsequently, midguts were dissected from a group of 40 mosquitoes, then washed and temporarily stored in a microtube filled with Schneider's Drosophila Medium kept on ice. After the dissection, the medium was discarded, and 400 ul of dissociation buffer was added into the microtube. The mixture was incubated on a rotator for 20-30 min at room temperature. Then, 400 ul of Schneider's Drosophila Medium was added to the microtube and mixed well. A total of 800 ul of the cell suspension was filtered with a 40 um Flowmi Cell Strainer to remove larger cell debris. To remove impurities and smaller cell debris, the filter was centrifuged over a density of approx. of 1.12 g/ml made with OptiPrep at 400× g RCF, 4 C for 20 min. Viable cell band was collected using a 200 ul pipette tip, mixed well in a new microtube and centrifuged at 400× g for 20 min again. The cell precipitation was washed with 1× PBS for several times and then resuspended with 200 ul of Schneider's Drosophila Medium.
Library construction was performed with Single Cell 3' v3 Chemistry according to the manufacturer's instructions.

tag: tissue

value: midgut

tag: strain

value: Rockefeller

value: Adult

value: 7 days


title: 10xATAC_D030_13_hu_Lobe_atac_lib

tag: ethnicity

value: 73 years


title: 10x3_D018_13_lib

source_name: macula lutea

value: macula lutea

value: gene symbol

tag: raw matrix_cellranger_assay_chemistry

tag: raw matrix_genome_annotation

value: GENCODE 32

value: UMI

value: snRNA-seq


title: 10xATAC_19_D6_hu_Lobe_atac_lib

value: peripheral region of retina

value: 10x scATAC-seq

value: male


title: CD4+ TCRb+CD44+, wild type control, 1

value: spleen

tag: cell type

value: memory CD4+ T cells

tag: genotype

value: WT

tag: treatment

value: cell sorting

value: ex-vivo

value: wildtype


title: 10xATAC_D026_13_hu_Lobe_atac_lib

value: European

tag: age

value: 81 years

value: FALSE

value: genomic coordinates

value: fragment ends

value: snATAC-seq


title: CD4+ TCRb+CD44+, STAT1GOF/CMVCre, 2


title: CD4+ TCRb+CD44+, STAT1GOF/CMVCre, 1


title: 10xATAC_D028_13_hu_Lobe_atac_lib

value: 67 years


title: control replicate 2

value: HUVEC

value: nonsilencing control siRNA


title: MigDC_pLN1_PBS

value: migratory dendritic cell

value: PBS

value: Balb/c


title: 10x3_D027_13_lib

value: macula lutea

value: male

value: 77 years

value: gene symbol

value: GENCODE 32

value: UMI

value: snRNA-seq


title: 10xATAC_19_D019_lobe_atac_lib

value: peripheral region of retina

value: 10x scATAC-seq

value: female

value: European

value: 82 years

value: FALSE


title: control replicate 1

value: HUVEC

value: nonsilencing control siRNA


title: 10x3_D026_13_lib

value: 81 years


title: AAEFMG, replicate2

description: 10x Genomics

extract_protocol:
!Sample_extract_protocol_ch1 = Female adult mosquitoes at 7 days after eclosion were anesthetized on ice. Subsequently, midguts were dissected from a group of 40 mosquitoes, then washed and temporarily stored in a microtube filled with Schneider's Drosophila Medium kept on ice. After the dissection, the medium was discarded, and 400 ul of dissociation buffer was added into the microtube. The mixture was incubated on a rotator for 20-30 min at room temperature. Then, 400 ul of Schneider's Drosophila Medium was added to the microtube and mixed well. A total of 800 ul of the cell suspension was filtered with a 40 um Flowmi Cell Strainer to remove larger cell debris. To remove impurities and smaller cell debris, the filter was centrifuged over a density of approx. of 1.12 g/ml made with OptiPrep at 400× g RCF, 4 C for 20 min. Viable cell band was collected using a 200 ul pipette tip, mixed well in a new microtube and centrifuged at 400× g for 20 min again. The cell precipitation was washed with 1× PBS for several times and then resuspended with 200 ul of Schneider's Drosophila Medium.
Library construction was performed with Single Cell 3' v3 Chemistry according to the manufacturer's instructions.

value: midgut

value: Rockefeller

tag: developmental stage

value: Adult

value: 7 days


title: 10xATAC_19_D5_hu_Lobe_atac_lib

value: male

value: Hispanic or Latin American

value: 53 years

value: genomic coordinates

value: fragment ends

value: snATAC-seq


title: 10x3_19_D010_lib

value: macula lutea

value: female

value: 88 years

value: gene symbol

value: GENCODE 32

value: UMI

value: snRNA-seq


title: 10x3_D028_13_lib

value: European

value: 67 years

value: FALSE


title: 10x3_19_D006_lib

value: >89 years


title: 10xATAC_D019_13_hu_Lobe_atac_lib

value: peripheral region of retina

value: 10x scATAC-seq

value: male

value: 82 years


title: 10x3_19_D008_lib

value: Hispanic or Latin American

value: 64 years


title: 10x3_D017_13_lib

value: macula lutea

value: 65 years


title: 10x3_D009_13_lib

value: Asian

value: 85 years


title: 10xATAC_19_D7_lobe_atac_lib

value: 66 years

value: genomic coordinates

value: fragment ends

value: snATAC-seq


title: 10x3_D019_13_lib

value: European

value: gene symbol

value: GENCODE 32

value: UMI

value: snRNA-seq


title: 10x3_19_D005_lib

value: male

value: 53 years

value: FALSE


title: 10xATAC_D027_13_hu_Lobe_atac_lib

value: peripheral region of retina

value: 10x scATAC-seq

value: 77 years


title: 10xATAC_19_D011_hu_Lobe_atac_lib

value: female

value: >89 years


title: 10x3_D030_13_Macula_lib

value: macula lutea

value: 73 years


title: 10x3_19_D003_lib

value: 86 years


title: DLBCL case [TXRF01_ARN_27800]

status: Public on Oct 18 2023

city: Leioa

first: Nerea

last: Bilbao-Aldaiturriaga

address: Sarriena neighbourhood without number

country: Spain

institute: University of the Basque Country

data_processing:
Libraries were sequenced Single Read, 50nts (v4) on Illumina HiSeq 2500 with a depth of approximately 10 million reads per sample.
Reads were trimmed for the presence of the small RNA adapter using Skewer and filtered removing every sequence shorter than 15 and longer than 40 bases.
Alignment to the reference genome (GRCh38) using ShortStack and the resulting alignments used by htseq-count for determining the number of tags per gene.
Every small RNA with less than 10 reads considering the sum of the reads in every condition was excluded, and we used the remaining genes for differential expression analysis with DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include DESEQ2 values for each sample comparing DLBCL cases with non-lymphoma controls

extract_protocol:
FFPE samples with the miRNeasy FFPE Kit (Qiagen, Hilden, Germany)
TruSeq small RNA Sample Prep Kit (Illumina)
Libraries were analyzed using Agilent DNA High Sensitivity chip

tag: subject status

value: DLBCL case

tag: subtype

value: unknown

tag: group

value: Group 2 - Refractory at diagnosis

tag: relapse

value: No


title: DLBCL case [TXRC02_ARN_27800]

value: Group 3 - Relapse at diagnosis


title: 10xATAC_19_D3_hu_Lobe_atac_lib

tag: assay

tag: Sex

value: European

tag: donor id

tag: raw matrix_feature_keys

value: genomic coordinates

value: fragment ends

value: snATAC-seq


title: 10x3_19_D011_lib

tag: tissue

value: FALSE

value: gene symbol

value: GENCODE 32

tag: raw matrix_value_units

value: UMI

tag: raw matrix_assays

value: snRNA-seq


title: 10xATAC_D017_13_hu_Lobe_atac_lib

value: peripheral region of retina

value: 10x scATAC-seq

value: male

tag: ethnicity

value: 65 years


title: DLBCL case [TX16_33618]

value: DLBCL case

value: unknown

value: Group 1 - complete remission at diagnosis


title: 10x3_D013_13_lib

value: macula lutea

value: 69 years

tag: raw matrix_cellranger_assay_chemistry

tag: raw matrix_genome_annotation


title: 10xATAC_19_D9_lobe_atac_lib

value: Hispanic or Latin American

value: 68 years

value: genomic coordinates


title: 10x3_19_D009_lib

value: FALSE


title: 10xATAC_19_D010_lobe_atac_lib

value: female

value: European

value: 88 years

value: fragment ends

value: snATAC-seq


title: DLBCL case [TX14_ARN_27800]

value: No


title: 10xATAC_D5_13_hu_Lobe_atac_lib

value: peripheral region of retina

value: 10x scATAC-seq

value: male

value: 80 years


title: DLBCL case [TX12_33617]

value: DLBCL case

value: unknown

value: Group 2 - Refractory at diagnosis


title: 10xATAC_D9_13_hu_Lobe_atac_lib

value: Asian

value: 85 years


title: 10xATAC_19_D8_lobe_atac_lib

value: Hispanic or Latin American

value: 64 years

value: genomic coordinates


title: 10xATAC_D021_13_hu_Lobe_atac_lib

value: European

value: 86 years

value: FALSE


title: DLBCL case [TX09_33618]

value: non-germinal center

value: Group 1 - complete remission at diagnosis


title: 10x3_19_D007_lib

value: macula lutea

value: 66 years

value: gene symbol

value: GENCODE 32

value: UMI

value: snRNA-seq


title: DLBCL case [TX07_ARN_27800]

value: DLBCL case

value: No


title: 10x3_D005_13_lib

value: male

value: 80 years


title: 10xATAC_D030_13_atac_lib

value: 10x scATAC-seq

value: female

value: 73 years

value: fragment ends

value: snATAC-seq


title: 10xATAC_D013_13_hu_Lobe_atac_lib

value: peripheral region of retina

value: European

value: 69 years

value: FALSE

value: genomic coordinates


title: DLBCL case [TXRF02_ARN_27800]

value: unknown

value: Group 2 - Refractory at diagnosis


title: DLBCL case [TXRC03_ARN_27800]

value: Group 3 - Relapse at diagnosis


title: DLBCL case [TXRC01_ARN_27800]

value: DLBCL case

value: germinal center


title: DLBCL case [TX06_33617]

value: Group 1 - complete remission at diagnosis

value: No


title: 10x3_19_D019_lib

value: macula lutea

value: 82 years

value: gene symbol

value: GENCODE 32

value: UMI

value: snRNA-seq


title: DLBCL case [TX05_ARN_27800]


title: DLBCL case [TX18_ARN_27800]

value: non-germinal center


title: DLBCL case [TX04_ARN_27800]


title: DLBCL case [TX01_33618]


title: Non-lymphoma control [TX-CO-17_2_33619]

source_name: Non-tumoral ganglia

value: Non-lymphoma control

value: Group 4 - controls


title: Non-lymphoma control [TX-CO-13_33619]


title: Non-lymphoma control [TX-CO-16_2_33619]


title: DLBCL case [TX02_ARN_27800]


title: DLBCL case [TX17_33618]


title: DLBCL case [TX15_33618]


title: 10x3_D021_13_lib

value: male

value: European

value: 86 years

value: FALSE


title: DLBCL case [TX13_33618]

value: DLBCL case


title: DLBCL case [TX10_ARN_27800]

value: unknown


title: Non-lymphoma control [TX-CO-07_33619]


title: Non-lymphoma control [TX-CO-08_33619]


title: DLBCL case [TX08_ARN_27800]

value: Group 1 - complete remission at diagnosis


title: Non-lymphoma control [TX-CO-04_33619]


title: Non-lymphoma control [TX-CO-02_1_33619]


title: Non-lymphoma control [TX-CO-01_33619]


title: DLBCL case [S-10_33618]

value: No


title: DLBCL case [TX11_ARN_27800]

value: germinal center


title: DLBCL case [TX03_33618]


title: Non-lymphoma control [TX-CO-14_1_33619]


title: DLBCL case [REC11B_33617]

value: Yes


title: Non-lymphoma control [TX-CO-15_2_33619]


title: Non-lymphoma control [TX-CO-11_1_33619]


title: Non-lymphoma control [TX-CO-10_2_33619]


title: Non-lymphoma control [TX-CO-12_2_33619]


title: DLBCL case [L-REC-7C_33617]


title: DLBCL case [L-REC-7B_33617]


title: DLBCL case [az-l-ref_3_33618]

value: Group 2 - Refractory at diagnosis


title: DLBCL case [AZ-L-RC-13_33617]


title: Non-lymphoma control [TX-CO-09_33619]


title: Non-lymphoma control [TX-CO-06_33619]


title: Non-lymphoma control [TX-CO-05_2_33619]


title: DLBCL case [S-07_33618]


title: Non-lymphoma control [TX-CO-03_1_33619]


title: DLBCL case [S-11_33618]


title: DLBCL case [S-09HC_25274]


title: DLBCL case [AZ-L-RC_duradera-18_27799]


title: DLBCL case [S-08_27798]


title: DLBCL case [AZ-L-RC_duradera-11_33618]


title: DLBCL case [REC-12A_33617]

value: Group 3 - Relapse at diagnosis


title: DLBCL case [17TJ01634_33617]


title: DLBCL case [17TJ01652_33618]


title: DLBCL case [AZ-L-RC_duradera-5_27798]


title: DLBCL case [AZ-L-Recaida-2A_33617]


title: DLBCL case [AZLRC17HC_25274]


title: DLBCL case [AZ-L-RC_duradera-4_27798]


title: DLBCL case [17TJ01532_27800]


title: DLBCL case [AZ-L-RC_duradera-22_27799]


title: DLBCL case [AZ-L-RC_duradera-12_27798]


title: DLBCL case [17TJ01537_33619]


title: DLBCL case [17TJ01520_27799]


title: DLBCL case [17TJ01525_33619]


title: DLBCL case [17TJ01630_33618]


title: DLBCL case [17TJ01534_27800]


title: DLBCL case [17TJ01529_33619]


title: DLBCL case [17TJ01518_27799]


title: DLBCL case [17TJ01511_33618]


title: DLBCL case [17TJ01522_27799]


title: DLBCL case [4647-09B_27799]


title: DLBCL case [17TJ01512_27799]


title: DLBCL case [17TJ01504_27800]


title: DLBCL case [17TJ01503_33618]


title: DLBCL case [17TJ01517_33618]


title: DLBCL case [17TJ01032_33617]


title: DLBCL case [17TJ01020_33617]


title: DLBCL case [17TJ01030_33617]


title: DLBCL case [17TJ01018_33617]


title: DLBCL case [17R01430_27798]

description: 17R01430_27798_ CCGTCC


title: DLBCL case [17TJ01024_33618]


title: DLBCL case [17TJ01026_33617]


title: DLBCL case [17TJ01527_33619]


title: DLBCL case [17R01427_27798]


title: DLBCL case [17R01426_27799]


title: DLBCL case [17TJ01531_33618]


title: DLBCL case [17R01431_27798]


title: DLBCL case [17R01424_27799]


title: DLBCL case [17R01421_27799]


title: DLBCL case [17R01416_27799]


title: DLBCL case [17R01422_27799]


title: DLBCL case [17TJ01501_33618]

value: unkown


title: DLBCL case [17R01428_27798]


title: DLBCL case [021C_33617]


title: DLBCL case [023A_33617]


title: DLBCL case [021A_33617]


title: DLBCL case [007B_33617]


title: DLBCL case [007A_33617]


title: Physcomitrella patens plate culture csRNA-seq r1

status: Public on Sep 28 2023

city: Pullman

first: Sascha

last: Duttke

state: Washington

address: BLS 202, 100 Dairy Road

department: School of Molecular Biosciences

institute: Washington State University

description:
csRNA-seq; nascent TSS mapping in P.patens cells; Experiment SD553
P.patens-Gransden-10.tss.txt

data_processing:
csRNA-seq (small capped RNAs, ~20-60 nt) and sRNA-seq reads (“input”) were trimmed of their adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20" none -f {csRNA_fastq_path}/*fastq.gz”)(Heinz et al. 2010). Reads were aligned to the appropriate genome using Hisat2 version 2.2.1 (Kim et. al. 2019) with parameters “hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_genome_index} -U {path_rimmed_csRNA or sRNA} -S {output_sam} 2> {mapping_stats}”. Hisat2 indices were then created for each genome used ("hisat2-build -p 40 genome.dna.toplevel.fa {Hisat2_indexfolder}") with exception for barely which required the addition of "--large-index" due to genome size. Tag directory folders were then created using HOMER makeTagDirectories ("makeTagDirectories {outputName} -omitSN -checkGC -fragLength 150 -single")(Heinz et. al. 2010). Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. This consolidates the aligned read information into a read/chromosome format along with other important alignment information. Peaks were called and annotated using HOMER ("findcsRNATSS.pl {csRNA} -o {output} -i {sRNA} -genome hg38 -size 150 -ntagThreshold 10") (Duttke et al. 2019) and annotatePeaks.pl ("annotatePeaks.pl {tss/tsr.txt} hg38 -strand + -fragLength 1 -rlog -d {listOfTagDirs} > {output}") (Heinz et. al. 2010) respectively (additional details available in the manuscript).
Transcription start sites (TSSs) and Transcription start regions (TSRs) were determined in this study. TSRs  were called using findcsRNATSS.pl (detailed above) while TSSs were called using getTSSfromReads.pl ("getTSSfromReads.pl -d {csRNA_tagdir} -dinput {sRNA_tagdir} -min 7 > {output_file}") (Heinz et. al. 2010). To ensure high quality TSSs, at least 7 per 10^7 aligned reads were required and TSS were required to be within called TSR regions.
Paired end total ribosomal RNA-depeleted RNA-seq libraries were trimmed using skewer (“time -p skewer -m mp {read1} {read2} -t 40 -o {trimmed_fastq_output}”) (Jiang et al. 2014) and aligned using Hisat2 (Kim et al. 2019) to ensure all data were processed as similar as possible (“hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_index} -1 {trimmed_RNAseq_R1} -2 {trimmed_RNAseq_R2} -S {output_sam} 2> {mapping_file}”). In this manuscript, total RNA-seq was exclusively used to determine RNA-stability as described in the csRNA-seq analysis.
5’GRO-seq peaks were called using HOMER’s “findPeaks {5GRO_tagdirectory} -i {GRO_tagdirectory} -style tss -F 3 -P 1 -L 2 -LP 1 -size 150 -minDist 200 -ntagThreshold 10 > 5GRO_TSRs.txt”. Detailed explanation of each parameter can be found at http://homer.ucsd.edu/homer/ngs/tss/index.html.
Assembly: TAIR10, Papaya1.0, Chlamydomonas_reinhardtii_v5.5, Drosophila melanogaster: dm6, ASM32608v1, Phypa V3, Selaginella moellendroffii: v1.0, Zea mays (rest): Zm-B73-REFERENCE-NAM-5.0, Zea mays : AGPv4.38 (STARR-seq)
Supplementary files format and content: bed files: Locations indicate TSS positions. TSS.txt files: text files containing tab delimited  information about found transcription start site culsters (TSRs). Motif file containing new line delimited motifs. Motif files: files containing motifs used with a ‘>’ indicating motif information followed by rows with nucleotide probability.
Library strategy: csRNA-Seq

organism: Physcomitrium patens

source_name: plate culture

growth_protocol: A.thaliana Col-0 mature leaves were collected from plants grown as described (M. Wang et al. 2023), while A.thaliana Col-0 suspension cells were grown in 250-mL baffled flasks containing 50 mL of growth medium (3.2 g/L Gamborg’s B-5 medium, 3 mM MES, 3% [v/v] Suc, 1.1 mg L−1 2,4-dichlorophenoxyacetic acid). The cultures were maintained at 23°C under continuous light on a rotary shaker (160 rpm) and kindly provided as a frozen pellet by Dr. Ashley M. Brooks. Barley (Hordeum vulgare) RNA was isolated by Dr. Pete Hedley from embryonic tissue (including mesocotyl and seminal roots; EMB) isolated from grain tissues 4 days past germination (Mascher et al. 2017). Physcomitrium (Physcomitrella) patens (Gransden) was grown on plates with BCDA medium in a growth cabinet at 21°C under 16h light. Selaginella moellendorffii was purchased from Plant Delights Nursery and grown at the window under normal daylight for 1 week prior to isolating RNA from stems and leaves. C. reinhardtii, which was kindly provided by Dr. Will Ansari and Dr. Stephen Mayfield (UC San Diego), was grown to late logarithmic phase in TAP (Tris–acetate–phosphate) medium at 23°C under constant illumination of 5000 lux on a rotary shaker. Adult 2nd and 3rd leaves from Z. mays L. cultivar B73 was kindly provided by Dr. Lauri Smith (UC San Diego). Plants were grown in 4-inch pots in a greenhouse (temp: 23°C-29°C) without supplemental lighting or humidification (humidity in the 15 hours following inoculation ranged between 70 and 90%) year round in La Jolla, CA. RNA from Z. mays L. cultivar B73 7d old shoot, root and leaves were grown in the Schmitz laboratory (University of Georgia) as described in (Ricci et al. 2019).

extract_protocol: csRNA-seq was performed as described in (S. H. Duttke et al. 2019). Small RNAs of ~20-60 nt were size selected from 0.4-3 µg of total RNA by denaturing gel electrophoresis. A 10% input sample was taken aside and the remainder enriched for 5’-capped RNAs. Monophosphorylated RNAs were selectively degraded by 1 hour incubation with Terminator 5´-Phosphate-Dependent Exonuclease (Lucigen). Subsequently, RNAs were 5’dephosporylated through 90 minutes incubation in total with thermostable QuickCIP (NEB) in which the samples were briefly heated to 75°C and quickly chilled on ice at the 60 minutes mark. Input (sRNA) and csRNA-seq libraries were prepared as described in (Hetzel et al. 2016) using RppH (NEB) and the NEBNext Small RNA Library Prep kit, amplified for 11-14 cycles.  Total RNA-Seq Library Preparation  Strand-specific, paired-end libraries were prepared from total RNA by ribosomal depletion using the Ribo-Zero Gold plant rRNA removal kit (Illumina, San Diego, CA). Samples were processed following the manufacturer’s instructions.

value: plate culture

tag: treatment


title: SP025L

status: Public on Sep 25 2023

city: Shanghai

first: Zilu

last: Wen

address: No. 2901, Caolang Road, Jinshan District, Shanghai

institute: SHANGHAI PUBLIC HEALTH CLINICAL CENTER

data_processing:
Mapping reads to the genome and transcriptome uses the STAR aligner.
Seurat 3.1 was used to process the unique molecular identifier (UMI) count matrix.
Genome_build: GRCh38-3.0
Supplementary_files_format_and_content: counts
Supplementary_files_format_and_content: h5

source_name: Fresh resected human lung tissue

extract_protocol:
Resected lung tissues were processed in the BSL2+ laboratory and digested with Collagenase IV (100 U/ml) and Benzonase (50 U/ml) in RPMI 1640 medium without serum for 45 min at room temperature with rocking. Debris was removed using Dead Cell Removal Kit (Miltenyi Biotec). Cells were collected by centrifugation, resuspended in 1x DPBS on ice, and passed through a 40mm strainer. Cell viability measured by trypan blue staining was above 75%.
Single cell samples were processed using Chromium Single Cell 5’ GEM, Library & Gel Bead Kit v3 and, after cDNA amplification, removed from BSL2+ laboratory for subsequent library construction and sequencing.

value: lung tissue


title: SP025H

value: lung tissue with 18F-FDG avidity


title: SP024L


title: SP023L


title: SP021H


title: SP021L


title: SP019L


title: SP020L


title: SP023H


title: DLBCL case [17R01423_27799]


title: SP024H


title: Mouse-Rat Chimera 2 heart at E10.5

status: Public on Sep 20 2023

city: Pamplona

first: Asier

last: Ullate-Agote

state: Navarra

address: Av. de Pío XII, 55

department: Hemato-Oncology

institute: CIMA

data_processing:
Demultiplexing, alignment to a  Mus musculus (GRCm39) and Rattus norvegicus (mRatBN7.2) combined reference and quantification using the annotation from Ensembl v106 was performed using 10X Genomics Cell Ranger (v7.0.0) for the chimera samples
Demultiplexing, alignment to Rattus norvegicus (mRatBN7.2) reference and quantification using the annotation from Ensembl v106 was performed using 10X Genomics Cell Ranger (v7.0.0) for the embrionic Rat Heart at E11.5
Downstream analysis steps (quality control filtering, normalization, integration, clustering and differential expression) were performed using the R package Seurat (v4.2.0) and doublets were retrieved with scDblFinder v1.9.4
For the mouse-rat chimeras, as a two-species reference was considered, the count matrices were separated into rat and mouse genes respectively. Cells that had 10-fold more UMIs for a species, were annotated as such species, with the rest being discarded as ambiguous. Those considered as multiplets by Cell Ranger were also filtered out.
Assembly: GRCm39 and mRatBN7.2
Supplementary files format and content: HDF5 Feature Barcode Matrix containing a Gene x Cells UMI count matrix.
Supplementary files format and content: GEM species classification CSV file for the chimeras.
Supplementary files format and content: metadata.xlsx includes information for the different cells in the dataset.

organism:
Mus musculus
Rattus norvegicus

source_name: Embrionic heart

extract_protocol:
To prepare single cells for RNA-sequencing, hearts from complemented chimeras at E10.5 (n=2, processed individually) or rat embryos at E11.5 (n=3, pooled) were micro-dissected and digested with 0.25% trypsin-EDTA (Gibco) for 10 minutes at 37ºC. Samples were pipetted every 5 minutes to assist tissue disaggregation. Digestion was stopped with DMEM-2% FBS followed by centrifugation at 600g for 5 minutes. Pellets were resuspended in 0.05% BSA-PBS and filtered through a 40µm strainer. Cell viabilities (70-90%) were determined using Cellometer (Nexcelom) Cell Counter.
scRNA libraries were prepared for sequencing using standard Illumina protocols

value: Embrionic heart


title: Embrionic Rat Heart E11.5

organism: Rattus norvegicus


title: DLBCL case [023B_33617]

value: non-germinal center


title: SP019H


title: OB_2941KO

status: Public on Aug 31 2023

city: Milwaukee

first: Demin

last: Wang

state: WI

address: 8727 West Watertown Plank Road

institute: Versiti Blood Research Institute

data_processing:
Raw sequencing data was de-multiplexed, reads were aligned to the Mus musculus mm10 genome and counts for each gene were quantified using Basepair software (https://www.basepairtech.com).
Read count normalization and differential expression analysis were conducted using DESeq2 v1.24.0.
Assembly: mm10
Supplementary files format and content: Normalized read counts for all samples

source_name: osteoblast cells

extract_protocol:
MSCs and OBs were sorted from wild-type and miR-9-1-deficient mice, lysed in TRIzol (LifeTechnologies), and mRNAs were then isolated using NEBNext poly(A) mRNA Magnetic Isolation Module (New England Biolabs). 0.5 ug of total RNA was used for the construction of sequencing libraries.
The libraries were constructed using NEBNext Ultra RNA library Prep kit for Illumina (New England Biolabs) and quantified using Kapa Library Quantification Kit (KapaBiosystems) and QubitFluorometer (ThermoFisher).

tag: cell type

value: osteoblast cells

tag: genotype


title: OB_2942KO


title: DLBCL case [021B_33617]

tag: subject status


title: OB_0035KO


title: OB_2996WT

value: Wild-type


title: OB_2944WT


title: OB_2945WT


title: MSC_2999KO

source_name: mesenchymal stem cells

value: mesenchymal stem cells


title: MSC_2941KO


title: MSC_2942KO


title: MSC_0035KO


title: MSC_2945WT


title: MSC_0036WT


title: MSC_2996WT


title: Mouse-Rat Chimera 1 heart at E10.5

tag: developmental stage


title: 113_CMV_KLRG1+/TIGIT+ [lib31133]

status: Public on Jun 30 2023

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2) was used to remove any remaining adapter sequence.
Reads were aligned by bowtie and TopHat v1.4.0 to GRCh38
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2)30, and HTSeq-count (v0.4.1).
Assembly: GRCh38
Supplementary files format and content: Processed data is in .csv format. Each row is a gene, each column is a sample.

source_name: CD8 T-cell

extract_protocol:
The indicated populations were isolated by flow cytometry, and  cells were resuspended in SMARTer v4 lysis reagents (Clontech). Cells were lysed and cDNA was synthesized. For the cell lines, stimulated or unstimulated cells were used for RNA extraction with QIAGEN RNeasy Mini kit and cDNA synthesized from this.
After amplification, sequencing libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina). Barcoded libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies). Single-read sequencing of the pooled libraries was carried out on a HiSeq2500 sequencer (Illumina) for 74 cycles, using TruSeq v3, and SBS kits (Illumina). Target read depths were ~5-10 million raw reads per sample.

value: CD8 T-cell

tag: stimulation

value: 1ug/ml coated anti-CD3 (clone UCHT1) w/ 2ug/ml soluble anti-CD28 (clone 28.2) 16 hours

tag: study group

value: CMV tetramer positive from Healthy Screened Control

tag: sort

tag: donor

value: female

tag: age


title: Aged Brain, BAI1

status: Public on Aug 16 2023

city: La Jolla

first: Xue

last: Lei

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

description:
BAI1-treated
10x Genomics Gene Expression Flex

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using cellranger software v7.1.0
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

organism: Mus

source_name: Brain

extract_protocol:
Freshly collected brains were fresh frozen in liquid nitrogen and stored at -80 C until tissues were sent for analysis. Fixed, single cell suspension were prepared from flash frozen mouse brain tissue using the Chromium Next GEM Single Cell Fixed RNA Preparation kit (10x Genomics) according to the user guide (CG000553, Rev B). Minced tissues were fixed for 24 hrs at 4C. Cell dissociation was performed using the gentleMACS Octo Dissociator (Miltenyi).
Libraries were constructed using the single-plex Chromium Fixed RNA Profiling kit (CG000477, Rev C). Probes were incubated for 20 hrs at 42C and 9 cycles were performed for the indexing PCR.

treatment_protocol: 20-month old mice were treated with the Bax inhibitor, BAI1,3 times a week for three months. Mice were sacrificed and tissues were fresh frozen and stored at -80 C until they were sent for analysis

value: Brain

value: 20-month old

value: WT

tag: strain


title: 113_Flu_KLRG1+/TIGIT+ [lib31132]

value: Flu tetramer positive from Healthy Screened Control

tag: Sex


title: OB_2999KO


title: 244_Flu_KLRG1+/TIGIT+ [lib31131]


title: 241_Flu_KLRG1+/TIGIT+ [lib31129]


title: 177_CMV_KLRG1+/TIGIT+ [lib31130]


title: 997_CMV_KLRG1+/TIGIT+ [lib31128]

value: male


title: 8_RCC_KLRG1-/TIGIT- [lib28991]

value: 1ug/ml coated anti-CD3 (clone UCHT1) w/ 2ug/ml soluble anti-CD28 (clone 28.2) 17 hours

value: RCC


title: 458_CMV_KLRG1+/TIGIT+ [lib31126]


title: 997_Flu_KLRG1+/TIGIT+ [lib31127]


title: OB_0036WT


title: 132_Flu_KLRG1+/TIGIT+ [lib31125]


title: 7_HC_KLRG1+/TIGIT+ [lib28988]

value: Healthy Screened Control


title: 6_RCC_KLRG1-/TIGIT- [lib28987]


title: 8_RCC_KLRG1+/TIGIT+ [lib28990]


title: 7_HC_KLRG1-/TIGIT- [lib28989]


title: 6_RCC_KLRG1+/TIGIT+ [lib28986]


title: 5_HC_KLRG1-/TIGIT- [lib28985]


title: MSC_2944WT


title: 4_RCC_KLRG1+/TIGIT+ [lib28982]


title: 3_HC_KLRG1+/TIGIT+ [lib28980]


title: 3_HC_KLRG1-/TIGIT- [lib28981]


title: 4_RCC_KLRG1-/TIGIT- [lib28983]


title: 5_HC_KLRG1+/TIGIT+ [lib28984]


title: 2_RCC_KLRG1-/TIGIT- [lib28979]


title: 2_RCC_KLRG1+/TIGIT+ [lib28978]


title: Aged Brain, Vehicle

description:
Control
10x Genomics Gene Expression Flex

tag: tissue

value: Vehicle


title: 1_HC_KLRG1+/TIGIT+ [lib28977]


title: 18_T1D_KLRG1-/TIGIT- [lib23907]

value: Type 1 Diabetic


title: 17_HC_KLRG1-/TIGIT- [lib23905]


title: 15_HC_KLRG1+/TIGIT+ [lib23900]


title: 18_T1D_KLRG1+/TIGIT+ [lib23906]


title: 14_T1D_KLRG1-/TIGIT- [lib23899]


title: 16_T1D_KLRG1-/TIGIT- [lib23903]


title: 13_HC_KLRG1+/TIGIT+ [lib23896]


title: 13_HC_KLRG1-/TIGIT- [lib23897]


title: 15_HC_KLRG1-/TIGIT- [lib23901]


title: 11_HC_KLRG1-/TIGIT- [lib23893]


title: 14_T1D_KLRG1+/TIGIT+ [lib23898]


title: 17_HC_KLRG1+/TIGIT+ [lib23904]


title: 11_HC_KLRG1+/TIGIT+ [lib23892]


title: Donor1736837_Control [lib12756]

data_processing:
Base-calling was performed automatically by Illumina real time analysis software and demultiplexing was performed on Illumina BaseSpace.
Hard trimming was performed in Galaxy; 1 3'-end base was removed from all reads using the FASTQ Trimmer tool (v1.0.0)
Quality-based trimming was performed in Galaxy; reads were trimmed from both ends using the FASTQ Quality Trimmer tool (v1.0.0) until minimum base quality for each read was >= 30.
Reads were aligned in Galaxy using TopHat (Tophat for Illumina tool, v.1.5.0)
Read counts per Ensembl gene ID were generated using htseq-count (htseq-count tool, v.0.4.1).
Assembly: GRCh38
Supplementary files format and content: Processed data is in .csv format. Each row is a gene, each column is a sample.

source_name: Whole blood

extract_protocol:
RNA was extracted from whole blood in collected in tempus.
Libraries were constructed from RNA using the Illumina TruSeq RNA Sample Preparation kit v2.

value: Whole blood

value: Control

tag: donor id

tag: hla

value: *1501, unknown


title: Donor1928619_Control [lib12757]

value: *0402, unknown


title: 12_T1D_KLRG1+/TIGIT+ [lib23895]

value: CD8 T-cell


title: Donor2894_Control [lib12763]

value: *01, unknown


title: Donor0398_Control [lib12752]

value: female


title: 12_T1D_KLRG1-/TIGIT- [lib23894]


title: Donor2741_Control [lib12761]


title: Donor2633_Control [lib12760]


title: Donor2601_Control [lib12759]

value: unknown


title: Donor0019_Control [lib12751]


title: Donor1671440_Control [lib12749]

value: *1501, Unknown


title: Donor1196414_Control [lib12753]


title: Donor1693775_Control [lib12747]


title: Donor1658067_Control [lib12755]


title: Donor1603583_Control [lib12745]

value: *0401, unknown


title: 16_T1D_KLRG1+/TIGIT+ [lib23902]


title: Donor1969720_Control [lib12750]


title: Donor1474132_Control [lib12754]


title: Donor2895_Control [lib12746]

value: *0401, Unknown


title: Donor1755527_Control [lib12742]

value: male


title: Donor1887470_RA [lib12740]

value: RA

value: *0404, Unknown


title: Donor1889030_Control [lib12741]


title: Donor1757_RA [lib12737]


title: Donor1148647_Control [lib12744]


title: Donor1763503_RA [lib12733]


title: Donor1964569_Control [lib12758]


title: Donor1971_RA [lib12731]


title: Donor1223_Control [lib12732]


title: Donor1216130_RA [lib12739]


title: Donor0328_Control [lib12736]


title: Donor1882537_Control [lib12730]


title: Donor1138178_Control [lib12738]


title: Donor1809718_RA [lib12727]


title: Donor1745_RA [lib12729]


title: Donor1386730_Control [lib12726]

value: *13, unknown


title: Donor1766850_RA [lib12723]


title: Donor1861319_RA [lib12721]

value: *1502, Unknown


title: Donor1550_Control [lib12722]


title: Donor2039_RA [lib12718]


title: Donor1705337_Control [lib12743]


title: Donor1792541_Control [lib12734]


title: Donor1105384_Control [lib12713]


title: Donor1287492_RA [lib12715]


title: Donor1724121_RA [lib12720]


title: Donor1894606_RA [lib12714]

value: *01, Unknown


title: Donor0761_Control [lib12719]

value: Whole blood


title: Donor1505124_Control [lib12711]

value: Control


title: Donor0762_Control [lib12728]


title: Donor1351026_RA [lib12712]


title: Donor1872502_RA [lib12710]


title: Donor1849948_RA [lib12706]


title: Donor0123_Control [lib12707]


title: Donor2622_Control [lib12705]


title: Donor1545392_RA [lib12725]


title: Donor1628991_RA [lib12702]


title: Donor3025_Control [lib12724]


title: Donor1232422_Control [lib12703]


title: Donor2900_Control [lib12716]

value: *0404, unknown


title: Donor1065567_RA [lib12700]


title: Donor1350778_Control [lib12699]


title: Donor1381209_RA [lib12698]

value: Unknown, Unknown


title: Donor2621_Control [lib12701]


title: Donor0025_Control [lib12697]


title: Donor1880735_RA [lib12696]


title: Donor1760_RA [lib12717]


title: Donor1777334_Control [lib12691]


title: Donor1041424_RA [lib12735]


title: Donor1376835_RA [lib12694]


title: Donor1175204_RA [lib12688]


title: Donor1721905_Control [lib12695]

value: Unknown


title: Donor1767881_Control [lib12709]

value: *1501, unknown


title: Donor1648186_RA [lib12708]


title: Donor1404335_RA [lib12704]

value: female


title: Donor1888425_RA [lib12692]


title: Donor1157256_Control [lib12687]


title: Donor1933530_RA [lib12690]


title: Donor1962511_Control [lib12689]


title: Donor1315694_Control [lib12693]


title: Donor1222158_Control [lib12685]


title: Donor1294142_RA [lib12686]


title: Donor1432996_RA [lib12684]


title: Donor0234_Control [lib12681]


title: Donor1969419_RA [lib12682]


title: Donor1504670_RA [lib12679]


title: Donor2896_Control [lib12678]


title: Donor1683832_RA [lib12680]


title: Donor1916608_Control [lib12683]


title: Donor1332072_RA [lib12677]


title: Donor1975726_RA [lib12671]


title: Donor0729_Control [lib12674]


title: Donor0328_Control [lib12670]


title: Donor2915_Control [lib12672]


title: Donor2850_Control [lib12668]


title: Donor1983389_RA [lib12675]


title: Donor1962139_RA [lib12667]


title: Donor1407226_RA [lib12665]


title: Donor1912_RA [lib12663]


title: Donor1329632_RA [lib12662]


title: Donor2854_Control [lib12664]


title: Donor1346496_RA [lib12673]


title: Donor1406860_RA [lib12661]


title: Donor0057_Control [lib12666]


title: Donor1495425_RA [lib12659]


title: Donor1133894_RA [lib12658]


title: Donor2765_Control [lib12676]


title: Donor1136_Control [lib12657]


title: Donor1381016_RA [lib12656]


title: Donor0783_Control [lib12652]


title: Donor1846671_RA [lib12655]


title: Donor1514468_Control [lib12654]


title: Donor1136160_RA [lib12653]


title: Donor0482_Control [lib12650]


title: Donor1483_RA [lib12649]


title: Donor1777997_RA [lib12651]


title: Donor1873412_RA [lib12669]


title: Donor0846_Control [lib12646]


title: Donor1647661_Control [lib12644]


title: Donor2794_Control [lib12648]


title: Donor1454758_RA [lib12647]


title: Donor1485897_RA [lib12645]

value: *0408, Unknown


title: Donor1946625_RA [lib12643]


title: Donor2692_Control [lib12642]


title: Donor1878766_RA [lib12641]

value: *13, Unknown


title: Donor1661108_RA [lib12639]


title: Donor1686004_RA [lib12637]


title: Donor1160560_RA [lib12636]


title: Donor2826_Control [lib12640]


title: Donor2620_Control [lib12638]

value: *03, unknown


title: Donor1945_Control [lib12634]

value: *0401, Unknown


title: Donor2636_Control [lib12630]


title: Donor2916_Control [lib12632]

value: male


title: Donor2027_RA [lib12635]

value: RA


title: Donor2640_Control [lib12628]


title: Donor1107671_RA [lib12633]


title: Donor1124429_RA [lib12631]

value: *1501, Unknown


title: Donor0456_Control [lib12626]


title: Donor1408361_Control [lib12624]

value: Not tested


title: Donor2627_Control [lib12660]


title: Donor2020_RA [lib12623]


title: Donor2788_Control [lib12622]


title: Donor1483288_RA [lib12619]


title: Donor0910_Control [lib12618]


title: Donor1978426_RA [lib12621]


title: Donor1880389_RA [lib12615]


title: Donor1751_RA [lib12617]

value: *0404, Unknown


title: Donor1814669_Control [lib12616]


title: Donor2665_Control [lib12620]


title: Donor1010996_RA [lib12613]


title: Donor1463987_Control [lib12612]


title: Donor2703_Control [lib12610]


title: Donor1287906_RA [lib12611]


title: Donor1306738_RA [lib12629]


title: Donor1503872_RA [lib12609]


title: Donor1506832_RA [lib12607]

value: *0405, Unknown


title: Donor2999_Control [lib12608]

value: Whole blood


title: Donor0737_Control [lib12606]

value: Control


title: Donor2774_Control [lib12604]


title: Donor1651069_RA [lib12605]


title: Donor2026_RA [lib12627]


title: Donor1050325_RA [lib12598]


title: Donor1140_Control [lib12602]


title: Donor0221_Control [lib12600]


title: Donor2658_Control [lib12597]


title: Donor2649_Control [lib12593]


title: Donor1756694_RA [lib12596]


title: Donor0867_Control [lib12614]


title: Donor1787900_RA [lib12594]


title: Donor2641_Control [lib12595]


title: Donor1960805_RA [lib12590]


title: Donor1977_Control [lib12588]


title: Donor2694_Control [lib12591]


title: Donor0203_Control [lib12586]


title: Donor0848_Control [lib12584]


title: Donor1505901_RA [lib12587]


title: Donor1792473_RA [lib12592]


title: Donor1723151_RA [lib12585]

value: *0401, unknown


title: Donor1786291_RA [lib12589]


title: Donor1036946_RA [lib12603]


title: Donor1674_RA [lib12583]


title: Donor2667_Control [lib12573]


title: Donor1959752_RA [lib12599]


title: Donor1743_Control [lib12575]


title: Donor1140436_Control [lib12577]


title: Donor1793904_RA [lib12581]


title: Donor2348_Control [lib12580]

value: unknown


title: Donor1116_Control [lib12571]


title: Donor1612_Control [lib12582]


title: Donor0349_Control [lib12568]


title: Donor0722_Control [lib12560]


title: Donor0271_Control [lib12558]


title: Donor2360_Control [lib12565]

value: *03, Unknown


title: Donor1600_Control [lib12563]


title: Donor1093602_RA [lib12555]


title: Donor1960585_RA [lib12557]


title: Donor2338_Control [lib12552]


title: Donor0950_Control [lib12556]


title: Donor1877555_RA [lib12551]


title: Donor1818623_RA [lib12553]


title: Donor0862_Control [lib12554]


title: Donor0367_Control [lib12550]


title: Donor1950288_RA [lib12547]


title: Donor2123_Control [lib12548]


title: Donor1162237_RA [lib12545]


title: Donor2365_Control [lib12546]


title: Donor1482623_RA [lib12543]


title: Donor2668_Control [lib12544]


title: Donor1772717_RA [lib12549]


title: Donor1049134_RA [lib12559]


title: Donor0207_Control [lib12542]


title: Donor2837_Control [lib12540]


title: Donor1775665_RA [lib12541]


title: Donor1048359_RA [lib12537]


title: Donor2660_Control [lib12538]


title: Donor1303002_RA [lib12539]

value: Unknown, Unknown


title: C57Bl_6J_IgG2

status: Public on Jun 06 2023

city: Cambridge

first: Loke CTR

last: Bioinformatics

address: Downing Street

department: Physiology building

country: United Kingdom

institute: Loke Centre for Trophoblast Research

data_processing:
50bp paired end sequencing was carried out on an Illumina HiSeq 2500 platform
Processing was performed by Babraham Bioinformatics Facility using the clusterflow fastq_bowtie2 pipeline, comprising adapter and quality trimming using trim galore v0.6.6 using default paired end parameters followed by mapping to the mouse GRCm38 genome assembly using bowtie2 v2.4.1. Mapped reads were imported into Seqmonk for data exploration and analysis.
500bp contiguous in silico probes were designed in Seqmonk and DMRs identified using the embedded EdgeR function (p<0.05, with multiple testing correction) and filtered for those with a LFC >1
Assembly: GRCm38
Supplementary files format and content: tab delimited text file with normalised read count quantitation for 5kb contiguous regions

source_name: E10.5 placenta

extract_protocol:
Genomic DNA was isolated and purified using the QIAamp Fast DNA Tissue Kit(Qiagen)
Genomic DNA was sonicated to yield 150–600 bp fragments, and adaptors for paired-end sequencing (Illumina) were ligated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs). Immunoprecipitations were carried out using 500ng DNA per sample, 1.25μg anti-5mC antibody (Eurogentec Cat# BI-MECY-0100, RRID:AB_2616058) and 10μL Dynabeads coupled with M-280 sheep anti-mouse antibody (Invitrogen). Pulled down DNA was amplified for 12 cycles with adapter-specific indexed primers. Final clean-up and size selection was carried out with AMPure-XP SPRI beads (Beckman Coulter).

value: E10.5 placenta

value: wildtype


title: hTSC-H3K4me3

status: Public on Jun 28 2023

city: Xiamen

first: Jinhua

last: Lu

address: No. 4221, Xiangan Road, Xiangan District, Xiamen city

institute: Xiamen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using HISAT2 with default parameters
MACS2 was used to call the peaks of these antibodies binding using default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: pileup peaks

source_name: human TSC

growth_protocol: Advanced DMEM/F12 supplemented with 0.1mM 2-mercaptoethanol, 0.2% FBS, 1% ITS-X supplement, 0.3% BSA, 0.5% Penicillin -Streptomycin, 1.5 μg/ml L-ascorbic acid, 0.5 μM A83-01, 50 ng/ml EGF, 1μM SB431542, 2 μM CHIR99021, 5 μM Y27632 and 0.8 mM VPA

extract_protocol:
ChIP was performed according to the reported previousl with slight modification. Briefly, about 2x10^6 TS cells were cross-linked with 1/15 volume of 16% formaldehyde (CST) at room temperature for 10 minutes and quenched with 1/10 volume of 1.25 M glycine for 15 minutes on ice. Cell lysate in lysis buffer III were sonicated using Bioruptor pico (Diagenode) and then incubated with 4 µg antibody overnight at 4℃ with rotation. Immunoprecipitated complexes were collected with 15 µl Protein A Dynabeads (Invitrogen, 10002D) for 1 hour at 4℃ with rotation. Subsequently, beads were washed sequentially once with low-salt buffer, twice with high-salt buffer, once with LiCl buffer, twice with TE, and then eluted in 400 µl of elution buffer for 30 min at 65℃. The eluates were incubation at 65℃ for 8 h to reverse the cross-linking. Next, eluates were treated with proteinase K for 1 h at 55℃ and then RNase A for 30 min at 37℃ before DNA was extracted and purified. The ChIP libraries were prepared using KAPA HyperPrep Kits (Roche, 07962347001) and then run on the Illumina sequencer Hiseq-Xten PE150.
The ChIP libraries were prepared using KAPA HyperPrep Kits (Roche, 07962347001) and then run on the Illumina sequencer Hiseq-Xten PE150 using standard Illumina protocols

value: Human trophoblast stem cells

tag: chip antibody

value: Anti-Histone H3 (tri methyl K4), Abcam, catalog number:ab8580


title: hTSC-input

value: none (input)


title: F2_Mtrr+_+_FGE_meDIP_rep_2

value: F2 Mtrr+/+


title: C57Bl_6J_IgG1


title: F2_Mtrr+_+_FGE_meDIP_rep_1


title: F2_Mtrr+_+_PN_meDIP_rep_7


title: F2_Mtrr+_+_PN_meDIP_rep_8


title: F2_Mtrr+_+_PN_meDIP_rep_5


title: F2_Mtrr+_+_PN_meDIP_rep_3


title: F2_Mtrr+_+_PN_meDIP_rep_2


title: F2_Mtrr+_+_PN_meDIP_rep_4


title: Mtrrgt_gt_FGR_meDIP_rep_5

value: Mtrrgt/gt


title: F2_Mtrr+_+_PN_meDIP_rep_1


title: Mtrrgt_gt_FGR_meDIP_rep_6


title: Mtrrgt_gt_FGR_meDIP_rep_4


title: Mtrrgt_gt_FGR_meDIP_rep_7


title: Mtrrgt_gt_FGR_meDIP_rep_2


title: Mtrrgt_gt_FGR_meDIP_rep_1


title: hTSC-H3K36me3

value: Tri-Methyl-Histone H3 (Lys36) (D5A7), Cell signaling Technology (CST); catalog number:#4909


title: Mtrrgt_gt_PN_meDIP_rep_4


title: Mtrrgt_gt_PN_meDIP_rep_3


title: Mtrrgt_gt_PN_meDIP_rep_2


title: Mtrrgt_gt_PN_meDIP_rep_7


title: Mtrrgt_gt_PN_meDIP_rep_5


title: Mtrrgt_gt_PN_meDIP_rep_1


title: C57Bl_6J_meDIP_rep_6


title: C57Bl_6J_meDIP_rep_7


title: F2_Mtrr+_+_PN_meDIP_rep_6


title: C57Bl_6J_meDIP_rep_4


title: C57Bl_6J_meDIP_rep_5


title: Mtrrgt_gt_PN_meDIP_rep_6


title: F2_Mtrr+_+_FGE_meDIP_rep_3


title: C57Bl_6J_meDIP_rep_8


title: C57Bl_6J_meDIP_rep_1


title: Mtrrgt_gt_FGR_meDIP_rep_3


title: F2_Mtrr+_+_FGE_rep_1

data_processing:
Libraries were pooled and sequenced on the Illumina NextSeq500 platform with 75-base-pair single-end reads.
Sequences were trimmed with Trim Galore! and aligned to GRCm38 mouse genome using STAR aligner
Alignments were processed using custom ClusterFlow (v0.5dev) pipelines and assessed using MultiQC (0.9.dev0). Gene quantification was determined with HTSeq- Counts (v0.6.1p1). Additional quality control was performed with rRNA and mtRNA counts script, feature counts (v 1.5.0- p2) and qualimap (v2.2).
Differential gene expression was performed with DESeq2 package (v1.22.2, R v3.5.2).
Assembly: GRCm38
Supplementary files format and content: tab delimited text file with RPKM values for each library

extract_protocol:
Whole E10.5 placentas were homogenized using lysing matrix D beads and total RNA was extracted using TRI Reagent according to the manufacturer’s instructions
Libraries were prepared using 200 ng of total RNA with the Illumina TruSeq stranded mRNA Library Preparation kit


title: C57Bl_6J_meDIP_rep_3


title: F2_Mtrr+_+_FGE_rep_3


title: F2_Mtrr+_+_PN_rep_3


title: F2_Mtrr+_+_PN_rep_2


title: F2_Mtrr+_+_PN_rep_1


title: F2_Mtrr+_+_FGE_rep_2


title: Mtrrgt_gt_FGR_rep_6


title: Mtrrgt_gt_FGR_rep_7


title: Mtrrgt_gt_FGR_rep_5


title: Mtrrgt_gt_FGR_rep_4


title: Mtrrgt_gt_FGR_rep_3


title: Mtrrgt_gt_FGR_rep_2


title: Mtrrgt_gt_PN_rep_14


title: Mtrrgt_gt_FGR_rep_1


title: Mtrrgt_gt_PN_rep_12


title: Mtrrgt_gt_PN_rep_13


title: Mtrrgt_gt_PN_rep_11


title: Mtrrgt_gt_PN_rep_10


title: Mtrrgt_gt_PN_rep_9


title: C57Bl_6J_meDIP_rep_2


title: Mtrrgt_gt_PN_rep_7


title: Mtrrgt_gt_PN_rep_6


title: F2_Mtrr+_+_PN_rep_4


title: Mtrrgt_gt_PN_rep_3


title: F2_Mtrr+_+_FGE_rep_4


title: Mtrrgt_gt_PN_rep_5


title: C57Bl_6J_rep_5


title: Mtrrgt_gt_PN_rep_2


title: Mtrrgt_gt_PN_rep_1


title: C57Bl_6J_rep_3


title: C57Bl_6J_rep_1


title: C57Bl_6J_rep_2


title: C57Bl_6J_rep_6


title: mouse_brain_SIMPLE

status: Public on May 04 2023

city: New York

first: Dongsheng

last: Bai

state: NY

address: 101 Avenue of the Americas

institute: New York Genome Center

data_processing:
Cut adapter step: The raw FASTQ files are firstly but the sequencing adapters with cutadapt software
Alignment step: After the cut adapter step, all the FASTQ files are mapped to the reference genome
BAM convert step:The alignment SAM results are converted to sorted BAM files with samtools software
Assembly: mm10
Supplementary files format and content: The genome browser track file showing the modification levels of each cluster of mouse brain cells.

source_name: brain

extract_protocol:
The formaldehyde fixed cells are collected and re-suspended in ice cold NIB buffer for nucleosome deplation; the nuclei pellets were tagmentated with identical barcoded assembled Tn5 followed 2 rounds of Ligation-based combinatorial barcoding; nuclei were lysed and gDNA purified with 1X SPRI beads; next, performs Second adaptor tagging and 5hmC transition and hmC-to-T recording; after the primer extension reaction, the dsDNA is subjected into 5mC specific labelling; the final library is amplified by Kapa HiFi uracil plus DNA polymerase and used 1.8X Ampure XP beads to purify the product. The final libraries were sequenced using a MGI-2000 platform (MGI) with the following read lengths: PE 150 + 8 + 150 (Read 1 + Index 1 + Read 2).
The formaldehyde fixed cells are collected and re-suspended in ice cold NIB buffer for nucleosome deplation; the nuclei pellets were tagmentated with identical barcoded assembled Tn5 followed 2 rounds of Ligation-based combinatorial barcoding; nuclei were lysed and gDNA purified with 1X SPRI beads; next, performs Second adaptor tagging and 5hmC transition and hmC-to-T recording; after the primer extension reaction, the dsDNA is subjected into 5mC specific labelling; the final library is amplified by Kapa HiFi uracil plus DNA polymerase and used 1.8X Ampure XP beads to purify the product. The final libraries were sequenced using a MGI-2000 platform (MGI) with the following read lengths: PE 150 + 8 + 150 (Read 1 + Index 1 + Read 2).

value: brain

tag: cell line

value: brain cells

value: WT

value: No treatment


title: Mtrrgt_gt_PN_rep_8


title: Mtrrgt_gt_PN_rep_4


title: t-VK12653, rep3

status: Public on Apr 04 2023

description: Vκ*MYC

data_processing:
Aligned to the Mus musculus GRCm38/mm10 genome using STAR
Normalization and Differential Gene Expression assay using DESeq2
Pre-ranked GSEA using clusterProfiler
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include Feature Counts, FPKM and TPM values for each sample

source_name: BM

extract_protocol:
Total RNA were isolated using RNeasy Micro Kit (Qiagen).
RNA-Seq libraries were prepared using SMARTer® Stranded Total RNA-Seq Kit v1 - Pico Input Mammalian (Takara Bio USA/Clontech).

value: BM

value: primary cells

value: CD138+B220- MM cells

value: V{kappa}{star}MYC


title: VQ-D5, rep2

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)

value: V{kappa}{star}MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)


title: VQ-D5, rep4

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)

source_name: LN

value: LN


title: VQ-D2, rep4

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)


title: VQ-D2, rep2

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)

source_name: Spleen

value: Spleen


title: GFP-hPNE/hTert Rep3

status: Public on Apr 20 2023

type: RNA

first: jerome

last: torrisani

address: 2 avenue Hubert Curien

institute: inserm

description:
A5
Biological replicate 3 of 3. GFP-hPNE/hTert controls

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE v2 microarray (8X60K, Design 039494) enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 039494_D_F_20120628). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 12 out of 15 microarrays or with a minimal weight of 2 per group from at least one experimental group. At this step, 37447 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 31018 rows each corresponding to a unique ProbeName (provided as Data table).

source_name: Pancreatic hPNE/hTert cell line

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: hPNE/hTer cells were grown in 75 % DMEM medium (4.5g/L Glucose-Life Technologies) + 25% M3 (Incell) medium + 2 mM L-glutamine (Life Technologies) + 5% Fetal Calf Serum (Life Technologies) + 10 nG/mL EGF (Sigma-Aldrich) + 750 nG/mL puromycine (Cayla-Invivogen)

extract_protocol: Total RNAs were extracted using Trizol following manufacturer's instructions

treatment_protocol: Cells stably over-express GFP, DNMT1, DNMT3A or DNMT3b after lentiviral transduction followed by antibiotics selection. Cells were harvested in exponential growth phase.

value: hTert-hPNE ATCC® CRL-4023

value: control


title: DNMT3a-hPNE/hTert Rep2

description:
C3
Biological replicate 2 of 4. DNMT3A-hPNE/hTert

value: DNMT3A overexpression


title: DNMT3a-hPNE/hTert Rep3

description:
C4
Biological replicate 3 of 4. DNMT3A-hPNE/hTert


title: DNMT1-hPNE/hTert Rep4

description:
B5
Biological replicate 4 of 4. DNMT1-hPNE/hTert

value: DNMT1 overexpression


title: DNMT1-hPNE/hTert Rep3

description:
B4
Biological replicate 3 of 4. DNMT1-hPNE/hTert


title: t-VK12653, rep4

description: Vκ*MYC


title: GFP-hPNE/hTert Rep2

description:
A3
Biological replicate 2 of 3. GFP-hPNE/hTert controls


title: t-VK12653, rep2

description: Vκ*MYC


title: C57Bl_6J_rep_4

value: E10.5 placenta

value: wildtype


title: DNMT1-hPNE/hTert Rep1

description:
B2
Biological replicate 1 of 4. DNMT1-hPNE/hTert


title: DNMT3b-hPNE/hTert Rep3

description:
D4
Biological replicate 3 of 4. DNMT3B-hPNE/hTert

value: DNMT3B overexpression


title: DNMT1-hPNE/hTert Rep2

description:
B3
Biological replicate 2 of 4. DNMT1-hPNE/hTert


title: DNMT3a-hPNE/hTert Rep1

description:
C2
Biological replicate 1 of 4. DNMT3A-hPNE/hTert


title: GFP-hPNE/hTert Rep1

description:
A2
Biological replicate 1 of 3. GFP-hPNE/hTert controls


title: DNMT3b-hPNE/hTert Rep4

description:
D5
Biological replicate 4 of 4. DNMT3B-hPNE/hTert


title: DNMT3b-hPNE/hTert Rep1

description:
D2
Biological replicate 1 of 4. DNMT3B-hPNE/hTert


title: DNMT3a-hPNE/hTert Rep4

description:
C5
Biological replicate 4 of 4. DNMT3A-hPNE/hTert


title: DNMT3b-hPNE/hTert Rep2

description:
D3
Biological replicate 2 of 4. DNMT3B-hPNE/hTert


title: t-VK12653, rep1

description: Vκ*MYC


title: VQ-D5, rep3

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)


title: VQ-D5, rep1

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)


title: VQ-D2, rep3

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)


title: VQ-D4, rep4

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)


title: VQ-D2, rep1

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)


title: VQ-D4, rep3

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)


title: VQ-D1, rep3

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)


title: VQ-D1, rep4

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)


title: VQ-D4, rep2

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)

source_name: Liver

value: Liver


title: VQ-D4, rep1

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)


title: Control, rep1


title: VQ-D4, BCR Heavy Chain

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)

data_processing:
demultiplexing and UMI extraction by MIGEC v1.2.9
mapping consencus sequences and assembling clonotypes by MiXCR v3.0.3
Repertoire clonal assembly and alignment to germline sequences by change-O toolkit
Assembly: mm10
Supplementary files format and content: tab-delimited files including clonal information of each assmple
Supplementary files format and content: tsv files including Igblast alignment information of each sample
Library strategy: Rep-Seq

extract_protocol:
Total RNA were isolated using RNeasy Micro Kit (Qiagen).
full length IgH and IgL chain libraries were generated as described in Nat Protoc. 2016 Sep;11(9):1599-616; DOI:10.1038/nprot.2016.093.


title: Control, rep2


title: VQ-D4, BCR Light Chain

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)


title: VQ-D5, BCR Heavy Chain

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)


title: VQ-D1, rep1

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)


title: Control, rep3


title: 4938, BCR Light Chain

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)

value: VQ-D2 derived cell line 4938


title: VQ-D2, BCR Light Chain

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)


title: VQ-D2, BCR Heavy Chain

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)


title: VQ-D1, BCR Heavy Chain

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)


title: VQ-D1, BCR Light Chain

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)


title: 4935, BCR Light Chain

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)

value: VQ-D2 derived cell line 4935


title: 4935, BCR Heavy Chain

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)

value: BM


title: VQ-D5, BCR Light Chain

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)

value: primary cells


title: 4938, BCR Heavy Chain

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)

value: CD138+B220- MM cells


title: MEP rep2

status: Public on Mar 30 2023

city: Santa Cruz

first: Camilla

last: Forsberg

state: California

address: 1156 High Street

institute: Institute for the Biology of Stem Cells, University of California Santa Cruz

data_processing:
data was processed using the ENCODE ATAC-seq Pipeline version 1.4.2
Parameters for pipeline were:  atac.multimapping=0, atac.smooth_win=150, atac.enable_idr=true, atac.idr_thresh=0.1
Master peaklist was generated by chromVAR v1.02 and the filterPeaks function using default parameters
Peaks were annotated using annotatePeaks.pl function in HOMER v4.10.2
Genome_build: mm10
Supplementary_files_format_and_content: Annotated Master peak-list output from chromVAR and HOMER

source_name: MEP

growth_protocol: Adult (8-12 weeks old) Wild-type C57/Bl6 mice were sacrificed and cells were harvested from  bone marrow and/or thymus.

extract_protocol:
Cells were collected after sorting into microcentrifuge tubes containing staining media (1xDPBS,1mM EDTA with 5% serum) and centrifuged at 500xg for 5 minutes at 4˚C . Cell pellet was washed with ice-cold 1xDPBS and centrifuged as above. Cells were lysed in (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) and centrifuged at 500xg for 10 minutes. Samples were suspended 25µL 2xTD Buffer, 2.5µL transposase (Illumina), and 22.5µL nuclease free water and incubated at 37˚C for 30 minutes at 600rpm. Samples were purified using the MinElute Reaction Clean up kit (Qiagen).
Library fragments were amplified using NEBnext PCR mastermix and custom Nextera primers, and size selected using Ampure XP Beads.

treatment_protocol: Bone marrow or thymic cells were stained with flourescent antibodies and sorted by FACS according to established markers.

value: Megakaryocitic-erythroid Progenitor

value: bone marrow


title: ProB rep1

source_name: ProB

value: B cell Progenitor


title: ProT rep2

source_name: ProT

value: T cell Progenitor

value: thymus


title: CMP rep2

source_name: CMP

value: Common Myeloid Progenitor


title: GMP rep1

source_name: GMP

value: Granulocyte/Macrophage Progenitor


title: ProB rep2


title: VQ-D1, rep2

description: Vκ*MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)

value: Spleen

value: V{kappa}{star}MYC; NrasLSL Q61R/+; IgG1-Cre (VQ)


title: MEP rep1


title: GMP rep2