title: RNA Seq_KO DP_repeat1

first: Yu

last: Xu

address: 320 Yueyang Road

institute: Shanghai Institue of Biochemistry and Cell Biology

data_processing:
We analysed the quality scores and other metrics using FASTQC.After quality filtration and the removal of sequencing adapters with Trim_galore (v0.5.0) In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from HISAT2 website directly.The RNA-seq reads were aligned to the mouse genome (grcm38) using HISAT2（v2.1.0）.
The only reads hitting no more than 2 genomic loci were used to quantify gene expression with featureCounts (v1.6.4)
The latest gene annotation files (gtf file) were downloaded from the ENSEMBL database. We analyzed these raw data using DESeq2 to assess variance and differential expression between sample groups.
Genome_build: Mus_musculus.Ensembl release 99
Supplementary_files_format_and_content: Tab-delimited text files include  reads count for each RNA-seq sample

source_name: RNA Seq_KO DP

growth_protocol: DP thymocytes were isolated by cell sorting (CD4+CD8+).

extract_protocol:
RNA was extracted, purified and checked for integrity using an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US).
Libraries were generated for sequencing using a NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H.  After end repair, adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed and PCR products were purified (AMPure XP system). The library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: strain background

tag: genotype/variation

value: Thymus

value: CD4+CD8+ double-positive (DP) thymocytes


title: RNA Seq_KO DP_repeat2

status: Public on May 21 2021

type: SRA

city: Shanghai

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type


title: RNA Seq_WT DP_repeat1

source_name: RNA Seq_WT DP


title: RNA Seq_WT DP_repeat2


title: Sample 40_AB1093

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used. (read2 used to read cell and molecule barcodes only)
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: *_metadata_s.txt: Meta data file associating each single cell with its amplification batch and index sorting readouts

molecule: polyA RNA

source_name: ND2 blood cDC

extract_protocol:
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}
single cell RNA-seq for gene expression quantitation

tag: strain

value: Blood

value: cDC

tag: selection marker

tag: infection

tag: time point

value: 2 weeks

value: ND


title: Sample 39_AB1092

source_name: ND1 blood cDC


title: T7051

city: Memphis

first: Liza

last: Makowski

state: Tennessee

address: 19 South Manassas St

department: Medicine- Heme Onc

country: USA

institute: UTHSC

description: lean mice fed low fat diet (LFD) receiving sham surgery

data_processing:
RNA degradation was examined by SCISSOR (shape changes in selecting sample outliers in RNA-seq) which uses unsupervised screening of a range of structural alterations in RNA-seq data.
Benjamini-Hochberg procedure was used to control false discovery rate (FDR) for adjusted P value.
Transcript-level abundance was imported into gene-level abundance with the R package tximport.
Genes with low expression were identified and filtered out from further analysis using filterByExpr function of the edgeR package in R software.
Voom transformation function was applied to normalize log2-cpm values using mean-variance trend in the limma software package.
ClaNC was used to create classifier genes that characterize the groups of interest for heatmap and tables.
Database for Annotation, Visualization and Integrated Discovery (DAVID ) v6.8 was used for pathway analysis.
Immune infiltration estimations based on bulk gene expression data from RNA-seq was plotted using TIMER2.0.
Genome_build: GRCm38

source_name: Tumor - breast cancer

growth_protocol: E0771 breast cancer cells were thawed from a 1 million cell aliquot stored in liquid nitrogen, plated and passed the same time for every injection.  E0771 cells were injected in the left fourth mammary fat pad of 22-week-old C57BL/6J females at 250,000 cells in 100μl of 75% RPMI / 25% Matrigel.

extract_protocol:
RNA was extracted from tumor tissue using RNeasy mini kit (QIAGEN, Germantown, MD).  The integrity of RNA was assessed using Agilent Bioanalyzer and samples with RIN >8.0 were used.
Libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kits (non-directional) for Illumina, following manufacturer protocols. mRNA was enriched using oligo-dT beads.
Libraries were sequenced on NovaSeq 6000 using paired-end 150 bp reads. There was no PhiX spike-in.

treatment_protocol:
Female mice were purchased at 3 weeks of age from Jackson Labs C57BL/6J (Jackson stock number: 000664), shipped to UTHSC, acclimated 1 week, then randomized to diets: high fat diet (HFD, D12492i – 60% kcal derived from fat from  Research Diets Inc., New Brunswick, NJ) or low fat diet (LFD, D12450Ji- 10% kcal derived from fat) from Research Diets Inc. (New Brunswick, NJ) for 16 weeks (age 4 weeks to 20 weeks old) before a 5 week surgery and cancer protocol..
Perioperative procedures were performed in accordance with the literature. Pre-operative measures included providing liquid diet (Ensure® Original Milk Chocolate Nutrition Shake, Abott) and DietGel recovery (Clear H2O, Portland, ME, ID# 72-06-5022) one day before surgery to all mice. Four hours before surgery, solid food was removed to reduce stomach contents. For 4 hours pre-surgery, mice were maintained half on half off a heat pad in clean cages. Surgery was performed under isoflurane anesthesia. Vertical sleeve gastrectomy (VSG) was performed as previously described. The stomach was clamped and the lateral 80% of the stomach was removed with scissors. The remaining stomach was sutured with 8-0 to create a tubular gastric sleeve. All treatment groups not receiving VSG had a sham surgery performed. For sham, an abdominal laparotomy was performed with exteriorization of the stomach. Light pressure with forceps was applied to the exteriorized stomach. For both VSG and sham surgeries, the abdominal wall was closed with 6-0 sutures and skin closed with staples. Mice received carprofen (5mg/kg, subcutaneous, once daily) as an analgesic immediately prior to and once daily for 3 days following surgery. Mice were given 1ml saline at time of surgery.  For 12 hours post-surgery, mice were maintained half on half off a recovery heat pad. Mice were provided Ensure® liquid diet (as above), DietGel recovery, and solid food pellets ad libitum for 48 hours post-surgery. HFD-fed DIO mice receiving VSG (“HFD-VSG”) were maintained on the same HFD for 5 weeks following surgery until euthanasia at study endpoint. Control groups that were lean (“LFD-Sham”) or DIO (“HFD-Sham”) were maintained on respective LFD or HFD diets following sham surgery. For dietary intervention weight loss, “Diet Switch” (DS) mice were formerly HFD-fed DIO switched to LFD ad libitum after sham similar to our previous work (8, 9). “Calorie restricted” (CR) mice were matched controls to the HFD-VSG mice by weight matching through restricting intake of HFD. On average, mice consumed 1.7g (ranging from 1.0-2.5 g or 8.84 kcal (5.2-13.0 kCal) per day of HFD. Mice were fed at the start of the dark cycle.

tag: cell syngeneic orthotopic transplant

value: E0771-luciferase cells

tag: mouse strain

value: Tumor - breast cancer

tag: treatment

value: LFD-Sham


title: T7054

description: caloric restriction (CR) to match weight loss in VSG cohort receiving sham surgery (weight match sham control)

value: CR-Sham


title: T7066

description: Formerly obese mice fed High fat diet (HFD) and switch to low fat diet (LFD) receiving sham surgery

value: DS-Sham


title: NSC-17-2-H3K27ac

city: Tokyo

first: Yosuke

last: Tanaka

address: 5-1-1, tsukiji, Chuo-ku

country: Japan

institute: National Cancer Center Research Institute

library_source: genomic

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to GRCh37 whole genome using Burrows - Wheeler Aligner  v0.7.17.
Duplicates were removed using the samtools rmdup, and replicate experiments were merged using samtools merge.
Peaks were called using MACS2 (version 2.0).
Genome_build: GRCh37
Supplementary_files_format_and_content: peak bed files

molecule: genomic DNA

organism: Homo sapiens

source_name: Human gastric cancer cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions.

tag: cell types

value: Human gastric cancer cells

tag: chip antibody

value: H3K27ac (D5E4, Cell Signaling Technology)


title: Sample 43_AB137

source_name: 2 weeks ND 1.6

value: liver

value: CD45+ Immune cells


title: miR148a-gKO3

city: Erlangen

first: Hans-Martin

last: Jäck

address: Glückstrasse 6

department: Molecular Immunology

country: Germany

institute: Universitätsklinikum Erlangen

data_processing:
Sequenced reads were trimmed for adaptor sequences and mapped to the GRCM38 mouse genome with STAR 2.5.4b
Gene-wise counts were generated with featureCounts 1.6.4
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Combined table with summarized gene-wise counts for each sample generated with featureCounts

source_name: Bone Marrow Plasma Cell

extract_protocol:
Plasma cells were FACS-purified from bone marrow (CD138+ TACI+) and sorted directly into Trizol (Qiagen) Lysis reagent. Total RNA was isolated with the miRNeasy Micro Kit (Qiagen).
Sequencing libraries were constructed with the Takara Clontech Smart-Seq v4 Low input kit according to manufacturers instructions and sequenced on Illumina Hiseq X instruments.

tag: genotype

value: bone marrow plasma cells (TACI+ CD138+)


title: Sample 38_AB1091

source_name: MCDD2 BM CDP

value: Bone marrow

value: CDP

value: Lin+ CD135+CSF1R+CD117int

value: MCDD


title: Sample 37_AB1090

source_name: MCDD1 BM CDP


title: T7022

description: Diet induced obese mice fed HFD, then receiving sham surgery

value: HFD-Sham


title: Sample 36_AB1089

source_name: ND2 BM CDP

value: 2 weeks


title: NSC-16-2-H3K27ac


title: NSC-17-1-H3K27ac


title: NSC-16-1-H3K27ac


title: NSC-15-2-H3K27ac


title: 10% Input Control Biological Replicate

city: Seattle

first: Anthony

middle: Scott

last: Castanza

state: Washington

address: 1959 NE Pacific St Box 357470

department: Pathology

institute: University of Washington

description:
AUTS2_RIP_vs_Input_FPKM_Table
AUTS2_RIP_vs_Input_cummeRbund_database
Input-B.205639

data_processing:
75bp Illumina reads were mapped to the GRCm38.p4 mouse reference genome (Gencode M11) with STAR version 2.5 by the NWGC at University of Washington
RIP-Seq BAM Files were filtered using SAMtools in Galaxy with the following flags -mapped -noqcfail -nopcrdup
A blacklist file was generated by retreiving alignments for tRNA, rRNA, chrM, and chrY for Gencode M14 from BioMart which were masked from downstream analysis
BAM files were masked against the blacklist and Quantified against the Gencode M14 annotation using CuffDiff version 2.2.1 on Galaxy
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include CuffDiff FPKM values for each Sample. CummeRbund sqlite files contain CuffDiff tracking and results database for each analysis

source_name: Cortex

extract_protocol:
Cortex from two P0.5 neonates was dissected under cold saline and pooled (per replicate). Freshly dissected tissue was prepared immediately for RNA-immunoprecipitation in accordance with the Millipore Magna-RIP protocol (Catalog No. 17-700)
Libraries were prepared with the CloneTech SMARTer Stranded protocol

tag: developmental stage

value: Cortex


title: T6080

value: E0771-luciferase cells


title: T7001

value: Tumor - breast cancer


title: T7021


title: T7017


title: T5855


title: Sample 35_AB1088

source_name: ND1 BM CDP

value: ND


title: NSC-15-1-H3K27ac


title: T5852

value: CR-Sham


title: T5746

value: DS-Sham


title: T5743


title: 10% Input Control

description:
AUTS2_RIP_vs_Input_FPKM_Table
AUTS2_RIP_vs_Input_cummeRbund_database
Input-A.205636


title: NSC-11-2-H3K27ac

value: Human gastric cancer cells


title: T70211


title: T6079


title: IgG Control RIP-Seq Biological Replicate

description:
AUTS2_RIP_vs_IgG_FPKM_Table
AUTS2_RIP_vs_IgG_cummeRbund_database
IgG-B.205638

tag: antibody

value: IgG


title: NSC-11-1-H3K27ac

value: H3K27ac (D5E4, Cell Signaling Technology)


title: IgG Control RIP-Seq

description:
AUTS2_RIP_vs_IgG_FPKM_Table
AUTS2_RIP_vs_IgG_cummeRbund_database
IgG-A.205635


title: T5740

value: LFD-Sham


title: NSC-10-2-H3K27ac


title: T5739


title: T5738

description: Diet induced obese mice fed HFD, then receiving bariatric surgery vertical sleeve gastrectomy (VSG)

value: HFD-VSG


title: NSC-10-1-H3K27ac


title: AUTS2 RIP-Seq

description:
AUTS2_RIP_vs_IgG_FPKM_Table
AUTS2_RIP_vs_IgG_cummeRbund_database
AUTS2_RIP_vs_Input_cummeRbund_database
Auts2-A.205634


title: T5737


title: NSC-6-2-H3K27ac


title: T5732


title: NSC-6-1-H3K27ac


title: T5731


title: T5730


title: Cop1_sgRNA2_IFNgamma_Rep1 (ATAC-Seq)

city: Boston

first: Xiaoqing

last: Wang

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

data_processing:
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 whole genome using BWA using the default parameters.
We used MACS2 for peak calling.
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 was applied to identify the differentially accessible regions.

source_name: 4T1 mouse breast cancer cells

extract_protocol:
ATAC-seq was performed on replicates (200,000 cells) by the Center for Functional Cancer Epigenetics at DFCI as previously described.
Genome-wide mapping of insertion ends by high-throughput sequencing allows for multidimensional assays of the regulatory landscape of chromatin with a relatively simple protocol.

treatment_protocol:
The assay of transposase accessible chromatin (ATAC-seq) uses hyperactive Tn5 transposase to simultaneously cut and ligate adapters for high-throughput sequencing at regions of increased accessibility.
we treated sgControl or sgCop1-transduced 4T1 cells with vehicle control or 20ng/ml IFNγ for 24 hrs

tag: cell line

tag: cancer type

value: breast cancer

value: breast

tag: sgrna

value: IFNg


title: Cop1_sgRNA2_IFNgamma_Rep2 (ATAC-Seq)

tag: tissue


title: NSC-4-1-H3K27ac


title: NSC-4-2-H3K27ac


title: Cop1_sgRNA1_IFNgamma_Rep1 (ATAC-Seq)


title: T5726


title: NSC-71-2-input


title: T5722


title: Cop1_sgRNA1_IFNgamma_Rep2 (ATAC-Seq)


title: T5720


title: Rosa26_sgRNA_IFNgamma_Rep2 (ATAC-Seq)


title: AUTS2 RIP-Seq Biological Replicate

description:
AUTS2_RIP_vs_IgG_FPKM_Table
AUTS2_RIP_vs_IgG_cummeRbund_database
AUTS2_RIP_vs_Input_cummeRbund_database
Auts2-B.205637


title: T5717


title: Cop1_sgRNA2_Rep2 (ATAC-Seq)

value: Vehicle


title: NSC-70-2-input


title: NSC-70-1-input


title: Cop1_sgRNA2_Rep1 (ATAC-Seq)


title: T5715


title: NSC-71-1-input


title: Cop1_sgRNA1_Rep2 (ATAC-Seq)


title: NSC-69-1-input


title: T886


title: Cop1_sgRNA1_Rep1 (ATAC-Seq)


title: T885

value: HFD-Sham


title: NSC-68-2-input


title: Rosa26_sgRNA_IFNgamma_Rep1 (ATAC-Seq)


title: Rosa26_sgRNA_Rep2 (ATAC-Seq)


title: T5716


title: T882


title: NSC-68-1-input


title: Rosa26_sgRNA_Rep1 (ATAC-Seq)


title: NSC-69-2-input


title: T866


title: NSC-67-2-input


title: D8_WT_C_TE#1

city: La Jolla

first: Ananda

last: Goldrath

state: CA

address: 9500 Gilman Dr

institute: UCSD

description:
SK-3YTT_B7
Processed_RNA_seq_D8_Brd4_KO.xlsx

data_processing:
Tophat
HT-Seq Count
DESeq from BioConductor
Genome_build: UCSC mm10 (GRCm38)
Supplementary_files_format_and_content: Processed_RNA_seq_D8_Brd4_KO.xlsx: Excel file

source_name: D8 P14 KLRG1loCD127hi

extract_protocol:
Total RNA was extracted in TRIZoL reagent.
PrepX RNA-seq library preparation kit (Integenex).

tag: age

value: 6-16 Weeks

value: Spleen


title: NSC-67-1-input


title: T850

value: E0771-luciferase cells


title: T848

value: Tumor - breast cancer


title: NSC-66-2-input


title: NSC-66-1-input


title: D8_WT_C_MP#1

description:
SK-3YTT_B9
Processed_RNA_seq_D8_Brd4_KO.xlsx

source_name: D8 P14 KLRG1hiCD127lo

tag: strain


title: T826


title: NSC-65-2-input


title: D8_WT_B_TE#1

description:
SK-3YTT_B4
Processed_RNA_seq_D8_Brd4_KO.xlsx


title: D8_WT_C_EEC#1

description:
SK-3YTT_B8
Processed_RNA_seq_D8_Brd4_KO.xlsx

source_name: D8 P14 KLRG1loCD127lo


title: T817


title: T809


title: D8_WT_B_MP#1

description:
SK-3YTT_B6
Processed_RNA_seq_D8_Brd4_KO.xlsx


title: NSC-65-1-input


title: T827


title: D8_WT_A_MP#1

description:
SK-3YTT_B3
Processed_RNA_seq_D8_Brd4_KO.xlsx


title: NSC-68

type: genomic

description: Patient derived cell lines

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Infinium Human methylation EPIC beads chip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio

label: Cy5 and Cy3

source_name: Human gastric cancer cell line

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from cell lines of gastric cancer using Qiagen Kit according to standard instructions

tag: cell type


title: NSC-64-2-input


title: D8_WT_B_EEC#1

description:
SK-3YTT_B5
Processed_RNA_seq_D8_Brd4_KO.xlsx


title: NSC-64

description: Patient derived cell lines


title: NSC-71

description: Patient derived cell lines


title: NSC-61

description: Patient derived cell lines


title: D8_WT_A_EEC#1

description:
SK-3YTT_B2
Processed_RNA_seq_D8_Brd4_KO.xlsx


title: NSC-63-1-input


title: NSC-69

description: Patient derived cell lines


title: NSC-70

description: Patient derived cell lines


title: NSC-56

description: Patient derived cell lines


title: NSC-67

description: Patient derived cell lines


title: T400

description: Formerly obese mice fed High fat diet (HFD) and switch to low fat diet (LFD) receiving sham surgery


title: NSC-50

description: Patient derived cell lines


title: NSC-51

description: Patient derived cell lines


title: A7022

description: Diet induced obese mice fed HFD, then receiving sham surgery

source_name: Mammary Fat Pad

extract_protocol:
RNA was extracted from uninjected mammary fat pad (contralateral to E0771 injected 4th mammary gland) tissue using kit specific for lipid rich tissue (Norgen Biotek, Ontario, Canada).  The integrity of RNA was assessed using Agilent Bioanalyzer and samples with RIN >8.0 were used.
Libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kits (non-directional) for Illumina, following manufacturer protocols. mRNA was enriched using oligo-dT beads.
Libraries were sequenced on NovaSeq 6000 using paired-end 150 bp reads. There was no PhiX spike-in.

value: Mammary fat pad adipose tissue (uninjected, contralateral) in E0771-luciferase breast cancer bearing mice

tag: lean or obese & diet exposure

value: Obese (high fat diet, HFD, 60% kcal from fat)

tag: surgery


title: NSC-61-2-input


title: NSC-60

description: Patient derived cell lines


title: NSC-57

description: Patient derived cell lines


title: NSC-58

description: Patient derived cell lines


title: A7054

description: caloric restriction (CR) to match weight loss in VSG cohort receiving sham surgery (weight match sham control)

tag: cell syngeneic orthotopic transplant

value: Formerly Obese (high fat diet, HFD, 60% kcal from fat)

value: CR-Sham


title: NSC-65

description: Patient derived cell lines

value: Human gastric cancer cells


title: NSC-66

description: Patient derived cell lines


title: NSC-61-1-input


title: D8_KO_C_MP#1

description:
SK-3YTT_C6
Processed_RNA_seq_D8_Brd4_KO.xlsx


title: NSC-49

description: Patient derived cell lines


title: NSC-63-2-input


title: D8_WT_A_TE#1

description:
SK-3YTT_B1
Processed_RNA_seq_D8_Brd4_KO.xlsx


title: NSC-46

description: Patient derived cell lines


title: NSC-63

description: Patient derived cell lines


title: A7006

tag: mouse strain

value: Formerly Obese (high fat diet, HFD, 60% kcal from fat) then fed low fat diet, LFD, (10% kcal from fat)

value: DS-Sham


title: A7001

description: lean mice fed low fat diet (LFD) receiving sham surgery

value: Lean (low fat diet, LFD, 10% kcal from fat)

value: LFD-Sham


title: NSC-58-2-input


title: NSC-60-2-input


title: NSC-47

description: Patient derived cell lines


title: NSC-44

description: Patient derived cell lines


title: NSC-39

description: Patient derived cell lines


title: NSC-40

description: Patient derived cell lines


title: D8_KO_A_TE#1

description:
SK-3YTT_B10
Processed_RNA_seq_D8_Brd4_KO.xlsx


title: A7051


title: NSC-48

description: Patient derived cell lines


title: D8_KO_B_EEC#1

description:
SK-3YTT_C2
Processed_RNA_seq_D8_Brd4_KO.xlsx


title: NSC-57-2-input


title: D8_KO_C_TE#1

description:
SK-3YTT_C4
Processed_RNA_seq_D8_Brd4_KO.xlsx


title: NSC-57-1-input


title: A7021


title: D8_KO_A_EEC#1

description:
SK-3YTT_B11
Processed_RNA_seq_D8_Brd4_KO.xlsx


title: A7017


title: D8_KO_C_EEC#1

description:
SK-3YTT_C5
Processed_RNA_seq_D8_Brd4_KO.xlsx


title: D8_JQ1_B_MP#1

description:
SK-3YTT_A6
Processed_RNA_seq_D8_JQ1.txt

data_processing:
Tophat
HT-Seq Count
DESeq from BioConductor
Genome_build: UCSC mm10 (GRCm38)
Supplementary_files_format_and_content: Processed_RNA_seq_D8_JQ1.txt: Tab-delimited text file


title: D8_KO_B_TE#1

description:
SK-3YTT_C1
Processed_RNA_seq_D8_Brd4_KO.xlsx


title: NSC-64-1-input


title: D8_KO_B_MP#1

description:
SK-3YTT_C3
Processed_RNA_seq_D8_Brd4_KO.xlsx


title: NSC-60-1-input


title: A5743


title: NSC-51-2-input


title: A6080


title: NSC-58-1-input


title: A6079


title: A5855


title: D8_KO_A_MP#1

description:
SK-3YTT_B12
Processed_RNA_seq_D8_Brd4_KO.xlsx


title: NSC-56-2-input


title: A5852


title: NSC-38

description: Patient derived cell lines


title: NSC-51-1-input


title: NSC-50-2-input


title: NSC-56-1-input


title: A5746


title: NSC-50-1-input


title: D8_JQ1_A_EEC#1

description:
SK-3YTT_A2
Processed_RNA_seq_D8_JQ1.txt


title: NSC-49-2-input


title: NSC-32

description: Patient derived cell lines


title: A5739


title: D8_JQ1_A_MP#1

description:
SK-3YTT_A3
Processed_RNA_seq_D8_JQ1.txt


title: A5737


title: NSC-49-1-input


title: A5738

description: Diet induced obese mice fed HFD, then receiving bariatric surgery vertical sleeve gastrectomy (VSG)

value: Formely Obese (high fat diet, HFD, 60% kcal from fat)

value: HFD-VSG


title: A5740


title: D8_JQ1_A_TE#1

description:
SK-3YTT_A1
Processed_RNA_seq_D8_JQ1.txt


title: NSC-26

description: Patient derived cell lines


title: D8_DMSO_B_TE#1

description:
SK-3YTT_A10
Processed_RNA_seq_D8_JQ1.txt


title: D8_DMSO_B_EEC#1

description:
SK-3YTT_A11
Processed_RNA_seq_D8_JQ1.txt


title: NSC-36

description: Patient derived cell lines


title: A5732


title: A5730


title: D8_DMSO_B_MP#1

description:
SK-3YTT_A12
Processed_RNA_seq_D8_JQ1.txt


title: NSC-37

description: Patient derived cell lines


title: D8_DMSO_A_TE#1

description:
SK-3YTT_A7
Processed_RNA_seq_D8_JQ1.txt


title: NSC-34

description: Patient derived cell lines


title: NSC-35

description: Patient derived cell lines


title: NSC-22

description: Patient derived cell lines


title: D8_JQ1_B_TE#1

description:
SK-3YTT_A4
Processed_RNA_seq_D8_JQ1.txt


title: A5726

description: Formerly obese mice fed High fat diet (HFD) and switch to low fat diet (LFD) receiving sham surgery


title: NSC-48-2-input


title: D8_JQ1_B_EEC#1

description:
SK-3YTT_A5
Processed_RNA_seq_D8_JQ1.txt


title: D8_DMSO_A_MP#1

description:
SK-3YTT_A9
Processed_RNA_seq_D8_JQ1.txt


title: A5731


title: NSC-48-1-input


title: D8_DMSO_A_EEC#1

description:
SK-3YTT_A8
Processed_RNA_seq_D8_JQ1.txt


title: NSC-47-2-input


title: A5722


title: NSC-47-1-input


title: LC-9: large cell MALT lymphoma 9

city: Ulm

first: Thomas

middle: FE

last: Barth

state: Select...

address: Albert-Einstein-Allee 11

institute: Ulm University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing:
GenomeStudio software (v2011.1; methylation module 1.9.0)
GenomeStudio software (v2011.1; methylation module 1.9.0) normalized avg. beta values. For data normalization, the intrinsic controls present on the array were used.

label: Cy3 and Cy5

source_name: gastric resection

extract_protocol: A tumor cell content of at least 70% was ensured based on morphologic inspection in every sample analyzed herein. Extraction of DNA from FFPE tissue was performed using the truXTRAC FFPE DNA micro Tube Kit (Covaris, USA) . DNA extraction from cryo-preserved material was performed using the QIAamp DNA Mini Kit (Qiagen, Germany).

tag: gender,age, tissue type

value: M, 79, cryopreserved

tag: gender

value: M

value: large cell MALT lymphoma

tag: tissue type

value: cryopreserved


title: LC-8: large cell MALT lymphoma 8

value: F, 75, cryopreserved

value: F


title: NSC-46-2-input

tag: cell types

tag: chip antibody


title: NSC-46-1-input


title: LC-7: large cell MALT lymphoma 7

value: F, 77, cryopreserved


title: T8.JQ1HI.EEC.D5.Sp.A#1

description:
ImmGen_Population_G06
Processed_RNA_seq_D5_JQ1.xlsx

data_processing:
Tophat
HT-Seq Count
DESeq from BioConductor
Genome_build: UCSC mm10 (GRCm38)
Supplementary_files_format_and_content: Processed_RNA_seq_D5_JQ1.xlsx: Excel file

source_name: D5 Spleen P14 KLRG1loCD127lo

value: 6-16 Weeks

value: Spleen


title: NSC-29

description: Patient derived cell lines


title: A5717

value: Mammary fat pad adipose tissue (uninjected, contralateral) in E0771-luciferase breast cancer bearing mice


title: NSC-23

description: Patient derived cell lines

value: Human gastric cancer cells


title: LC-6: large cell MALT lymphoma 6

value: F, 64, cryopreserved


title: NSC-44-2-input


title: NSC-28

description: Patient derived cell lines


title: T8.DMSO.EEC.D5.Sp.B#1

description:
ImmGen_Population_G05
Processed_RNA_seq_D5_JQ1.xlsx


title: A5715


title: NSC-44-1-input


title: LC-5: large cell MALT lymphoma 5

value: F, 41, cryopreserved


title: NSC-24

description: Patient derived cell lines


title: T8.DMSO.EEC.D5.Sp.A#1

description:
ImmGen_Population_G04
Processed_RNA_seq_D5_JQ1.xlsx


title: LC-4: large cell MALT lymphoma 4

value: F, 62, cryopreserved


title: A886

description: caloric restriction (CR) to match weight loss in VSG cohort receiving sham surgery (weight match sham control)

value: Formerly Obese (high fat diet, HFD, 60% kcal from fat)

value: CR-Sham


title: NSC-40-2-input


title: T8.JQ1HI.EEC.D5.Sp.B#1

description:
ImmGen_Population_G07
Processed_RNA_seq_D5_JQ1.xlsx


title: A5716

description: Diet induced obese mice fed HFD, then receiving sham surgery

value: Obese (high fat diet, HFD, 60% kcal from fat)

value: HFD-Sham


title: A885


title: T8.shCD19.EEC.D5.Sp.D#1

description:
ImmGen_Population_F07
Processed_RNA_seq_D5_JQ1.xlsx


title: LC-3: large cell MALT lymphoma 3

value: M, NA, cryopreserved

value: M


title: NSC-15

description: Patient derived cell lines


title: A882

value: Formely Obese (high fat diet, HFD, 60% kcal from fat)

value: HFD-VSG


title: LC-2: large cell MALT lymphoma 2

value: M, 74, cryopreserved

value: large cell MALT lymphoma

value: cryopreserved


title: NSC-39-2-input


title: T8.shCD19.EEC.D5.Sp.C#1

description:
ImmGen_Population_F05
Processed_RNA_seq_D5_JQ1.xlsx

value: 6-16 Weeks

value: Spleen


title: NSC-40-1-input

value: Human gastric cancer cells


title: A866

value: Mammary fat pad adipose tissue (uninjected, contralateral) in E0771-luciferase breast cancer bearing mice


title: NSC-11

description: Patient derived cell lines


title: NSC-39-1-input


title: T8.shBrd4.2.EEC.D5.Sp.A#1

description:
ImmGen_Population_F04
Processed_RNA_seq_D5_JQ1.xlsx


title: NSC-38-2-input


title: NSC-20

description: Patient derived cell lines


title: A5720

description: lean mice fed low fat diet (LFD) receiving sham surgery

value: Lean (low fat diet, LFD, 10% kcal from fat)

value: LFD-Sham


title: ComLC-10: large cell component of composite lymphoma 10

value: F, 75, cryopreserved

value: F


title: A863

value: Obese (high fat diet, HFD, 60% kcal from fat)


title: T8.shCD19.EEC.D5.Sp.B#1

description:
ImmGen_Population_F03
Processed_RNA_seq_D5_JQ1.xlsx


title: A850


title: ComLC-9: large cell component of composite lymphoma 9

value: M, 62, cryopreserved


title: NSC-38-1-input


title: T8.shBrd4.1.EEC.D5.Sp.B#1

description:
ImmGen_Population_F02
Processed_RNA_seq_D5_JQ1.xlsx


title: NSC-37-2-input


title: NSC-16

description: Patient derived cell lines


title: LC-1: large cell MALT lymphoma 1

value: M,NA, cryopreserved


title: A848


title: ComLC-8: large cell component of composite lymphoma 8

value: M, 55, cryopreserved

value: M


title: T8.shCD19.EEC.D5.Sp.A#1

description:
ImmGen_Population_F01
Processed_RNA_seq_D5_JQ1.xlsx


title: NSC-18

description: Patient derived cell lines


title: ComLC-7: large cell component of composite lymphoma 7

value: M, 58, cryopreserved


title: A832

description: Diet induced obese mice fed HFD, then receiving bariatric surgery vertical sleeve gastrectomy (VSG)

value: Formely Obese (high fat diet, HFD, 60% kcal from fat)

value: HFD-VSG


title: T8.shBrd4.1.EEC.D5.Sp.A#1

description:
ImmGen_Population_E12
Processed_RNA_seq_D5_JQ1.xlsx


title: NSC-36-2-input


title: ComLC-6: large cell component of composite lymphoma 6

value: F, 73, cryopreserved

value: cryopreserved


title: NSC-10

description: Patient derived cell lines


title: T8.shBrd4.2.EEC.D5.Sp.B#1

description:
ImmGen_Population_F06
Processed_RNA_seq_D5_JQ1.xlsx

value: 6-16 Weeks

value: Spleen


title: ComLC-5: large cell component of composite lymphoma 5

value: M, 68, cryopreserved


title: NSC-35-2-input

value: Human gastric cancer cells


title: A826

value: Mammary fat pad adipose tissue (uninjected, contralateral) in E0771-luciferase breast cancer bearing mice


title: NSC-6

description: Patient derived cell lines


title: A809

value: HFD-Sham


title: NSC-36-1-input


title: NSC-37-1-input


title: ComLC-4: large cell component of composite lymphoma 4

value: F, 82, cryopreserved

value: F


title: ComLC-2: large cell component of composite lymphoma 2

value: F, 74, cryopreserved


title: A400

description: Formerly obese mice fed High fat diet (HFD) and switch to low fat diet (LFD) receiving sham surgery

value: Formerly Obese (high fat diet, HFD, 60% kcal from fat) then fed low fat diet, LFD, (10% kcal from fat)

value: DS-Sham


title: ComLC-3: large cell component of composite lymphoma 3

value: M, 46, cryopreserved

value: M


title: SUM190PT_LapatinibHerceptin_3

type: RNA

city: Drammen

first: Lisa

middle: Svartdal

last: Normann

address: Wergelands gate 10

department: Department of Research and Innovation

country: Norway

institute: Vestre Viken Health Trust

description:
SUM190PT_LapatinibHerceptin_3
120807_253118113776_S01_miRNA_107_Sep09_1_4

hyb_protocol: Agilent miRNA Labeling Reagent and Hybridization Kit, Protocol v.2.3.

scan_protocol: Scanning on Agilent scanner G2565B and Feature Extraction (FE) v10.7.3.1 was used to extract signals

data_processing: Samples were processed using Feature Extraction (FE) version 10.7.3.1 (Agilent Technologies). Quality was assessed by the quality control parameters in FE. The data were log2-transformed and for each sample, considering only expressed miRNAs, the data were median centered. All non-expressed miRNAs across samples were set to a common minimum value.

source_name: Breast cancer cell line

growth_protocol: HER2 positive breast cancer cell lines

extract_protocol: miRNeasy Mini kit according to manufaturer's protocol (Qiagen)

treatment_protocol: Cells were treated with trastuzumab (10 µg/ml) and/or lapatinib (100 nM) for 24 hours before RNA extraction.

value: Breast cancer cell line

value: HER2 positive breast cancer


title: NSC-34-1-input

source_name: Human gastric cancer cells


title: SUM190PT_LapatinibHerceptin_1

description:
SUM190PT_LapatinibHerceptin_1
120807_253118113485_S01_miRNA_107_Sep09_1_4

label_protocol: Agilent miRNA Labeling Reagent and Hybridization Kit, Protocol v.2.3.


title: ComLC-1: large cell component of composite lymphoma 1

value: M, 77, cryopreserved


title: A827

value: Obese (high fat diet, HFD, 60% kcal from fat)


title: BPR_n1

city: Taipei

first: Ya-Ju

last: Yu

address: 5F ,No 1, Sec 1, Jen-Ai Rd

country: Taiwan

institute: National Taiwan University College of Medicine Graduate Institute of Immunology

description: SMARTer, 200 cells

data_processing:
cDNA samples were sequenced by Illumina NovaSeq 6000.
Paired-end reads were filtered by Trimmomatic (v0.38).
Read pairs from each sample were aligned to the reference genome by the HISAT2 software (v2.1.0).
FeatureCounts (v1.6.0) was used to count the reads numbers mapped to individual genes.
Trimmed Mean of M-values normalization (TMM) was performed DEGseq (v1.36.1)
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files

source_name: BPR (B cells from pDC R848 coculture system)

growth_protocol: Purified B and pDCs were cultured in 200 μl complete RPMI medium (RPMI 1640 with 10% FBS, hyclone, 10 μg/ml gentamycin, and 50μM β-ME, Sigma) in 96-well U bottom plates at 37°C in 5% CO2 humidified incubator.

extract_protocol:
SMARTer® Stranded RNA-Seq Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: wo/with R848 (1μg/ml)

tag: cell isolation

value: Sorted primary cells

tag: treatment


title: SUM190PT_Lapatinib_2

description:
SUM190PT_Lapatinib_2
120807_253118113485_S01_miRNA_107_Sep09_2_4

tag: cell line


title: SUM190PT_Lapatinib_3

description:
SUM190PT_Lapatinib_3
120807_253118113506_S01_miRNA_107_Sep09_2_4


title: SUM190PT_LapatinibHerceptin_2

description:
SUM190PT_LapatinibHerceptin_2
120807_253118113506_S01_miRNA_107_Sep09_1_4


title: Com(SC+LC)-3: composite lymphomas including both the large and small-cell components 3

value: F, 73, FFPE

value: FFPE


title: BR_n2

description: SMARTer, 200 cells

source_name: BR (with R848)

value: Spleen


title: NSC-32-2-input

value: Human gastric cancer cells


title: Com(SC+LC)-2: composite lymphomas including both the large and small-cell components 2

value: cryopreserved


title: BR_n1

description: SMARTer, 200 cells


title: Com(SC+LC)-1: composite lymphomas including both the large and small-cell components 1

value: F, 55, cryopreserved


title: NSC-29-2-input


title: SUM190PT_Lapatinib_1

description:
SUM190PT_Lapatinib_1
120807_253118113505_S01_miRNA_107_Sep09_2_4


title: NSC-4

description: Patient derived cell lines


title: WT (wildtype)

city: Beijing

first: Chunsheng

last: Han

state: Beijing

address: 1-5 Beichen West Road, Chaoyang District

department: Institute of Zoology

institute: Chinese Academy of Sciences

description: 10X genomics

data_processing:
Trimmed FASTQ files (26 bp cell barcode and UMI Read1, 8 bp i7 index, and 100 bp Read2), were generated using the CellRanger (Version 1.3.1) “mkfastq” command. The Cell Ranger “mkref” function with default settings was used to process the genomic sequence (Mus musculus genome GRCm38) and the annotation file for read alignment. We removed cells with low quality using the following thresholds: 1) UMIs or gene numbers beyond 3 median absolute deviations away from the median determined by the “isOutlier” function of the Scater package (Version 1.14.6); 2) the ratio of mitochondria over 0.2.
The filtered gene expression data were analyzed by the Seurat package (Version 3.2.2). Global scaling normalization was applied with the “NormalizeData” function via the “LogNormalize” method with a scale factor 10,000. The top 2000 variable genes were identified by the “FindVariableGenes” function and used for principal component analysis. Significant principal components that were enriched with low p value (<1×10-5) genes were used for cell clustering. Using the graph-based clustering approach implemented in the “FindClusters” function of the Seurat package, with a resolution of 0.2, a seed of 323 and otherwise default parameters, cells were clustered and re-clustered by UMAP aligned coordinates and the resulting clusters were consistent with the mapping of known markers.
DEGs between WT and KO spermatocytes from scRNA-seq were identified by the “FindMarkers” function of the Seurat package using the “Wilcox” test, which returned “p_val_adj” using the Bonferroni correction and the log-transformed fold change, “avg_logFC”, and the cutoff was set to p_val_adj < 0.05.
Genome_build: GRCm38
Supplementary_files_format_and_content: raw counts

source_name: WT testicular cells

extract_protocol:
Single-cell suspensions were generated from adult WT and KO mouse testes using a two-step enzymatic digestion approach58. Mice were sacrificed, and then the testes were removed and decapsulated. The seminiferous tubules were cut into small pieces and incubated in DPBS containing 1 mg/ml Collagenase I (Gibco) at 37ºC for five minutes with gentle shaking. The dispersed seminiferous tubules and cells were collected by centrifugation at 100 g for two minutes at 4ºC. The pellet was washed once with DPBS and digested in 0.25% Trypsin (Gibco) containing 1 mg/ml DNase I (AppliChem) at 37ºC for five minutes with gentle shaking. The suspension was added with FBS (Vistech) to terminate digestion. Then, cells were collected by centrifugation at 600 g for five minutes and washed with 0.04% BSA/DPBS. The cells were then filtered through a 40-μm cell strainer (BD Falcon), and cell debris was removed by FACS. The cells were resuspended at a concentration of 1 million cells per ml in 0.04% BSA/DPBS.
Chromium Next GEM Single-cell 3’ GEM Library and Gel Bead Kit V3.1 (10× Genomics, 1000121) and Chromium Next GEM Chip G Single Cell Kit (10× Genomics, 1000120) were used for cell capture and cDNA synthesis. The cell suspension was loaded onto the Chromium single-cell controller (10× Genomics) to generate single-cell gelbead emulsions (GEMs) according to the manufacturer's instruction. About 20,000 cells were added to each channel, and the target recovery rate was estimated to be 13,000 cells. Captured cells were lysed and the released RNA was barcoded through reverse transcription in individual GEMs. Reverse transcription was performed using a T series Multi-Block Thermal Cycler (LongGene). The following procedure was used: 53°C for 45 min, 85°C for 5 min, and 4°C forever. The quality of the generated cDNA was assessed by the Agilent 2100, which was performed by Emei Tongde (Beijing, China). Sequencing (performed by NovoGene, Beijing) was performed on the Illumina NovaSeq 6000 sequencer with 150 bp (PE150) paired-end reads.

value: Total testicular cells

value: adult

value: testis

tag: genotype

value: WT


title: KO (knockout)

description: 10X genomics

source_name: KO testicular cells

tag: tissue


title: NSC-29-1-input


title: ComSC-2: small cell component of composite lymphoma 2

value: M, 81, FFPE

tag: age


title: SUM190PT_Herceptin_3

description:
SUM190PT_Herceptin_3
120807_253118113505_S01_miRNA_107_Sep09_1_4


title: SUM190PT_Herceptin_1

description:
SUM190PT_Herceptin_1
120807_253118113484_S01_miRNA_107_Sep09_1_4


title: NSC-28-2-input


title: ComSC-1: small cell component of composite lymphoma 1

value: M


title: Sample 34_AB10817

source_name: MCDD PIC 2

tag: strain

value: liver lymph nodes

value: PIC (T + cDC)

tag: selection marker

tag: infection

tag: time point

value: 2 weeks

value: MCDD


title: Sample 33_AB10816

source_name: MCDD PIC 1

tag: cell type


title: SC-6: small cell MALT lymphoma 6

value: M, 75, FFPE

value: small cell MALT lymphoma


title: NSC-32-1-input


title: SUM190PT_Control_2

description:
SUM190PT_Control_2
120807_253118113484_S01_miRNA_107_Sep09_2_4

value: Breast cancer cell line

value: HER2 positive breast cancer


title: NSC-26-2-input

value: Human gastric cancer cells


title: NSC-28-1-input


title: SUM190PT_Herceptin_2

description:
SUM190PT_Herceptin_2
120807_253118113504_S01_miRNA_107_Sep09_1_4


title: SUM190PT_Control_1

description:
SUM190PT_Control_1
120807_253118113776_S01_miRNA_107_Sep09_2_4


title: Sample 32_AB10815

source_name: ND PIC 2

value: ND


title: SUM190PT_Control_3

description:
SUM190PT_Control_3
120807_253118113504_S01_miRNA_107_Sep09_2_4


title: NSC-26-1-input


title: SC-4: small cell MALT lymphoma 4

value: F, 49, cryopreserved

value: F

value: cryopreserved


title: Sample 31_AB10814

source_name: ND PIC 1


title: NSC-17

description: Patient derived cell lines


title: SC-3: small cell MALT lymphoma 3

value: F, 80, cryopreserved


title: NSC-24-2-input


title: SKBR3_LapatinibHerceptin_3

description:
SKBR3_LapatinibHerceptin_3
120807_253118113506_S01_miRNA_107_Sep09_1_2


title: SKBR3_LapatinibHerceptin_2

description:
SKBR3_LapatinibHerceptin_2
120807_253118113485_S01_miRNA_107_Sep09_1_2


title: NSC-24-1-input


title: SKBR3_LapatinibHerceptin_1

description:
SKBR3_LapatinibHerceptin_1
120807_253118113505_S01_miRNA_107_Sep09_1_2


title: NSC-23-2-input


title: SC-5: small cell MALT lymphoma 5

value: M, 42, cryopreserved


title: NSC-23-1-input


title: Sample 27_AB10810

source_name: DC ND 2

value: cDC


title: Sample 28_AB10811

source_name: DC ND 6


title: BPR_n2

description: SMARTer, 200 cells

value: Spleen

value: Sorted primary cells


title: HPD group3

city: Nice Cedex 3

first: Maria

last: Stathopoulou

address: 151 Route de Saint-Antoine de Ginestière

country: France

institute: Inserm

description: small RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads has been first filtered against pre-formated fasta file including, SOLiD P1 and P2 adaptors, SOLiD barcodes, polynucleotides (polyA,polyT,polyC and polyG), ribosomal RNAs. Genome alignment was performs against mm9 release using Bowtie aligner allowing 2 mismatchs after discarding SOLiD adaptor. Read count was performs using custom Java class based on the parsing of .bam alignment file and sequential annotation using .gff annotation files gathering genomic positions of microRNAs (mirbase release 18), UCSC tRNAs tracks table, Ensembl ncRNAs (release 69) and fRNAdb. Differential expression analysis has been performed with the DESeq R (bionconductor) package. DESeq size factor normalization. Genome_build: mm9 Supplementary_files_format_and_content: Not normalized table counts of features identified within all samples.
Annotation through the pipeline SPORTS1.0
Generation of normalized abundance measurements through DESeq2
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: excel files with number of read counts

organism: Rattus norvegicus

source_name: spermatozoa

growth_protocol: Male Wistar rats at the age of 10 weeks, weighing approximately 330 g, were housed (2 rats per cage) and divided into two groups. One group was fed with standard diet (SD group) . The other group was fed with a high-protein diet (HPD) for 2 to 3 months (HPD group)

extract_protocol:
Sperm were collected from epididym, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Wistar

value: spermatozoa

value: 5-months old rat

value: wild type

tag: diet

value: High Protein (HPD)


title: SKBR3_Lapatinib_3

description:
SKBR3_Lapatinib_3
120807_253118113485_S01_miRNA_107_Sep09_2_2

value: Breast cancer cell line


title: HPD group2

description: small RNA


title: NSC-22-2-input


title: SC-1: small cell MALT lymphoma 1

tag: gender,age, tissue type

value: F, 68, cryopreserved

value: small cell MALT lymphoma


title: Sample 26_AB10809

source_name: DC ND 1

value: liver lymph nodes

value: 2 weeks

value: ND


title: Sample 30_AB10813

source_name: DC MCDD 2

value: MCDD


title: Sample 25_AB10808

source_name: T MCDD 6

value: T


title: HPD group1

description: small RNA


title: NSC-22-1-input

value: Human gastric cancer cells


title: SKBR3_Lapatinib_2

description:
SKBR3_Lapatinib_2
120807_253118113505_S01_miRNA_107_Sep09_2_2

value: HER2 positive breast cancer


title: SD group3

description: small RNA

value: Standard (SD)


title: SKBR3_Lapatinib_1

description:
SKBR3_Lapatinib_1
120807_253118113504_S01_miRNA_107_Sep09_2_2


title: Sample 29_AB10812

source_name: DC MCDD 1

value: cDC


title: Sample 24_AB10807

source_name: T MCDD 2


title: SKBR3_Herceptin_3

description:
SKBR3_Herceptin_3
120807_253118113504_S01_miRNA_107_Sep09_1_2

source_name: Breast cancer cell line


title: SC-2: small cell MALT lymphoma 2

source_name: gastric resection

value: M, 62, cryopreserved

tag: gender

value: M

value: cryopreserved


title: SKBR3_Herceptin_2

description:
SKBR3_Herceptin_2
120807_253118113484_S01_miRNA_107_Sep09_1_2


title: Sample 23_AB10806

source_name: T MCDD 1


title: SKBR3_Herceptin_1

description:
SKBR3_Herceptin_1
120807_253118113776_S01_miRNA_107_Sep09_1_2


title: NSC-20-1-input

source_name: Human gastric cancer cells


title: SD group2

description: small RNA

value: Wistar

value: spermatozoa

value: 5-months old rat

value: wild type


title: SKBR3_Control_3

description:
SKBR3_Control_3
120807_253118113484_S01_miRNA_107_Sep09_2_2

value: Breast cancer cell line


title: NSC-18-2-input


title: Sample 22_AB10805

source_name: T ND 6

value: liver lymph nodes


title: NSC-18-1-input


title: Sample 21_AB10804

source_name: T ND 2

value: 2 weeks


title: SKBR3_Control_2

description:
SKBR3_Control_2
120807_253118113776_S01_miRNA_107_Sep09_2_2


title: Sample 20_AB10803

source_name: T ND 1

value: ND


title: LDLR KO_3_LPS 12 hours

city: New Haven

first: Alberto

last: Canfrán-Duque

state: CT

address: 10 Amistad

department: Comparative Medicine

institute: Yale University

data_processing:
Using the PartekFlow® software, version 8.0.19.0405 (Partek, Inc., St. Louis, MO) the reads were aligned with the STAR algorithm to the mouse genome mmu10.
To estimate the transcript expression abundance we used Quantify to annotation model (Partek E/M) algorithm.
Genome_build: mmu10
Supplementary_files_format_and_content: quantification matrix

source_name: Thioglycollated elicited periotneal macrophages

growth_protocol: Thioglycollate-elicited peritoneal macrophages were mantain in RPMI with 10%FBS for a total of 14 hours.

extract_protocol:
After the treatment thioglycollate-elicited peritoneal macrophages were harvested and RNA was isolated Total RNA from liver samples treated with ASOs as described above was extracted and purified using a RNA isolation Kit (Qiagen) followed by DNAse treatment to remove genomic contamination using RNA MinElute Cleanup (Qiagen).
rRNA was depleted from RNA samples using Ribo-Zero rRNA Removal Kit (Illumina). RNA libraries were performed using TrueSeq Small RNA Library preparation (Illumina).
Libraries were sequenced for 45 cycles on Illumina HiSeq 2000 platform (1 x 100bp read length).

treatment_protocol: Thioglycollate-elicited peritoneal macrophages were treated with 100 ng/ml of LPS for 4 hours or 12 hours or kept untreated.

tag: strain/genotype

value: macrophage

value: 100 ng/ml LPS for 12 hours


title: NSC-20-2-input

tag: cell types

value: Human gastric cancer cells


title: LDLR KO_2_LPS 12 hours


title: NSC-17-1-input

tag: chip antibody


title: Sample 19_AB10519

source_name: LLN MCDD LLN PIC 3

value: PIC (T + cDC)

value: MCDD


title: LDLR KO_1_LPS 12 hours


title: NSC-17-2-input


title: SKBR3_Control_1

description:
SKBR3_Control_1
120807_253118113777_S01_miRNA_107_Sep09_2_4

value: HER2 positive breast cancer


title: Sample 18_AB10518

source_name: LLN ND LLN PIC 3


title: NSC-16-2-input


title: Sample 17_AB10517

source_name: LLN DC MCDD 5

value: cDC


title: LDLR KO_3_LPS 4 hours

value: 100 ng/ml LPS for 4 hours


title: LDLR KO_2_LPS 4 hours


title: NSC-16-1-input


title: KPL4_LapatinibHerceptin_1

description:
KPL4_LapatinibHerceptin_1
120807_253118113484_S01_miRNA_107_Sep09_2_3


title: KPL4_LapatinibHerceptin_2

description:
KPL4_LapatinibHerceptin_2
120807_253118113504_S01_miRNA_107_Sep09_2_3


title: KPL4_LapatinibHerceptin_3

description:
KPL4_LapatinibHerceptin_3
120807_253118113505_S01_miRNA_107_Sep09_2_3


title: NSC-15-2-input


title: SD group1

description: small RNA

source_name: spermatozoa

value: Standard (SD)


title: KPL4_Lapatinib_3

description:
KPL4_Lapatinib_3
120807_253118113484_S01_miRNA_107_Sep09_1_3


title: LDLR KO_1_LPS 4 hours


title: Sample 15_AB10515

source_name: LLN DC MCDD 3


title: LDLR KO_3_Mock

value: Mock treated


title: LDLR KO_2_Mock


title: NSC-11-2-input


title: NSC-11-1-input


title: Sample 14_AB10514

source_name: LLN T MCDD 5

value: T


title: KPL4_Lapatinib_2

description:
KPL4_Lapatinib_2
120807_253118113776_S01_miRNA_107_Sep09_1_3


title: LDLR KO_1_Mock


title: NSC-10-1-input


title: NSC-10-2-input


title: Sample 16_AB10516

source_name: LLN DC MCDD 4


title: KPL4_Herceptin_3

description:
KPL4_Herceptin_3
120807_253118113776_S01_miRNA_107_Sep09_2_3


title: KPL4_Herceptin_2

description:
KPL4_Herceptin_2
120807_253118113506_S01_miRNA_107_Sep09_2_3


title: KPL4_Lapatinib_1

description:
KPL4_Lapatinib_1
120807_253118113506_S01_miRNA_107_Sep09_1_3


title: Sample 10_AB10510

source_name: LLN DC ND 3


title: Sample 9_AB10509

source_name: LLN DC ND 2


title: Sample 11_AB10511

source_name: LLN T ND 6


title: Sample 13_AB10513

source_name: LLN T MCDD 4


title: NSC-6-2-input


title: NSC-6-1-input


title: KPL4_Herceptin_1

description:
KPL4_Herceptin_1
120807_253118113485_S01_miRNA_107_Sep09_2_3

source_name: Breast cancer cell line


title: KPL4_Control_3

description:
KPL4_Control_3
120807_253118113485_S01_miRNA_107_Sep09_1_3


title: Sample 8_AB10508

source_name: LLN T ND 5


title: NSC-15-1-input

source_name: Human gastric cancer cells


title: NSC-4-2-input


title: KPL4_Control_2

description:
KPL4_Control_2
120807_253118113505_S01_miRNA_107_Sep09_1_3


title: BT474_LapatinibHerceptin_3

description:
BT474_LapatinibHerceptin_3
120807_253118113504_S01_miRNA_107_Sep09_2_1


title: KPL4_Control_1

description:
KPL4_Control_1
120807_253118113504_S01_miRNA_107_Sep09_1_3


title: NSC-4-1-input


title: Sample 12_AB10512

source_name: LLN T MCDD 3


title: Sample 6_AB10506

source_name: LLN T ND 3


title: CRISPR_expt2_rep2

city: Bronx

first: Andrew

last: Johnston

state: NY

address: 1301 Morris Park Avenue

department: Genetics

institute: Albert Einstein College of Medicine

data_processing:
Sequencing reads were base-called and trimmed using Picard v2.17.1 and trim_galore v0.3.7
Reads were aligned to hg38 and counted using STAR v2.6.0c with  ensembl release 79 gtf and the following parameters: --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --sjdbOverhang 99
Gene counts were normalized by selecting the 1000 housekeeping genes with the lowest coefficient of variation among the samples for use in the RUVg command within the RUVseq v1.10.0 package. House keeping genes were defined previously and can be found here: (https://www.tau.ac.il/~elieis/HKG/).
Differentially expressed genes were finally determined by DESeq2 v1.16.1
Genome_build: hg38 ensembl release 79
Supplementary_files_format_and_content: Raw_gene_counts.txt is a table of the raw counts as counted by STAR. DE_gene_table.txt contains the genes differentially expressed between CRISPR transfected and control cells lines

source_name: Embryonic kidney

growth_protocol: Cells were cultured in Dulbecco's Modified Eagle Medium (DMEM, Gibco # 11965-092), supplemented with 10% fetal bovine serum, 100 units/mL penicillin, 100 µg/mL streptomycin, and 1% non-essential amino acids. Cultures were kept in culture  at 37 ºC in a 5% CO2 incubator.

extract_protocol:
Cell pellets were treated with QIAzol lysis reagent (Qiagen) and total RNA was isolated using the miRNAeasy kit (Quiagen) combined with on column DNAse (Qiagen) treatment according to manufacaturer's instructions.
RNA-seq libraries were prepared from 1 ng of total RNA using the SMART-Seq HT Kit (Takara) combined with Nextera XT kit (Illumina), according to manufacturers' instructions. Briefly, a one-step cDNA synthesis and ds cDNA amplification was conducted with 3' SMART-Seq CDS Primer II A for priming, and SMART-Seq HT oligonucleotide for template switching at the 5' end of the transcript. Then, cDNA was purified with the Agencourt AMPure XP kit, tagmented, and PCR amplified with appropriate index primers.

treatment_protocol: A total of 1 million cells were were transferred to a 100 mm Petri dish 24 h prior to transfection . Cells were transfected using lipofectamine 2000 reagent and  a total of 5.4 pmol of DNA plasmids for 48 h. Cells that did not receive any plasmid, received transfection reagents only.

tag: transfected vectors


title: Sample 5_AB10020

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used. (read2 used to read cell and molecule barcodes only)
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: *_metadata_s.txt: Meta data file associating each single cell with its amplification batch and index sorting readouts

source_name: LLN T  MCDD 1


title: BT474_LapatinibHerceptin_2

description:
BT474_LapatinibHerceptin_2
120807_253118113484_S01_miRNA_107_Sep09_2_1


title: BT474_LapatinibHerceptin_1

description:
BT474_LapatinibHerceptin_1
120807_253118113505_S01_miRNA_107_Sep09_2_1


title: CRISPR_expt2_rep1


title: Sample 3_AB10016

source_name: LLN PIC  MCDD doublet 2


title: Sample 4_AB10019

source_name: LLN DC  MCDD 1


title: CRISPR_expt1_rep2


title: Sample 2_AB10015

source_name: LLN PIC MCDD doublet 1


title: CRISPR_expt1_rep1


title: Control_expt2_rep2


title: Control_expt2_rep1


title: Sample 1_AB10014

source_name: LLN PIC ND doublet 1


title: BT474_Lapatinib_3

description:
BT474_Lapatinib_3
120807_253118113776_S01_miRNA_107_Sep09_1_1


title: BT474_Lapatinib_2

description:
BT474_Lapatinib_2
120807_253118113506_S01_miRNA_107_Sep09_1_1


title: Sample 7_AB10507

source_name: LLN T ND 4


title: Control_expt1_rep2


title: BT474_Lapatinib_1

description:
BT474_Lapatinib_1
120807_253118113485_S01_miRNA_107_Sep09_1_1


title: BT474_Herceptin_2

description:
BT474_Herceptin_2
120807_253118113485_S01_miRNA_107_Sep09_2_1


title: BT474_Herceptin_3

description:
BT474_Herceptin_3
120807_253118113506_S01_miRNA_107_Sep09_2_1


title: BT474_Herceptin_1

description:
BT474_Herceptin_1
120807_253118113776_S01_miRNA_107_Sep09_2_1


title: Control_expt1_rep1


title: CD34_expt2_rep2

value: sgRNA-dCas9-VP160-P2A-EGF, 6 CD34-gRNAs


title: Neutro BM WT Rep2

city: Montpellier

first: Gwendal

last: Lazennec

address: 1682 rue de la valsiere

institute: CNRS

data_processing:
Raw sequencing data was quality-controlled with the FastQC program. Low quality reads were trimmed or removed using Trimmer (minimum length: 120 bp).
Reads were aligned to the mouse reference genome (mm10 build) with the Star tool.
Gene counts were obtained by read counting software Htseq.
Genome_build: mm10
Supplementary_files_format_and_content: txt files

source_name: Bone marrow

extract_protocol:
Neutrophils were purified by flow cytometry, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow

value: neutrophils

value: FVB WT

value: 10 weeks

value: WT

tag: housing

value: SOPF


title: Neutro BM WT Rep3


title: CD34_expt2_rep1

tag: cell line


title: Neutro Tum PyMT-Cxcr2-/- Rep4

source_name: Mammary tumor

value: Mammary tumor

tag: genotype


title: Neutro BM WT Rep1

tag: tissue


title: BT474_Control_3

description:
BT474_Control_3
120807_253118113505_S01_miRNA_107_Sep09_1_1

value: Breast cancer cell line


title: BT474_Control_2

description:
BT474_Control_2
120807_253118113504_S01_miRNA_107_Sep09_1_1


title: NSC-35-1-input

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to GRCh37 whole genome using Burrows - Wheeler Aligner  v0.7.17.
Duplicates were removed using the samtools rmdup, and replicate experiments were merged using samtools merge.
Peaks were called using MACS2 (version 2.0).
Genome_build: GRCh37
Supplementary_files_format_and_content: peak bed files

value: Human gastric cancer cells


title: Neutro Tum PyMT-Cxcr2-/- Rep3

tag: age


title: NSC-34-2-input


title: CD34_expt1_rep1


title: Neutro Tum PyMT-Cxcr2-/- Rep2

tag: strain


title: ATAC-Seq Co-culture rep3 + dnAP-1

city: Stanford

first: Helen

middle: M

last: Blau

address: 269 Campus Dr

department: Baxter Laboratories

institute: Stanford University

description: Co-culture rep3 + dnAP-1

data_processing:
Default Illumina base calling implementation
Reads were trimmed, and then mapped to concatenated human and mouse genome using Bowtie 2
reads mapping to chrM and those with MAPQ <10 were removed
peaks were called with MACS 2
Genome_build: hg38/mm10
Supplementary_files_format_and_content: bigwig read pileup centered at Tn5 29bp footprint

source_name: human fibroblast + mouse ESC co-culture

growth_protocol: Fibroblasts are grown in 10% FBS + DMEM. ESCs are grown with 10% FBS, 10% KSR, LIF, beta-mercaptoethanol in KO DMEM

extract_protocol:
Cells were pelleted and permeabilized in hypotonic buffer with 0.1% IGEPAL CA-630. Nuclei were treated with transposase from Illumina (Cat FC-121-1030)
Fragments were amplified with NEBNext PCR master mix and Nextera indices for 8-12 cycles

treatment_protocol: To induce dnAP-1 in fibroblasts, doxycycline was added at the beginning of the co-culture step at 1000 ng/ml

value: human lung fibroblast

tag: treatment

value: dnAP-1 (Tet-On)


title: RiSQ052_SpikeinSTD_primary_4

city: Bunkyo-ku

first: Tetsushi

last: Iida

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Biological Visualization

institute: The Institute for Quantitative Biosciences (IQB), The University of Tokyo

description:
Spike-in standard DNA cocktail for RisCQ-seq, synthetic 466bp DNA and DNA-rNMP fragments based on phiX174RF1 sequence, experimental replicate 4, STD1, STD1-rAG, STD1-rCU, STD2, STD2-rAG, STD2-rCU, TruSeqHT-compatible adaptor ligation, gel purification, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, SNP detection of DNA-rNMP fragments, fragment-composition check sample
processed data file: STD_primary.tsv

data_processing:
library strategy: RiSQ-seq
Basecalls performed using Real Time Analysis (RTA) 1.18.42
Background reads and rNMP reads were mapped to EF4.68 assembly using bowtie 1.0.0 with paired-end mapping.
Mapped pair reads (SAM) were converted to fragments and rNMP position (BED) by AWK scripts.
PCR-amplified reads were also converted to rNMP position (BED) by AWK scripts, and adjusted to PCR-free library scale.
Compute read coverage to single-base bin files using bedtools 2.24.0.
rNMP detection efficiency of each sample preparation was estimated from spiked-in standards by linear regression model using R 3.2.1 (lm).
rNMP accumulation level at each  42 base bin was estimated by normalization of total rNMP counts by total background counts with spiked-in standard adjustment.
For nuclear genome, rNMP reads were from PCR-amplified reads adjusted to PCR-free scale.
Genome_build: S. cerevisiae, S288C genome, EF4.68
Supplementary_files_format_and_content: Bedgraph files include rNMP accumlation level, damage per million (dpm); BED file includes biased mapping region with abberant score of rNMP level by mapping bias.

organism: Sinsheimervirus phiX174

source_name: Synthetic DNA

growth_protocol: Yeast strains were exponentially grown in two flasks of 500ml 1% Bacto Yeast Extract (BD), 2% Bacto Peptone and 2% Glucose (Wako) (YPD) or low glucose media with 0.05% Glucose (CR) around 1x10^7 cells/ml and arrested cell-cycle by addition of alpha-factor at final concentration 5 ug/ml for 2.5 hour at 30C with shaking (222 rpm) in INNOVA43 shaker.

extract_protocol:
Yeast spheloplasts were lysed in pre-warmed lysis buffer (50 mM Tris-Cl pH7.5, 0.2 M NaCl, 0.1 M EDTA, 5% SDS) at 65°C by gentle pipetting and inversions. After phenol-chloroform extraction twice, nucleic acids were precipitated with twice volume of 99% ethanol, and the precipitates were rinsed with 70% ethanol. Dried nucleic acids were treated by RNase A (Wako) in 500 µl of RNase buffer (10 mM Tris-Cl pH7.5, 1 mM EDTA, 0.5 mg/ml RNase A) at 37°C for 2 h. After phenol-chloroform extraction twice, genomic DNAs were purified by ethanol precipitation.
RiSQ-seq was performed with sheared genomic DNAs. Ten µg of total DNA was sheared in microTUBE (Covaris) by Covaris M220 (peak power 140W, duty factor 10%, cycle/burst 200 and duration 1 minute). Agarose-gel purified DNA (400-450 bp range) was end-repaired by KAPA library preparation kit for Illumina (Kapa Biosystems) supplement with 2 mM ATP and 2.5 mM dNTP. One µg of the size-selected DNA and  25ng of spike-in standard cocktail were used for a primary library. Pre-primary library was prepared by KAPA library preparation kit and Illumina TruSeqHT-compatible adaptors (IDT). Free 3'-OH ends of the pre-primary library were masked by terminal deoxynucleotidyl transferase (Takara) with 0.25 mM ddNTP (Roche) for 1 hour at 37°C. The fully ligated library was purified by size-selection with agarose-gel electrophoresis (primary library). For RNaseH-digested samples, 100 ng of the primary library was digested using 1xThermoPol reaction buffer, 3.75 units of RNase H and RNase HII (New England Biolabs) overnight (18 hours) at 37°C. Thirty ng of the primary library with or without RNaseH digestion was heat denatured at 100°C for 3 minutes and chilled at 0°C for 5 minutes. The denatured library was incubated with 10 µM of 701ss adaptor and 750 units of T4 DNA ligase (Kapa Biosystems) overnight (12 hours) at 20°C for secondary-adaptor ligation. After three times of library purification with AMPureXP beads (Beckman Coulter), complementary strand of the libraries were synthesized in 25 µl reaction mixture with 16 units of BstPolymerase LF, 1xThermoPol reaction buffer (New England Biolabs), 0.25 mM dNTP and 4µM of TruHTAmp7Rv primer at 65°C for 10 minutes. The size-selected libraries were directly used for paired-end sequencing by MiSeq sequencer (Illumina) to identify location of fragments and 3'-end of nicks generated with or without RNaseH treatment. For PCR-amplified sample, 5 ng of the double-stranded libraries were amplified using 5 µM of primers TruHTAmp5Fw and TruHTAmp701allSRv, using KAPA real time library amplification kit (Kapa Biosystems). Libraries were then purified with AMPureXP beads (target range over 300 bp) and sequenced as PCR-amplified samples.

tag: molecule subtype

value: Synthetic DNA


title: Neutro BM WT Rep4


title: RiSQ051_SpikeinSTD_primary_3

description:
Spike-in standard DNA cocktail for RisCQ-seq, synthetic 466bp DNA and DNA-rNMP fragments based on phiX174RF1 sequence, experimental replicate 3, STD1, STD1-rAG, STD1-rCU, STD2, STD2-rAG, STD2-rCU, TruSeqHT-compatible adaptor ligation, gel purification, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, SNP detection of DNA-rNMP fragments, fragment-composition check sample
processed data file: STD_primary.tsv


title: ATAC-Seq Co-culture rep2 + dnAP-1

description: Co-culture rep2 + dnAP-1


title: RiSQ050_SpikeinSTD_primary_2

description:
Spike-in standard DNA cocktail for RisCQ-seq, synthetic 466bp DNA and DNA-rNMP fragments based on phiX174RF1 sequence, experimental replicate 2, STD1, STD1-rAG, STD1-rCU, STD2, STD2-rAG, STD2-rCU, TruSeqHT-compatible adaptor ligation, gel purification, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, SNP detection of DNA-rNMP fragments, fragment-composition check sample
processed data file: STD_primary.tsv


title: Neutro Tum PymT Rep4

value: FVB-PyMT

value: PyMT


title: Neutro Tum PymT Rep3


title: ATAC-Seq Co-culture rep3

description: Co-culture rep3

value: no dnAP-1 (control)


title: RiSQ049_SpikeinSTD_primary_1

description:
Spike-in standard DNA cocktail for RisCQ-seq, synthetic 466bp DNA and DNA-rNMP fragments based on phiX174RF1 sequence, experimental replicate 1, STD1, STD1-rAG, STD1-rCU, STD2, STD2-rAG, STD2-rCU, TruSeqHT-compatible adaptor ligation, gel purification, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, SNP detection of DNA-rNMP fragments, fragment-composition check sample
processed data file: STD_primary.tsv


title: Neutro Tum PymT Rep2


title: BT474_Control_1

description:
BT474_Control_1
120807_253118113484_S01_miRNA_107_Sep09_1_1

value: HER2 positive breast cancer


title: RiSQ048_STD_RH_4_rNMP

description:
Synthetic 466bp DNA and DNA-rNMP fragments based on phiX174RF1 sequence, standard DNA mixture 4, STD1, STD1-rAG, STD1-rCU, STD2, STD2-rAG, STD2-rCU, TruSeqHT-compatible adaptor ligation, gel purification, RNaseH digestion, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, secondary index fraction, rNMP-detection sample
processed data file: STD_pilot_experiments.tsv


title: CD34_expt1_rep2

value: sgRNA-dCas9-VP160-P2A-EGF, 6 CD34-gRNAs


title: RiSQ047_STD_RH_4_Bg

description:
Synthetic 466bp DNA and DNA-rNMP fragments based on phiX174RF1 sequence, standard DNA mixture 4, STD1, STD1-rAG, STD1-rCU, STD2, STD2-rAG, STD2-rCU, TruSeqHT-compatible adaptor ligation, gel purification, RNaseH digestion, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, primary index fraction, background sample
processed data file: STD_pilot_experiments.tsv


title: Neutro Tum PyMT-Cxcr2-/- Rep1


title: ATAC-Seq Co-culture rep1

description: Co-culture rep1


title: RiSQ046_STD_RH_3_rNMP

description:
Synthetic 466bp DNA and DNA-rNMP fragments based on phiX174RF1 sequence, standard DNA mixture 3, STD1, STD1-rAG, STD1-rCU, STD2, STD2-rAG, STD2-rCU, TruSeqHT-compatible adaptor ligation, gel purification, RNaseH digestion, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, secondary index fraction, rNMP-detection sample
processed data file: STD_pilot_experiments.tsv


title: RiSQ045_STD_RH_3_Bg

description:
Synthetic 466bp DNA and DNA-rNMP fragments based on phiX174RF1 sequence, standard DNA mixture 3, STD1, STD1-rAG, STD1-rCU, STD2, STD2-rAG, STD2-rCU, TruSeqHT-compatible adaptor ligation, gel purification, RNaseH digestion, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, primary index fraction, background sample
processed data file: STD_pilot_experiments.tsv


title: ATAC-Seq Homokaryon

description: Homokaryon

source_name: human fibroblast fusion

value: homokaryon


title: Ad-GFP-m-ACOT1 rep4

city: Toronto

first: Marc

last: Angeli

state: Ontario

address: 101 College street

department: Multi Organ Transplant

country: Canada

institute: University Health Network

description: Gene Expression Data from mouse liver ACOT1 overexpression vector

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

label_protocol: standard Affymetrix protocol

extract_protocol: 6-8-week-old male C57BL/6 mice were housed in sterilized, individually-ventilated cages. After 1 week of acclimation, animals received free access to High Fat, High Carbohydrate Diet (HFD) for 16 weeks. HFHC diets consisted of 58%kcal fat diet (D12330 High-fat Diet from Research diets) supplemented with enriched water 42g/L carbohydrates at a ratio of 45% sucrose and 55% fructose on a 12:12-h light-dark cycle. injections of either an Adenoviral vector (with Adenoviral type 5 backbone) containing Ad-GFP-m-ACOT1 or Ad-GFP at 1x109 PFU were performed weekly for 4 weeks (Vector Biolabs). The mouse ACOT1 gene was placed with a Tag/Marker eGFP under the same CMV promoter

treatment_protocol: tail vein injections of either an Adenoviral vector (with Adenoviral type 5 backbone) containing Ad-GFP-m-ACOT1 or Ad-GFP at 1x109 PFU were performed weekly for 4 weeks after 16 weeks of HF diet

value: ACOT1 overexpression


title: Ad-GFP-m-ACOT1 rep1


title: Ad-GFP-m-ACOT1 rep3


title: Ad-GFP rep4

description: Gene Expression Data from Mouse liver empty vector

source_name: Ad-GFP

value: Control


title: ATAC-Seq Co-culture rep1 + dnAP-1

description: Co-culture rep1 + dnAP-1


title: Ad-GFP-m-ACOT1 rep2


title: Ad-GFP rep5


title: RiSQ044_STD_RH_2_rNMP

description:
Synthetic 466bp DNA and DNA-rNMP fragments based on phiX174RF1 sequence, standard DNA mixture 2, STD1, STD1-rAG, STD1-rCU, STD2, STD2-rAG, STD2-rCU, TruSeqHT-compatible adaptor ligation, gel purification, RNaseH digestion, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, secondary index fraction, rNMP-detection sample
processed data file: STD_pilot_experiments.tsv


title: A4_3D_F3

city: Sheffield

first: Dr. Kai

last: Erdmann

state: South Yorkshire

address: Western Bank

department: Biomedical Science

country: United Kingdom

institute: University of Sheffield

description: Cultured in OrganoPlate for 4 days

data_processing:
raw data was pre-processed using a workflow consisting of trimming reads to remove adapters, indexes and bad quality bases using Trimmomatric
quality control on trimmed reads using FastQC
Filtered reads were aligned / mapped to the reference genome build using STAR
pseudo-mapped against the reference transcriptome using Kallisto
The mapping quality was assessed focusing on coverage of splice junctions; rates of splicing in known or novel junctions; read-coverage of splice-junctions; gene-body coverage and potential 5’-3’ bias; insertions-deletions: the rate of occurrence and the lengths using QoRTS
The estimated counts from the Kallisto abundance estimations (at the transcript level) were summarized at the gene-level by using the R package txtimport using Ensembl annotations and DESeq2 (R/Bioconductor package) is used to fit a negative binomial model to the data
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: TPMs_kallisto_genesummarized text file

source_name: Proximal tubule kidney cells (HK2 Cell Line)

growth_protocol: 3 biological replicates of cells were cultured in organ-on-chip platform of OrganoPlates for 4 days to form 3D tubules with fluid flow applying physiologically relevant shear stress.

extract_protocol:
Column purification using RNeasy Micro Kit (74004, Qiagen) was used to extract total RNA with DNASE-I treament to remove gDNA.
RNA library preparation with polyA selection for sequencing with Illumina HiSeq, 2x150bp configuration, single index, per lane. ~350M raw paired-end reads per lane per sample was provided after sequencing

treatment_protocol: OCRL1 gene was knocked-out using gene editing technology (CRISPR-Cas9) and two different clones with different mutations were chosen (A3 & A4) to compare with willd-type HK_2 cell line.

value: Proximal tubule kidney cells

tag: culture conditions

tag: platform methods

value: Poly-A capture; 2*150 bp PE sequencing


title: Ad-GFP rep3


title: RiSQ043_STD_RH_2_Bg

description:
Synthetic 466bp DNA and DNA-rNMP fragments based on phiX174RF1 sequence, standard DNA mixture 2, STD1, STD1-rAG, STD1-rCU, STD2, STD2-rAG, STD2-rCU, TruSeqHT-compatible adaptor ligation, gel purification, RNaseH digestion, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, primary index fraction, background sample
processed data file: STD_pilot_experiments.tsv


title: ATAC-Seq Fibroblast rep4

description: Fibroblast rep4

source_name: human fibroblast

tag: cell type


title: ATAC-Seq Fibroblast rep3

description: Fibroblast rep3


title: ATAC-Seq Co-culture rep2

description: Co-culture rep2


title: A4_3D_F2

description: Cultured in OrganoPlate for 4 days


title: A4_3D_F1

description: Cultured in OrganoPlate for 4 days


title: A3_3D_F3

description: Cultured in OrganoPlate for 4 days


title: ATAC-Seq Fibroblast rep2

description: Fibroblast rep2


title: RiSQ041_STD_RH_1_Bg

description:
Synthetic 466bp DNA and DNA-rNMP fragments based on phiX174RF1 sequence, standard DNA mixture 1, STD1, STD1-rAG, STD1-rCU, STD2, STD2-rAG, STD2-rCU, TruSeqHT-compatible adaptor ligation, gel purification, RNaseH digestion, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, primary index fraction, background sample
processed data file: STD_pilot_experiments.tsv


title: ATAC-Seq Fibroblast rep5

description: Fibroblast rep5


title: Neutro Tum PymT Rep1

value: neutrophils

value: 10 weeks

value: SOPF


title: A3_3D_F2

description: Cultured in OrganoPlate for 4 days


title: ATAC-Seq Fibroblast rep1

description: Fibroblast rep1


title: Ad-GFP rep1


title: RiSQ040_STD_primary_4

description:
Synthetic 466bp DNA and DNA-rNMP fragments based on phiX174RF1 sequence, standard DNA mixture 4, STD1, STD1-rAG, STD1-rCU, STD2, STD2-rAG, STD2-rCU, TruSeqHT-compatible adaptor ligation, gel purification, heat denatured library, complementary-strand synthesis, PCR-free sequencing, SNP detection of DNA-rNMP fragments, fragment-composition check sample
processed data file: STD_pilot_experiments.tsv


title: Ad-GFP rep2


title: CONTROL_DC

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

institute: Weizmann Institute of Science

description: Control

data_processing:
10x genomics pipeline
hg38
Genome_build: refdata-cellranger-GRCh38-1.2.0.tar.gz
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: mixed samples from multple patients

extract_protocol:
Liver biopsies from bariatric surgery patients were collected in RPMI (Supplemented with 10%FBS) and immediately transported on ice to the laboratory. A section of tissue was formalin fixed for histopathological evaluation; however, the bulk of the tissue was digested using Miltenyi Tumor dissociation Kit (cat no. 130-095-929) as per the manufacturer’s instructions. Single cell suspensions thus generated were stored in Liquid nitrogen in FBS+20% DMSO until further processing. For sorting and scRNAseq of DCs obtained from control and NASH livers, the stored cells were thawed in a 37oC water bath, washed once with complete media and once with FACS buffer (PBS+2% FBS). After FC blocking, cells were stained for 30 min and washed once with FACS buffer and once with sorting buffer (PBS+0.5mM EDTA). Sorting was carried out at DKFZ cytometry facility using BD FACS Aria. Bulk-sorted CD45+ Lin- CD11c+ were then processed for 10X (10X Genomics).
10x v.3; Single cell RNA-seq 3’ : 28bp R1 and 91 bp R2

tag: clinic status

value: Healthy

value: mixed samples from multple patients

tag: Sex

value: pooled male and female

value: sorted DCs

tag: sofa score

tag: clinical outcome


title: RiSQ039_STD_primary_3

description:
Synthetic 466bp DNA and DNA-rNMP fragments based on phiX174RF1 sequence, standard DNA mixture 3, STD1, STD1-rAG, STD1-rCU, STD2, STD2-rAG, STD2-rCU, TruSeqHT-compatible adaptor ligation, gel purification, heat denatured library, complementary-strand synthesis, PCR-free sequencing, SNP detection of DNA-rNMP fragments, fragment-composition check sample
processed data file: STD_pilot_experiments.tsv

value: Synthetic DNA


title: NASH_DC

description: NASH

value: NASH


title: WT_3D_F3

description: Cultured in OrganoPlate for 4 days

value: WT


title: RiSQ038_STD_primary_2

description:
Synthetic 466bp DNA and DNA-rNMP fragments based on phiX174RF1 sequence, standard DNA mixture 2, STD1, STD1-rAG, STD1-rCU, STD2, STD2-rAG, STD2-rCU, TruSeqHT-compatible adaptor ligation, gel purification, heat denatured library, complementary-strand synthesis, PCR-free sequencing, SNP detection of DNA-rNMP fragments, fragment-composition check sample
processed data file: STD_pilot_experiments.tsv


title: WT_3D_F2

description: Cultured in OrganoPlate for 4 days


title: RiSQ042_STD_RH_1_rNMP

description:
Synthetic 466bp DNA and DNA-rNMP fragments based on phiX174RF1 sequence, standard DNA mixture 1, STD1, STD1-rAG, STD1-rCU, STD2, STD2-rAG, STD2-rCU, TruSeqHT-compatible adaptor ligation, gel purification, RNaseH digestion, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, secondary index fraction, rNMP-detection sample
processed data file: STD_pilot_experiments.tsv


title: ATAC_WT_repeat2

city: Shanghai

first: Yu

last: Xu

address: 320 Yueyang Road

institute: Shanghai Institue of Biochemistry and Cell Biology

data_processing:
Raw data from the sequencer were first undergone quality control using FastQC
After quality filtration and the removal of sequencing adapters with Trim_galore，Illumina adapter sequence and low quality (phred score < 20) at the 3′ end were trimmed. The paired reads were removed if any of the two reads does not meet the minimum length (20 bp)
Reads were aligned to the mouse genome (mm10) using BOWTIE2 with the parameter”--very sensitive –X 2000” to ensure that fragments up to 2 kb were allowed to align. For all data files duplicates and mitochondrial reads were removed using GATK4/Picard(v4.1.5.0).
Different summary plots and heatmap versions generated by deepTools(v3.4.1)
MACS2 (v2.1.4) was used for peak calling with parameters “--nomodel -B -g mm”.
Genome_build: mm10
Supplementary_files_format_and_content: peak files output from MACS2, including bed and narrowpeak files

source_name: ATAC_WT_DP thymocytes

extract_protocol:
50,000 sorted DP thymocytes in FACS Buffer were pelleted by centrifugation at 500 RCF for 5 minutes at 4°C in a pre-cooled fixed-angle centrifuge. Then cells were lysed in lysis buffer (10 mM Tris-HCL, 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40) and nucleuses were enriched.
50 ul transposase mixture (10 ul of 5x TTBL, 5 ul of TTE Mix V50, 35 ul of nuclease-free water) (Cat# TD501-01, Vazyme) was added to nucleuses and the pellet was disrupted by pipetting. Transposition reactions were incubated at 37°C for 30 minutes. Transposed DNA was purified using a VAHTS DNA Clean beads (Cat# N411-01-AA, Vazyme) and purified DNA was eluted in 26 ul nuclease-free water. Transposed fragments were amplified and purified according to the standard protocols of TruePrep DNA Library Prep Kit V2 for Illumina (Cat# TD501-01, Vazyme) . The library quality was assessed on the Agilent Bioanalyzer 2100 system. Libraries were quantified by qPCR prior to sequencing.

tag: strain background

tag: genotype/variation

value: Thymus

value: CD4+CD8+ double-positive (DP) thymocytes


title: RiSQ037_STD_primary_1

description:
Synthetic 466bp DNA and DNA-rNMP fragments based on phiX174RF1 sequence, standard DNA mixture 1, STD1, STD1-rAG, STD1-rCU, STD2, STD2-rAG, STD2-rCU, TruSeqHT-compatible adaptor ligation, gel purification, heat denatured library, complementary-strand synthesis, PCR-free sequencing, SNP detection of DNA-rNMP fragments, fragment-composition check sample
processed data file: STD_pilot_experiments.tsv


title: cabozantinib_1uM_48h

first: Yu-Hsuan

last: Fu

address: No.1, Chang-Te St

department: Department of Clinical Laboratory Sciences and Medical Biotechnology

institute: National Taiwan University

data_processing:
Sequencing was sequenced on Illumina NovaSeq 6000 platform.
Paired-end sequencing alignment toward hg19 and reads mapping to known genes (feature counts)were performed by Rsubread.
Differentially expressed genes (DEGs) identification between groups were conducted with EBSeq, with a threshold of fold change ≥ 2 or ≤ 0.5 and p-value of ≤ 0.05.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *csvt: comma-separated values of row and normalized counts for each known gene (EntrezID, and HGNC symbol) in columns and sample in rows.

source_name: Asynchronous cells

growth_protocol: Cancer cells were cultured in RPMI medium suppled with 10% FBS

extract_protocol:
Total RNAs were isolated with NucleoSpin® RNA kit (Macherey-Nagel); The final library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.
Strand-specific RNA library were built by TruSeq stranded protocols from Illumina

treatment_protocol: Cells were exposure for 48 h to 1uM cabozantinib (XL184) or to the vehicle control (DMSO).

value: erythroid leukemia K562

value: bone marrow

tag: cell phenotype

value: Asynchronous cells

value: 1uM cabozantinib


title: DMSO_48h

tag: cell line

value: DMSO


title: WT_3D_F1

description: Cultured in OrganoPlate for 4 days

value: Proximal tubule kidney cells

tag: genotype

value: Poly-A capture; 2*150 bp PE sequencing


title: ATAC_WT_repeat1

tag: tissue


title: A3_3D_F1

description: Cultured in OrganoPlate for 4 days


title: ATAC_KO_repeat2

source_name: ATAC_KO_DP thymocytes


title: ATAC_KO_repeat1


title: s.NJA01801.B06

status: Public on May 20 2021

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

data_processing:
Sequencing reads were trimmed, adapter sequences removed
Reads aligned to the mm10 reference assembly using STAR with default parameters
Duplicate reads were removed using picard
Transcript counts were obtained using HTSeq35 and mm10 UCSC exon/transcript annotations
Single cell profiles with the following features were deemed to be of poor quality and removed: 1) cells with less than a specified total number of valid counts in exonic regions (1.8x104 and 4x104 for the mouse gut and sorted multiplets dataset, respectively), 2) cells with low actin TPM, and 3) cells with high fractions of ERCC reads. To determine a cut-off for actin TPM, we used the normal distribution with empirical mean and standard deviation from log2 transformed actin TPM, which is normally distributed in successful experiments. The cut-off was set to the 0.01 quantile (eg. the lower 0.01 % of the bell curve). A similar strategy was used for fractions of ERCC reads, samples with a log2 transformed fraction of ERCC reads above the 0.99 % quantile were rejected.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: htseq-format of raw counts

source_name: colon

growth_protocol: Small intestine and colon were removed from C57BL/J wild-type mice and kept on ice in phosphate buffered saline (PBS). Lumina of colon and small intestine were washed three times with PBS and adipose tissue connected to the exterior of the small intestine or colon was removed. Colon and small intestine were opened longitudinally, and any remaining mucous on covering the epithelial layer was gently rubbed off. Tissues were washed once in PBS before being cut into 0.5 - 1 mm long fragments. Colon fragments were immersed in 10mM EDTA-PBS and incubated for 105 minutes on ice, with shaking every 15 minutes. Small intestinal fragments were similarly immersed in 10mM EDTA-PBS on ice and shaken. After 15 minutes, small intestinal fragments were allowed to settle at the bottom and the supernatant was discarded and replaced with new 10mM EDTA-PBS and shaken vigorously. This procedure was repeated 1-2 times, with supernatant fractions investigated through light microscopy before discarding, in order to enrich for crypts. Small intestinal fragments were then incubated on ice for 45-60 minutes for a total of 105 minutes. Following EDTA-PBS treatment fractions were triturated 10-15 times. Colon fractions were strained through a 100 um filter while small intestinal fractions were strained through a 70 um filter. Fractions were centrifuged at 300g for 5 minutes and dissociated using TrypLE Express (Invitrogen) at 37°C for 15-20 minutes. Enzymatic dissociation was supervised using light microscopy during regular intervals to obtain an appropriate amount of single cells and multiplets. Dead cells were removed using Dead Cell Removal Kit (Miltenyi Biotec) according to the manufacturer's protocol before staining for FACS sorting was performed.

extract_protocol:
For mouse intestine, cells were stained with FITC anti-CD326 and 7AAD (Sony Biotechnology) in order to monitor number of epithelial cells and select live cells. Additionally, paneth cells were enriched using Brilliant Violent anti-CD24. For spleen, cells were sorted with only 7AAD to remove dead cells, not other antibodies. Single cells were distinguished from multiplets using FSC-H and FSC-W gating and the gating scheme was visually confirmed via phase contrast microscopy (Fig. 1a). Cells were sorted into 384- or 96-well plates containing hypotonic lysis buffer using a SH800S FACS sorter (Sony). Plates were sealed immediately after sorting with microseal F foil (Biorad) and centrifuged at 4000g at 4°C for 5 min before being frozen on dry ice and stored at -80°C.
Single-cell and multiplet RNA-Seq libraries were generated as described. Briefly, single-cells collected in 384-well plates were lysed, followed by reverse transcription with template-switch using an LNA-modified template switch oligo to generate cDNA. After 21 cycles of pre-amplification, DNA was purified and analysed on an automated Fragment Analyzer (Advanced Analytical). Each cell’s cDNA fragment profile was individually inspected and only wells with successful amplification products (concentration higher than 0.06 ng/ul) and with no detectable RNA degradation were selected for final library preparation. Tagmentation assays and barcoded sequencing libraries were prepared using Nextera XT kit (Illumina) according to the manufacturer's instructions. Barcoded libraries were pooled and subjected to 75 bp paired-end sequencing on the Illumina NextSeq 500 instrument.

value: colon

tag: facs cellnumber

value: Singlet

tag: age (days)


title: s.NJA01801.B09

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title: s.NJA01801.B01


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title: s.NJA01803.E14


title: s.NJA01803.F09


title: s.NJA01803.E13


title: s.NJA01803.E08


title: s.NJA01803.E10


title: s.NJA01803.E09


title: s.NJA01803.E11


title: s.NJA01803.E07


title: s.NJA01803.E06


title: s.NJA01803.F05


title: s.NJA01803.E05


title: s.NJA01803.E20


title: s.NJA01803.E15


title: s.NJA01803.D24


title: s.NJA01803.D23


title: s.NJA01803.D22


title: s.NJA01803.D19


title: s.NJA01803.D16


title: s.NJA01803.D17


title: s.NJA01803.D18


title: s.NJA01803.D15


title: s.NJA01803.D13


title: s.NJA01803.D10


title: s.NJA01803.D11


title: s.NJA01803.D12


title: s.NJA01803.D06


title: s.NJA01803.D09


title: s.NJA01803.D04


title: s.NJA01803.D05


title: s.NJA01803.E04


title: s.NJA01803.D14


title: s.NJA01803.D07


title: s.NJA01803.D03


title: s.NJA01803.D02


title: s.NJA01803.D08


title: s.NJA01803.E02


title: s.NJA01803.E01


title: s.NJA01803.E03


title: s.NJA01803.D21


title: s.NJA01803.D20


title: s.NJA01803.C24


title: s.NJA01803.D01


title: s.NJA01803.C19


title: s.NJA01803.C20


title: s.NJA01803.C22


title: s.NJA01803.C23


title: s.NJA01803.C16


title: s.NJA01803.C13


title: s.NJA01803.C14


title: s.NJA01803.C09


title: s.NJA01803.C11


title: s.NJA01803.C10


title: s.NJA01803.C12


title: s.NJA01803.C08


title: s.NJA01803.C15


title: s.NJA01803.C03


title: s.NJA01803.C07


title: s.NJA01803.B23


title: s.NJA01803.C06


title: s.NJA01803.C04


title: s.NJA01803.C01


title: s.NJA01803.C05


title: s.NJA01803.B24


title: s.NJA01803.C02


title: s.NJA01803.B21


title: s.NJA01803.B19


title: s.NJA01803.B18


title: s.NJA01803.B16


title: s.NJA01803.B15


title: s.NJA01803.B14


title: s.NJA01803.B20


title: s.NJA01803.B13


title: s.NJA01803.B12


title: s.NJA01803.B17


title: s.NJA01803.B09


title: s.NJA01803.B07


title: s.NJA01803.B05


title: s.NJA01803.B06


title: s.NJA01803.B10


title: s.NJA01803.B08


title: s.NJA01803.A04


title: s.NJA01803.A09


title: s.NJA01803.A06


title: s.NJA01803.A08


title: s.NJA01803.A14


title: s.NJA01803.A07


title: s.NJA01803.A10


title: s.NJA01803.B03


title: s.NJA01803.A18


title: s.NJA01803.A17


title: s.NJA01803.A24


title: s.NJA01803.A02


title: s.NJA01803.A12


title: s.NJA01803.A19


title: s.NJA01803.A11


title: s.NJA01803.A13


title: s.NJA01803.B04


title: s.NJA01803.A16


title: m.NJD00101.P24

value: Multiplet


title: s.NJA01803.A01


title: m.NJD00101.P22


title: s.NJA01803.A03


title: s.NJA01803.A20


title: s.NJA01803.B02


title: s.NJA01803.A15


title: m.NJD00101.P21


title: m.NJD00101.P20


title: m.NJD00101.P19


title: m.NJD00101.P17


title: m.NJD00101.P18


title: m.NJD00101.P15


title: m.NJD00101.P14


title: m.NJD00101.P07


title: m.NJD00101.P05


title: m.NJD00101.O23


title: m.NJD00101.P11


title: m.NJD00101.P08


title: m.NJD00101.P13


title: m.NJD00101.P02


title: m.NJD00101.P10


title: m.NJD00101.O11


title: m.NJD00101.O10


title: m.NJD00101.O14


title: m.NJD00101.P06


title: m.NJD00101.O13


title: m.NJD00101.O18


title: m.NJD00101.P01


title: m.NJD00101.O16


title: m.NJD00101.P12


title: m.NJD00101.O12