title: Newly diagnosed MM_72

value: multiple myeloma


title: Healthy adult 10_PB_bL

status: Public on Jun 01 2022

type: SRA

city: New York City

first: Ramin

last: Herati

state: NY

address: 429 E. 29th Street, room 308

country: USA

institute: NYU School of Medicine

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-128_PB_bL_S54

library_source: transcriptomic

data_processing:
FASTQ files were trimmed using Trimmomatic 0.32.
Bcl2fastq2 v2.20 was used to convert bcl files to fastq format.
Alignment done using STAR 2.5.2a against the hg38 reference genome.
The aligned files were processed using PORT 0.8.5 gene-based normalization (https://github.com/itmat/Normalization).
Genome_build: HG38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells

extract_protocol:
Peripheral blood mononuclear cells were sorted by FACS and checked for purity. Then, RNA was isolated using Qiagen RNeasy Micro Plus kit (Cat#74034) according to manufacturer's instructions.
Libraries were constructed using the TakaraBio SMART-Seq® HT Kit (Cat#634437) and indexing adapters added using Illumina Nextera XT (Cat#FC-131-1024) as per manufacturer's instructions.

tag: individual

value: Healthy adult 10

tag: therapy

value: Healthy control

tag: time point

value: Baseline

tag: cell type

value: PBMC

tag: cell subset

value: Antibody-secreting B cells


title: Healthy adult 11_ABC_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-129_ABC_oW_S81

value: Healthy adult 11

value: One week after flu vaccine

value: Activated B cells


title: SSp5C1

city: Zhengzhou

first: Qian

last: Bai

address: JING BA ROAD

country: China

institute: The second affiliated hospital of Zhengzhou University

data_processing:
Poly-N, adapter and low-quality were removed by in-house perl scripts ，Quality control analysis was performed by ng_qc.
Clean reads were aligned to the mus musculus ensembl 92 using HISAT2(Langmead,  B.et al) v2.0.4. HISAT2 was run with ‘--rna-strandness RF’, other parameters were set  as default.
The mapped reads of each sample were assembled by StringTie (v1.3.1) (Mihaela  Pertea.et al. 2016) in a reference-based approach. StringTie uses a novel network flow  algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in  each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the  FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of  exon per million fragments mapped, calculated based on the length of the fragments  and reads count mapped to this fragment.
Genome_build: mus_musculus_Ensembl_92
Supplementary_files_format_and_content: raw_FPKM

organism: Mus musculus

source_name: spinal trigeminal nucleus caudalis

extract_protocol:
RNA was harvested using Trizol reagent.
A total amount of 3 μg RNA per sample was used as input material for the RNA sample  preparations. Firstly, ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA  Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol  precipitation. Subsequently, sequencing libraries were generated using the rRNAdepleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®  (NEB, USA) following manufacturer’s recommendations.

tag: strain

tag: tissue

value: spinal trigeminal nucleus caudalis

tag: age

value: 8 weeks


title: Healthy adult 10_naiveB_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-128_naiveB_bL_S52

value: Naïve B cells


title: CSp5C1


title: CTG3

source_name: trigeminal ganglia

value: trigeminal ganglia


title: Healthy adult 10_ABC_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-128_ABC_bL_S53


title: Habenula_SUI8

type: RNA

city: Seoul

first: Hyeijung

last: Yoo

address: Goryeodaero 73

department: Department of anatomy

country: South Korea

institute: Korea University College of Medicine

description: gene expression data from suicide subjects

hyb_protocol: Hybridization cocktails containing biotin-labeled DNA fragments for the target and hybridization controls were prepared. The target was then hybridized to the GeneChip Human Gene 2.0 ST arrays (Affymetrix) in a GeneChip Hybridization Oven 640 (Affymetrix). Chips were washed and stained with streptavidin phycoerythrin conjugate using GeneChip Hybridization, Wash and Stain kit (Affymetrix) on the GeneChip Fluidics Station 450 according to Affymetrix recommendations.

scan_protocol: GeneChip arrays were scanned with the GeneChip Scanner 3000 7G (Affymetrix). Raw scanned images (.DAT) as well as processed DAT files (.CEL) were acquired using Affymetrix GeneChip Command Console software (AGCC).

data_processing: Raw data CEL files from Affymetrix were imported into Expression Console1.1. RMA(Robust Multi-array Average) Normalization method was used for normalization

label: biotin

source_name: Habenula

label_protocol: 200 ng of total RNA was amplified and labeled using the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix), following the manufacturer’s instructions.

extract_protocol: RNAs longer than approximately 200 nucleotides were purified from each Hb tissue using RNeasy Mini kits according to the manufacturer’s instructions (Qiagen GmbH, Hilden, Germany).

tag: group

value: suicide

value: habenula

tag: gender

value: male


title: Newly diagnosed MM_69

city: Rotterdam

first: Mark

last: van Duin

address: Wytemaweg 80

country: Netherlands

institute: Erasmus MC

hyb_protocol: 13 ug of fragmented and biotin labeled cRNA hybridized to the microarray in an Affymetrix GeneChip® Hybridization Oven 645 and washed / stained in Affymetrix GeneChip Fluidics Station FS450DX2v2

scan_protocol: Affymetrix GeneChip® System 3000Dx v.2

data_processing: MAS5.0 (Bioconductor affy package v1.36.2) default values with a trimmed mean target intensity value set to 1500. Values below 30 were truncated.

source_name: bone marrow aspirate

label_protocol: Affymetrix GeneChip® 3' IVT PLUS Reagent Kit or Gene Profiling MDx IVD Expression Reagent Kit in accordance with Affymetrix protocols.

extract_protocol: RNeasy

treatment_protocol: Patients were treatment naive

value: Male

tag: age category

value: bone marrow aspirate

tag: disease state


title: Newly diagnosed MM_67

value: Female

value: multiple myeloma


title: Habenula_SUI6


title: Newly diagnosed MM_68


title: CTG2


title: Habenula_SUI9


title: Habenula_SUI10


title: Habenula_SUI7


title: Newly diagnosed MM_70


title: Newly diagnosed MM_65


title: Newly diagnosed MM_66


title: SSp5C2


title: Healthy adult 9_naiveB_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-127_naiveB_oW_S75

value: Healthy adult 9

value: Healthy control


title: CTG1


title: Newly diagnosed MM_64


title: Habenula_SUI5


title: Habenula_SUI4


title: Healthy adult 9_naiveB_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-127_naiveB_bL_S57

value: Baseline

value: PBMC


title: STG3


title: Habenula_SUI3


title: Healthy adult 9_HiHi_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-127_HiHi_oW_S76

value: One week after flu vaccine

value: ICOS+CD38+ cTfh


title: STG2


title: Healthy adult 9_ABC_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-127_ABC_bL_S58

value: Activated B cells


title: Newly diagnosed MM_62


title: Habenula_SUI2


title: STG1

value: 8 weeks


title: Habenula_SUI1


title: Healthy adult 8_HiHi_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-126_HiHi_oW_S14

value: Healthy adult 8


title: Newly diagnosed MM_61


title: Habenula_CTL10

description: gene expression data from healthy control

value: control


title: Newly diagnosed MM_63


title: Healthy adult 9_PB_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-127_PB_bL_S59

value: Antibody-secreting B cells


title: Healthy adult 7_naiveB_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-125_naiveB_oW_S77

value: Healthy adult 7

value: Naïve B cells


title: Healthy adult 7_HiHi_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-125_HiHi_oW_S79


title: P9_1

city: Beijing

first: Yujie

last: Tian

address: No.1 Tsinghua Park

institute: Tsinghua University

data_processing:
The raw data obtained was filtered by SOAPnuke (v1.5.2) to get clean data.
After filtering the raw data, the clean reads were then aligned to the reference genome mm10 (NCBI assembly of the mouse genome) by using Bowtie2.
The gene expression levels of each sample were calculated by using RSEM and normalized by calculation of the FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) value.
Differential expression was analyzed by DEGseq package.
Differential expressed genes for each pairwise comparison were defined as q-value < 0.001 and absolute value of log2 fold change ≥ 2.
Genome_build: mouse (mm10)
Supplementary_files_format_and_content: Tab-delimited text files include counts and FPKM values for every gene in each Sample.

molecule: polyA RNA

source_name: CD115-Ly6C- CDPs

extract_protocol:
Purified mRNA was fragmented by adding an appropriate amount of the interrupting reagent under high-temperature conditions, and the first and second strand cDNA was synthesized using the fragmented mRNA as a template. The fragment size was then selected and amplified by PCR, then the constructed library was qualified with Agilent 2100 Bioanalyzer and ABI StepOne Plus Real-Time PCR System and conducted sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: wildtype

value: 6-8 week

value: bone marrow

value: CD115-Ly6C- CDPs


title: P8_2

source_name: CD115+Ly6C+ CDPs

value: CD115+Ly6C+ CDPs


title: Habenula_CTL9

value: habenula

value: male


title: Newly diagnosed MM_59

value: Male

value: bone marrow aspirate

value: multiple myeloma


title: Newly diagnosed MM_58


title: P8_1


title: Newly diagnosed MM_60

value: Female


title: P9_2


title: Habenula_CTL8


title: Habenula_CTL7


title: Habenula_CTL6


title: Newly diagnosed MM_57


title: Newly diagnosed MM_55


title: Habenula_CTL5


title: P7_1

source_name: CD115+Ly6C- CDPs

value: CD115+Ly6C- CDPs


title: Healthy adult 7_ABC_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-125_ABC_oW_S78

value: Healthy control

value: One week after flu vaccine

value: PBMC

value: Activated B cells


title: Healthy adult 7_naiveB_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-125_naiveB_bL_S55

value: Healthy adult 7

value: Baseline

value: Naïve B cells


title: Newly diagnosed MM_56


title: P7_2

value: wildtype

value: 6-8 week

value: bone marrow


title: Healthy adult 6_HiHi_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-122_HiHi_oW_S74

value: Healthy adult 6

value: ICOS+CD38+ cTfh


title: SW620_Reversed

type: genomic

city: Houston

first: Ganiraju

last: Manyam

state: TX

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Center

hyb_protocol: The aCGH analysis of colorectal cancer cell lines was carried out on Agilent Human Genome CGH Microarray 44A arrays (G4410A) with commercially available normal genomic DNA (Promega, Madison, WI) used as the control reference. The pre-annealed sample mixtures as prepared above, were applied to Agilent gasketted cover slips, and then the Agilent Human Genome CGH Microarray 44A arrays were placed over the loaded coverslips. Assembly of the Agilent Hybridization Chambers was completed and hybridization was carried out at 65 °C for about 40 hours in a rotisserie hybridization oven. After removing the arrays from the hybridization chambers, they were washed once in wash buffer I (2X, 0.005% Triton X102) for 5 min., once in wash buffer II ( 0.006X SSPE,  0.005% N-lauoylsarcosine), and then dried in Stabilization and Drying solution (proprietary wash buffer from Agilent which also serves to scavenge ozone and improve the robustness  of the fluorescence signal intensity). A total of four normal female genomic DNA vs. normal male genomic DNA hybridizations were performed to calibrate the hybridization analysis in terms of variation due to noise. For each  cell line, dye-swap hybridization was performed to produce at least two replicates. The data from the replicates were combined and further analyzed.

scan_protocol: Genomic arrays were scanned with the Agilent DNA Microarray scanner and fluorescence intensities, normalization and ratios obtained using the

data_processing:
Agilent Feature Extraction Software (v7.5.1) was used for background subtraction; the ploidy obtained from SKY for each cell line was used to generate ploidy correction factors (PCF) that were applied to the Feature Extraction treated data for each array. The dye swaps were averaged for each cell line. Regions of chromosomal gain and loss were identified by Circular Binary Segmentation (CBS),at a significance level of p=0.01.  using open source open source R library DNAcopy.
Matrix table includes normalized copy number estimate obtained after applying CBS algorithm

molecule: genomic DNA

label_protocol: The cell line and normal genomic DNA were diluted to a concentration of 25ng/pl and lp.1 was used in a phi-29 amplification step using the Qiagen Repli-g amplification kit according to Agilent-manufacturer’s protocol, omitting the initial denaturing step. Amplified DNA was digestedmodified with Rsa I and Alu I enzymes (NEB, Ipswich, MA), cleaned up with Qiaquick Miniprep columns, and visualized on a 1% agarose gel. The labeling of 6pg amplified, digested DNA with either cyanine 3 (Cy3)-dUTP or cyanine 5 (Cy5)-dUTP (Perkin Elmer, Waltham, MA) was carried out with the Invitrogen BioPrime Random Labeling Kit. Unincorporated labeled nucleotides were removed using MicroconYM-30 filters (Millipore, Billerica, MA). Differentially labeled cell line and normal DNAs were combined with Agilent 1 OX Control Targets, Human COT-1 DNA, Yeast tRNA and Agilent In Situ 2X Hybridization buffer. Samples were denatured at 95°C for 3 minutes and then allowed to pre-anneal at 37 °C for 30 min.

growth_protocol: SW480 and SW620 were cultured according to ATCC protocol; KM12 cell lines were grown according to published protocols of the laboratory from which they were obtained (Morikawa et al, 1988)

extract_protocol: Genomic DNA was isolated from cells using theQiagen DNeasy DNA Extraction Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocols and stored at -20 °C.

source_name: SW620 colon cancer cell line

value: SW620 colon cancer cell line


title: Healthy adult 5_PB_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-121_PB_oW_S66

value: Healthy adult 5

value: Antibody-secreting B cells


title: Healthy adult 6_ABC_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-122_ABC_oW_S73


title: Healthy adult 6_naiveB_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-122_naiveB_oW_S72


title: Habenula_CTL3

value: control

value: habenula

value: male


title: SW620_Forward

source_name: normal genomic DNA (Promega, Madison, WI)


title: SW480_Reversed

value: normal genomic DNA (Promega, Madison, WI)

source_name: SW480 colon cancer cell line

value: SW480 colon cancer cell line


title: Healthy adult 7_ABC_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-125_ABC_bL_S56

value: Healthy control

value: PBMC

value: Activated B cells


title: SW480_Forward


title: Newly diagnosed MM_53

value: Male

value: bone marrow aspirate

value: multiple myeloma


title: Habenula_CTL2


title: Healthy adult 5_PB_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-121_PB_bL_S48

value: Baseline


title: Healthy adult 5_naiveB_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-121_naiveB_oW_S64

value: One week after flu vaccine

value: Naïve B cells


title: KM12SM_Reversed

source_name: KM12SM colon cancer cell line

value: KM12SM colon cancer cell line


title: KM12SM_Forward


title: Newly diagnosed MM_54


title: Newly diagnosed MM_51


title: Newly diagnosed MM_52

value: Female


title: KM12L4A_Forward

source_name: KM12L4A colon cancer cell line

value: KM12L4A colon cancer cell line


title: KM12L4A_Reversed


title: Habenula_CTL4

value: control


title: Newly diagnosed MM_49


title: ABOS1048

city: Lille

first: Denis

middle: A

last: Mogilenko

address: 1 Rue du Professeur Calmette, BP245

country: France

institute: INSERM

hyb_protocol: Following fragmentation, 5.5µg of ssDNA were hybridized for 16 hr at 45C on GeneChip® HuGene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner GCS3000.

data_processing: Microarray data were background-corrected and normalized using the robust multi-array average (RMA) algorithm by using affy R package

source_name: Omental adipose tissue

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip WT Terminal Labeling Kit: Affymetrix).

extract_protocol: Trizol extraction of total RNA followed by RNeasy Mini Kit (Qiagen) was performed according to the manufacturer's instructions.

value: Omental adipose tissue

value: female

tag: bmi

tag: type 2 diabetes (t2d)

value: Yes


title: Habenula_CTL1

value: habenula

value: male


title: Healthy adult 5_HiHi_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-121_HiHi_bL_S49

value: Healthy adult 5

value: Healthy control

value: PBMC

value: ICOS+CD38+ cTfh


title: ABOS1049


title: Newly diagnosed MM_50

value: Male

value: bone marrow aspirate

value: multiple myeloma


title: Newly diagnosed MM_48


title: ABOS1043

value: No


title: Newly diagnosed MM_47


title: Healthy adult 5_naiveB_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-121_naiveB_bL_S46

value: Baseline

value: Naïve B cells


title: Healthy adult 5_HiHi_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-121_HiHi_oW_S67

value: One week after flu vaccine


title: ABOS1042


title: ABOS1024


title: Healthy adult 3_PB_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-119_PB_oW_S70

value: Healthy adult 3

value: Antibody-secreting B cells


title: Newly diagnosed MM_46

value: Female


title: KM12C_Reversed

value: normal genomic DNA (Promega, Madison, WI)

source_name: KM12C colon cancer cell line

value: KM12C colon cancer cell line


title: Healthy adult 5_ABC_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-121_ABC_oW_S65

value: Activated B cells


title: KM12C_Forward


title: Healthy adult 5_ABC_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-121_ABC_bL_S47

value: Healthy adult 5


title: ABOS1013

value: Omental adipose tissue

value: female

value: Yes


title: ABOS938


title: ABOS979


title: ABOS923


title: ABOS912


title: Healthy adult 4_PB_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-120_PB_bL_S44

value: Healthy adult 4

value: Healthy control

value: PBMC


title: Newly diagnosed MM_44

value: Male

value: bone marrow aspirate

value: multiple myeloma


title: Newly diagnosed MM_43


title: Healthy adult 4_HiHi_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-120_HiHi_bL_S45

value: Baseline

value: ICOS+CD38+ cTfh


title: Newly diagnosed MM_41


title: ABOS951

value: No


title: Mmp13 knock out 3

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation uisng lumi package in R

source_name: calvaria cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

value: Mmp13 knockout

value: calvaria cells


title: Healthy adult 3_naiveB_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-119_naiveB_bL_S50

value: Healthy adult 3

value: Naïve B cells


title: Healthy adult 3_naiveB_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-119_naiveB_oW_S68

value: One week after flu vaccine


title: Wildtype 3

value: wild type


title: Mmp13 knock out 2


title: Newly diagnosed MM_42

value: Female


title: Healthy adult 3_PB_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-119_PB_bL_S51

value: Antibody-secreting B cells


title: Newly diagnosed MM_45


title: HC EE rep3

city: Warsaw

first: Adria-Jaume

last: Roura

address: Ludwika Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology, Polish Academy of Sciences

description:
HC_ENR_rep3
EE_experiment_raw_counts_matrix.featureCounts.txt

data_processing:
Illumina-specific adapters, low quality 5’ and 3’ bases and short reads were removed in FASTQ files using Trimmomatic tool (version 0.36).
RNA sequencing reads were aligned to a reference mouse genome sequence (mm10) using the STAR aligner (version 2.6.1b) enabling the twopassMode Basic.
Duplicates were identified and marked using Picard Tools (version 2.17.1) and resulting RNAseq mapped reads were summarized and counted by genes using featureCounts (version 1.5.3), in paired (-p), reverse stranded mode (-s 2) and only considering reads with MAPQ values of 3 or higher.
Low-expressed genes were pre-filtered and a differentially expressed genes analysis was performed using DESeq2 (version 1.24.0).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: MINO_experiment_raw_counts_matrix.featureCounts.txt: Matrix table with raw gene counts for every gene and every sample - minocycline experiment.
Supplementary_files_format_and_content: EE_experiment_raw_counts_matrix.featureCounts.txt: Matrix table with raw gene counts for every gene and every sample - environmental enrichment experiment.

source_name: HC CD11b+

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols.

value: hippocampus

tag: treatment

value: CUMS protocol + env. enrichment


title: Wildtype 2


title: ABOS895

value: Omental adipose tissue

value: female


title: Wildtype 1


title: Newly diagnosed MM_40

value: Male

value: bone marrow aspirate


title: Newly diagnosed MM_39

value: multiple myeloma


title: ABOS851

value: Yes


title: Newly diagnosed MM_37


title: Newly diagnosed MM_36


title: ABOS866


title: HC VEH rep3

description: EE_experiment_raw_counts_matrix.featureCounts.txt

value: CUMS protocol + vehicle


title: ABOS842

value: No


title: Healthy adult 1_HiHi_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-101_HiHi_oW_S13

source_name: Peripheral blood mononuclear cells

value: Healthy adult 1

value: Healthy control

value: PBMC

value: ICOS+CD38+ cTfh


title: Healthy adult 1_ABC_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-101_ABC_bL_S11

value: Baseline

value: Activated B cells


title: Healthy adult 2_HiHi_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-117_HiHi_oW_S16

value: Healthy adult 2

value: One week after flu vaccine


title: Newly diagnosed MM_38

value: Female


title: anti-PD1-treated adult 10_naiveB_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-032_naiveB_oW_S86

value: anti-PD1-treated adult 10

value: Naïve B cells


title: Healthy adult 3_HiHi_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-119_HiHi_oW_S71

value: Healthy adult 3


title: HC EE rep2

description:
HC_ENR_rep2
EE_experiment_raw_counts_matrix.featureCounts.txt

value: hippocampus

value: CUMS protocol + env. enrichment


title: ABOS856

value: Omental adipose tissue

value: female


title: Newly diagnosed MM_31

value: Male

value: bone marrow aspirate

value: multiple myeloma


title: HC EE rep1

description:
HC_ENR_rep1
EE_experiment_raw_counts_matrix.featureCounts.txt


title: Newly diagnosed MM_29


title: Mmp13 knock out 1

value: Mmp13 knockout

value: calvaria cells


title: Newly diagnosed MM_30


title: inVitro_D270_pos_brep6

city: Dresden

first: Marius

last: Ader

address: Fetscherstrasse 105

department: Center for Regenerative Therapies Dresden

country: Germany

institute: TU Dresden

data_processing:
basecalling:
Basecalls were done with Illumina bcl2fastq version 2.19.1 (Illumina NextSeq 500 files) and 2.20.0 (Illumina NovaSeq 6000 files).
xenograft filtering:
A xengsort (v2021-05-27) index based on human and mouse genome and transcript sequences obtained form Ensembl92 was built (parameter:  -k 25  -n 4496607845 --type 3FCVbb --unaligned  --hashfunctions linear945:linear9123641:linear349341847  -p 4 --fill 0.88 -T 1 --shortcutbits 0). Mouse reads were identified with xengsort (parameter: --threads 20 --chunksize 16.0 --prefetch 1) and removed, that is, only reads uniquely assigned to human were kept.
mapping:
Xenograft-filtered reads were aligned to the human reference genome hg38 using the aligner gsnap (v2020-12-16) with Ensembl 92 human splice sites as support (parameter: --gunzip -A sam -t 11 --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -n 1 -m 0.6 -s EnsemblGene-92.ss.hg38.iit -N 0 --read-group-id=L62689_H6x6C52Lc --read-group-name=H6x6C52Lc --read-group-library=L62689 --read-group-platform=illumina --action-if-cigar-error noprint fastq/L62689_H6x6C52Lc_R1.fastq.gz fastq/L62689_H6x6C52Lc_R2.fastq.gz).
counts per feature:
Uniquely mapped reads were compared based on their overlap to Ensembl 92 human gene annotations using featureCounts (v2.0.1) to create a table of fragments per human gene and sample (parameter: featureCounts -a EnsemblGene-92.hg38.TR.gtf -s 0 -p -o bfx1362.hg38.e92.txt -Q 1 -T 8).
Assembly: hg38
Supplementary files format and content: bfx1362.hg38.e92.txt.gz is a tab-separated file with the output from FeatureCounts. Each row represents a gene and the columns contain the gene information followed by the sample counts.

source_name: in vitro generated human retinal organoids

growth_protocol: Detailed description of the human retinal organoid generation protocol can be found in the supplementary methods of the manuscript.

extract_protocol:
Detailed description of retrieval and sorting of human cells from murine eyecups as well as dissociation and sorting of cells from human retinal organoids in vitro can be found in the methods section of the manuscript.
RNAseq was based on Smart-seq2 sensitive full-length transcriptome profiling and modified from Picelli et. al., 2013 (Picelli et al., 2013).

treatment_protocol: Detailed description of the transplantation procedure can be found in the methods of the manuscript.

tag: alternative name

tag: cell line

value: mCar-GFP in PGP1 human iPSC

tag: origin

value: inVitro

tag: total age_in_days

tag: fraction

value: pos

tag: dissociation protocol

value: Retinal organoids were dissociated as described in the methods of the manuscript, filtered and sorted directly into lysis buffer.


title: Newly diagnosed MM_34

value: Female


title: PFC VEH rep2

source_name: PFC CD11b+

tag: strain

value: pre-frontal cortex

tag: cell type

value: CUMS protocol + vehicle


title: HC VEH rep2

tag: tissue


title: Newly diagnosed MM_33


title: anti-PD1-treated adult 10_PB_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-032_PB_oW_S88

tag: individual

value: anti-PD1-treated adult 10

tag: therapy

tag: time point

value: One week after flu vaccine

value: PBMC

tag: cell subset

value: Antibody-secreting B cells


title: Newly diagnosed MM_35

tag: gender

tag: age category

tag: disease state


title: Newly diagnosed MM_26


title: PFC EE rep3

description:
PFC_ENR_rep3
EE_experiment_raw_counts_matrix.featureCounts.txt

tag: treatment

value: CUMS protocol + env. enrichment


title: Newly diagnosed MM_32

value: Male


title: PFC EE rep2

description:
PFC_ENR_rep2
EE_experiment_raw_counts_matrix.featureCounts.txt


title: anti-PD1-treated adult 10_ABC_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-032_ABC_oW_S87

value: Activated B cells


title: HC NAIVE rep2

description: MINO_experiment_raw_counts_matrix.featureCounts.txt

value: hippocampus

value: Naive control group


title: inVitro_D270_pos_brep4

tag: alternative name

value: in vitro generated human retinal organoids


title: HC VEH rep1


title: Healthy adult 3_ABC_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
FS1819-119_ABC_oW_S69

value: Healthy adult 3

value: Healthy control


title: PFC VEH rep3


title: anti-PD1-treated adult 9_PB_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-031_PB_bL_S42

value: anti-PD1-treated adult 9

value: Baseline


title: Newly diagnosed MM_27

value: Female

value: bone marrow aspirate

value: multiple myeloma


title: anti-PD1-treated adult 9_HiHi_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-031_HiHi_oW_S61

value: ICOS+CD38+ cTfh


title: ABOS844

value: Omental adipose tissue

value: female

tag: bmi

tag: age

tag: type 2 diabetes (t2d)

value: Yes


title: PFC EE rep1

description:
PFC_ENR_rep1
EE_experiment_raw_counts_matrix.featureCounts.txt

value: pre-frontal cortex

value: CUMS protocol + env. enrichment


title: ABOS824

value: No


title: anti-PD1-treated adult 10_HiHi_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-032_HiHi_oW_S89

value: anti-PD1-treated adult 10

value: One week after flu vaccine

value: PBMC


title: HC CUMS_M rep3

value: hippocampus

value: CUMS protocol + minocycline


title: anti-PD1-treated adult 9_naiveB_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-031_naiveB_oW_S60

value: anti-PD1-treated adult 9

value: Naïve B cells


title: anti-PD1-treated adult 9_naiveB_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-031_naiveB_bL_S40

value: Baseline


title: Newly diagnosed MM_23

value: Male

value: bone marrow aspirate


title: inVitro_D270_neg_brep3

value: in vitro generated human retinal organoids

tag: cell line

value: mCar-GFP in PGP1 human iPSC

tag: origin

value: inVitro

tag: total age_in_days

tag: fraction

value: neg

value: Retinal organoids were dissociated as described in the methods of the manuscript, filtered and sorted directly into lysis buffer.


title: HC NAIVE rep1

tag: strain

tag: tissue

tag: cell type

value: Naive control group


title: PFC VEH rep1

description: EE_experiment_raw_counts_matrix.featureCounts.txt

value: pre-frontal cortex

value: CUMS protocol + vehicle


title: HC CUMS_M rep1


title: Newly diagnosed MM_28

value: Female

value: multiple myeloma


title: inVitro_D270_pos_brep3

value: pos

tag: dissociation protocol


title: inVitro_D270_neg_brep2


title: HC CUMS rep3

value: hippocampus

value: CUMS protocol


title: inVitro_D270_pos_brep2


title: anti-PD1-treated adult 8_naiveB_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-030_naiveB_bL_S37

tag: individual

value: anti-PD1-treated adult 8

tag: therapy

tag: time point

value: PBMC

tag: cell subset

value: Naïve B cells


title: anti-PD1-treated adult 8_HiHi_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-030_HiHi_oW_S63

value: One week after flu vaccine

value: ICOS+CD38+ cTfh


title: HC CUMS_M rep2

tag: treatment

value: CUMS protocol + minocycline


title: Newly diagnosed MM_25

tag: gender

value: Male

tag: age category

value: bone marrow aspirate

tag: disease state


title: inVitro_D270_pos_brep1

tag: alternative name

value: in vitro generated human retinal organoids

value: mCar-GFP in PGP1 human iPSC

value: inVitro

value: Retinal organoids were dissociated as described in the methods of the manuscript, filtered and sorted directly into lysis buffer.


title: anti-PD1-treated adult 9_HiHi_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-031_HiHi_bL_S43

value: anti-PD1-treated adult 9

value: Baseline


title: inVitro_D270_neg_brep1

tag: cell line

value: neg


title: HC CUMS rep2

value: hippocampus


title: anti-PD1-treated adult 9_ABC_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-031_ABC_bL_S41

value: Activated B cells


title: Newly diagnosed MM_24

value: Female

value: multiple myeloma


title: anti-PD1-treated adult 8_PB_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-030_PB_bL_S38

value: anti-PD1-treated adult 8

value: PBMC

value: Antibody-secreting B cells


title: inVitro_D200_pos_trep3

tag: origin

value: pos


title: PFC NAIVE rep2

value: pre-frontal cortex

value: Naive control group


title: anti-PD1-treated adult 8_ABC_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-030_ABC_oW_S62

value: One week after flu vaccine


title: HC CUMS rep1

value: CUMS protocol


title: Newly diagnosed MM_21

value: bone marrow aspirate


title: Newly diagnosed MM_19

value: Male


title: anti-PD1-treated adult 7_naiveB_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-028_naiveB_bL_S32

value: anti-PD1-treated adult 7

value: Naïve B cells


title: inVitro_D200_pos_trep2

value: in vitro generated human retinal organoids

value: mCar-GFP in PGP1 human iPSC

value: inVitro

tag: total age_in_days

value: Retinal organoids were dissociated as described in the methods of the manuscript, filtered and sorted directly into lysis buffer.


title: inVitro_D200_pos_trep1

tag: fraction


title: PFC NAIVE rep1

tag: strain


title: Newly diagnosed MM_18

value: Female

tag: tissue

value: multiple myeloma


title: Newly diagnosed MM_22


title: Newly diagnosed MM_17


title: PFC CUMS_M rep3

tag: cell type

value: CUMS protocol + minocycline


title: anti-PD1-treated adult 8_HiHi_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-030_HiHi_bL_S39

value: anti-PD1-treated adult 8

value: Baseline

value: PBMC

value: ICOS+CD38+ cTfh


title: Newly diagnosed MM_16


title: Newly diagnosed MM_20


title: inVitro_D200_neg

value: neg

tag: dissociation protocol


title: exVivo_D200_10w_pos_brep4

value: exVivo

tag: age donor_cells

tag: time in_vivo

value: pos

value: Whole murine eye cups containing transplanted human cones were dissociated with papain as described in the methods section of the manuscript, filtered and sorted directly into lysis buffer.


title: anti-PD1-treated adult 7_ABC_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-028_ABC_bL_S33

tag: individual

value: anti-PD1-treated adult 7

tag: therapy

tag: time point

value: Activated B cells


title: Newly diagnosed MM_15

tag: gender

value: Male

value: bone marrow aspirate


title: exVivo_D200_10w_pos_brep3

value: in vitro generated human retinal organoids

value: mCar-GFP in PGP1 human iPSC


title: PFC CUMS_M rep1

description: MINO_experiment_raw_counts_matrix.featureCounts.txt

value: pre-frontal cortex

tag: treatment


title: PFC CUMS_M rep2


title: anti-PD1-treated adult 7_HiHi_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-028_HiHi_bL_S34

tag: cell subset


title: anti-PD1-treated adult 6_HiHi_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-027_HiHi_bL_S31

value: anti-PD1-treated adult 6


title: anti-PD1-treated adult 6_naiveB_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-027_naiveB_bL_S30

value: Naïve B cells


title: PFC CUMS rep2

value: CUMS protocol


title: exVivo_D200_10w_pos_brep2

tag: alternative name


title: exVivo_D200_10w_pos_brep1_trep3

tag: cell line


title: PFC CUMS rep1


title: Newly diagnosed MM_14

value: Female

tag: age category

tag: disease state

value: multiple myeloma


title: anti-PD1-treated adult 6_ABC_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-027_ABC_oW_S36

value: One week after flu vaccine

value: PBMC


title: Newly diagnosed MM_13


title: exVivo_D200_10w_pos_brep1_trep2

tag: origin

value: exVivo

tag: total age_in_days

tag: fraction


title: VA_6_S6: EVs3

city: Trento

first: Maria Caterina

last: Mione

address: Via Sommarive 9

department: CIBIO

country: Italy

institute: University of Trento

data_processing:
Basecalls performed using CASAVA (Illumina Inc.)
Reads were aligned to the reference genome Danio rerio assembly GRCz11 using STAR [PMID: 23104886] with recommended options and thresholds (version 2.5).
HTSeq-count (version 0.9.1) [PMID: 25260700 ] was used to generate raw gene counts.
EdgeR package (version 3.24.3) [PMID: 19910308] was used to normalize counts to Trimmed Mean of M-values (TMM) for visualization methods.
Differential expression analysis was performed using DESeq2 package (version 1.22.2) and for significance testing, the Wald test was used.
Genome_build: GRCz11
Supplementary_files_format_and_content: tab-delimited text files include COUNTS values for each Sample

organism: Danio rerio

growth_protocol: Melanomas were induced in developing zebrafish through the Gal4/UAS system, using the kita:Gal4 driver line and the injection of a UAS:HRASV12G plasmid

extract_protocol:
RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit (Norgen) following manufacturer’s instructions, subjected to DNase-I (Thermo Fisher Scientific) treatment and subsequently purified using phenol-chloroform
Libraries were constructed using Clontech SMARTer smRNA-Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

tag: cell type

value: extracellular vesicles

tag: strain


title: VA_5_S5: EVs2


title: anti-PD1-treated adult 5_PB_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-026_PB_bL_S24

value: anti-PD1-treated adult 5

value: Baseline

value: Antibody-secreting B cells


title: anti-PD1-treated adult 5_naiveB_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-026_naiveB_bL_S22


title: anti-PD1-treated adult 5_HiHi_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-026_HiHi_bL_S25

value: ICOS+CD38+ cTfh


title: Newly diagnosed MM_12

value: Male

tag: tissue

value: bone marrow aspirate


title: Newly diagnosed MM_10


title: CH_1h_n3

city: Frankfurt

first: Tobias

last: Schmid

address: Theodor-Stern-Kai 7

department: Institute of Biochemistry I

institute: Goethe University Frankfurt

description:
Summary_Total_Counts_1hLabeling.txt
Summary_TtoC_Counts_1hLabeling.txt

data_processing:
Bcl2fastq conversion and demultiplexing of pooled libraries was carried out in Illumina BaseSpace.
Length trimming to 75 nt as well as quality-, adapter- and polyA-trimming was carried out with Cutadapt.
Umi2index
Reads were aligned to the human genome (GRCh38) using STAR with the following parameters: --alignEndsType EndToEnd --outSAMattributes MD NH --outFilterMultimapNmax 1 --clip5pNbases 12.
Transcript counts (total and T-to-C) were determined using HTSeq-count.
RNA half-lives were determined using GRAND-SLAM. bam-files of the 8h-labeling experiment (without washout) and corresponding bam-files of unlabeled samples were used as input.
Differential gene expression analysis of total counts and T-to-C counts was performed using DeSeq2.
Assembly: GRCh38
Supplementary files format and content: Text files containing total or T-to-C count data.

source_name: acute myeloid leukemia

growth_protocol: Monocytic THP-1 were cultured in RPMI with 10% FCS, 100 U/mL penicillin, and 100 µg/mL streptomycin.

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit according the instructions with the modification that dithiothreitol (DTT) was added in all washing steps (0.1 mM) and to the final eluate (1 mM). Afterwards, extracted total RNA was alkylated using 10 mM iodoacetamide (in 50 mM sodium phosphate buffer, pH 8, 50% DMSO). After 15 minutes incubation at 50°C, the reaction was quenched by addition of 20 mM DTT, followed by subsequent ethanol precipitation.
cDNA libraries were generated with the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD with Illumina with the UMI Second Strand Synthesis Module for QuantSeq (Lexogen). Library sequencing (single-read; 75 or 150 cycles) was performed on a NextSeq 500 sequencer using a High Output Kit v2.

treatment_protocol: Hypoxic incubations were performed in a hypoxia workstation with 5% CO2 and 1% O2 for 8h (acute hypoxia = AH) or 72h (chronic hypoxia = CH). For metabolic RNA-Seq, the cells were labeled for 1h with 300 µM 4-thiouridine (4sU) or for 8h with 4x 30 µM 4SU every 2h.

value: THP-1 monocytes

tag: 4su labeling

tag: 4su washout

value: no washout

value: chronic hypoxia (72h 1% O2)


title: AH_1h_n3

value: acute hypoxia (8h 1% O2)


title: VA_4_S4: EVs1


title: Newly diagnosed MM_11

source_name: bone marrow aspirate


title: anti-PD1-treated adult 5_ABC_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-026_ABC_oW_S35

tag: individual

tag: therapy

value: Activated B cells


title: exVivo_D200_10w_pos_brep1_trep1

value: in vitro generated human retinal organoids

value: mCar-GFP in PGP1 human iPSC

tag: age donor_cells

tag: time in_vivo

value: pos

tag: dissociation protocol

value: Whole murine eye cups containing transplanted human cones were dissociated with papain as described in the methods section of the manuscript, filtered and sorted directly into lysis buffer.


title: VA_24_S14: Melanoma3

value: Melanocytes


title: Newly diagnosed MM_8

tag: gender

value: multiple myeloma


title: VA_23_S13: Melanoma2


title: N_1h_n3

tag: treatment

value: normoxia


title: anti-PD1-treated adult 5_ABC_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-026_ABC_bL_S23

value: anti-PD1-treated adult 5

tag: time point

value: Baseline

value: PBMC

tag: cell subset


title: VA_22_S12: Melanoma1


title: CH_1h_n2


title: Newly diagnosed MM_9

value: Male

tag: age category

tag: disease state


title: AH_1h_n2


title: anti-PD1-treated adult 4_naiveB_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-025_naiveB_oW_S26

value: anti-PD1-treated adult 4

value: One week after flu vaccine

value: Naïve B cells


title: KO HFD_rep3

first: CheolJun

last: Choi

address: 1, Gwanak-ro, Gwanak-gu, 29-310

institute: Seoul National University

data_processing:
bcl2fastq2-v2.20.0 package was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.38. (Trimmomatic option : ILLUMINACLIP:[TruSeq3-PE-2.fa]:2:30:10:5:true ,LEADING:3 , TRAILING:3 , SLIDINGWINDOW:4:15, MINLEN:36)
To estimate expression levels, the RNA-Seq reads were mapped to Mus musculus genome (mm10) using HISAT2 version 2.1.0, which is capable of reporting split-read alignments across splice junctions and determined using StringTie version 1.3.4d software in default options.
The read count data of filtered genes was normalized by RLE (Relative Log Expression) normalization with DESeq2. The nbinomWaldTest function in DESeq2 was used to test for differential expression. The output prints foldChange, p-value and FDR values which corrected by the Benjamin-Hochberg procedure.  DEGs was determined by |fold change|>=2 and p-value <0.05. For DEGs, hierarchical clustering analysis was performed with complete linkage method and Euclidean distance as a measure of similarity.
Gene-enrichment analysis and KEGG pathway analysis for DEGs were also performed based on Gene Ontology (http://geneontology.org/) and KEGG pathway (https://www.genome.jp/kegg/) database respectively. All statistical analysis and visualization of differentially expressed genes was conducted using R.3.5.1 (www.r-project.org).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include baseMean values for each Comparison

source_name: gonadal white adipose tissue

growth_protocol: Mice were fed a NCD or HFD and were kept on a 12-h light/12-h dark cycle with free access to food and water at 22±1 °C.

extract_protocol:
RNA was isolated using Trizol reagent (Invitrogen) and processed as per manufacturer’s instructions.
Libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit, according to the manufacturer’s

treatment_protocol: Mice were fed a NCD or HFD for 8 weeks at the age of 6 weeks. Tamoxifen treatment were performed at 1 weeks and 5weeks of HFD feeding for 5 days.

value: gonadal white adipose tissue

tag: Sex

tag: genotype

value: Gja1floxed Csf1r creER

value: 8 weeks of HFD feeding and Tamoxifen treatment


title: anti-PD1-treated adult 4_HiHi_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-025_HiHi_oW_S29

tag: cell type

value: ICOS+CD38+ cTfh


title: Newly diagnosed MM_6

tag: tissue

value: bone marrow aspirate


title: N_1h_n2

value: THP-1 monocytes

tag: 4su labeling

value: no washout


title: anti-PD1-treated adult 4_ABC_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-025_ABC_oW_S27

value: Activated B cells


title: anti-PD1-treated adult 4_PB_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-025_PB_oW_S28

value: Antibody-secreting B cells


title: KO HFD_rep2

tag: strain


title: anti-PD1-treated adult 3_HiHi_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-023_HiHi_oW_S18

tag: individual

value: anti-PD1-treated adult 3


title: Newly diagnosed MM_4

value: Female

value: multiple myeloma


title: N_1h_n1

tag: 4su washout

value: normoxia


title: Newly diagnosed MM_7

value: Male


title: KO NCD_rep3

value: 8 weeks of NCD feeding and Tamoxifen treatment


title: AH_1h_n1

value: acute hypoxia (8h 1% O2)


title: Newly diagnosed MM_3


title: anti-PD1-treated adult 3_HiHi_bL

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-023_HiHi_bL_S15

tag: therapy

value: Baseline

value: PBMC


title: Newly diagnosed MM_5


title: anti-PD1-treated adult 2_naiveB_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-022_naiveB_oW_S19

value: anti-PD1-treated adult 2

value: One week after flu vaccine

value: Naïve B cells


title: CH_8h6h_n3

description:
Summary_Total_Counts_8hLabeling.txt
Summary_TtoC_Counts_8hLabeling.txt

value: chronic hypoxia (72h 1% O2)


title: KO NCD_rep1

value: gonadal white adipose tissue

value: Gja1floxed Csf1r creER


title: Newly diagnosed MM_2

value: bone marrow aspirate


title: KO NCD_rep2


title: anti-PD1-treated adult 2_HiHi_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-022_HiHi_oW_S21

value: ICOS+CD38+ cTfh


title: anti-PD1-treated adult 2_ABC_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-022_ABC_oW_S20

value: Activated B cells


title: inVitro_D270_pos_brep5

tag: alternative name

value: in vitro generated human retinal organoids

tag: cell line

value: mCar-GFP in PGP1 human iPSC

tag: origin

value: inVitro

tag: total age_in_days

tag: fraction

value: pos

value: Retinal organoids were dissociated as described in the methods of the manuscript, filtered and sorted directly into lysis buffer.


title: KO HFD_rep1

value: Male

tag: treatment

value: 8 weeks of HFD feeding and Tamoxifen treatment


title: WT HFD_rep3

value: 8 weeks of HFD feeding


title: WT HFD_rep2


title: CH_1h_n1

value: THP-1 monocytes

value: no washout


title: CH_8h1h_n3


title: WT HFD_rep1


title: HCT116_Reversed

value: normal genomic DNA (Promega, Madison, WI)

source_name: HCT116 colon cancer cell line

value: HCT116 colon cancer cell line


title: Newly diagnosed MM_1

tag: gender

tag: age category

value: multiple myeloma


title: FL B cells from BM 114

city: RENNES

first: Celine

last: Pangault

address: 2, avenue du Léon Bernard

department: Medical School of Rennes

institute: Rennes University Hospital

description: Cells were purified using FACSARIA sorting

hyb_protocol: Following fragmentation, cARN were hybridized on GeneChip Human U133Plus2 arrays

scan_protocol: GeneChips were scanned using the Genechip Scanner Affymetrix 3000

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC). Normalization was performed sing the Robust Multiarray Analysis (RMA) method. Dataset was then filtering by eliminating PS with no expression in all dataset and/or no gene symbol annotations.

source_name: B tumor cells purified from follicular lymphoma bone marrow

label_protocol: Biotinylated cRNA were amplified according to the small sample labeling protocol (Affymetrix, Santa Clara, CA)

growth_protocol: FL B cells were purified by FACSARIA strategy from FL bone marrow samples using CD20hiCD44loCD38posIgDnegCD138negCD34neg phenotype.

extract_protocol: RNA extraction was  performed using Qiazol (Qiagen, Valencia, CA) according to the manufacturer's instructions.

tag: status

value: FL patient

value: Bone marrow


title: FL B cells from BM 115


title: CH_8h3h_n3

value: chronic hypoxia (72h 1% O2)


title: Sample 110519 from ADM D0

city: Los Angeles

first: Hesamedin

last: Hakimjavadi

state: California

address: 4650 Sunset Blvd

department: Pathology and Laboratory Medicine

institute: Childrens Hospital Los Angeles

data_processing:
Quality control of sequences were performed using Trime Glore 0.5.0
low quality and adapter trimmed using Trim Glore 0.5.0
Read were aligned using Hisat2 (v 2.2.1) againes indexed human genome (Homo_sapiens.GRCh38)
Read were quatified using featureCounts from subread package 2.0.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Transcript read counts, rowes are transcript values, columns are samples

source_name: pancreatic acinar cells

growth_protocol: The acinar clusters were collected from fresh islet-depleted cell fractions containing digested acinar clusters from cadaveric pancreas donors

extract_protocol:
Total RNA was extracted from Trizol lysate using Qiagen miRNesay Mini Kit
The preparation was performed using the reagents provided in the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760S, New England Biolabs,USA), in conjunction with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and the NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs, NEB #6440s)

treatment_protocol: 0 days vs. 6 days of three-dimensional (3-D) culture of acinar cells on Matrigel

value: pancreatic acinar cells

tag: time

tag: race

value: Hispanic

value: Female

tag: bmi


title: WT NCD_rep3

tag: tissue

value: gonadal white adipose tissue

tag: Sex

tag: genotype

value: 8 weeks of NCD feeding


title: HCT116_Forward

source_name: normal genomic DNA (Promega, Madison, WI)


title: AH_8h1h_n3

tag: cell type

tag: 4su labeling

tag: 4su washout

value: acute hypoxia (8h 1% O2)


title: FL B cells from BM 110


title: FL B cells from BM 113


title: WT NCD_rep1

tag: strain

value: Male


title: AH_8h6h_n3


title: WT NCD_rep2


title: Sample 101719 from ADM D0

tag: individual

value: White


title: CH_8h_n3


title: N_8h6h_n3

value: normoxia


title: FL B cells from BM 109


title: Sample 101519 from ADM D0


title: dDM_24

city: New Haven

first: Stephen

middle: M

last: Strittmatter.

state: Connecticut

address: 295 Congress Ave, BCMM Rm433

department: Neurology

institute: Yale University

data_processing:
Samples under went two rounds snRNA sequencing, to increase sequencing depth, using Illumina NoveSeq 5000/6000 software for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Assembly: mm10 whole genome using 3.0.0_premrna with parameters chemistry=SC3Pv3
Seurat (Butler et al., 2018 was used to generate seurat objects of single nuclei transcriptomic datasets, with pre-processing and quality control analysis
Nuclei doublet idenitification and removal using DoubletFinder (McGinnis CS, et. Al)
Log-normalization and multi-dataset reference-based integration with dimensionally reduced UMAP generation using Seurat

source_name: Cortex and hippocampus

growth_protocol: Miced were aged to 12months (average of 53.7+3.0 weeks)

extract_protocol:
Cerebral cortex and hippocampus from each brain was dissected and the two regions were processed together for each mouse. Nuclei isolated by sucrose density gradient centrifugation were processed for mRNA profiles with the 10X Genomics platform
RNA libraries were prepared for sequencing using standard Illumina protocols
Other: snRNAseq

treatment_protocol: Wild-type (WT), APP/PS1, and dKI mice were treated with vehicle or SAM for 35-39 days.

value: hTau/APPNL-G-F

tag: disease state

value: AD

tag: treatment group

value: SAM


title: Sample 071620 from ADM D6

value: Black


title: AH_8h_n3

value: THP-1 monocytes

value: no washout

tag: treatment


title: anti-PD1-treated adult 1_HiHi_oW

description:
FINAL_master_list_of_gene_counts_MIN.Fastqs.txt
19616-021_HiHi_oW_S17

value: anti-PD1-treated adult 1

tag: therapy

tag: time point

value: One week after flu vaccine

value: PBMC

tag: cell subset

value: ICOS+CD38+ cTfh


title: N_8h3h_n3


title: N_8h1h_n3


title: dDF_233

value: Female


title: Sample 121219 from ADM D0

value: pancreatic acinar cells

tag: time

tag: gender


title: Sample 071020 from ADM D6

tag: race

tag: bmi


title: dDF_496

tag: Sex


title: 6047_SP_t12w

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.36.1).

source_name: Adipose tissue biopsy from subject 6047, after treatment with a 25% Caloric Restriction diet with Normal Protein content (t12w)

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: The current study was part of a previously published double-blind randomized intervention study (Backx et al, PMID: 26471344). The study was highly controlled, as 90% of the daily energy intake was provided by the University. Subjects were recruited by publishing advertisements in local newspapers and by sending out general e-mails to an e-mail list of persons who had indicated their interest in participating in studies of our university. Subjects were included based on the following criteria: BMI 27-40 kg/m2, Waist circumference male:≥102 cm, female:≥88cm, and Willingness and ability to comply with the protocol. Subjects were excluded based on the following exclusion criteria: Renal insufficiency, co-morbidities, Type 1 & 2 diabetics (Fasting glucose level ≥ 7 mmol/L), Cancer, COPD, Participation in weight loss program 3 months before the intervention, Participation of any heavy resistance-type exercise training (>1 wk) the last 2 y, Intentional or unintentional weight loss (>3 kg in the last 3 months), Severe loss appetite, Diagnosed allergy to milk products, Gastric bypass, Supplements or medication use for weight loss, Participation in any other intervention trial, Women could only participate if they are postmenopausal (last period  ≥ a year ago). The study protocol was approved by the Medical Ethical Committee of Wageningen University and written informed consent was obtained before study participation. The study was registered at clinicaltrials.gov as NCT01915030.

extract_protocol: Total RNA was prepared from the abdominal subcutaneous adipose biopsies using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNeasy columns. RNA integrity was checked on chip analysis (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 7.0).

treatment_protocol: Sixty-one overweight and obese healthy women (n=25) and men (n=36), aged 55-70 years, were randomly assigned to either a high-protein diet (HP-ER; 1.7 g protein/kg per day) or normal protein diet (NP-ER; 0.9 g protein/kg per day), during a 12-week 25% energy intake restriction. A subcutaneous adipose tissue biopsy was taken under local anesthesia under fasted conditions before and after the intervention from 22 participants.

tag: subjectid

tag: protein content restricted diet

value: normal

tag: time of sampling (before/after)

value: after

tag: time of sampling (wk)

tag: sexe

tag: date of birth (dd-mm-yyyy)

tag: screening bmi (kg/m2)

tag: screening body fat percentage (fm)

tag: screening glucose (mmol/l)


title: CH_8h6h_n2

tag: cell type

tag: 4su labeling

tag: 4su washout

tag: treatment

value: chronic hypoxia (72h 1% O2)


title: Sample 071020 from ADM D0

tag: individual

tag: time

value: White

tag: gender


title: N_8h_n3

value: normoxia


title: dVM_913

tag: strain

value: hTau/APPNL-G-F

tag: Sex

value: Male

tag: disease state

tag: treatment group

value: Vehicle


title: dVF_59

value: AD


title: dVM_914


title: 6047_SP_t0w

source_name: Adipose tissue biopsy from subject 6047, before treatment with a 25% Caloric Restriction diet with Normal Protein content (t0w)

tag: subjectid

tag: protein content restricted diet

tag: time of sampling (before/after)

value: before

tag: time of sampling (wk)

value: t=0 (baseline)


title: 6092_SP_t12w

source_name: Adipose tissue biopsy from subject 6092, after treatment with a 25% Caloric Restriction diet with Normal Protein content (t12w)

tag: sexe

tag: date of birth (dd-mm-yyyy)

tag: screening bmi (kg/m2)

tag: screening body fat percentage (fm)


title: 6012_SP_t12w

source_name: Adipose tissue biopsy from subject 6012, after treatment with a 25% Caloric Restriction diet with Normal Protein content (t12w)

tag: screening glucose (mmol/l)


title: 6121_HP_t0w

source_name: Adipose tissue biopsy from subject 6121, before treatment with a 25% Caloric Restriction diet with High Protein content (t0w)

value: high


title: CH_8h3h_n2

tag: cell type

value: THP-1 monocytes

tag: 4su labeling

tag: 4su washout

tag: treatment


title: 6092_SP_t0w

source_name: Adipose tissue biopsy from subject 6092, before treatment with a 25% Caloric Restriction diet with Normal Protein content (t0w)


title: Sample 063020 from ADM D6

tag: individual

tag: time

tag: race

value: Hispanic

tag: gender

tag: bmi


title: 6121_HP_t12w

source_name: Adipose tissue biopsy from subject 6121, after treatment with a 25% Caloric Restriction diet with High Protein content (t12w)

tag: subjectid

tag: protein content restricted diet


title: CH_8h1h_n2


title: Sample 071620 from ADM D0

value: Black


title: 6112_HP_t12w

source_name: Adipose tissue biopsy from subject 6112, after treatment with a 25% Caloric Restriction diet with High Protein content (t12w)

tag: time of sampling (before/after)

tag: time of sampling (wk)


title: dDM_25

tag: strain

tag: Sex

tag: disease state

tag: treatment group

value: SAM


title: Sample 063020 from ADM D0

tag: cell type

value: pancreatic acinar cells

value: Female


title: Sample 103119 from ADM D0


title: Sample 061520 from ADM D6


title: AH_8h6h_n2

tag: 4su labeling

value: acute hypoxia (8h 1% O2)


title: 6087_SP_t12w

source_name: Adipose tissue biopsy from subject 6087, after treatment with a 25% Caloric Restriction diet with Normal Protein content (t12w)

value: normal

value: after

tag: sexe

tag: date of birth (dd-mm-yyyy)

tag: screening bmi (kg/m2)

tag: screening body fat percentage (fm)

tag: screening glucose (mmol/l)


title: CH_8h_n2

source_name: acute myeloid leukemia

tag: 4su washout

value: no washout

tag: treatment

value: chronic hypoxia (72h 1% O2)


title: Sample 061520 from ADM D0

tag: individual

tag: time

tag: race

value: White

tag: gender

value: Male

tag: bmi


title: WDM_607

tag: strain

value: hTau/APPNL-G-F

tag: Sex

value: Wildtype


title: WDF_272

tag: disease state

tag: treatment group


title: WDM_608


title: AH_8h1h_n2

tag: cell type

tag: 4su labeling


title: Sample 100419 from ADM D0


title: AH_8h_n2


title: dVF_60

value: AD

value: Vehicle


title: WVM_976


title: N_8h6h_n2

value: THP-1 monocytes

value: normoxia


title: AH_8h3h_n2


title: Sample 121319 from ADM D6


title: Sample 060220 from ADM D0

value: Black


title: N_8h3h_n2


title: WVM_221


title: N_8h1h_n2


title: Sample 121019 from ADM D6


title: Sample 060220 from ADM D6


title: WVF_270


title: Sample 110519 from ADM D6

value: Hispanic


title: WDF_68

value: SAM


title: N_8h_n2


title: N_unlabeled_n2

description:
N_unlabeled_n2_total.txt
N_unlabeled_n2_TtoC.txt

value: no labeling


title: Sample 103119 from ADM D6

value: pancreatic acinar cells


title: WVF_271

value: Female


title: CH_8h6h_n1


title: Sample 102319 from ADM D0


title: Sample 102319 from ADM D6


title: Sample 101519 from ADM D6


title: TGD_565

value: APPswe/PSEN-delta-E9 line


title: Sample 101719 from ADM D6


title: 6087_SP_t0w

source_name: Adipose tissue biopsy from subject 6087, before treatment with a 25% Caloric Restriction diet with Normal Protein content (t0w)

tag: subjectid

tag: protein content restricted diet

value: normal

tag: time of sampling (before/after)

value: before

tag: time of sampling (wk)

value: t=0 (baseline)

tag: sexe

tag: date of birth (dd-mm-yyyy)


title: TGV_955

value: Male


title: TGD_552


title: TGD_488


title: CH_8h1h_n1

tag: 4su washout

tag: treatment

value: chronic hypoxia (72h 1% O2)


title: CH_8h_n1

value: no washout


title: Sample 121219 from ADM D6

tag: individual

tag: time

tag: race

value: White


title: TGD_563

tag: strain

value: AD


title: CH_8h3h_n1

value: THP-1 monocytes


title: AH_8h6h_n1

value: acute hypoxia (8h 1% O2)


title: TGV_502

tag: Sex

value: Vehicle


title: Sample 100419 from ADM D6

tag: gender

tag: bmi


title: AH_8h3h_n1

tag: cell type


title: Sample 121319 from ADM D0


title: 6129_SP_t12w

source_name: Adipose tissue biopsy from subject 6129, after treatment with a 25% Caloric Restriction diet with Normal Protein content (t12w)

value: after

tag: screening bmi (kg/m2)

tag: screening body fat percentage (fm)

tag: screening glucose (mmol/l)


title: TGV_554

tag: disease state

tag: treatment group


title: TGV_501


title: 6129_SP_t0w

source_name: Adipose tissue biopsy from subject 6129, before treatment with a 25% Caloric Restriction diet with Normal Protein content (t0w)

tag: subjectid

tag: protein content restricted diet

tag: time of sampling (before/after)

tag: time of sampling (wk)

tag: sexe


title: Sample 121019 from ADM D0

tag: individual

tag: time


title: AH_8h1h_n1

tag: 4su labeling

tag: 4su washout

tag: treatment


title: WTD_961

tag: strain

tag: Sex

value: Wildtype

value: SAM


title: AH_8h3h_n3

tag: cell type


title: 6012_SP_t0w

source_name: Adipose tissue biopsy from subject 6012, before treatment with a 25% Caloric Restriction diet with Normal Protein content (t0w)

tag: date of birth (dd-mm-yyyy)

tag: screening bmi (kg/m2)

tag: screening body fat percentage (fm)


title: AH_8h_n1


title: 6112_HP_t0w

source_name: Adipose tissue biopsy from subject 6112, before treatment with a 25% Caloric Restriction diet with High Protein content (t0w)

value: high

tag: screening glucose (mmol/l)


title: 6124_HP_t12w

source_name: Adipose tissue biopsy from subject 6124, after treatment with a 25% Caloric Restriction diet with High Protein content (t12w)

tag: subjectid

value: Female


title: 6086_HP_t0w

source_name: Adipose tissue biopsy from subject 6086, before treatment with a 25% Caloric Restriction diet with High Protein content (t0w)

tag: protein content restricted diet


title: WTD_564

source_name: Cortex and hippocampus

value: APPswe/PSEN-delta-E9 line

tag: disease state

tag: treatment group


title: Empty

city: Cincinnati

first: Kwangmin

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Basecalls performed using CASAVA version 1.4
The quality of paired reads were checked using FASTQC (v0.11.7)
Reads were aligned with STAR (v2.5) against mm10
RNA targets of RNA-binding proteins were detected using HyperTRIBE (v1.0.0)
Genome_build: mm10
Supplementary_files_format_and_content: BedGraph and tab-delimited HyperTRIBE output files

growth_protocol: Cells grown in RPMI with 10% FCS and pen/strep.

extract_protocol:
Total RNA was harvested using the Zymo Quick-RNA Miniprep kit
Standard Illumina protocols were used
library strategy: HyperTRIBE

treatment_protocol: Cells were transduced with the indicated pGK-GFP retroviral supernatants generated in 293T cells and grown for 7 days.

tag: cell line

value: human leukemia cell line

tag: transgene


title: WTD_954


title: ADAR alone

value: ADARcd


title: 6108_HP_t12w

source_name: Adipose tissue biopsy from subject 6108, after treatment with a 25% Caloric Restriction diet with High Protein content (t12w)

tag: time of sampling (before/after)

tag: time of sampling (wk)

tag: sexe


title: WTV_957


title: DDX41-ADAR


title: CB_2

first: Penyun

last: Li

address: 27 Taiping Road, Haidian District

institute: Beijing Institute of Pharmacology and Toxicology

data_processing:
Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Hisat2 v2.0.5
Supplementary_files_format_and_content: Matrix table with raw gene counts and FPKM for every gene and every sample

source_name: MDA-MB-231 cells

extract_protocol:
Total RNA was extracted with Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: MDA-MB-231 cells

tag: tissue

value: Breast cancer tissue

tag: treatment

value: Treated with CB1


title: WTD_483

tag: strain

tag: Sex

value: Male


title: CB_3


title: N_8h_n1

tag: cell type

tag: 4su labeling

tag: 4su washout

value: no washout

value: normoxia


title: WTV_952


title: N_8h1h_n1

value: THP-1 monocytes


title: N_8h3h_n1


title: N_8h6h_n1


title: WTV_951


title: 6086_HP_t12w

source_name: Adipose tissue biopsy from subject 6086, after treatment with a 25% Caloric Restriction diet with High Protein content (t12w)

tag: date of birth (dd-mm-yyyy)

tag: screening bmi (kg/m2)

tag: screening body fat percentage (fm)

tag: screening glucose (mmol/l)


title: CB_1


title: N_unlabeled_n1

description:
N_unlabeled_n1_total.txt
N_unlabeled_n1_TtoC.txt

value: no labeling


title: HU-PRELP-5_S20

city: London

first: Alex

last: Leung

state: London

address: 11-43 Bath Street

country: United Kingdom

institute: UCL Institute Of Ophthalmology

data_processing:
Data demultiplexed and converted to fastq ising Ilumina bcl2fastq conversion software v2.19
Sequenced reads were converted into BAM files and aligned to hg38 genome using HISAT2 at UseGalaxy.com
Reads per transcript counted using FeatureCounts at UseGalaxy.com
Samples pooled and differential expression of genes calculated using DESeq2 at UseGalaxy.com
Assembly: hg38
Supplementary files format and content: tab-delimited text files from FeatureCounts contain raw counted reads, per gene, per row, for each sample
Supplementary files format and content: tab-delimited text file from DESeq2 contain log2 fold change of each read between pooled control and treated samples per gene with p and q-values

source_name: HUVEC - PRELP conditioned media treated

growth_protocol: Cells were maintained up to passage six in endothelial cell growth media in T25 flasks. Media was replaced every 2-3 days and cells passaged at 80% confluency

extract_protocol:
Fresh retinal tissuRNA was extracted using a PureLink RNA Mini Kit (ThermoFisher)
Samples were prepared a KAPA mRNA HyperPrep Kit and library constructed using standard Ilumina protocols

treatment_protocol: 5 replicates of 1 million cells were seeded into 6-well plates and treated with conditioned media from 293T that either did or did not express PRELP for 24 h

value: Umbilical vein endothelial cells

value: PRELP-treated


title: 6108_HP_t0w

source_name: Adipose tissue biopsy from subject 6108, before treatment with a 25% Caloric Restriction diet with High Protein content (t0w)

tag: subjectid

tag: protein content restricted diet

value: before

value: t=0 (baseline)


title: Treated-ATAC-Rep2

city: Atlanta

first: Yoonhee

last: Jung

state: Georgia

address: 615 Michael Street

department: Human Genetics

institute: Emory university

library_source: genomic

data_processing:
All libraries were sequenced using an Illumina Hiseq v4 sequencer and 50 bp paired-end format. Paired reads were aligned to mouse reference genome mm10 using Bowtie2.  ATAC-seq reads were aligned using default parameters except -X 2000 -m 1. Duplicates were removed using Samtools.  To adjust for fragment size, we aligned all reads as + strands offset by +4 bp and – strands offset by -5 bp (Buenrostro et al. 2013). To separate nucleosome-free (THSS)  and  mono-nucleosome (Nucleosome) fragments, we chose reads 50-115 bp 180-247 bp in length, respectively. Mono-nucleosome reads were analyzed using DANPOS2 (Chen et al. 2013). MACS was used for peak calling with nucleosome-free reads (Liu 2014). For generating wiggle files, we combined each replicates.
Assembly: hg38

source_name: Treated-ATAC

extract_protocol:
ATAC-seq was carried out using the Omni-ATAC protocol. After cells were counted, the nuclei were isolated with Lysis Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin. The purified nuclei pellet was then resuspended in the transposase reaction mix containing 0.05% digitonin and incubated for 30 min at 37°C. Following incubation, cells were treated with Proteinase K at 55°C for 2 h, and gDNA was isolated by phenol:chloroform:isoamyl alcohol and EtOH precipitation. Library amplification was done with 2x KAPA HiFi mix (Kapa Biosystems) and 1.25 µM indexed primers using the following PCR conditions: 72°C for 5 min; 98°C for 30 s; and 10-11 cycles at 98°C for 10 s, 63°C for 30 s, and 72°C for 1 min. Libraries were paired-end sequenced on Illumina Hiseq2500 v4 or NovaSeq 6000 instruments.
Library amplification was done with 2x KAPA HiFi mix and 1.25 µM indexed primers using the following PCR conditions: 72°C for 5 min; 98°C for 30 s; and 10-11 cycles at 98°C for 10 s, 63°C for 30 s, and 72°C for 1 min.

tag: strain background

value: treated


title: HU-PRELP-3_S18


title: Vector_3

tag: cell line

value: Treated with DMSO


title: WTV_487

value: APPswe/PSEN-delta-E9 line

tag: disease state

value: Wildtype

tag: treatment group

value: Vehicle


title: Treated-ATAC-Rep1


title: Vector_2

value: MDA-MB-231 cells

tag: tissue


title: 6107_SP_t0w

source_name: Adipose tissue biopsy from subject 6107, before treatment with a 25% Caloric Restriction diet with Normal Protein content (t0w)

value: normal

tag: time of sampling (before/after)

tag: time of sampling (wk)

tag: sexe


title: 6084_HP_t0w

source_name: Adipose tissue biopsy from subject 6084, before treatment with a 25% Caloric Restriction diet with High Protein content (t0w)

value: high


title: 6124_HP_t0w

source_name: Adipose tissue biopsy from subject 6124, before treatment with a 25% Caloric Restriction diet with High Protein content (t0w)

value: Female


title: 6080_SP_t12w

source_name: Adipose tissue biopsy from subject 6080, after treatment with a 25% Caloric Restriction diet with Normal Protein content (t12w)

value: after

value: Male


title: 6107_SP_t12w

source_name: Adipose tissue biopsy from subject 6107, after treatment with a 25% Caloric Restriction diet with Normal Protein content (t12w)


title: CTL-ATAC-Rep2

source_name: CTL-ATAC

value: control


title: 6080_SP_t0w

source_name: Adipose tissue biopsy from subject 6080, before treatment with a 25% Caloric Restriction diet with Normal Protein content (t0w)


title: HU-PRELP-2_S17

tag: cell type

tag: treatment


title: HU-PRELP-4_S19


title: 6084_HP_t12w

source_name: Adipose tissue biopsy from subject 6084, after treatment with a 25% Caloric Restriction diet with High Protein content (t12w)


title: 6055_HP_t0w

source_name: Adipose tissue biopsy from subject 6055, before treatment with a 25% Caloric Restriction diet with High Protein content (t0w)


title: 6064_SP_t12w

source_name: Adipose tissue biopsy from subject 6064, after treatment with a 25% Caloric Restriction diet with Normal Protein content (t12w)


title: RS_2

data_processing:
Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Hisat2 v2.0.5
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

value: Breast cancer tissue

value: Treated with RSL3


title: 6064_SP_t0w

source_name: Adipose tissue biopsy from subject 6064, before treatment with a 25% Caloric Restriction diet with Normal Protein content (t0w)


title: HU-PRELP-1_S16

value: Umbilical vein endothelial cells

value: PRELP-treated


title: 6044_HP_t12w

source_name: Adipose tissue biopsy from subject 6044, after treatment with a 25% Caloric Restriction diet with High Protein content (t12w)


title: 6077_HP_t12w

source_name: Adipose tissue biopsy from subject 6077, after treatment with a 25% Caloric Restriction diet with Normal Protein content (t12w)


title: 6078_HP_t0w

source_name: Adipose tissue biopsy from subject 6078, before treatment with a 25% Caloric Restriction diet with High Protein content (t0w)

value: before

value: t=0 (baseline)


title: 6044_HP_t0w

source_name: Adipose tissue biopsy from subject 6044, before treatment with a 25% Caloric Restriction diet with High Protein content (t0w)


title: 6078_HP_t12w

source_name: Adipose tissue biopsy from subject 6078, after treatment with a 25% Caloric Restriction diet with High Protein content (t12w)


title: Vector_1

source_name: MDA-MB-231 cells

value: Treated with DMSO


title: 6055_HP_t12w

source_name: Adipose tissue biopsy from subject 6055, after treatment with a 25% Caloric Restriction diet with High Protein content (t12w)


title: CTL-ATAC-Rep1


title: HUVEC-5_S15

source_name: HUVEC - control conditioned media treated

value: Control


title: RS_1


title: HUVEC-4_S14


title: ER_3

value: Treated with erastin


title: 6039_HP_t12w

source_name: Adipose tissue biopsy from subject 6039, after treatment with a 25% Caloric Restriction diet with High Protein content (t12w)


title: ER_2


title: HUVEC-3_S13


title: ER_1


title: HUVEC-2_S12


title: NC_3


title: 6054_SP_t12w

source_name: Adipose tissue biopsy from subject 6054, after treatment with a 25% Caloric Restriction diet with Normal Protein content (t12w)


title: 6077_HP_t0w

source_name: Adipose tissue biopsy from subject 6077, before treatment with a 25% Caloric Restriction diet with High Protein content (t0w)


title: 6054_SP_t0w

source_name: Adipose tissue biopsy from subject 6054, before treatment with a 25% Caloric Restriction diet with Normal Protein content (t0w)


title: NC_2


title: 6076_SP_t12w

source_name: Adipose tissue biopsy from subject 6076, after treatment with a 25% Caloric Restriction diet with Normal Protein content (t12w)


title: ImPACCT-02-004-Biopsy-C-RNA

city: Utrecht

first: Onno

last: Kranenburg

address: Heidelberglaan 100

institute: UMC Utrecht

data_processing:
Illumina NextSeq500 High Output: 1x 75 bp
Quality control on the sequence reads from the raw FASTQ files was done with FastQC (v0.11.4)
Reads were aligned to the reference genome fasta (Homo_sapiens.GRCh37) using star (v2.4.2a) aligner
Readgroup were added using Picard (v1.141)
Readcounts were generated using the HTSeq-count (v0.6.1) with the Homo_sapiens.GRCh37.74.gtf gtf file as annotation
Normalization was done using R-packages DeSeq (v1.18.0) and edgeR (v3.8.6)
Genome_build: Homo_sapiens.GRCh37
Supplementary_files_format_and_content: tab-delimited text files include raw reads count for each sample
Supplementary_files_format_and_content: tab-delimited text file with size factor normalized (DESeq) read counts of all samples

source_name: Colorectal cancer

extract_protocol:
In brief, biopsies were homogenized using the tissue homogenizing CKMix ceramic beads (Precellys, P000918-LYSK0-A) and subsequently processed for RNA isolation using the column-based RNA isolation (RNeasy Kit, Qiagen). RNA yield and quality were evaluated using spectrometry (Nanodrop 2000/200c, Thermo Fisher) and the BioAnalyzer (2100 Bioanalyzer, Agilent), respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Colorectal cancer

tag: subject id

tag: rf cms4 probability

tag: imatinib

value: Pre-imatinib


title: NC_1

value: MDA-MB-231 cells


title: H95_86616095024_v1: Newly diagnosed MM_123

city: Rotterdam

first: Mark

last: van Duin

address: Wytemaweg 80

institute: Erasmus MC

data_processing:
Paired end sequencing was performed on an Illumina NovaSeq 6000 using 101 cycles for each mate.
Fastq files were constructed using bcl2fastq (v2.20.0.422).
Illumina universal adapters   were removed using trim_galore (v0.4.4).
Pseudo counts were measured on the trimmed Fastq files using  salmon (v1.3.0) using the default settings.
Salmon performed according to reference DOI:10.1038/NMETH.4197
Genome_build: GRCh37
Supplementary_files_format_and_content: Salmon, read counts

source_name: bone marrow aspirate

growth_protocol: primary human tissue

extract_protocol:
RNeasy
RNA Seq libraries were generated with the mRNA HyperPrep Kit (KAPA, catalog number 08105952001/KK8544), according to manufacturer’s instructions.

value: multiple myleoma

tag: gender

tag: age

value: bone marrow aspirate


title: 6039_HP_t0w

source_name: Adipose tissue biopsy from subject 6039, before treatment with a 25% Caloric Restriction diet with High Protein content (t0w)

tag: subjectid

value: high

value: Female

tag: date of birth (dd-mm-yyyy)

tag: screening bmi (kg/m2)

tag: screening body fat percentage (fm)

tag: screening glucose (mmol/l)


title: ImPACCT-02-004-Biopsy-A-RNA

tag: disease state


title: ImPACCT-02-004-Biopsy-B-RNA


title: Anti-PD-1 Responder

city: Pittsburgh

first: Bowen

last: Dong

state: Pennsylvania

address: 4200 Fifth Ave, Pittsburgh, PA 15260

institute: University of Pittsburgh

description: single cell RNA

data_processing:
cellranger was used to generate the fastq files using mkfastq
cellranger was used to generate the barcode and gene expression count matrix using mouse mm10 reference genome
Seurat R package was used for downstream analysis.
Assembly: mm10
Supplementary files format and content: gene expression count matrix

source_name: bladder urothelial cancer cells

growth_protocol: Tumor dissociated cells (2 X 10 6) from TKO organoid in 50% Matrigel/medium were subcutaneously injected into the right flank of ~8 weeks old male C57 BL/6J mice from Jackson Lab

extract_protocol:
Tumor from each group were dissected and processed for single cell dissociation. Duplicates from same group were mixed and sequenced as one sample.
Single cell libraries are generated using the 10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1.   The resulting libraries are evaluated on D1000 screentape using a TapeStation 4200 (Agilent Technologies), and quantitated using Kapa Biosystems qPCR quantitation kit for Illumina. The resulting pool is then loaded into the appropriate NovaSeq Reagent cartridge and sequenced on a NovaSeq6000 following the manufacturer’s recommended protocol (Illumina Inc.)

treatment_protocol: Mice group was treated for 2 weeks with an anti-PD1 antibody (BioXcell, RMP1-14, 200 μg, intraperitoneally twice weekly, Catalog: BP0146) or a control IgG (BioXcell, 2A3, 200 μg, intraperitoneally twice weekly, Catalog: BP0089).

tag: tissue

value: bladder urothelial carcinoma xenograft

tag: tumor cell genotype

value: Trp53, Rb1, PTEN mutations

tag: host strain

value: C57 BL/6J


title: Anti-PD-1 Non-responder

description: single cell RNA


title: H95_65014493851_v1: Newly diagnosed MM_122


title: Control IgG2a

description: single cell RNA

value: Control IgG2a


title: si287_3

city: Guangzhou

first: Lan

last: Yang

state: Guangdong

address: 1838 North Guangzhou Street

department: Department of Plastic and Aesthetic Surgery

institute: Nanfang Hospital of Southern Medical University

data_processing:
Illumina Casava software was used for basecalling.
Cutadapt software was used for data filtering. Data filtering steps required at least 10 bp Overlap, and 20% base false rate was permitted.
HISAT2 software (http://ccb.jhu.edu/software/hisat2/index.shtml), with the parameter of microexon-search and library-type=fr-firststrand, was used for reads alignment.
Genome_build: GRCh38.98
Supplementary_files_format_and_content: Processed_Data_Matrix.xlsx includes raw gene counts and FPKM values for every gene and every sample.

source_name: THP1 cells

growth_protocol: THP1 cells were cultured in RPMI-1640 medium (Gibco, Gaithersburg, MD, USA) with 10% fetal bovine serum (FBS, Gibco, USA) and 1% penicillin/streptomycin (Gibco, USA) at 37°C in a 5% CO2 humidified incubator.

extract_protocol:
1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes to construct cDNA library which was paired-end (PE) sequenced using Illumina sequencing platforms based on Next-Generation Sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: THP1 cells were induced into macrophages with 50 ng/ml phorbol 12-myristate 13-acetate (PMA) stimulation for 48 h. Then, the cells were treated with 200 nM NC or hsa_circ_0004287 siRNA (GenePharma, Shanghai, China) with Lipofectamine RNAiMAX reagent (Invitrogen, USA) for 48 h and subjected to 200 ng/mL LPS stimulation for 3 h.

tag: cell line

value: 50 ng/ml PMA, 48 h

value: THP1-derived macrophages

tag: sirna

value: 200 nM hsa_circ_0004287 siRNA, 48 h

tag: stimulation

value: 200 ng/ml LPS, 3 h


title: 6053_HP_t12w

source_name: Adipose tissue biopsy from subject 6053, after treatment with a 25% Caloric Restriction diet with High Protein content (t12w)

tag: protein content restricted diet

tag: time of sampling (before/after)

value: after

tag: time of sampling (wk)

tag: sexe

value: Male


title: ImPACCT-01-058-Biopsy-C-RNA

value: Colorectal cancer

tag: subject id

tag: rf cms4 probability

tag: imatinib


title: HUVEC-1_S11

tag: cell type

value: Umbilical vein endothelial cells

tag: treatment

value: Control


title: ImPACCT-01-058-Biopsy-B-RNA

value: Pre-imatinib


title: si287_2


title: ImPACCT-01-058-Biopsy-A-RNA


title: si287_1


title: Normal female WT-1

data_processing:
Fastq files generated with CASAVA
Sequenced reads were mapped to GRCm38 reference GENCODE annotation M22 using STAR aligner
Read counts are obtained using Subread
Assembly: GRCm38
Supplementary files format and content: Raw counts csv file format

source_name: bladder normal urothelial cells

growth_protocol: Tumor dissociated cells (2 X 10 6) from TKO organoid in 50% Matrigel/medium were orthotopically injected into bladder wall. 2 X 10 6 MB49 cells or TKO cells were intravesically injected into bladder luman by catheter, which bladder was pretreated with 0.1% poly-L-lysine. Normal male bladder cell were directly scratched from dissected bladder tissue.

extract_protocol:
Tumor were dissected and frozen on dry ice, and the purification of total and small RNAs is prepared using the miRNeasy mini kit (Qiagen).  10-50 mg of frozen tissue samples, with the addition of 700 ul of Qiazol reagent, are  homogenized using Navy Rhino tubes in a Bullet Blender Homogenizer (Next Advance) for 5 minutes. After chloroform extraction, The sample is then applied to the miRNeasy Mini spin column. On-column DNAse digestion is also performed to remove any residual genomic DNA contamination. Quantitative assessment of the purified total RNA is then accomplished by using a Qubit Broad Range RNA kit (Thermofisher), and concentration is determined by Ribogreen fluorescent binding to isolated RNA.
The sequencing libraries are prepared with the RNA HyperPrep Kit with RiboErase (HMR)kit (Roche Sequencing Solutions), from 500ng total RNA, following the manufacturer’s instructions. The resulting pool is then loaded into the appropriate NovaSeq Reagent cartridge, as determined by the number of sequencing cycles desired, and sequenced on a NovaSeq6000 following the manufacturer’s recommended protocol (Illumina Inc.).

value: bladder mucosa

tag: strain


title: Normal female WT-2


title: ImPACCT-01-013-Biopsy-C-RNA

tag: disease state


title: TKO-ortho-2

tag: tissue

value: bladder orthotopic tumor


title: ImPACCT-01-013-Biopsy-B-RNA


title: NC_3

value: 200 nM NC siRNA, 48 h


title: TKO-ortho-1


title: NC_2


title: ImPACCT-01-013-Biopsy-A-RNA


title: TKO-intra-2

value: bladder intravesical tumor


title: NC_1


title: ImPACCT-01-006-Biopsy-C-RNA


title: TKO-intra-1


title: ImPACCT-01-006-Biopsy-B-RNA


title: H95_33221184711_v1: Newly diagnosed MM_121

value: bone marrow aspirate

tag: gender

value: Female

tag: age

value: multiple myleoma


title: MB49-intra-3

value: C57 BL/6J


title: 6053_HP_t0w

source_name: Adipose tissue biopsy from subject 6053, before treatment with a 25% Caloric Restriction diet with High Protein content (t0w)

tag: subjectid

value: high

value: before

value: t=0 (baseline)

tag: date of birth (dd-mm-yyyy)

tag: screening bmi (kg/m2)

tag: screening body fat percentage (fm)

tag: screening glucose (mmol/l)


title: Mono-enriched-PBMC_sPg_3hr_subj6

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.28.2).

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with 4 µg/ml sPg, subject 6

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Leukocyte cones (n=7) were purchased from the National Blood Service (Cambridge, UK) and peripheral blood mononuclear cells (PBMC) isolated by Lymphoprep (Axis Shield Diagnostics Ltd, Scotland) density gradient centrifugation. PBMC were further enriched for monocytes by a second density gradient centrifugation over Percoll (Sigma-Aldrich Ltd, UK) density medium, and were re-suspended at 1.10^6 cells/ml in RPMI-1640 medium (Sigma-Aldrich), supplemented with 10 % Fetal Calf Serum (PAA Laboratories Ltd, UK), 2 mM L-glutamine (Sigma-Aldrich), 100 U/ml penicillin (Sigma-Aldrich) and 100 μg/ml streptomycin (Sigma-Aldrich).

extract_protocol: Total RNA was purified using an Abi Prism 6100 Nucleic Acid PrepStation (Applied Biosystems, UK) following manufacturer’s instructions and including a wash step with AbsoluteRNA wash solution (Applied Biosystems), again as per manufacturer’s instructions. On occasions and to increase nucleotide concentration, a second purification procedure was performed using RNeasy MinEluteTM Cleanup Kit (Qiagen Ltd, UK) according to manufacturer’s protocol. Samples were stored at -80 °C until further microarray processing.

treatment_protocol: Culture and stimulation of monocyte-enriched PBMC were performed in sterile 15 ml Falcon tubes (Starlab UK Ltd, UK) at 1.10^6 cells/ml and at 37 °C/ 5 % CO2. Freshly isolated monocyte-enriched PBMC were rested overnight, following which they were replenished with Dulbecco’s Modified Eagle’s Medium (Sigma-Aldrich), supplemented with 10 % Fetal Calf Serum, 2 mM L-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin. 5.10^6 cells were then stimulated for 3 hr with vehicle, synthetic AMCP nanoparticles or with a final concentration of 4 µg/ml soluble peptidoglycan (from Escherichia coli; Source BioScience plc, UK), alone or trapped within synthetic AMCP (AMCP/sPg). After challenge, stimulants were removed and cells washed twice in Hank’s Balanced Salt Solution (Sigma-Aldrich) before being lysed with Nucleic Acid Purification Solution (Life Technologies Ltd, UK) and stored at -80 °C prior to RNA isolation.

value: blood

value: cultured monocyte-enriched peripheral blood mononuclear cells

value: 4 µg/ml sPg (Escherichia coli, soluble, purified)


title: MB49-intra-2


title: 6076_SP_t0w

source_name: Adipose tissue biopsy from subject 6076, before treatment with a 25% Caloric Restriction diet with Normal Protein content (t0w)

tag: protein content restricted diet

value: normal

tag: time of sampling (before/after)

tag: time of sampling (wk)

value: Male


title: H95_81233173985_v1: Newly diagnosed MM_120


title: H95_37926530551_v1: Newly diagnosed MM_119


title: MB49-intra-1


title: Mono-enriched-PBMC_sPg_3hr_subj3

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with 4 µg/ml sPg, subject 3

tag: subject id


title: ImPACCT-01-005-Biopsy-C-RNA

value: Colorectal cancer

tag: rf cms4 probability

tag: imatinib

value: Pre-imatinib


title: Mono-enriched-PBMC_sPg_3hr_subj4

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with 4 µg/ml sPg, subject 4

tag: cell type

tag: treatment


title: H95_54317412108_v1: Newly diagnosed MM_118

tag: disease state


title: ImPACCT-01-005-Biopsy-B-RNA


title: Mono-enriched-PBMC_AMCPsPg_3hr_subj7

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with synthetic AMCP/sPg nanoparticles, subject 7

tag: tissue


title: Mono-enriched-PBMC_sPg_3hr_subj7

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with 4 µg/ml sPg, subject 7


title: Mono-enriched-PBMC_sPg_3hr_subj5

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with 4 µg/ml sPg, subject 5


title: Mono-enriched-PBMC_sPg_3hr_subj2

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with 4 µg/ml sPg, subject 2


title: H95_40862784553_v1: Newly diagnosed MM_117

tag: gender


title: Mono-enriched-PBMC_sPg_3hr_subj1

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with 4 µg/ml sPg, subject 1


title: Mono-enriched-PBMC_AMCPsPg_3hr_subj5

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with synthetic AMCP/sPg nanoparticles, subject 5

value: synthetic AMCP/sPg nanoparticles


title: cKO_LSK3

city: Chengdu

first: Quanming

last: An

address: 26 Huacai road,Chenghua District

institute: Institute of Blood Transfusion, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS & PUMC)

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary files format and content: The gene expression raw counts were provided in the Myh9_gene_data_fkpm.csv file.

source_name: LSK cells from Myh9fl/fl;Mx1-cre mice bone marrow 4 days after first poly I:C injection

growth_protocol: Mice were bred in SPF level experimental animal house. Genotyping were performed between 4-5 weeks old. Myh9fl/fl;Mx1-cre and littermate Myh9;no cre were used for experiment.

extract_protocol:
4 days after first poly I:C injection, 100,000 of LSK cells from Myh9fl/fl;Mx1-cre or littermate Myh9;no cre mice were sorted separately into 500 µL DPBS-BSA buffer (0.5% BSA) using a 1.5 mL Eppendorf tube. After a single wash, RNA was harvested using Trizol reagent. Illumina Truseq RNA Sample Prep kit (Cat#FC-122-1001) was used with 1ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequecing using standard Illumina protocols.

treatment_protocol: Two doses of 5mg/kg body weight poly I:C were injected into Myh9fl/fl;Mx1-cre and littermate Myh9;no cre mice every other day. LSK cells were sorted 4 days after first injection.

value: bone marrow cells

tag: strain

tag: genotype


title: cKO_LSK2


title: ImPACCT-01-005-Biopsy-E-RNA

source_name: Colorectal cancer


title: ImPACCT-01-006-Biopsy-A-RNA


title: Mono-enriched-PBMC_AMCPsPg_3hr_subj6

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with synthetic AMCP/sPg nanoparticles, subject 6


title: RS_3

city: Beijing

source_name: MDA-MB-231 cells

tag: cell line

value: MDA-MB-231 cells

value: Breast cancer tissue

value: Treated with RSL3


title: ImPACCT-02-004-III-2-RNA

value: Post-imatinib


title: H95_79165043271_v1: Newly diagnosed MM_115

source_name: bone marrow aspirate

value: bone marrow aspirate

tag: age

value: multiple myleoma


title: cKO_LSK1


title: Mono-enriched-PBMC_AMCPsPg_3hr_subj3

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with synthetic AMCP/sPg nanoparticles, subject 3


title: ImPACCT-02-004-II-2-RNA


title: CTRL_LSK3

source_name: LSK cells from Myh9fl/fl;no cre mice bone marrow 4 days after first poly I:C injection

value: Myh9fl/fl;no cre


title: Mono-enriched-PBMC_AMCPsPg_3hr_subj1

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with synthetic AMCP/sPg nanoparticles, subject 1


title: CTRL_LSK2


title: Mono-enriched-PBMC_AMCPsPg_3hr_subj4

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with synthetic AMCP/sPg nanoparticles, subject 4


title: H95_46043575096_v1: Newly diagnosed MM_114


title: CTRL_LSK1


title: ImPACCT-01-058-II-1-RNA


title: H95_27354837176_v1: Newly diagnosed MM_116


title: H95_42724425741_v1: Newly diagnosed MM_111

value: Female


title: ImPACCT-01-058-I-2-RNA


title: Mono-enriched-PBMC_AMCP_3hr_subj7

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with synthetic AMCP nanoparticles, subject 7

value: blood


title: H95_28299419011_v1: Newly diagnosed MM_110


title: ImPACCT-01-013-III-2-RNA


title: Mono-enriched-PBMC_AMCPsPg_3hr_subj2

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with synthetic AMCP/sPg nanoparticles, subject 2

value: cultured monocyte-enriched peripheral blood mononuclear cells


title: ImPACCT-01-058-III-1-RNA


title: ImPACCT-01-013-II-2-RNA


title: H95_75510431627_v1: Newly diagnosed MM_112


title: Mono-enriched-PBMC_AMCP_3hr_subj5

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with synthetic AMCP nanoparticles, subject 5

value: synthetic AMCP nanoparticles


title: Mono-enriched-PBMC_AMCP_3hr_subj6

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with synthetic AMCP nanoparticles, subject 6