title: sgRNA_ANTIPRO3_SS4_1 [ANTIPRO3_SS4_1-280122890]

description: NO capture sequencing data


title: sgRNA_AC083843_5 [AC083843_5_SS4-280084739]

status: Public on Dec 05 2021

type: SRA

city: Gent

first: Eric

middle: James

last: de Bony de Lavergne

state: <None>

address: 10 corneel heymanslaan, UZ Campus, building Block B, Entry 36

department: Biomolecular Medecine

country: Belgium

institute: University of Ghent

description: NO capture sequencing data

library_source: transcriptomic

data_processing:
FastQC (v0.11.8) was used for data quality control
polyA read-through and low-quality reads were removed via bbduk (BBMap v38.26)
Reads were mapped with STAR (v2.6.0c) against the hg38 reference genome, and gene counts were determined via HTSeq (v.0.11.0)
Genome_build: hg38
Supplementary_files_format_and_content: count table

molecule: total RNA

organism: Homo sapiens

source_name: HEK293T cell line

growth_protocol: 12,000 cells per well were seeded in 96-well plates (Corning, cat. no. 3596) in 180 µl of RPMI cell culture medium with 10% fetal calf serum

extract_protocol:
72 hours after transfection, cells were lysed with SingleShot lysis buffer
Quantseq (Lexogen)

treatment_protocol: 24 hours after seeding, sgRNAs were transfected with lipofectamine reagent CRISPRMAX

tag: cell line

tag: modification

tag: treatment

value: sgRNA transfected


title: sgRNA_AC083843_6 [AC083843_6_SS4-280123892]

description: NO capture sequencing data


title: pC2_CLSY2-3xF_ins2_smRNA-seq

city: La Jolla

first: Julie

middle: Ann

last: Law

state: CA

address: 10010 North Torrey Pines Rd

department: PLANT MOLECULAR AND CELLULAR BIOLOGY LABORATORY

country: USA

institute: The Salk Institute for Biological Studies

data_processing:
Illumina Casava software used for basecalling and demultiplexing.
Read Filtering, Mapping, and cluster calling: The adapters were removed from the de-multiplexed reads using cutadapt (v1.9.1) and trimmed reads longer that 15nt were mapped to the TAIR10 genome using ShortStack (v3.8.1) with the following options: --mismatches 1 and either --mmap f, to include multi-mapping reads, or --mmap n, to include only unique mapping reads. Only perfectly matched read or reads with a single 3’ mismatch were used to call smRNA clusters using ShortStack with the --mincov 20, --pad 100, --dicermin 21 and dicermax 24 options, to generate Tag Directories using the using the makeTagDirectory script from the HOMER with the -format sam -mis 1 and -keepAll options, and to make genome browser tracks specifically for the 24nt sized smRNAs using the makeUCSCfile script from HOMER with the -fragLength 24 and -norm 10000000 options.
TAIR10
Supplementary_files_format_and_content: bedGraph file, including header and chr#, start position, end position and normalized value (rp10M).

organism: Arabidopsis thaliana

source_name: stage 12 and younger flower buds (Fl)

growth_protocol: Growth conditions and tissue collection for 15 day old aerial rosettes (Ar) and 25 day old leaves (Lv) for all genotypes were as follows: seeds were sterilized with bleach and plated on half strength Linsmaier and Skoog medium (1/2 LS) supplemented with 1% agar. After three days stratification in the dark at 4℃, plants were grown in the Percival growth chamber (GCU-36L5) under 16h-light and 8h-dark cycle at 22℃ for 7 days and then were transplanted onto soil in Salk’s green house with long day conditions. At day 15 and day 25 of total growth, aerial rosette tissue (whole seedling without roots) or the first and second true leaves (without petioles) were collected from~40 plants as the Ar and Lv samples, respectively, immediately frozen in liquid nitrogen, and kept at -80°C until use. Growth conditions and tissue collection for mature, unfertilized ovules (Ov) were as follows: seeds were grown from soil in Salk’s greenhouse with long day conditions and un-opened flower buds (stage 10-12) were dissected to obtain carpels using a tweezer and then fixed on a double-side tape on a glass slide. Subsequently, carpels were dissected under dissection microscope using a needle and ovules were collected with the vacuum-based micro-aspiration device as detailed below. After collection, ovules for RNA extraction were quickly mixed with 100 µL trizol (Invitrogen, Cat# 15596018), flash frozen in liquid nitrogen and preserved at -80℃ until use, while ovules for DNA preparation were preserved in the same way without trizol. For each genotype, > 300 carpels were dissected and over 10,000 ovules were collected.

extract_protocol:
Total RNAs were isolated using Trizol reagent (Life Tech, Cat# 15596018) following the manual and dissolved in 250μL RNase-free water. 2.0 µg of total RNA from Ar and Lv tissues, or ~0.5ug of total RNA from Ov, were used for smRNA enrichment through a polyethylene glycol (PEG) precipitation step. One volume of a 20% PEG 8000/2M NaCl solution was added to each RNA sample, mixed well and kept on ice for more than 30 minutes (min) and then centrifuged at 13,000rpm for 15min at 4°C. The supernatant, containing the small RNAs, was collected and precipitated with 1 volume of cold isopropanol, mixed and incubated on ice for 30min. Then the small RNA samples were recovered by centrifuged at 13,000rpm for 30min at 4°C. The resulting small RNA samples were run on 15% polyacrylamide-8M urea gels and performed size-selection of fragments from 17-29 nucleotide (nt) following the ZR-small RNA ladder (zymo research, Cat# R1090). The small RNAs in the gels were recovered by incubating with 0.3M NaCl overnight, filtering the gels and add 2.5 volumes of 100% ethanol and 3μL of glycogen for precipitation over 2 hours (h) at -80°C.
The small RNAs were used for library preparation with the NEBnext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Cat# E7300) following the user’s manual. The final library products were further purified using an 8% polyacrylamide gel to excise 130-160nt products relative to the pBR322 DNA-MspI Digest ladder (New England Biolabs, Cat# E7323AA). The purified libraries were pooled and sequenced (single end 50 bp, SE50) on a HiSeq 2500 machine (Illumina).

tag: ecotype

value: Columbia

tag: tissues

value: stage 12 and younger flower buds (Fl)

tag: genotype

value: pC2::CLSY2-3xF clsy2-2


title: sgRNA_AC083843_4 [AC083843_4_SS4-280091746]

description: NO capture sequencing data


title: pC2_3xF-CLSY2_ins1_smRNA-seq

value: pC2::3xF-CLSY2 clsy2-2


title: sgRNA_AC083843_3 [AC083843_3_SS4-280081719]

description: NO capture sequencing data


title: pC3_3xF-CLSY3_ins2_smRNA-seq

value: pC3::3xF-CLSY3 clsy3-1


title: clsy2-2_smRNA-seq


title: PSP advanced 6

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: PSP advanced stage

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

extract_protocol: RNA samples were extracted from cerebrospinal fluid using 3D-Gene extraction reagent from liquid sample(Toray Industries Inc., Tokyo, Japan).

tag: subject status

value: PSP advanced stage

tag: age

tag: Sex

value: Male

tag: tissue/cell type

value: cerebrospinal fluid


title: sgRNA_AC083843_10 [AC083843_10_SS4-280081718]

description: NO capture sequencing data


title: PSP advanced 5


title: PSP advanced   1


title: PSP advanced  4


title: PSP advanced  3


title: PSP advanced   2


title: i48-Healthy3-Random-4000_S24

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

data_processing:
HiSat2 (v2.0.5) and FeatureCounts (v1.6.3)
Genome_build: hg19
Supplementary_files_format_and_content: healthy_counts.tsv.gz and diseased_counts.tsv.gz- a compressed tsv file. A gene-count matrix with columns for samples and rows for genes. The values represent the gene abundance count for the given sample

molecule: polyA RNA

source_name: Healthy tendon fibroblasts (P2 primary cells)

extract_protocol:
Cells were lifted from scaffolds with Trypsin at 37oc for 5 mins. Cell suspension was then centrifuged for 5 minutes at 1500rpm, the supernatant was removed, and the cell pellets were resuspended in 300ul of Trizol and stored at -80C prior to RNA extraction. RNA was extracted using Direct-zol RNA Miniprep kits (Zymo Research, USA), following the manufacturer’s instructions. RNA was quantified using a NanoDropTM 2000 spectrophotometer and standardised to 100ng of RNA in 50ul of nuclease free water.
Library prep was performed using Nebnext Ultra II directional RNA library prep kit for Illumina with Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, USA), following the manufacturer’s instructions

treatment_protocol: Primary healthy tendon fibroblasts [Hamstring derived] and primary diseased tendon fibroblasts [Massive rotator cuff tears derived] at passage 2 (P2) were cultured on 8 scaffold variants for 7 days.  Initial seeding density was ~40,000 cells/cm2.  All conditions were performed in biological triplicate (n=3 donors).

tag: disease state

value: Healthy

tag: scaffold alignment

value: Random

tag: scaffold fiber diameter (nm)


title: i47-Healthy3-Random-2000_S1


title: pC1_3xF-CLSY1_ins2_smRNA-seq

value: pC1::3xF-CLSY1 clsy1-7


title: PSP early 5

source_name: PSP early stage

value: PSP early stage

value: Female


title: PSP early 3


title: PSP early 4


title: nrpd1-4_pol-iv_rep1_smRNA-seq


title: 3M-052_DCs_D28 4

city: Stanford

first: Madeleine

last: Scott

address: 729 Lagunita Dr

institute: Stanford

data_processing:
Cellranger 3.1.0
Seurat 3.6.3 used for all downstream processing
Genome_build: mm10
Supplementary_files_format_and_content: gene expression matrices (mtx)

organism: Mus musculus

source_name: lymph node

extract_protocol:
PBMC isolation directly after blood sample collection
10x Single Cell 3' v3

tag: strain

tag: tissue

value: lymph node

tag: day

tag: flow sort category

value: DCs


title: i46-Healthy3-Random-1000_S6


title: Control 8

source_name: Control

value: Control


title: sgRNA_AC083843_2 [AC083843_2_SS4-280121908]

description: NO capture sequencing data

tag: cell line

value: sgRNA transfected


title: sgRNA_AC083843_1 [AC083843_1_SS4-280084738]

description: NO capture sequencing data

tag: modification


title: pC1_3xF-CLSY1_ins1_smRNA-seq

value: Columbia


title: PSP early 1


title: Control 7


title: Control 6


title: PSP early 2


title: i45-Healthy3-Random-300_S19


title: clsy1-7_smRNA-seq

value: stage 12 and younger flower buds (Fl)


title: i44-Healthy3-Aligned-4000_S13

value: Aligned


title: Control 4


title: Control 3


title: i42-Healthy3-Aligned-1000_S7


title: Erythroblast, C2

city: Jinan

first: Zhiyuan

last: Lu

state: Shandong

address: 6699 Qingdao road

department: School of Pharmaceutical Sciences & Institute of Materia Medica

country: China

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)  by (1) Removing reads  containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base  quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown  base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored  in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2(v2.0.4) .
Bowtie2 (v2.2.5)  was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12)
Differential expression was performed using DESeq2 (version 1.4.5).
Genome_build: GCF_000001635.26, GRCm38.p6
Supplementary_files_format_and_content: CHO-C_RawReadCounts.txt, CHO-C_NormalizedReadCounts.txt

source_name: Erythroblast

growth_protocol: TER119-negative fetal liver erythroblasts were purified and cultured in Epo containing medium

extract_protocol:
Total RNA was extracted using the TRIzol reagent. RNA quality and quantity were determined using a Nano Drop and Agilent 2100 bioanalyzer
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end  repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases  reads were generated on DNBSEQ platform.

treatment_protocol: Treated with or without cholesterol (40 μM) for 30 h

tag: treatment

value: untreated

value: Fetal liver

tag: cell type

value: Erythroblast


title: Erythroblast, C3


title: Erythroblast, CHO3

value: cholesterol for 30 hours


title: Control 2

value: cerebrospinal fluid


title: Erythroblast, CHO1


title: WT bovine fetal fibroblast cell-rep2

city: Hohhot

first: xueqiao

last: wang

address: No.24，zhaojun Street

institute: Inner Mongolia University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Bos taurus

source_name: fetal fibroblast cell

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 50-60 days after pregnancy

value: Primary culture to obtain fetal fibroblasts

value: wild-type


title: Erythroblast, C1


title: i41-Healthy3-Aligned-300_S15

value: Healthy


title: i40-Healthy2-Random-4000_S14

value: Random


title: WT bovine fetal fibroblast cell-rep3


title: Control 1

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Global normalization was applied to all microarray data.

value: Male


title: WT bovine fetal fibroblast cell-rep1


title: Control 5


title: i39-Healthy2-Random-2000_S9


title: Kidney, P0

city: Kuamomoto

first: Shunsuke

last: Tanigawa

state: Kumamoto

address: 2-2-1 Chuou-ku honjyo

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

data_processing:
Sequencing and making Fastq files by illumina HiSeq X Ten. Read length: Read1:26, Index read 1(i7):8, Read2:98.
Cell Ranger v2.0.0 software was used to perform alignment and gene and UMI counting each cell.
Genome_build: GRCm38_93
Supplementary_files_format_and_content: Cell Ranger output files:  barcodes.tsv.gz, features.tsv.gz, matrix.mtx

source_name: Kidney

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium. Reverse transcription was performed in droplet.
library construction was performed by using Chromium Single Cell 3ʹ Reagent Kits v2.

value: Kidney

value: Wild type


title: ES cell-derived kidney organoids, iSP1

source_name: ES cell-derived kidney organoids

value: ES cell-derived kidney organoids


title: i36-Healthy2-Aligned-4000_S8


title: i37-Healthy2-Random-300_S17


title: i38-Healthy2-Random-1000_S10


title: fat-1 transgenic bovine fetal fibroblast cell-rep3

value: fat-1 transgenic


title: fat-1 transgenic bovine fetal fibroblast cell-rep2


title: Erythroblast, CHO2


title: i43-Healthy3-Aligned-2000_S4


title: ES cell-derived kidney organoids, ndiS1


title: ago3 - Alternaria alternata (AC) [ago3_Alternaria_AC_87]

city: Irapuato

first: Alfredo

last: Herrera Estrella

state: Guanajuato

address: Libr. Norte carr. León, Km 9.6

department: LANGEBIO

country: Mexico

institute: CINVESTAV

data_processing:
Preprocessing with FastQC and Trimmomatic
Alingment to T. atroviride genome with Hisat2
Normalization
Differential expresion analysis with EdgeR and Limma packages
Genome_build: Trichoderma atroviride v2.0 (https://mycocosm.jgi.doe.gov/Triat2/Triat2.home.html)
Supplementary_files_format_and_content: Gene matrix in csv format

organism: Trichoderma atroviride

source_name: ago3 - Alternaria alternata (AC)

growth_protocol: PDA medium in Petri dishes, complete darkness at 27°C

extract_protocol:
TRIzol RNA extraction
Illumina TruSeq RNA sample prep V2

treatment_protocol: Mycelium frozen in liquid nitrogen

value: mutant

tag: time point

value: After contact

value: Mycelium

tag: replicate

value: Replicate 3


title: dcr2 control [dcr2_control_89]

source_name: dcr2 control

tag: genotype

value: Control


title: WT control [WT_control_88]

source_name: WT control


title: ago3 - Alternaria alternata (BC) [ago3_Alternaria_BC_85]

source_name: ago3 - Alternaria alternata (BC)

value: Before contact


title: ago3 control [ago3_control_90]

source_name: ago3 control


title: Kidney, E11.5

value: ICR


title: Kidney, E15.5


title: ago3 - R. solani AG5 (AC) [dcr2_Alternaria_AC_84]

source_name: ago3 - R. solani AG5 (AC)


title: ago3 - Alternaria alternata (C) [ago3_Alternaria_C_86]

source_name: ago3 - Alternaria alternata (C)

value: At the contact


title: i34-Healthy2-Aligned-1000_S11

value: Aligned


title: i35-Healthy2-Aligned-2000_S2


title: fat-1 transgenic bovine fetal fibroblast cell-rep1

tag: age

value: 50-60 days after pregnancy

value: Primary culture to obtain fetal fibroblasts


title: ago3 - R. solani AG5 (C) [dcr2_Alternaria_C_83]

source_name: ago3 - R. solani AG5 (C)


title: Kidney, E9.5


title: AdCre_2

city: Nashville

first: Masoud

last: Ghamari-Langroudi

state: TN

address: 8435 MRB #IV, 2215 Garland ave

institute: Vanderbilt University

description: male diet -induced obese (20 weeks on HFD)

data_processing:
mRNA library preparation (poly A enrichment)
NovaSeq PE150
Quantification Analysis

extract_protocol: Total RNA was extracted in Trizol reagent, DNase treated and  cleaned using Rneasy columns (Qiagen)

value: epididymal white adipose tissue (eWAT)

value: 28 weeks old

value: adiponectin-Cre controls (AdCre)

value: vehicle


title: AdCre_1


title: AdCre_3


title: i32-Healthy1-Random-4000_S3

value: Healthy

value: Random


title: AdKO_3

value: adipose tissue specific HDAC6 KO mice (AdKO)


title: i33-Healthy2-Aligned-300_S5


title: AdCre_4


title: ago3 - R. solani AG5 (BC) [dcr2_Alternaria_BC_82]

source_name: ago3 - R. solani AG5 (BC)

value: mutant


title: AdKO_4


title: sgRNA_ANTIPRO3_SS1_2 [ANTIPRO3_SS1bis_2-280086704]

description: NO capture sequencing data

source_name: HEK293T cell line

value: sgRNA transfected


title: i31-Healthy1-Random-2000_S20

source_name: Healthy tendon fibroblasts (P2 primary cells)


title: i30-Healthy1-Random-1000_S21


title: AdKO_1


title: AdKO_2


title: TubA_3

value: 25 weeks old

value: HDAC6 global knockout

value: tubastatin A-HCl


title: ago3 - R. solani AG2 (AC) [WT_Alternaria_AC_81]

source_name: ago3 - R. solani AG2 (AC)

value: After contact

value: Mycelium

value: Replicate 3


title: TubA_4


title: Human GBM Tumor sample 1 [F3pos_CD44neg_VII]

city: New York

first: Mungunsarnai

last: Ganbold

state: NYC

address: 417 East 68st

department: Brain Tumor Center

institute: MSKCC

description:
SMARTerAmpSeq
humanGBM_bulkRNA_F3sort.csv

data_processing:
All single-cell 3' RNA-seq data were processed from raw fastq files to count matrices with SEQC (see https://github.com/dpeerlab/seqc)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: patient derived xenograft glioblastoma cells

extract_protocol:
Mouse brain was dissected, and tumor tissues were dissociated into single cells and FACS sorted for live cells. Human PDX tumor cells were further processed on ChromiumTM instrument (10X Genomics) after mouse cell depletion.
RNA libraries were amplified with SMARTerAmpSeq kit for buk RNA sequencing, or  prepared following the manual “Single Cell 3’ Reagent Kits v2 User Guide” (CG00052 Rev E) provided by the 10X Genomics for single cell RNA sequencing.

tag: tumor grade

value: glioblastoma

value: untreated


title: ago3 - R. solani AG2 (C) [WT_Alternaria_C_80]

source_name: ago3 - R. solani AG2 (C)

value: At the contact


title: i29-Healthy1-Random-300_S22


title: dcr2 - Alternaria alternata (AC) [ago3_AG5_AC_78]

source_name: dcr2 - Alternaria alternata (AC)


title: ago3 - R. solani AG2 (BC) [WT_Alternaria_BC_79]

source_name: ago3 - R. solani AG2 (BC)

value: Before contact


title: TubA_2

value: epididymal white adipose tissue (eWAT)


title: Veh_4

value: vehicle


title: sgRNA_ANTIPRO2_SS4_1 [ANTIPRO2_SS4_1-280088748]

description: NO capture sequencing data


title: Veh_3


title: i28-Healthy1-Aligned-4000_S18

value: Healthy

value: Aligned


title: dcr2 - Alternaria alternata (C) [ago3_AG5_C_77]

source_name: dcr2 - Alternaria alternata (C)


title: Veh_2


title: Veh_1


title: dcr2 - Alternaria alternata (BC) [ago3_AG5_BC_76]

source_name: dcr2 - Alternaria alternata (BC)


title: i26-Healthy1-Aligned-1000_S23


title: dcr2 - R. solani AG5 (AC) [dcr2_AG5_AC_75]

source_name: dcr2 - R. solani AG5 (AC)


title: i27-Healthy1-Aligned-2000_S12


title: i25-Healthy1-Aligned-300_S16


title: T-WT-5

city: Milan

first: Marco

last: Filipuzzi

address: Via Giuseppe Ripamonti, 435

country: Italy

institute: IEO

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_quality_trimmer -Q33 -t 20 -l 10 -v -i ; fastq_masker -Q33 -q 20 -r -N -v -i
alignment with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-inds --library-type fr-unstranded -G gtffile reffile fastqfile
removing duplicate reads: samtools rmdup -S bamfile
quantifying transcript abundance with cufflinks version 2.0.2: cufflinks -p 16 --GTF gtffile -u --library-type fr-unstranded --compatible-hits-norm bamfile
Genome_build: mm9
Supplementary_files_format_and_content: text file with RPKM

source_name: Lymph nodes

extract_protocol:
B-cells of pretumoral mice were sorted with CD19+ magnetic beads and MACS colums (Mylteni Biotech, Cat, No.130-121-301) and resuspended in RNA lysis buffer (Zymo, #R1054), while bulk population isolated from full blown lymphomas were directly resuspenden in RNA lysis buffer.Total RNA was purified from these lysates onto Quick-RNA Miniprep columns (Zymo, #R1054) and treated on-column with DNaseI. RNA quality was checked with the Agilent 2100 Bioanalyser (Agilent Technologies), then 0.5-1 µg used to prepare libraries for RNA-Seq with the TruSeq stranded total RNA Sample Prep Kit (Illumina, #20020596) following manufacturer instruction. RNA-seq libraries were then run on the Agilent 2100 Bioanalyser (Agilent Technologies) for quantification and quality control and then sequenced on Illumina NovaSeq.
Strand Specific RNA-Seq

value: Lymph nodes

value: CD19-Cre; E{mu}-myc; Pcgf6+/+

tag: treatment protocol


title: dcr2 - R. solani AG5 (BC) [dcr2_AG5_BC_73]

source_name: dcr2 - R. solani AG5 (BC)

value: mutant


title: T-KO-6

value: CD19-Cre; E{mu}-myc; Pcgf6-/-


title: i23-Disease3-Random-2000_S1

source_name: Diseased tendon fibroblasts (P2 primary cells)

tag: disease state

value: Diseased

value: Random


title: T-WT-2


title: dcr2 - R. solani AG5 (C) [dcr2_AG5_C_74]

source_name: dcr2 - R. solani AG5 (C)


title: T-WT-4


title: T-KO-5


title: T-KO-3


title: i24-Disease3-Random-4000_S13

tag: scaffold alignment


title: TubA_1

value: 25 weeks old

value: HDAC6 global knockout

value: tubastatin A-HCl


title: i22-Disease3-Random-1000_S11

tag: scaffold fiber diameter (nm)


title: T-KO-2

tag: strain


title: dcr2 - R. solani AG2 (C) [WT_AG5_C_71]

source_name: dcr2 - R. solani AG2 (C)

tag: tissue

value: Mycelium

value: Replicate 3


title: T-WT-3


title: T-KO-4


title: T-KO-1


title: T-WT-1


title: i21-Disease3-Random-300_S23


title: dcr2 - R. solani AG2 (AC) [WT_AG5_AC_72]

source_name: dcr2 - R. solani AG2 (AC)

value: After contact


title: P-WT-3

source_name: B-cells

value: B-cells


title: P-WT-4


title: i19-Disease3-Aligned-2000_S20


title: i18-Disease3-Aligned-1000_S12


title: i17-Disease3-Aligned-300_S6


title: P-KO-2


title: P-WT-1


title: i16-Disease2-Random-4000_S4


title: P-KO-1


title: C-WT-2

value: CD19-Cre; Pcgf6+/+


title: WT - R. solani AG5 (C) [dcr2_AG2_C_65]

source_name: WT - R. solani AG5 (C)

value: Wild type

value: At the contact


title: dcr2 - R. solani AG2 (BC) [WT_AG5_BC_70]

source_name: dcr2 - R. solani AG2 (BC)

value: Before contact


title: i14-Disease2-Random-1000_S22


title: WT - R. solani AG5 (BC) [dcr2_AG2_BC_64]

source_name: WT - R. solani AG5 (BC)


title: C-KO-1

value: CD19-Cre; Pcgf6-/-


title: i13-Disease2-Random-300_S21


title: WT - Alternaria alternata (AC) [ago3_AG2_AC_69]

source_name: WT - Alternaria alternata (AC)


title: P-KO-4


title: WT - R. solani AG2 (C) [WT_AG2_C_62]

source_name: WT - R. solani AG2 (C)


title: WT - R. solani AG2 (BC) [WT_AG2_BC_61]

source_name: WT - R. solani AG2 (BC)


title: i11-Disease2-Aligned-2000_S5

value: Aligned


title: LY_WT_H3K4me1

library_source: genomic

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_masker -Q33 -q 20 -r -N -v -i
Alignment to mm9 with bwa version 0.6.2; bwa aln -t 16 reffile -fastqfile| bwa samse -n 1 reffile - fastqfile | samtools view -q 1 -ut reffile - |samtools sort - bamfile
Removing duplicate reads: samtools rmdup -sS bamfile
Transcription factors (MYC, Pol2) peak calling with MACS version 2.0.9; macs2 -t samplebam -c inputbam --mfold=7,30 -g mm -p 0.00001
Genome_build: mm9
Supplementary_files_format_and_content: bed files with enriched regions

molecule: genomic DNA

source_name: Stabilized in vitro lymphomas

growth_protocol: Cells were isolated from infiltated lymph nodes of sick mice (CD19-Cre; Eμ-myc; Pcgf6+/+; CD19-Cre; Eμ-myc; Pcgf6-/- or CD19-Cre; Eμ-myc; Mga-/-). Upon isloation, cells were grown in B cell medium composed of DMEM medium (Dulbecco’s Modified Eagle Medium) and IMDM medium (Iscove’s Modified Dulbecco’s Medium) in a 1:1 ratio and additionated of 10% fetal bovine serum (FBS) (Cytivia, CHA115L), 2 mM L-glutamine (Invitrogen Life Technologies, Paisley, UK), 1% non-essential amino acids (NEAA), 1% penicillin/streptomycin and 25 mM β-mercaptoethanol.

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 250 bp were immunoprecipitated using different antibodies.
Libraries were prepared for Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection with AMPure beads and PCR with index primers.

value: Stabilized in vitro lymphomas

value: stabilized in vitro lymphoma B cells

value: CD19-Cre; E{mu}-myc; Pcgf6+/+

tag: chip antibody

value: H3K4me1, Abcam (ab8895)


title: LY_WT_PCGF6


title: LY_PCGF6KO_H3K4me3

value: CD19-Cre; E{mu}-myc; Pcgf6-/-

value: H3K4me3, Active Motif (#39159)


title: i12-Disease2-Aligned-4000_S7

value: Diseased


title: C-KO-2


title: i20-Disease3-Aligned-4000_S16


title: C-KO-3


title: LY_WT_H2AK119Ub

value: H2AK119Ub, Cell Signaling (#8240)


title: C-WT-1


title: P-WT-2


title: i15-Disease2-Random-2000_S3

value: Random


title: LY_WT_H3K27me3

value: H3K27me3, Cell Signaling (#9733)


title: P-KO-3

value: B-cells


title: C-WT-3

value: CD19-Cre; Pcgf6+/+


title: WT - R. solani AG5 (AC) [dcr2_AG2_AC_66]

source_name: WT - R. solani AG5 (AC)

value: Wild type

value: After contact

value: Mycelium

value: Replicate 3


title: i09-Disease2-Aligned-300_S14

value: Aligned


title: WT - R. solani AG2 (AC) [WT_AG2_AC_63]

source_name: WT - R. solani AG2 (AC)


title: LY_WT_H3K27ac

value: Stabilized in vitro lymphomas

value: H3K27ac, Abcam (ab4729)


title: LY_WT_H3K4me3

value: stabilized in vitro lymphoma B cells

value: CD19-Cre; E{mu}-myc; Pcgf6+/+


title: C-KO-4

value: CD19-Cre; Pcgf6-/-


title: ago3 control [ago3_control_60]

source_name: ago3 control

value: mutant

value: Control

value: Replicate 2


title: LY_PCGF6KO_PCGF6

value: CD19-Cre; E{mu}-myc; Pcgf6-/-


title: WT - Alternaria alternata (BC) [ago3_AG2_BC_67]

source_name: WT - Alternaria alternata (BC)

value: Before contact


title: i10-Disease2-Aligned-1000_S8

value: Diseased


title: WT - Alternaria alternata (C) [ago3_AG2_C_68]

source_name: WT - Alternaria alternata (C)

value: At the contact


title: LY_PCGF6KO_H3K4me1

value: H3K4me1, Abcam (ab8895)


title: dcr2 control [dcr2_control_59]

source_name: dcr2 control


title: LY_PCGF6KO_H3K27me3

value: H3K27me3, Cell Signaling (#9733)


title: WT control [WT_control_58]

source_name: WT control

value: Wild type

value: Mycelium


title: ago3 - Alternaria alternata (AC) [ago3_Alternaria_AC_57]

source_name: ago3 - Alternaria alternata (AC)

value: After contact


title: LY_PCGF6KO_H2AK119Ub

value: Stabilized in vitro lymphomas

value: H2AK119Ub, Cell Signaling (#8240)


title: i08-Disease1-Random-4000_S18

source_name: Diseased tendon fibroblasts (P2 primary cells)

value: Random


title: LY_PCGF6KO_H3K27ac

value: stabilized in vitro lymphoma B cells

value: H3K27ac, Abcam (ab4729)


title: ago3 - R. solani AG5 (AC) [dcr2_Alternaria_AC_54]

source_name: ago3 - R. solani AG5 (AC)

value: mutant


title: i07-Disease1-Random-2000_S2


title: LY_MGAKO_H3K4me3

value: CD19-Cre; E{mu}-myc; Mga-/-

value: H3K4me3, Active Motif (#39159)


title: dcs, Day 28 9_S9_L003

description: dcs, Day 28

data_processing:
Cellranger 3.1.0
ArchR was used for all downstream analyses
Genome_build: mm10
Supplementary_files_format_and_content: Gene scores as interpreted by ArchR (integration around TSS)
Supplementary_files_format_and_content: Matrix table with estimated gene scores for every gene and every cell
Supplementary_files_format_and_content: features (genes)
Supplementary_files_format_and_content: barcodes per cell
Supplementary_files_format_and_content: phenotypic information for each cell
Supplementary_files_format_and_content: estimated gene scores

source_name: Lymph Nodes

extract_protocol:
Lymph nodes were harvested and flow sorted
DNA libraries were prepared for sequencing using standard Illumina protocols

value: Day 28

value: dcs


title: ago3 - Alternaria alternata (C) [ago3_Alternaria_C_56]

source_name: ago3 - Alternaria alternata (C)

value: Replicate 2


title: ago3 - Alternaria alternata (BC) [ago3_Alternaria_BC_55]

source_name: ago3 - Alternaria alternata (BC)

value: Before contact


title: LY_MGAKO_H3K27ac


title: i05-Disease1-Random-300_S10

value: Diseased


title: dcs, Day 28 9_S9_L005

description: dcs, Day 28


title: ago3 - R. solani AG5 (C) [dcr2_Alternaria_C_53]

source_name: ago3 - R. solani AG5 (C)

value: At the contact


title: ago3 - R. solani AG5 (BC) [dcr2_Alternaria_BC_52]

source_name: ago3 - R. solani AG5 (BC)


title: Input


title: i03-Disease1-Aligned-2000_S24

value: Aligned


title: i06-Disease1-Random-1000_S19


title: dcs, Day 28 9_S9_L001

description: dcs, Day 28


title: dcs, Day 28 9_S9_L004

description: dcs, Day 28


title: dcs, Day 28 9_S9_L002

description: dcs, Day 28


title: LY_MGAKO_H3K27me3

value: H3K27me3, Cell Signaling (#9733)


title: LY_MGAKO_PCGF6


title: ago3 - R. solani AG2 (AC) [WT_Alternaria_AC_51]

source_name: ago3 - R. solani AG2 (AC)

value: After contact

value: Mycelium


title: LY_MGAKO_H3K4me1

source_name: Stabilized in vitro lymphomas

value: Stabilized in vitro lymphomas

value: H3K4me1, Abcam (ab8895)


title: i01-Disease1-Aligned-300_S15


title: dcs, Day 1 8_S8_L005

description: dcs, Day 1

value: Day 1


title: LY_MGAKO_H2AK119Ub

value: stabilized in vitro lymphoma B cells

value: H2AK119Ub, Cell Signaling (#8240)


title: i04-Disease1-Aligned-4000_S9


title: dcs, Day 1 8_S8_L004

description: dcs, Day 1


title: ago3 - R. solani AG2 (C) [WT_Alternaria_C_50]

source_name: ago3 - R. solani AG2 (C)

value: mutant


title: i02-Disease1-Aligned-1000_S17


title: dcs, Day 1 8_S8_L003

description: dcs, Day 1


title: MDA-MB-231 UBE3D KD rep3

city: Boston

first: Huiyun

last: Liu

state: Massachusetts

address: 150 Harrison Avenue, Jaharis building, Room 401A

institute: Tufts university school of medicine

description: rRNA depleted RNAs

data_processing:
Reads were trimmed using cutadapt v1.8.1
Trimmed reads were aligned to the hg38 annotation of human genome using STAR v2.5.2b
DESeq2 was used to analyze differential gene expression.
The raw read counts were normalized using reads per kilobase of transcript per million mapped reads (RPKM)
The significance of differential expression was estimated for each gene using the Wald test and then corrected for multiple comparisons using the Benjamini and Hochberg procedure (Padj)
Visualization of the generated data was achieved using ggplot2 and EnhancedVolcano.
GO enrichment analyses were performed using Metascape
Downstream of Genes (DoG) transcripts were identified using DoGFinder
Differential expression analysis of normalized read counts in DoG regions was performed using DESeq2, with shrinking of log2 fold changes using ashr
Eulerr was used to generate proportional Venn diagrams for overlap analysis.
Normalized reads maps were visualized using Jbrowse
Genome_build: hg38
Supplementary_files_format_and_content: "metadata_MDA-MB-231_UBE3D_KO.csv" contains sample metadata, "gene_shUBE3DvsCTRL.csv" contains differential gene expression analysis in UBE3D KD samples compared to control shRNA samples, "DoG_shUBE3DvsCTRL.csv" contains differential expressed DoGs in UBE3D KD samples compared to control shRNA samples

source_name: Human triple negative breast cancer cell line

growth_protocol: The MDA-MB-231 cells were cultured in Dulbecco’s modified Eagle medium (DMEM) with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (10,000 U/mL).

extract_protocol:
Total RNA from control or UBE3D KD cells was prepared using TRIzol Reagent
Total RNA samples depleted of rRNA were converted to cDNA using random primers.
75bp pair-end stranded sequencing was done by Realseq, Inc.

treatment_protocol: Inducible shRNAs against UBE3D was integrated into human genome by lentivirus and UBE3D expression was knocked down by adding dxoxycycline

tag: sample type

value: Pooled


title: dcs, Day 1 8_S8_L002

description: dcs, Day 1


title: dcs, Day 1 8_S8_L001

description: dcs, Day 1


title: dcr2 - Alternaria alternata (AC) [ago3_AG5_AC_48]

source_name: dcr2 - Alternaria alternata (AC)


title: dcs, Day 0 7_S7_L005

description: dcs, Day 0

value: Day 0


title: dcs, Day 0 7_S7_L004

description: dcs, Day 0

value: dcs


title: MDA-MB-231 control rep3

description: rRNA depleted RNAs


title: dcs, Day 0 7_S7_L003

description: dcs, Day 0


title: dcr2 - Alternaria alternata (BC) [ago3_AG5_BC_46]

source_name: dcr2 - Alternaria alternata (BC)

value: Replicate 2


title: MDA-MB-231 control rep2

description: rRNA depleted RNAs


title: dcr2 - R. solani AG5 (C) [dcr2_AG5_C_44]

source_name: dcr2 - R. solani AG5 (C)


title: MDA-MB-231 control rep1

description: rRNA depleted RNAs


title: dcs, Day 0 7_S7_L002

description: dcs, Day 0


title: dcs, Day 0 7_S7_L001

description: dcs, Day 0


title: dcr2 - R. solani AG2 (AC) [WT_AG5_AC_42]

source_name: dcr2 - R. solani AG2 (AC)


title: pdcs, Day 28 6_S6_L005

description: pdcs, Day 28

value: Day 28

value: pdcs


title: ago3 - R. solani AG2 (BC) [WT_Alternaria_BC_49]

source_name: ago3 - R. solani AG2 (BC)

value: Before contact


title: MDA-MB-231 UBE3D KD rep1

description: rRNA depleted RNAs


title: MDA-MB-231 UBE3D KD rep2

description: rRNA depleted RNAs


title: pdcs, Day 28 6_S6_L004

description: pdcs, Day 28


title: dcr2 - Alternaria alternata (C) [ago3_AG5_C_47]

source_name: dcr2 - Alternaria alternata (C)

value: At the contact


title: hESC v101 3

city: Heidelberg

first: Alicia

last: Roig Merino

address: Im Neuenheimer Feld 242

country: Germany

institute: DKFZ

description:
200757770002_L
replicate 3

hyb_protocol: Standard Illumina Hybridisation Protocol (Whole-Genome Gene Expression  Direct Hybridization Assay Guide)  750 ng of cRNA were hybridized for 17 hr at 58°C on Illumina Human HT-12-Microarray.

scan_protocol: Standard Illumina Scanning Protocol (Whole-Genome Gene Expression  Direct Hybridization Assay Guide)  (Whole-Genome Gene Expression  Direct Hybridization Assay Guide)

data_processing: data were normalised using quantile normalisation with R using function normalize.quantiles from Bioconductor package preprocessCore

label: Biotin, Cy3-Streptavidin

source_name: EBNA

label_protocol: The Illumina TotalPrep RNA Amplification Kit (life technologies) was used to generate single-stranded cRNA from input amounts of 200ng total RNA

growth_protocol: hESC were grown on mitotically inactivated MEFs on 0,1% gelatin-coated plates and cultured in hESC media containing DMEM/F-12 +Glutamax (Gibco) supplemented with 20% Knockout Serum replacement (Gibco), 1% PenStrep (Gibco), 1% NEAA (Gibco) and 0,1mM beta-mercaptoethanol (Gibco). FGF2 (Peprotech) was added freshly to a final concentration of 10ng/ul

extract_protocol: RNA was extracted using RNeasy Mini Kit (Qiagen) following the manufacturers' instructions. DNAseI treatment (Ambion DNA-free kit, Invitrogen) was performed according to manufacturers' instructions

value: Human Embryonic Stem Cells

tag: gender

value: male

value: embryo


title: hESC v101 2

description:
200757770002_K
replicate 2


title: dcr2 - R. solani AG2 (C) [WT_AG5_C_41]

source_name: dcr2 - R. solani AG2 (C)

value: Mycelium


title: hESC v85 2

description:
200757770002_H
replicate 2

source_name: nSMAR


title: hESC v85 1

description:
200757770002_G
replicate 1


title: hESC v71 3

description:
200757770002_F
replicate 3

source_name: pSMAR


title: hESC v101 1

description:
200757770002_J
replicate 1


title: hESC v85 3

description:
200757770002_I
replicate 3


title: hESC v71 2

description:
200757770002_E
replicate 2


title: dcr2 - R. solani AG5 (AC) [dcr2_AG5_AC_45]

source_name: dcr2 - R. solani AG5 (AC)

value: After contact


title: dcr2 - R. solani AG2 (BC) [WT_AG5_BC_40]

source_name: dcr2 - R. solani AG2 (BC)


title: WT - Alternaria alternata (AC) [ago3_AG2_AC_39]

source_name: WT - Alternaria alternata (AC)

value: Wild type


title: dcr2 - R. solani AG5 (BC) [dcr2_AG5_BC_43]

source_name: dcr2 - R. solani AG5 (BC)


title: pdcs, Day 28 6_S6_L003

description: pdcs, Day 28

source_name: Lymph Nodes


title: pdcs, Day 28 6_S6_L001

description: pdcs, Day 28


title: WT - Alternaria alternata (C) [ago3_AG2_C_38]

source_name: WT - Alternaria alternata (C)


title: WT - Alternaria alternata (BC) [ago3_AG2_BC_37]

source_name: WT - Alternaria alternata (BC)


title: pdcs, Day 28 6_S6_L002

description: pdcs, Day 28


title: WT - R. solani AG5 (AC) [dcr2_AG2_AC_36]

source_name: WT - R. solani AG5 (AC)


title: pdcs, Day 1 5_S5_L005

description: pdcs, Day 1

value: Day 1


title: OP50, replicate 3

city: Montreal

first: J Alex

last: Parker

state: Quebec

address: 900 rue St-Denis

country: Canada

institute: CRCHUM, Université de Montréal

data_processing:
Basecalls performed using Illumina RTA 1.17.21.3.
Samples demultiplexed using bcl2fastq from Illumina CASAVA 1.8.2 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.5.1b
Readcounts were computed by STAR during sequence alignment based on annotations from Ensembl version 84
Expression values were also computed using RSEM version 1.2.28 based on Ensembl version 84 transcript annotations
Genome_build: WBcel235
Supplementary_files_format_and_content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary_files_format_and_content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column)

organism: Caenorhabditis elegans

source_name: N2 C. elegans fed with OP50

growth_protocol: Worms were grown on on OP50, Bifidobacterium animalis subsp. lactis B94 or Lacticaseibacillus rhamnosus HA-114 on NGM plates at 20 degrees.

extract_protocol:
Trizol extraction and Qiagen Rneasy column purification
KAPA RNA Stranded PolyA

value: fed with OP50

value: Whole worms

value: Mixed population


title: clsy1-7_2-2_3-1_4-1_Ov_rep2_smRNA-seq

data_processing:
Illumina Casava software used for basecalling and demultiplexing.
Read Filtering, Mapping, and cluster calling: The adapters were removed from the de-multiplexed reads using cutadapt (v1.9.1) and trimmed reads longer that 15nt were mapped to the TAIR10 genome using ShortStack (v3.8.1) with the following options: --mismatches 1 and either --mmap f, to include multi-mapping reads, or --mmap n, to include only unique mapping reads. Only perfectly matched read or reads with a single 3’ mismatch were used to call smRNA clusters using ShortStack with the --mincov 20, --pad 100, --dicermin 21 and dicermax 24 options, to generate Tag Directories using the using the makeTagDirectory script from the HOMER with the -format sam -mis 1 and -keepAll options, and to make genome browser tracks specifically for the 24nt sized smRNAs using the makeUCSCfile script from HOMER with the -fragLength 24 and -norm 10000000 options.
TAIR10
Supplementary_files_format_and_content: bedGraph file, including header and chr#, start position, end position and normalized value (rp10M).

source_name: unfertilized ovules (Ov)

tag: ecotype

value: Columbia

tag: tissues

value: unfertilized ovules (Ov)


title: OP50, replicate 1

tag: treatment


title: pdcs, Day 1 5_S5_L003

description: pdcs, Day 1


title: OP50, replicate 2


title: WT - R. solani AG5 (BC) [dcr2_AG2_BC_34]

source_name: WT - R. solani AG5 (BC)

tag: time point

value: Replicate 2


title: nprd1-4_Ov_rep2_smRNA-seq


title: clsy3-1_4-1_Ov_rep2_smRNA-seq


title: Lacticaseibacillus rhamnosus HA-114, replicate 2

source_name: N2 C. elegans fed with HA-114

value: fed with HA-114


title: WT - R. solani AG5 (C) [dcr2_AG2_C_35]

source_name: WT - R. solani AG5 (C)

tag: replicate


title: Lacticaseibacillus rhamnosus HA-114, replicate 3


title: clsy4-1_rep2_smRNA-seq

tag: genotype


title: clsy1-7_2-2_Ov_rep2_smRNA-seq


title: WT - R. solani AG2 (C) [WT_AG2_C_32]

source_name: WT - R. solani AG2 (C)


title: shh1-1_Ov_rep2_smRNA-seq


title: WT - R. solani AG2 (AC) [WT_AG2_AC_33]

source_name: WT - R. solani AG2 (AC)


title: pdcs, Day 0 4_S4_L005

description: pdcs, Day 0

value: Day 0

tag: age

value: pdcs


title: hESC O 3

description:
200757770002_C
replicate 3

source_name: Control

tag: cell type


title: pdcs, Day 1 5_S5_L004

description: pdcs, Day 1


title: hESC v71 1

description:
200757770002_D
replicate 1

source_name: pSMAR


title: pdcs, Day 1 5_S5_L001

description: pdcs, Day 1


title: hESC O 1

description:
200757770002_A
replicate 1


title: hESC O 2

description:
200757770002_B
replicate 2


title: WT - R. solani AG2 (BC) [WT_AG2_BC_31]

source_name: WT - R. solani AG2 (BC)

value: Before contact


title: Lacticaseibacillus rhamnosus HA-114, replicate 1


title: Bifidobacterium animalis subsp. lactis B94, replicate 2

source_name: N2 C. elegans fed with B94

value: fed with B94


title: pdcs, Day 0 4_S4_L004

description: pdcs, Day 0


title: Bifidobacterium animalis subsp. lactis B94, replicate 1


title: clsy2-2_rep2_smRNA-seq


title: ago3 control [ago3_control_30]

source_name: ago3 control

value: mutant

value: Control

value: Replicate 1


title: dcr2 control [dcr2_control_29]

source_name: dcr2 control

value: Mycelium


title: clsy1-7_rep2_smRNA-seq


title: WT_Ov_rep4_smRNA-seq

value: wild-type


title: pdcs, Day 0 4_S4_L003

description: pdcs, Day 0

source_name: Lymph Nodes


title: pdcs, Day 0 4_S4_L002

description: pdcs, Day 0


title: pdcs, Day 1 5_S5_L002

description: pdcs, Day 1

value: Day 1


title: clsy3-1_rep2_smRNA-seq


title: Human GBM Tumor sample 1 TMZ 2 [180327-1_TMZ 2]

description: 10X single cell RNA sequencing

source_name: patient derived xenograft glioblastoma cells

tag: tumor grade

value: glioblastoma

value: temozolomide treated


title: pdcs, Day 0 4_S4_L001

description: pdcs, Day 0


title: Human GBM Tumor sample 1 TMZ 1 [180327-1_TMZ 1]

description: 10X single cell RNA sequencing


title: ago3 - Alternaria alternata (AC) [ago3_Alternaria_AC_27]

source_name: ago3 - Alternaria alternata (AC)

value: After contact


title: cd11b+pdca1+, Day 28 3_S3_L005

description: cd11b+pdca1+, Day 28

value: Day 28


title: Human GBM Tumor sample 8 [161129-2]

description: 10X single cell RNA sequencing

value: untreated


title: Hippocampus KO rep8

city: Barcelona

first: Arnau

last: Hervera

address: Baldiri Reixac 15-21

country: Spain

institute: IBEC

data_processing:
Reads were aligned with the STAR mapper to release M14 of the Mus musculus Gencode version of the genome (GRMm38/mm10 assembly) (https://www.gencodegenes.org/mouse/release_M14.html).
A raw count of reads per gene was also obtained with STAR (-quantMode TranscriptomeSAM GeneCounts option). The R/Bioconductor package DESeq2 was used to assess differential expression between experimental groups (Wald statistical test + false discovery rate correction). Prior to processing the differential expression analysis, genes for which the sum of raw counts across all samples was less than two were discarded.
Genome_build: GRMm38/mm10 assembly
Supplementary_files_format_and_content: One report per sample that shows quality of each base, duplication levels, etc
Supplementary_files_format_and_content: Summary per sample (table, the number of reads and the uniquely mapping rates
Supplementary_files_format_and_content: Raw count of reads per gene, as calculated by STAR

source_name: Hippocampus

extract_protocol:
Hippocampi were extracted, flash frozen on dry ice, and RNA was harvested using RNAEasy Mini kit (Qiagen). 500 ng of total RNA was used for poly(A)-mRNA selection using Oligo (dT) magnetic beads and subsequently fragmented to approximately 300bp. cDNA was synthesized using reverse transcriptase (SuperScript II, Invitrogen) and random primers. The second strand of the cDNA incorporated dUTP in place of dTTP.
Libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit v2 according to the manufacturer's protocol. Briefly, double-stranded DNA was further used for library preparation. dsDNA was subjected to A-tailing and ligation of the barcoded Truseq adapters. All purification steps were performed using AMPure XP Beads. Library amplification was performed with PCR using the primer cocktail supplied in the kit. Final libraries were analyzed using Agilent DNA 1000 chip to estimate the quantity, check the size distribution, and then quantified by qPCR using the KAPA Library Quantification Kit (KapaBiosystems, Merck, Darmstadt, Germany) before amplification Illumina's cBot. Libraries were sequenced 1 x 50bp on Illumina's HiSeq 2500.

value: Hippocampus

tag: age (weeks)


title: Hippocampus KO rep7


title: ago3 - Alternaria alternata (C) [ago3_Alternaria_C_26]

source_name: ago3 - Alternaria alternata (C)

value: At the contact


title: Human GBM Tumor sample 7 [160810-1]

description: 10X single cell RNA sequencing


title: cd11b+pdca1+, Day 28 3_S3_L004

description: cd11b+pdca1+, Day 28


title: Hippocampus KO rep6


title: cd11b+pdca1+, Day 28 3_S3_L003

description: cd11b+pdca1+, Day 28


title: ago3 - Alternaria alternata (BC) [ago3_Alternaria_BC_25]

source_name: ago3 - Alternaria alternata (BC)


title: Human GBM Tumor sample 6 [180911-1]

description: 10X single cell RNA sequencing


title: ago3 - R. solani AG5 (AC) [dcr2_Alternaria_AC_24]

source_name: ago3 - R. solani AG5 (AC)


title: Human GBM Tumor sample 4 [160830-1]

description: 10X single cell RNA sequencing


title: cd11b+pdca1+, Day 28 3_S3_L002

description: cd11b+pdca1+, Day 28


title: WT control [WT_control_28]

source_name: WT control

value: Wild type


title: ago3 - R. solani AG5 (BC) [dcr2_Alternaria_BC_22]

source_name: ago3 - R. solani AG5 (BC)


title: ago3 - R. solani AG5 (C) [dcr2_Alternaria_C_23]

source_name: ago3 - R. solani AG5 (C)


title: Hippocampus KO rep5


title: cd11b+pdca1+, Day 28 3_S3_L001

description: cd11b+pdca1+, Day 28


title: cd11b+pdca1+, Day 1 2_S2_L005

description: cd11b+pdca1+, Day 1


title: cd11b+pdca1+, Day 1 2_S2_L004

description: cd11b+pdca1+, Day 1


title: Hippocampus KO rep1


title: Hippocampus KO rep2


title: Hippocampus KO rep4


title: ago3 - R. solani AG2 (AC) [WT_Alternaria_AC_21]

source_name: ago3 - R. solani AG2 (AC)


title: Human GBM Tumor sample 2 [180518-1]

description: 10X single cell RNA sequencing


title: cd11b+pdca1+, Day 1 2_S2_L003

description: cd11b+pdca1+, Day 1


title: Human GBM Tumor sample 5 [180709-1]

description: 10X single cell RNA sequencing


title: ago3 - R. solani AG2 (C) [WT_Alternaria_C_20]

source_name: ago3 - R. solani AG2 (C)


title: Hippocampus WT rep8

value: PRNP+/+


title: cd11b+pdca1+, Day 1 2_S2_L002

description: cd11b+pdca1+, Day 1


title: Hippocampus WT rep7


title: ago3 - R. solani AG2 (BC) [WT_Alternaria_BC_19]

source_name: ago3 - R. solani AG2 (BC)

value: Before contact


title: dcr2 - Alternaria alternata (AC) [ago3_AG5_AC_18]

source_name: dcr2 - Alternaria alternata (AC)


title: Hippocampus KO rep3


title: cd11b+pdca1+, Day 1 2_S2_L001

description: cd11b+pdca1+, Day 1


title: LG20M2(treated)

city: Baoding

first: Chunqing

last: Li

state: Hebei Province

address: Number 180,  Wusi east street

institute: Hebei University

data_processing:
The purity of RNA was assessed with NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). The concentration of RNA was tested with Qubit® 3.0 Flurometer (Life Technologies, CA, USA). The integrity of RNA was confirmed with Agilent 2100 RNA Nano 6000 Assay Kit (Agilent Technologies, CA, USA).
All samples in this study passed quality control with a minimum RNA integrity number of 8.0.Qualified libraries were sequenced using Illumina platform. The sequencing strategy was PE150.
3 µg of RNA per sample as the input material for RNA sample preparation. RNA-seq libraries were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) .The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia)
Cufflinks v2.1.1 was used to analyse differentially expressed genes between metformin and control groups. Transcript abundance representing the level of gene expression was measured by fragments per kilobase of exon model per million mapped fragments (FPKM).
Genome_build: Homo_sapiens.GRCh38.91.chr
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: Huh-7 cell

extract_protocol:
control and treated Huh-7cells were harvested using Trizol reagent. Tanscriptome sequencing trial was carried out by ANOROAD (Beijing, China). Six cDNA libraries were constructed.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: protocol

value: cell in vitro

tag: time

value: 48 hours

tag: cell line

tag: agent

value: metformin


title: LG20M3(treated)


title: Hippocampus WT rep6

tag: tissue


title: Human GBM Tumor sample 3 [170911-1]

description: 10X single cell RNA sequencing


title: Human GBM Tumor sample 1 [180327-1]

description: 10X single cell RNA sequencing


title: LG20M1(treated)


title: dcr2 - Alternaria alternata (BC) [ago3_AG5_BC_16]

source_name: dcr2 - Alternaria alternata (BC)

value: mutant

value: Replicate 1


title: ly6c+, Day 28 12_S12_L004

description: ly6c+, Day 28

tag: strain


title: LG6(Control)

value: Control


title: ly6c+, Day 28 12_S12_L005

description: ly6c+, Day 28


title: Hippocampus WT rep5


title: Hippocampus WT rep4


title: dcr2 - R. solani AG5 (C) [dcr2_AG5_C_14]

source_name: dcr2 - R. solani AG5 (C)

value: Mycelium


title: Hippocampus WT rep3


title: dcr2 - R. solani AG5 (AC) [dcr2_AG5_AC_15]

source_name: dcr2 - R. solani AG5 (AC)


title: ly6c+, Day 28 12_S12_L002

description: ly6c+, Day 28

source_name: Lymph Nodes


title: LG5(Control)


title: Hippocampus WT rep2


title: dcr2 - R. solani AG5 (BC) [dcr2_AG5_BC_13]

source_name: dcr2 - R. solani AG5 (BC)


title: dcr2 - Alternaria alternata (C) [ago3_AG5_C_17]

source_name: dcr2 - Alternaria alternata (C)


title: A549-ATOH8-SMAD3_CHIP

city: Guangzhou

first: Ximeng

address: Zhongshan Road No.2 Yuexiu district

institute: SUN YAT-SEN UNIVERSITY

data_processing:
Basecalls performed using FastQC v0.11.8.
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2-align-s version 2.3.4.3.
Peaks were called using macs2 2.2.7.1.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *_peaks.txt: Tab-delimited text files include peaks.

source_name: A549 cells with retroviral ATOH8 stably transduced

growth_protocol: The cells were grown in DMEM (Termo Fisher) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (penicillin 100 U ml–1 and streptomycin 10 μg ml–1).

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols.

value: Lung adenocarcinoma cell line

value: stable transduction with ATOH8

tag: chip antibody


title: ly6c+, Day 1 11_S11_L004

description: ly6c+, Day 1

value: Day 1


title: A549-ATOH8-SMAD3_input


title: A549-ATOH8-FLAG_CHIP

value: FLAG


title: ly6c+, Day 1 11_S11_L005

description: ly6c+, Day 1


title: dcr2 - R. solani AG2 (C) [WT_AG5_C_11]

source_name: dcr2 - R. solani AG2 (C)


title: dcr2 - R. solani AG2 (BC) [WT_AG5_BC_10]

source_name: dcr2 - R. solani AG2 (BC)


title: A549-ATOH8-FLAG_input


title: ly6c+, Day 28 12_S12_L003

description: ly6c+, Day 28

value: Day 28


title: ly6c+, Day 1 11_S11_L003

description: ly6c+, Day 1


title: rapamycin-pretreated EpCAM CAR-T cells 3

city: hefei

first: zhigang

last: nian

state: anhui

address: 443 Huang-Shan Road

department: school of life science

institute: university of science and technology of China

description: ExpressionProfile.txt

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house  perl scripts.
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.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each  gene.And then 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

source_name: T cells

growth_protocol: CAR-T cells were geenrated using lentiviruses.

extract_protocol:
Sequencing libraries were generated using NEBNext® UltraTM  RNA Library Prep Kit for Illumina® (NEB, USA)
the library preparations were  sequenced on an Illumina Novaseq platform

treatment_protocol: rapamycin-pretreated EpCAM CAR-T cells were treated with 20  nM rapamycin

value: EpCAM CAR T cells treated with rapamycin

tag: culture

value: culture 6 days in vitro


title: Ang_Los_1

city: Córdoba

first: Eduardo

last: Muñoz

address: Avda Menéndez Pidal s/n

institute: Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), University of Córdoba

data_processing:
Raw reads were pre-processed with fastp (v0.20.0), using a cut windows size of 4 bp with a required mean quality of 15 and a required total length of 20 bp for a read to pass the filter.
Then, reads were aligned against the GRCm38 genome (v84) from ENSEMBL with HISAT (v2.1.0).
The count matrix was obtained from the alignments using the corresponding ENSEMBL annotation file with featureCounts (v2.0.0).
Normalization and differential expression analysis were performed with edgeR (v3.30.0), excluding genes with less than 15 counts across all samples.
Next, the functional analysis was performed through a pre-ranked gene set enrichment analysis with the fgsea package (v1.14.0), ranking genes by the edgeR estimated log transformed fold change and using the functional categories defined by MSigDb hallmarks for Mus musculus (V7.0).
Genome_build: ENSEMBL GRCm38 (v84)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

source_name: Heart

extract_protocol:
RNA samples were extracted from heart samples using Qiazol lysis reagent.
300 ng of RNA per sample were used to construct a cDNA library capturing mRNA through Oligo-dT beads with polyA tails (Illumina TruSeq RNA Library Prep Kit v2, #RS-122-2001).
The cDNA library was sequenced on an Illumina Hiseq 2500 system, generating single end 50 bp reads and obtaining ~30 million reads per sample.

tag: group

value: Ang II + Losartan


title: ly6c+, Day 1 11_S11_L002

description: ly6c+, Day 1


title: Ang_Los_3


title: Ang_Ehp_3

value: Ang II + EHP-101


title: LG4(Control)


title: rapamycin-pretreated EpCAM CAR-T cells 2

description: ExpressionProfile.txt

tag: treatment


title: WT - Alternaria alternata (C) [ago3_AG2_C_8]

source_name: WT - Alternaria alternata (C)

value: Wild type

tag: time point

value: At the contact


title: ly6c+, Day 1 11_S11_L001

description: ly6c+, Day 1


title: Ang_Ehp_2


title: ly6c+, Day 28 12_S12_L001

description: ly6c+, Day 28


title: ly6c+, Day 0 10_S10_L005

description: ly6c+, Day 0

value: Day 0


title: rapamycin-pretreated EpCAM CAR-T cells 1

description: ExpressionProfile.txt


title: WT - Alternaria alternata (BC) [ago3_AG2_BC_7]

source_name: WT - Alternaria alternata (BC)

value: Before contact

tag: replicate


title: Hippocampus WT rep1

source_name: Hippocampus

value: Hippocampus

tag: genotype

value: PRNP+/+


title: dcr2 - R. solani AG2 (AC) [WT_AG5_AC_12]

source_name: dcr2 - R. solani AG2 (AC)

value: mutant

value: After contact

value: Replicate 1


title: Ang_Los_2


title: Ang_Ehp_1


title: WT - Alternaria alternata (AC) [ago3_AG2_AC_9]

source_name: WT - Alternaria alternata (AC)

value: Mycelium


title: Ang_3

value: Ang II


title: ly6c+, Day 0 10_S10_L004

description: ly6c+, Day 0

tag: age


title: EpCAM CAR-T cells 3

description: ExpressionProfile.txt

value: EpCAM  CAR


title: WT - R. solani AG5 (C) [dcr2_AG2_C_5]

source_name: WT - R. solani AG5 (C)


title: EpCAM CAR-T cells 2

description: ExpressionProfile.txt


title: EpCAM CAR-T cells 1

description: ExpressionProfile.txt


title: ly6c+, Day 0 10_S10_L003

description: ly6c+, Day 0


title: Ang_1


title: ly6c+, Day 0 10_S10_L002

description: ly6c+, Day 0


title: Ang_2


title: Control_3 (Ang II control)

value: Control


title: WT - R. solani AG2 (AC) [WT_AG2_AC_3]

source_name: WT - R. solani AG2 (AC)


title: T cells 2

description: ExpressionProfile.txt

value: untreatment


title: WT - R. solani AG5 (AC) [dcr2_AG2_AC_6]

source_name: WT - R. solani AG5 (AC)


title: ly6c+, Day 0 10_S10_L001

description: ly6c+, Day 0


title: T cells 1

description: ExpressionProfile.txt

value: culture 6 days in vitro


title: T cells 3

description: ExpressionProfile.txt


title: WT - R. solani AG2 (BC) [WT_AG2_BC_1]

source_name: WT - R. solani AG2 (BC)


title: Control_2 (Ang II control)


title: Control_1 (Ang II control)


title: WT - R. solani AG5 (BC) [dcr2_AG2_BC_4]

source_name: WT - R. solani AG5 (BC)


title: Colon DSS day0

city: Solna

first: Ludvig

middle: Ale

last: Larsson

state: Stockholm

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: SciLifeLab

data_processing:
Library strategy: Spatial Transcriptomics
bcl2fastq command line tool was used for base calling
Sequence reads were trimmed for adapter sequence (Template Switch Oligo) and polyA homopolymers using cutadapt (-g XAAGCAGTGGTATCAACGCAGAGTACATGGG;max_error_rate=0.1 -a AAAAAAAAAA ;max_error_rate=0--overlap 5 -n 2)
Reads were mapped, annotated and demultiplexed using the spaceranger v1.0.0 command line tool
Annotated reads were quantified and mapped to the Hematoxylin and Eosin image using the spaceranger v1.0.0 command line tool
Genome_build: mm10 (Ensembl 93)
Supplementary_files_format_and_content: raw_feature_bc_matrix.h5  (Matrix with raw counts for every gene and every spot)
Supplementary_files_format_and_content: filtered_feature_bc_matrix.h5  (Matrix with raw counts for every gene and every spot, filtered to include spots under tissue)
Supplementary_files_format_and_content: tsv  (Matrix with normalized values. Normalization was done using variance stabilizing transformation as implemented in the R package sctransform v0.2.1 and Seurat v3.1.5)
Supplementary_files_format_and_content: tif  (Hematoxylin and Eosin (HE) image in TIF format)
Supplementary_files_format_and_content: png  (Low resolution Hematoxylin and Eosin (HE) image in PNG format)
Supplementary_files_format_and_content: json  (Scalefactors in json format)
Supplementary_files_format_and_content: csv  (Table with array and pixel coordinates)

source_name: Colon

extract_protocol:
Mouse colonic tissues were collected either on day 0 (without any exposure to DSS) or on day14 after exposure to DSS, Swisrolled and frozen in OCT. Mouse colonic tissues (day0 and day14) were cryo-sectioned (10uM) and placed on the already barcoded spots (6.5mm x 6.5mm) on the glass slide.
RNA libraries were prepared for sequencing following the 10x Genomics Visium protocol
Spatial Transcriptomics (Visium)

treatment_protocol: Wild type C57BL/6J mice were exposed to DSS in drinking water for 7 days and then allowed to recover for 7 more days.

value: colon

value: wild type

value: control


title: WT - R. solani AG2 (C) [WT_AG2_C_2]

source_name: WT - R. solani AG2 (C)

value: Wild type

value: At the contact


title: Colon DSS day14

value: DSS


title: Scripps registry recVTE_26

status: Public on Dec 04 2021

type: genomic

city: La Jolla

first: Hiroshi

last: Deguchi

state: Ca

address: 10550 N Torrey pines Rd

institute: The Scripps Research Institute

hyb_protocol: Samples were hybridized with Axiom® Exome Genotyping Array (Affymetrix) and scanned at DNA Core Laboratory of the Scripps Research Institute.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: The genotype for each SNP for each subject was determined using the Affymetrix Genotyping Console (version 4.1.4)

label: biotin

source_name: recVTE

label_protocol: not provided

growth_protocol: EDTA Blood was collected and white blood cells were separated by centrifuge in the presence of Ficol

extract_protocol: DNA were extracted from white blood cells using commercial kit.

tag: sample id

tag: diagnosis

value: Recurrent venous thromboembolism (recVTE)


title: Scripps registry recVTE_23


title: Scripps registry recVTE_24


title: Scripps registry recVTE_31


title: Scripps registry recVTE_32


title: Scripps registry recVTE_25


title: Scripps registry recVTE_28


title: Scripps registry recVTE_30


title: Scripps registry recVTE_27


title: Scripps registry recVTE_29


title: Scripps registry recVTE_22


title: Scripps registry recVTE_21


title: Scripps registry recVTE_20


title: Scripps registry recVTE_18


title: Scripps registry recVTE_16


title: Scripps registry recVTE_15


title: Scripps registry recVTE_14


title: Scripps registry recVTE_12


title: Scripps registry recVTE_10


title: Scripps registry recVTE_11


title: Scripps registry recVTE_9


title: Scripps registry recVTE_19


title: Scripps registry recVTE_17


title: Scripps registry recVTE_8


title: Scripps registry recVTE_6


title: Scripps registry recVTE_5


title: Scripps registry recVTE_7


title: Scripps registry recVTE_4


title: Scripps registry recVTE_3


title: Scripps registry VTE_70

source_name: VTE

value: Venous thromboembolism (VTE)


title: Scripps registry VTE_72


title: Scripps registry recVTE_2


title: Scripps registry recVTE_1


title: Scripps registry VTE_69


title: Scripps registry VTE_71


title: Scripps registry VTE_67


title: Scripps registry VTE_68


title: Scripps registry recVTE_13


title: Scripps registry VTE_66


title: Scripps registry VTE_65


title: Scripps registry VTE_64


title: Scripps registry VTE_62


title: Scripps registry VTE_63


title: HEK293_1

city: Goettingen

first: Markus

middle: T.

last: Bohnsack

address: Humboldtallee 23

department: Institute for Molecular Biology

institute: Goettingen University

data_processing:
Raw data were quality checked using FastQC and all read had a Phred score >33
Sequencing reads were mapped to the rDNA sequence (Genbank: U13369.1) using STAR (version 2.7.0d; Dobin and Gingeras, 2015). All reads mapping to the rDNA were discarded. --readFilesCommand zcat
--outSAMattributes All   --outSAMtype BAM SortedByCoordinate
--outReadsUnmapped Fastx
Remaining reads were mapped to the human reference genome gencode (GRCh39.29) using STAR (version 2.7.0d; Dobin and Gingeras, 2015). --limitBAMsortRAM 21470000000 --genomeLoad NoSharedMemory \ --sjdbOverhang 50 --outSAMattributes All --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM --outSAMstrandField intronMotif --outReadsUnmapped Fastx
Expression of different transcript isoforms was estimated using RSEM (version 1.3.3) (rsem-calculate-expression --bam --no-bam-output)
The EB-Seq package (R version 3.6.3; EB-Seq version 1.2.0) was run using default settings (rsem-run-ebseq--ngvector)
Genome_build: GRCh39.p13

source_name: HEK293 cell culture

growth_protocol: HEK293 Flp-In T-Rex cells were grown at 37°C in 5% CO2 in high glucose DMEM supplemented with 10% foetal calf serum.

extract_protocol:
Total RNA was extracted using TRI reagent (Sigma) according to the manufacturer's instructions. DNase treatment was performed using TURBO Dnase at 37°C for 15 min and RNA was re-purified using the RNA clean and concentrator kit (Zymo Research) according to the manufacturer's instructions.
Ribosomal RNA depletion was performed and libraries were constructed by TruSeq total RNA library preparation (Illumina) according to the maufacturer's instructions.

value: HEK293 Flp-In T-Rex cells


title: UMB1949

city: Grand Rapids

first: Jeffrey

last: MacKeigan

state: MI

address: 400 Monroe Ave NW

institute: Michigan State University

data_processing:
Reads were filtered and aligned to hg19 using Subread.
Raw read counts were obatined using FeatureCounts from Subread package.
Counts per million (CPM) were calculated, log2 transformed, and TMM normalized using voom.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are TSV in the format of gene name, gene symbol, chromsome, chromsome location, log2 counts per million

source_name: renal angiomyolipoma

growth_protocol: DMEM with 10% FBS and 250 U/mL penicillin-streptomycin at 37 °C with 5% CO2.

extract_protocol:
RNA was isolated using an acid phenol–chloroform extraction and the mirVana kit (Ambion). RNA integrity was confirmed using a BioAnalyzer 2100 (Agilent) and concentrations were determined using a Qubit 2.0. fluorometer (Invitrogen).
NEBNext

tag: cell type

value: renal angiomyolipoma derived cell

value: TSC2 V1362LfsTer50


title: 621-102

value: TSC2 R611Q


title: Scripps registry VTE_61


title: Scripps registry VTE_57


title: Scripps registry VTE_44


title: Scripps registry VTE_53


title: Scripps registry VTE_42


title: Scripps registry VTE_55


title: Scripps registry VTE_56


title: Scripps registry VTE_46


title: Scripps registry VTE_47


title: Scripps registry VTE_60


title: Scripps registry VTE_51


title: Scripps registry VTE_52


title: Scripps registry VTE_41


title: Scripps registry VTE_59


title: Scripps registry VTE_43


title: Scripps registry VTE_54


title: Scripps registry VTE_49


title: Scripps registry VTE_48


title: Scripps registry VTE_58


title: LEPR+ MSC - LT𝛽R-Ig [INJ-4]

city: Seoul

first: Jungmin

last: Choi

state: Seoul

address: 73, Goryeodae-ro, Seongbuk-gu

department: Department of Biomedical Sciences

country: South Korea

institute: Korea University College of Medicine

data_processing:
Sequencing reads were trimmed for bases with base quality score less than 20
Trimmed sequencing reads were aligned to mouse transcriptome mm10 using HISAT2
Transcript abundances were estimated by HTSeq-count
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file

source_name: LEPR+ MSC - LT𝛽R-Ig

extract_protocol:
Long bones were flushed with HBSS supplemented with 2% heat-inactivated FBS, 1% Penicillin/Streptomycin, 1% L-glutamine, 1% HEPES and 200 U/ml Collagenase IV. The flush out was digested for 30 min at 37C.  CD45+ and Ter119+ hematopoietic cells were magnetically depleted. The remaining cells were stained with antibodies against CD45, Ter119, CD31, CD144, LEPR and DAPI. Living CD45- Ter119- CD31- CD144- LEPR+ cells were FACS sorted into DMEM/10% FBS and re-sorted with the same strategy directly into 350 μL RLT plus buffer (Qiagen) with 3.5 μL β-mercaptoethanol. RNA was extracted from the lysates using the RNeasy® Plus Micro Kit (Qiagen)
RNA sequencing was performed using the Illumina HiSeq2500 system, with paired-end 2 x 76 bp read length

treatment_protocol: Mice were injected with 150μg control IgG1 (anti-hen egg lysozyme, HEL-Ig (CTR)) or LT𝛽R-Ig decoy (INJ) intravenously once per week for 3 weeks before bone marrow cell isolation and sorting.

value: BM LEPR+ MSC

value: bone marrow

value: LTbetaR-Ig


title: Scripps registry VTE_50


title: Scripps registry VTE_45


title: LEPR+ MSC - LT𝛽R-Ig [INJ-3]


title: Scripps registry VTE_40


title: P35_15467 Run3

city: Coventry

first: Jan

middle: J

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

institute: University of Warwick

data_processing:
Transcriptomic maps of paired-end reads were generated using bowtie-2.2.3, samtools-0.1.19, and tophat-2.0.12 against the hg19 reference genome (2014)
Transcript counts were assessed by HTSeq-0.6.1 using the reverse strand setting and intersection-non-empty mode and counts were assigned to gene ids.
Genome_build: hg19
Supplementary_files_format_and_content: Count and TPM data in .XLS format

source_name: P35_15467_endometrial cells

extract_protocol:
RNA was purified using RNA STAT-60 (AMS Bio) according to manufacturer's instructions and treated using Amplification Grade DNase I (Invitrogen) followed by ethanol precipitation and clean-up. Quality control, library preparation and sequencing were performed by the Wellcome Trust Centre for Human Genetics.
Libraries were prepared using the Illumina TruSeq Stranded mRNA sample prep kit according to manufacturer's instructions.  Paired-end 75bp sequencing was performed on Illumina HiSeq4000.

tag: lh+

tag: nk

tag: previous losses

tag: previous live births

tag: outcome after biopsy

value: Miscarriage

value: Endometrial cells


title: P36_15285 Run3

source_name: P36_15285_endometrial cells

value: Ongoing


title: HEK293_2

tag: cell line


title: Scripps registry VTE_39


title: Scripps registry VTE_38


title: LEPR+ MSC - LT𝛽R-Ig [INJ-2]

tag: tissue

tag: strain


title: Scripps registry VTE_36


title: Scripps registry VTE_34


title: LEPR+ MSC - LT𝛽R-Ig [INJ-1]


title: LEPR+ MSC - control [CTR-4]

source_name: LEPR+ MSC - control

value: HEL-Ig


title: Scripps registry VTE_26


title: Scripps registry VTE_33


title: Scripps registry VTE_35


title: P33_15410 Run3

source_name: P33_15410_endometrial cells


title: Scripps registry VTE_30


title: Scripps registry VTE_31


title: P29_15281 Run3

source_name: P29_15281_endometrial cells


title: LEPR+ MSC - control [CTR-3]


title: LEPR+ MSC - control [CTR-2]


title: Scripps registry VTE_28


title: LEPR+ MSC - control [CTR-1]


title: P32_15377 Run3

source_name: P32_15377_endometrial cells

value: Live birth


title: Scripps registry VTE_27


title: Scripps registry VTE_29


title: Scripps registry VTE_32


title: Scripps registry VTE_25


title: Scripps registry VTE_23


title: Scripps registry VTE_24


title: P27_15205 Run3

source_name: P27_15205_endometrial cells


title: lncRAP2_Dsi2_rep2

city: Cambridge

first: Juan

middle: R

last: Alvarez-Dominguez

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
Sequencing reads were aligned to the mouse genome (mm9; NCBI Build 37) using STAR v2.6.1 (Dobin et al., 2013) provided with a splice junctions databse (NCBIM37.67) and with default parameters and “--sjdbScore 2". Mapped reads from multiple sequencing lanes were merged using samtools (Li et al 2009). Gene expression based on NCBIM37.67 annotations was determined using HTSeq (Anders et al. 2015) in “union” mode.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files containing Htseq output for each sample

growth_protocol: Primary pre-adipocytes were harvested from 2-4 week-old mice subcutaneous (inguinal) white adipose tissue and differentiated in culture as described (Sun et al., 2011).

extract_protocol:
Total RNA was isolated using TRizol or QIazol reagent (LifeTechnologies/Ambion) and a miRNAeasy kit (Qiagen).
Directional cDNA libraries were prepared using an Illumina TruSeq Stranded polyA kit, pooled, and sequenced on an Illumina NextSeq platform in High Output mode across multiple lanes.

treatment_protocol: RNAi was performed as described (Isidor et al., 2016). On day 4 of differentiation, adipocytes were transfected with 5 nM siRNA (Sigma-Aldrich) using 5 μl/ml Lipofectamine RNAiMAX diluted in Opti-MEM I Reduced Serum Medium (Life Technologies). Cultures were analysed on day 6 of differentiation.


title: lncRAP2_Dsi2_rep3

value: subcutaneous (inguinal) white adipose tissue


title: P34_15443 Run3

source_name: P34_15443_endometrial cells


title: P30_15287 Run3

source_name: P30_15287_endometrial cells


title: P31_15307 Run3

source_name: P31_15307_endometrial cells


title: P28_15274 Run3

source_name: P28_15274_endometrial cells


title: lncRAP2_Dsi1_rep3


title: Scripps registry VTE_21


title: Scripps registry VTE_22


title: lncRAP2_Dsi1_rep2


title: Scripps registry VTE_19


title: P26_15177 Run3

source_name: P26_15177_endometrial cells


title: Scripps registry VTE_16


title: Scripps registry VTE_20


title: Igf2bp2_Dsi2_rep3


title: Igf2bp2_Dsi2_rep2


title: Scripps registry VTE_18


title: P24_15124 Run3

source_name: P24_15124_endometrial cells


title: lncRAP2_Dsi1_rep1


title: Scripps registry VTE_17

source_name: VTE


title: Scripps registry VTE_13


title: Scripps registry VTE_14


title: Scripps registry VTE_12


title: P22_15067 Run3

source_name: P22_15067_endometrial cells


title: P23_15121 Run3

source_name: P23_15121_endometrial cells


title: Scripps registry VTE_11


title: P21_15041 Run3

source_name: P21_15041_endometrial cells


title: Scripps registry VTE_10


title: Igf2bp2_Dsi1_rep2


title: Scripps registry VTE_37


title: Igf2bp2_Dsi1_rep1


title: P20_15033 Run3

source_name: P20_15033_endometrial cells


title: Scripps registry VTE_9


title: Scripps registry VTE_8


title: P25_15174 Run3

source_name: P25_15174_endometrial cells


title: Scripps registry VTE_15


title: Scripps registry VTE_6


title: neg_Dsi_rep3


title: Igf2bp2_Dsi1_rep3


title: neg_Dsi_rep2


title: Scripps registry VTE_4


title: neg_Dsi_rep1


title: Scripps registry VTE_2


title: Scripps registry control_211

source_name: control

value: healthy


title: Scripps registry VTE_1


title: Scripps registry control_210


title: P15_14248 Run3

source_name: P15_14248_endometrial cells


title: Scripps registry VTE_7


title: P16_14263 Run3

source_name: P16_14263_endometrial cells


title: px3_GM

first: Sylvain

last: Meloche

address: 2950, Chemin de Polytechnique

institute: Institute of Research in Immunology and Cancer

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.17 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extrimities and mapped to the mouse reference genome using STAR version 2.5.1b.
Readcounts were computed by STAR during sequence alignment based on annotations from Gencode version M13 based on Ensembl 88.
Expression values were also computed using RSEM version 1.2.28 based on Gencode version M13 transcript annotations
Genome_build: GRCm38
Supplementary_files_format_and_content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary_files_format_and_content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column)

source_name: Control stable cell line at GM

extract_protocol:
Trizol extraction and Qiagen Rneasy column purification
KAPA RNA Stranded PolyA
RNAseq (poly-A purification)

treatment_protocol: For analysis of proliferating C2C12 cells, the cells were cultured in growth medium (GM). For analysis of differentiating C2C12 cells, the cells were switched to  differentiation medium (DM) for 2 days (DM2).

value: Muscle

tag: condition

value: transfected with control plasmid


title: px3_DM2

source_name: Control stable cell line at DM2

tag: treatment


title: Scripps registry control_208


title: P14_14231 Run3

source_name: P14_14231_endometrial cells


title: P17_14292 Run3

source_name: P17_14292_endometrial cells


title: Scripps registry control_209


title: px2_GM


title: Scripps registry control_207


title: Scripps registry control_206


title: P13_14226 Run3

source_name: P13_14226_endometrial cells


title: Scripps registry control_205


title: P19_14388 Run3

source_name: P19_14388_endometrial cells


title: Scripps registry VTE_5

value: Venous thromboembolism (VTE)


title: P18_14331 Run3

source_name: P18_14331_endometrial cells


title: P12_14221 Run3

source_name: P12_14221_endometrial cells


title: Scripps registry VTE_3

source_name: VTE


title: px2_DM2


title: Scripps registry control_204


title: Scripps registry control_202


title: Scripps registry control_203


title: P11_14180 Run3

source_name: P11_14180_endometrial cells


title: px1_DM2


title: Scripps registry control_201


title: mk53_GM

source_name: Stable cell line depleted of MK5 at GM

value: transfected with px459-Mk5sg


title: Scripps registry control_198


title: Scripps registry control_199


title: Scripps registry control_200


title: P10_14131 Run3

source_name: P10_14131_endometrial cells


title: Scripps registry control_195


title: Scripps registry control_196


title: P8_14114 Run3

source_name: P8_14114_endometrial cells


title: Scripps registry control_192


title: Scripps registry control_191


title: P7_14060 Run3

source_name: P7_14060_endometrial cells


title: Scripps registry control_197

source_name: control


title: mk53_DM2

source_name: Stable cell line depleted of MK5 at DM2


title: Scripps registry control_190


title: px1_GM


title: mk52_DM2


title: Scripps registry control_193


title: mk51_DM2


title: Scripps registry control_189


title: P9_14120 Run3

source_name: P9_14120_endometrial cells


title: P6_14056 Run3

source_name: P6_14056_endometrial cells


title: P5_14046 Run3

source_name: P5_14046_endometrial cells


title: Scripps registry control_188


title: Scripps registry control_187


title: e33_GM

source_name: Stable cell line depleted of ERK3 at GM

value: transfected with px459-Mapk6sg


title: P4_14043 Run3

source_name: P4_14043_endometrial cells


title: P3_14033 Run3

source_name: P3_14033_endometrial cells


title: Scripps registry control_186


title: Scripps registry control_185


title: Scripps registry control_184


title: Scripps registry control_194


title: mk52_GM


title: P2_13244 Run3

source_name: P2_13244_endometrial cells


title: e32_GM


title: mk51_GM


title: Scripps registry control_183


title: P1_13063 Run3

source_name: P1_13063_endometrial cells


title: Scripps registry control_182


title: Scripps registry control_181


title: P36_15285 Run2

source_name: P36_15285_endometrial cells


title: e32_DM2

source_name: Stable cell line depleted of ERK3 at DM2


title: e31_GM


title: P35_15467 Run2

source_name: P35_15467_endometrial cells


title: Scripps registry control_178


title: e31_DM2


title: Scripps registry control_177


title: Scripps registry control_179


title: Scripps registry control_176


title: P34_15443 Run2

source_name: P34_15443_endometrial cells


title: e33_DM2


title: Cortex TMRM low_8

city: Hangzhou

first: DANYANG

last: HE

state: Zhejiang

address: 600 Dunyu Road Sandun Town

department: School of Life Sciences

institute: Westlake Univeristy

data_processing:
cl2fastq was used to generate fastq files
Reads passed quality control were mapped to mm10 using TopHat 2.0.10 with default parameters
Transcripts were assembled with Cufflinks-2.0.2
Gene differential expression was analyzed by DESeq2

source_name: TMRM low_8

extract_protocol:
RNA were extracted from cells using RNAClean XP beads (Backman)  Smart-seq 2
cDNA librarby was generated with NextSeq 500/550 v2.5 Kit by manufacturing protocol

tag: strain background

value: Postnaral day 9

value: cortex

tag: subset

value: low microglia


title: P33_15410 Run2

source_name: P33_15410_endometrial cells


title: Scripps registry control_175


title: Cortex TMRM low_7

source_name: TMRM low_7


title: Scripps registry control_173

source_name: control


title: P32_15377 Run2

source_name: P32_15377_endometrial cells


title: Scripps registry control_172


title: Cortex TMRM low_6

source_name: TMRM low_6


title: P31_15307 Run2

source_name: P31_15307_endometrial cells


title: Scripps registry control_170


title: Scripps registry control_171


title: Scripps registry control_169


title: Scripps registry control_180


title: P30_15287 Run2

source_name: P30_15287_endometrial cells


title: Scripps registry control_167


title: Cortex TMRM low_4

source_name: TMRM low_4


title: Scripps registry control_166


title: Scripps registry control_165


title: Scripps registry control_174


title: Cortex TMRM low_3

source_name: TMRM low_3


title: Scripps registry control_164


title: Scripps registry control_163


title: P28_15274 Run2

source_name: P28_15274_endometrial cells


title: Scripps registry control_162


title: P27_15205 Run2

source_name: P27_15205_endometrial cells


title: P29_15281 Run2

source_name: P29_15281_endometrial cells


title: Scripps registry control_161


title: Cortex TMRM low_1

source_name: TMRM low_1


title: Cortex TMRM low_2

source_name: TMRM low_2


title: Scripps registry control_160


title: Scripps registry control_159


title: Cortex TMRM high_10

source_name: TMRM high_10

value: high microglia


title: P25_15174 Run2

source_name: P25_15174_endometrial cells


title: Scripps registry control_158


title: P26_15177 Run2

source_name: P26_15177_endometrial cells


title: Cortex TMRM low_5

source_name: TMRM low_5


title: Scripps registry control_168


title: Scripps registry control_157


title: P24_15124 Run2

source_name: P24_15124_endometrial cells


title: Scripps registry control_155

source_name: control


title: Cortex TMRM high_8

source_name: TMRM high_8


title: Scripps registry control_156


title: P23_15121 Run2

source_name: P23_15121_endometrial cells


title: Scripps registry control_153


title: Scripps registry control_154


title: Cortex TMRM high_7

source_name: TMRM high_7


title: P22_15067 Run2

source_name: P22_15067_endometrial cells


title: Scripps registry control_150


title: Scripps registry control_151


title: Cortex TMRM high_6

source_name: TMRM high_6


title: Scripps registry control_152


title: Scripps registry control_149


title: P21_15041 Run2

source_name: P21_15041_endometrial cells


title: Cortex TMRM high_5

source_name: TMRM high_5


title: Scripps registry control_148


title: P20_15033 Run2

source_name: P20_15033_endometrial cells


title: Scripps registry control_147


title: Cortex TMRM high_4

source_name: TMRM high_4


title: Cortex TMRM high_9

source_name: TMRM high_9


title: P19_14388 Run2

source_name: P19_14388_endometrial cells


title: P18_14331 Run2

source_name: P18_14331_endometrial cells


title: P17_14292 Run2

source_name: P17_14292_endometrial cells


title: Scripps registry control_143


title: Cortex TMRM high_2

source_name: TMRM high_2


title: Cortex TMRM high_1

source_name: TMRM high_1


title: P16_14263 Run2

source_name: P16_14263_endometrial cells


title: Scripps registry control_141

source_name: control


title: Scripps registry control_139


title: P15_14248 Run2

source_name: P15_14248_endometrial cells


title: Scripps registry control_140


title: Scripps registry control_137


title: P14_14231 Run2

source_name: P14_14231_endometrial cells


title: Scripps registry control_136


title: P9_Het_1 [02102018_p9_1_het]

description:
02102018_p9_1_het
processed data file:
microglia.matrix.mtx, microglia.genes.tsv, microglia.barcode.tsv

data_processing:
bulk RNAseq: map to mm10 using Bowtie 2 with default parameters
bulk RNAseq: RSEM were used for calculating counts
scRNA-seq data: the 10x Genomics Cell Ranger Single Cell Software Suite 2.0.1 was used to perform sample demultiplexing and single cell UMI counting
Genome_build: mm10
Supplementary_files_format_and_content:
For bulkRNAseq data: tab-delimited text files include counts values for each sample.
For scRNA-seq data:
mtx, a gene by cell count matrix in the sparse matrix market format
barcodes.tsv, cell names (colname names of the count matrix)
genes.tsv, gene names (row names of the count matrix)
matrix.tsv, the coordinates of cells form projecting cells measured from single-cell RNA-sequencing to the bulk ImmGen dataset

growth_protocol: Briefly, brains were digested enzymatically with papain then mechanically dissociated to generate a single cell suspension, followed by density gradient separation with 40% Percoll. Cell suspensions were then positively selected for CD11b expression by CD11b magnetic bead (Miltenyi) separation using the MACS system. CD11b purified mouse microglia were cultured in PDL-coated plates at in a defined culture media containing DMEM/F-12 (Thermo Fisher Scientific, 11320033), 100U/ml penicillin, 100ug/ml streptomycin, 5 ug/ml N-acetyl cysteine, 1X N-2 Supplement (Gibco), and 10ng/ml M-CSF (R&D) with 2.5% heat inactivated FCS (Sigma).

extract_protocol:
RNA were extracted from cells using RNAClean XP beads (Backman)
10x single cell RNA-seq, Smart-seq 2

treatment_protocol: For IL33 stimulation and compound treatment assays, microglia at 7-9 days in vitro (DIV) were pretreated with 0.2uM GSK-J4 (Cayman Chemicals) for 1h and then stimulated with 200ng/ml IL33 (Biolegend) for 3hrs.

value: postnatal day 9

tag: genotype/variation

value: ST2 Het

tag: tissue/cell type

tag: experiment type

value: 3'-end scRNA-seq


title: Scripps registry control_134

tag: sample id

tag: diagnosis


title: P9_Het_2 [02102018_p9_2_het]

description:
02102018_p9_2_het
processed data file:
microglia.matrix.mtx, microglia.genes.tsv, microglia.barcode.tsv

tag: age

value: postnatal day9


title: P9_KO_1 [02102018_p9_1_ko]

description:
02102018_p9_1_ko
processed data file:
microglia.matrix.mtx, microglia.genes.tsv, microglia.barcode.tsv

value: ST2 KO


title: P9_KO_2 [02102018_p9_2_ko]

description:
02102018_p9_2_ko
processed data file:
microglia.matrix.mtx, microglia.genes.tsv, microglia.barcode.tsv


title: P12_14221 Run2

source_name: P12_14221_endometrial cells

tag: lh+

tag: nk

value: Live birth

tag: cell type

value: Endometrial cells


title: P13_14226 Run2

source_name: P13_14226_endometrial cells

tag: previous losses

tag: previous live births

tag: outcome after biopsy

value: Miscarriage


title: Scripps registry control_132

value: healthy


title: Scripps registry control_135


title: Scripps registry control_144


title: Scripps registry control_133


title: Scripps registry control_146


title: Scripps registry control_130


title: Scripps registry control_131


title: P28_cortex_2 [03232018_p28ctx_2]

description:
03232018_p28ctx_2
processed data file:
microglia.matrix.mtx, microglia.genes.tsv, microglia.barcode.tsv

value: postnatal day28

value: wild type


title: Scripps registry control_129


title: P11_14180 Run2

source_name: P11_14180_endometrial cells


title: Cortex TMRM high_3

source_name: TMRM high_3

tag: tissue


title: Scripps registry control_142


title: Scripps registry control_128


title: P9 cortex_2 [03232018_p9ctx_2]

description:
03232018_p9ctx_2
processed data file:
microglia.matrix.mtx, microglia.genes.tsv, microglia.barcode.tsv

source_name: P9 cortex


title: Scripps registry control_145


title: Scripps registry control_138


title: P10_14131 Run2

source_name: P10_14131_endometrial cells


title: P28_cortex_1 [03232018_p28ctx_1]

description:
03232018_p28ctx_1
processed data file:
microglia.matrix.mtx, microglia.genes.tsv, microglia.barcode.tsv


title: Scripps registry control_125


title: P8_14114 Run2

source_name: P8_14114_endometrial cells


title: P9_14120 Run2

source_name: P9_14120_endometrial cells


title: Scripps registry control_127


title: Scripps registry control_126


title: P7_14060 Run2

source_name: P7_14060_endometrial cells

value: Ongoing


title: Scripps registry control_124


title: Scripps registry control_123


title: Scripps registry control_122


title: MG_IL33_7 [G6_S30]

description:
G6_S30_R1_001
processed data file:
rsem.genes.counts.matrix

value: postnatal day 5-8

value: Primary microglia culture

value: full length bulk RNA-seq


title: P9 cortex_1 [03232018_p9ctx_1]

description:
03232018_p9ctx_1
processed data file:
microglia.matrix.mtx, microglia.genes.tsv, microglia.barcode.tsv

value: cortex


title: MG_IL33_6 [G5_S29]

description:
G5_S29_R1_001
processed data file:
rsem.genes.counts.matrix


title: P5_14046 Run2

source_name: P5_14046_endometrial cells


title: MG_IL33_4 [G3_S27]

description:
G3_S27_R1_001
processed data file:
rsem.genes.counts.matrix


title: Scripps registry control_117


title: Scripps registry control_121


title: Scripps registry control_119


title: Scripps registry control_118


title: P3_14033 Run2

source_name: P3_14033_endometrial cells


title: Scripps registry control_116


title: Scripps registry control_113


title: P4_14043 Run2

source_name: P4_14043_endometrial cells


title: MG_IL33_5 [G4_S28]

description:
G4_S28_R1_001
processed data file:
rsem.genes.counts.matrix


title: P6_14056 Run2

source_name: P6_14056_endometrial cells


title: Scripps registry control_115


title: MG_IL33_3 [G2_S26]

description:
G2_S26_R1_001
processed data file:
rsem.genes.counts.matrix


title: Scripps registry control_111


title: Scripps registry control_120


title: MG_IL33_2 [G1_S25]

description:
G1_S25_R1_001
processed data file:
rsem.genes.counts.matrix


title: Scripps registry control_112


title: P2_13244 Run2

source_name: P2_13244_endometrial cells


title: Scripps registry control_114

source_name: control


title: MG_IL33_1 [F12_S24]

description:
F12_S24_R1_001
processed data file:
rsem.genes.counts.matrix


title: Scripps registry control_108


title: Scripps registry control_109


title: P36_15285 Run1

source_name: P36_15285_endometrial cells


title: P1_13063 Run2

source_name: P1_13063_endometrial cells


title: MG_Medium_7 [F11_S23]

description:
F11_S23_R1_001
processed data file:
rsem.genes.counts.matrix


title: Scripps registry control_106


title: P35_15467 Run1

source_name: P35_15467_endometrial cells


title: MG_Medium_6 [F10_S22]

description:
F10_S22_R1_001
processed data file:
rsem.genes.counts.matrix


title: Scripps registry control_107


title: Scripps registry control_105


title: MG_Medium_5 [F9_S21]

description:
F9_S21_R1_001
processed data file:
rsem.genes.counts.matrix


title: P34_15443 Run1

source_name: P34_15443_endometrial cells


title: Scripps registry control_110


title: Scripps registry control_104


title: P33_15410 Run1

source_name: P33_15410_endometrial cells


title: Scripps registry control_103


title: Scripps registry control_100


title: Scripps registry control_102


title: MG_Medium_3 [F7_S19]

description:
F7_S19_R1_001
processed data file:
rsem.genes.counts.matrix


title: Scripps registry control_101


title: Scripps registry control_98


title: MG_Medium_2 [F6_S18]

description:
F6_S18_R1_001
processed data file:
rsem.genes.counts.matrix


title: P32_15377 Run1

source_name: P32_15377_endometrial cells


title: Scripps registry control_97


title: MG_Medium_1 [F5_S17]

description:
F5_S17_R1_001
processed data file:
rsem.genes.counts.matrix


title: P31_15307 Run1

source_name: P31_15307_endometrial cells


title: P30_15287 Run1

source_name: P30_15287_endometrial cells


title: Scripps registry control_99


title: Scripps registry control_94


title: Tau-GFP Neg MG_8 [F4_S16]

description:
F4_S16_R1_001
processed data file:
rsem.genes.counts.matrix

source_name: Tau-GFP Neg MG

value: postnatal day 10

value: Mapttm1(EGFP)Klt carrier

value: Cortex


title: P28_15274 Run1

source_name: P28_15274_endometrial cells


title: Tau-GFP Neg MG_7 [F2_S14]

description:
F2_S14_R1_001
processed data file:
rsem.genes.counts.matrix


title: Tau-GFP Plus MG_8 [F3_S15]

description:
F3_S15_R1_001
processed data file:
rsem.genes.counts.matrix

source_name: Tau-GFP Plus MG


title: Scripps registry control_92


title: Scripps registry control_95


title: P27_15205 Run1

source_name: P27_15205_endometrial cells


title: Scripps registry control_93


title: MG_Medium_4 [F8_S20]

description:
F8_S20_R1_001
processed data file:
rsem.genes.counts.matrix


title: Scripps registry control_91


title: P26_15177 Run1

source_name: P26_15177_endometrial cells


title: Tau-GFP Neg MG_6 [E12_S12]

description:
E12_S12_R1_001
processed data file:
rsem.genes.counts.matrix


title: Scripps registry control_87


title: Tau-GFP Plus MG_7 [F1_S13]

description:
F1_S13_R1_001
processed data file:
rsem.genes.counts.matrix


title: Scripps registry control_89


title: Scripps registry control_88


title: P25_15174 Run1

source_name: P25_15174_endometrial cells


title: Scripps registry control_85


title: Scripps registry control_86


title: Scripps registry control_96


title: Tau-GFP Plus MG_6 [E11_S11]

description:
E11_S11_R1_001
processed data file:
rsem.genes.counts.matrix


title: P29_15281 Run1

source_name: P29_15281_endometrial cells


title: Scripps registry control_84


title: P23_15121 Run1

source_name: P23_15121_endometrial cells


title: Tau-GFP Neg MG_5 [E10_S10]

description:
E10_S10_R1_001
processed data file:
rsem.genes.counts.matrix


title: P24_15124 Run1

source_name: P24_15124_endometrial cells


title: Scripps registry control_90

source_name: control


title: Tau-GFP Plus MG_5 [E9_S9]

description:
E9_S9_R1_001
processed data file:
rsem.genes.counts.matrix


title: P22_15067 Run1

source_name: P22_15067_endometrial cells


title: Scripps registry control_83


title: Scripps registry control_79


title: Scripps registry control_81


title: Scripps registry control_80


title: Scripps registry control_78


title: Tau-GFP Neg MG_4 [E8_S8]

description:
E8_S8_R1_001
processed data file:
rsem.genes.counts.matrix


title: P21_15041 Run1

source_name: P21_15041_endometrial cells


title: Scripps registry control_77


title: Scripps registry control_76


title: P20_15033 Run1

source_name: P20_15033_endometrial cells


title: Tau-GFP Neg MG_3 [E6_S6]

description:
E6_S6_R1_001
processed data file:
rsem.genes.counts.matrix


title: Scripps registry control_75


title: Scripps registry control_73


title: Scripps registry control_74


title: Scripps registry control_72


title: Tau-GFP Neg MG_2 [E4_S4]

description:
E4_S4_R1_001
processed data file:
rsem.genes.counts.matrix


title: Scripps registry control_71


title: Tau-GFP Plus MG_4 [E7_S7]

description:
E7_S7_R1_001
processed data file:
rsem.genes.counts.matrix