title: BMDM_2

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
Base calling and de-multipexing using CASAVA version 1.8.2.
Alignment was performed with HiSat2 version 2.0.6 and SAMtools version 0.1.19 using the default parameters and option --dta.
Transcriptome assembly was performed using StringTie version 1.3.2d with default parameters for each sample individually guided by GENCODE vM10 transcriptome annotation, followed by merging of the assemblies using the stringtie --merge function.
Transcript abundances were estimated by re-running StringTie using the merged transcriptome assembly with options -B -e.
Data analysis and visualization was done in R using Ballgown.
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated file (transcriptExpression.csv) containing transcript annotation, coverage as well as FPKM values determined using Ballgown. GTF file (Stringtie_mergedTranscripts.gtf) containing the merged StringTie assembly results.

source_name: BMDM

growth_protocol: Murine bone marrow cells  isolated from tibia and femur by scraping and flushing the inner surface were differentiated in vitro for 8 days using M-CSF.

extract_protocol:
RNA was isolated with trizol and miRNeasy micro kit (Qiagen) according to the manufacturer’s protocol.
Library construction was performed according to the manufacturer´s instructions using the Tru-Seq RNA library preparation kit v2. 100 ng of RNA was converted into cDNA libraries
75 bp single-end run was performed on a HiSeq1500

treatment_protocol: No treatment.

tag: mouseid


title: Control 3

status: Public on Jun 29 2020

type: SRA

city: Liege

first: Alexia

last: Hulin

address: Avenue de l'hopital 1

department: Cardiovascular Science

country: Belgium

institute: GIGA

library_source: transcriptomic

data_processing:
Raw reads were demultiplexed and adapted-trimmed using Illumina software v2.17
the first three nucleotides of each read were removed using FATSX Toolkit,
Reads aligned to oryCun2 reference genome using Tophat v2.1.1
Quality of sequencing data was controlled using Picard tools
Raw gene counts were generating using Htseq count
Independent filtering was done to remove uninformative genes using HTSFilter. Unwanted variations were identified using svaseq() and RUVr() in R Bioconductor package RUVSeq
Genome_build: oryCun2
Supplementary_files_format_and_content: tab-delimited text files include Raw gene counts for each Sample with column header corresponding to treatment (Control w1 to w5, Serotonin s1 to s5, Pergolide p1 to p5 and dexfenfluramine d1 to d5)

molecule: total RNA

organism: Oryctolagus cuniculus

source_name: Tricuspid valve

extract_protocol:
Tricuspid valves were flash frozen and total RNA was extracted using the miRNease mini Kit (quiagen)
Library were prepared using the SMARTer Stranded RNA-Seq Kit  (Clontech)

treatment_protocol: 16 weeks oral administration of serotonin (80 mg/Kg/day), pergolide (0.5 mg/Kg/day), dexfenfluramine (20mg/Kg/day) or water

tag: strain

value: New Zealand white rabbit

tag: tissue

value: Tricuspid valve

tag: treatment

value: control


title: endometrium_biopsy, day20, early-mid-secretory, 10x

city: Stanford

first: Wanxin

last: Wang

state: CA

address: James H Clark Center, 318 Campus Drive, room E300

country: USA

institute: Stanford Univeristy

description:
ct_endo_10x.rds
meta_celltypes_samplename.csv
umap_endo_10x.csv
endo_29

data_processing:
Raw reads in the *.fastq files were aligned to reference (GRCh38-3.0.0) and quantified using cellranger (3.1.0).
Downstream data analysis was performed in R using customized scripts and the Seurat package.
Raw counts were normalized to log transformed transcripts per million (log(TPM+1)) using NormalizeData() function in Seurat.
Genome_build: GRCh38-3.0.0
Supplementary_files_format_and_content: Raw counts and descriptive details for cells
ct_endo_10x.rds - raw counts for all 10x platform captured post-quality-filtered cells analyzed in this study
meta_celltypes_samplename.csv - cell type identity and sample (biopsy) of origin for each cell analyzed
umap_endo_10x.csv - umap coordinates for each cell analyzed

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
GEM generation & barcoding, reverse-transcription, cDNA generation were done following the manufacture’s protocol (Single cell 3’ reagent kits v3.1, Chromium Next GEM Chip G, 10x Genomics).
Library construction were done following the manufacture’s protocol (Single cell 3’ reagent kits v3.1, Chromium Next GEM Chip G, 10x Genomics).

tag: Sex

value: female

tag: disease state

value: healthy

tag: fecundity

value: fertile

tag: time in menstrual cycle

tag: phase

value: early-mid-secretory

value: endometrium biopsy


title: Control 2


title: endometrium_biopsy, day17, 10x

description:
ct_endo_10x.rds
meta_celltypes_samplename.csv
umap_endo_10x.csv
endo_14

value: early-secretory


title: Control 1


title: Serotonin 5

value: 16 weeks serotonin (80 mg/Kg/day) oral administration


title: breast tumour 115A

type: RNA

city: London

first: Alice

last: Gao

state: London

address: 237 Fulham Road

department: Breast Cancer Now

country: United Kingdom

institute: The Institute of Cancer Research

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol of iScan

data_processing: The data was filtered to remove any non-expressed probes using the detection p-value from Illumina. Across all samples probes for which the intensity values were not significantly different (p>0.01) from the negative controls were removed from the analysis. Following filtering the data was transformed and normalized using variance-stabilizing transformation and robust spline normalization (RSN) method in the lumi package in R. The RSN combines the features of quantile and loess normalization

label: biotin

source_name: breast tumour

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

extract_protocol: mRNA from baseline (A) and surgery (B) tumour biopsies were extracted with RNeasy Mini Kit (Qiagen), as per the manufacturer's instructions, and quantification performed using the Agilent 2100 Bioanalyzer (Santa Clara, CA, USA).

tag: timepoint

value: baseline(A)

value: breast tumour


title: Control 5


title: BMDM_1

country: Germany

organism: Mus musculus

tag: genetic background


title: cloneIDs_from_10X_54

city: Solna

first: Michael

last: Ratz

address: Solnavägen 9

department: CMB

country: Sweden

institute: Karolinska Institute

description: amplicon library

data_processing:
Chromium: Sequencing reads were processed with Cell Ranger v2.2.0 (Chromium v2) or Cell Ranger v3.0.1 (Chromium v3); Visium: Sequencing reads were processed with Space Ranger 1.0.0
Genome_build: mm10 with additional sequence representing the H2B-EGFP-N transgene
Supplementary_files_format_and_content: Chromium: filtered gene count matrix; Visium: filtered gene count matrix, aligned images, spot coordinates

source_name: brain cells

growth_protocol: mice were kept in standard housing conditions

extract_protocol:
Targeted PCR for enrichment of cloneIDs on full length cDNA obtained from sample 10x54
Chromium: Brains were dissected and single cell dissociations prepared using the Papain dissociation system with manual trituration. Purified single cell suspensions were processed according to the manufacturer's instructions. Visium: Brains were fresh frozen, 10 µm cryosections mounted and fixed on a Visium glass slide +/- immunostaining and libraries prepared according to the manufacturer's instructions. Amplicon: full length cDNA obtained during Chromium or Visium library preparation.
10X Genomics Chromium Single Cell 3' v2 and v3; 10X Visium Spatial Gene Expression; Nested PCR

treatment_protocol: barcoding of progenitor cells was achieved via in utero microinjection

tag: region

value: hippocampus

tag: age

value: barcoded

tag: replicate

tag: technology

value: Chromium Single Cell 3' v3


title: cloneIDs_from_10X_53

description: amplicon library

extract_protocol:
Targeted PCR for enrichment of cloneIDs on full length cDNA obtained from sample 10x53
Chromium: Brains were dissected and single cell dissociations prepared using the Papain dissociation system with manual trituration. Purified single cell suspensions were processed according to the manufacturer's instructions. Visium: Brains were fresh frozen, 10 µm cryosections mounted and fixed on a Visium glass slide +/- immunostaining and libraries prepared according to the manufacturer's instructions. Amplicon: full length cDNA obtained during Chromium or Visium library preparation.
10X Genomics Chromium Single Cell 3' v2 and v3; 10X Visium Spatial Gene Expression; Nested PCR

value: striatum


title: cloneIDs_from_10X_52

description: amplicon library

extract_protocol:
Targeted PCR for enrichment of cloneIDs on full length cDNA obtained from sample 10x52
Chromium: Brains were dissected and single cell dissociations prepared using the Papain dissociation system with manual trituration. Purified single cell suspensions were processed according to the manufacturer's instructions. Visium: Brains were fresh frozen, 10 µm cryosections mounted and fixed on a Visium glass slide +/- immunostaining and libraries prepared according to the manufacturer's instructions. Amplicon: full length cDNA obtained during Chromium or Visium library preparation.
10X Genomics Chromium Single Cell 3' v2 and v3; 10X Visium Spatial Gene Expression; Nested PCR

value: cortex


title: breast tumour 112B

value: surgery(B)


title: BMDM_3


title: Serotonin 4

value: New Zealand white rabbit

value: Tricuspid valve


title: breast tumour 157B

value: female


title: breast tumour 173A


title: breast tumour 195A


title: breast tumour 157A


title: brain5_str

description: gene expression library

extract_protocol:
Brains were dissected and single cell dissociations prepared using the Papain dissociation system with manual trituration. Purified single cell suspensions were processed according to the manufacturer's instructions.
Chromium: Brains were dissected and single cell dissociations prepared using the Papain dissociation system with manual trituration. Purified single cell suspensions were processed according to the manufacturer's instructions. Visium: Brains were fresh frozen, 10 µm cryosections mounted and fixed on a Visium glass slide +/- immunostaining and libraries prepared according to the manufacturer's instructions. Amplicon: full length cDNA obtained during Chromium or Visium library preparation.
10X Genomics Chromium Single Cell 3' v2 and v3; 10X Visium Spatial Gene Expression; Nested PCR

value: control


title: Serotonin 3


title: Serotonin 2


title: breast tumour 153B


title: brain4_str

description: gene expression library


title: brain5_cx

description: gene expression library


title: breast tumour 82B


title: breast tumour 153A


title: Serotonin 1


title: breast tumour 82A


title: brain4_hc

description: gene expression library


title: NR-45103_10_min_DSN

city: Jerusalem

first: Iddo

middle: Z.

last: Ben-Dov

address: Ein Kerem

department: Nephrology and Hypertension

country: Israel

institute: Hadassah Medical Center

description:
sha_mapped_reads.txt.gz
Eat

data_processing:
HiSeq 2500 standard base-calling
Mapping to Schistosoma sp. genomes using miRDeep2's mapper.pl
Genome_build: SchistoDB-38_SmansoniPuertoRico_Genome.fasta; SchistoDB-38_SjaponicumAnhui_Genome.fasta; SchistoDB-38_ShaematobiumEgypt_Genome.fasta
Supplementary_files_format_and_content: Compressed text files which are derived from miRDeep2's mapper.pl script output, using default parameters. Reads were mapped against the respective species genome.

organism: Schistosoma haematobium

extract_protocol:
TRIzol extraction followed by glycogen-fascilitated isopropanol precipitation
ligation & gel-based small RNA cDNA library (see PMID: 24489795)

tag: Stage

value: adult

tag: [rna], ng/µl

tag: host

value: hamster

tag: barcode

tag: cdna cleavage by duplex specific nuclease?

value: 10 min

tag: 3' adapter sequence

value: TAGGATCGTATGCTGTCCTCTGTGGAATTCT


title: NR-45102_10_min_DSN

description:
sha_mapped_reads.txt.gz
Bat

tag: strain

tag: Sex

value: male

value: TAACGTCGTATGCTGTCCTCTGTGGAATTCT


title: Dam-WT_rep3

city: Beijing

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

country: China

institute: State Key Laboratory of Stem Cell and Reproductive Biology

description:
DamID sequencing of WT hMSCs.
DamID sequencing of WT hMSCs.

library_source: genomic

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 human refference genome using bowtie2 or histat2 software.
Genome_build: hg19
Supplementary_files_format_and_content: Txt file of read count for RNA-seq. bw file fof RPKM normalized read cout for each 10 bp bin size for others sequencing data.

molecule: genomic DNA

source_name: Mesenchymal stem cell

growth_protocol: Human MSCs (hMSCs) were cultured in MEMa (Thermo Fisher Scientific) medium supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific (Cat:10099-141, Lot:1616964)), 0.1 mM non-essential amino acids (Thermo Fisher Scientific), 1% penicillin/streptomycin (Thermo Fisher Scientific), and 1 ng/ml bFGF (Joint Protein Central, Incheon, Korea).

extract_protocol:
For DamID-seq, genomic DNA were isolated using DNeasy Blood & Tissue Kit (Qiagen). For ChIP-seq, DNA was isolated sing phenol-chloroform-isoamylalcohol extraction and ethanol precipitation. For RNA-seq, total RNA was extracted in TRIzol (Thermo Fisher Scientific) and genomic DNA was removed using a DNA-free kit (Thermo Fisher Scientific)
For ATAC-seq, library amplified and purified using TruePrep DNA Library Prep Kit V2 for Illumina(Vazyme Biotech). For DamID-seq, the DNA library was constructed using aNEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. For ChIP-seq, the enriched fragments were constructed into libraries without the incorporation of spike-in controls via KAPA Hyper Prep Kits with PCR Library Ampli?cation/Illumina series (KK8504) following the manufacturer’s instructions. For RNA-seq, sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.
DamID-seq, ATAC-seq, ChIP-seq, and RNA-seq

tag: cell type

value: Mesenchymal stem cell

tag: genotype

value: WT hMSCs

tag: passage


title: Dam-WT_rep2


title: Dam-WT_rep1

description:
DamID sequencing of WT hMSCs.
DamID sequencing of WT hMSCs.
WT_Dam-EMD_vs_Dam.bw


title: brain3_hc

description: gene expression library

value: hippocampus

tag: treatment

value: barcoded


title: NR-44216_10_min_DSN

description:
host: Bulinus spp. snails
sha_mapped_reads.txt.gz
dct

value: Egyptian

value: not applicable

value: cercariae

value: Bulinus

value: TCCGTTCGTATGCTGTCCTCTGTGGAATTCT


title: brain4_cx

description: gene expression library

value: cortex

value: Chromium Single Cell 3' v3


title: NR-44215_10_min_DSN

description:
host: Bulinus spp. snails
sha_mapped_reads.txt.gz
bmt

value: miracidia

value: TCATCTCGTATGCTGTCCTCTGTGGAATTCT


title: Dam-SIRT7_KO_rep3

description:
DamID sequencing of SIRT7 deficient hMSCs.
DamID sequencing of SIRT7 deficient hMSCs.

value: SIRT7 defecient hMSCs


title: brain3_str

description: gene expression library

value: striatum


title: NR-45103_5_min_DSN

description:
sha_mapped_reads.txt.gz
Eaf

value: female

value: adult

value: hamster

value: 5 min

value: TAGGATCGTATGCTGTCCTCTGTGGAATTCT


title: Dam-SIRT7_KO_rep2

value: Mesenchymal stem cell


title: brain3_cx

description: gene expression library

value: barcoded


title: NR-45102_5_min_DSN

description:
sha_mapped_reads.txt.gz
Baf

value: male

value: TAACGTCGTATGCTGTCCTCTGTGGAATTCT


title: NR-44216_5_min_DSN

description:
host: Bulinus spp. snails
sha_mapped_reads.txt.gz
dcf

value: Egyptian

value: not applicable

value: cercariae

value: Bulinus


title: brain2_str

description: gene expression library

value: Chromium Single Cell 3' v2


title: brain2_hc

description: gene expression library

value: hippocampus


title: brain2_cx

description: gene expression library

value: cortex


title: Dam-EMD-WT_rep3

value: WT hMSCs


title: breast tumour 80B

value: female

tag: timepoint

value: surgery(B)

tag: tissue

value: breast tumour


title: breast tumour 107B


title: NR-44215_5_min_DSN

description:
host: Bulinus spp. snails
sha_mapped_reads.txt.gz
bmf

value: miracidia

value: 5 min

value: TCATCTCGTATGCTGTCCTCTGTGGAATTCT


title: NR-45103

description:
sha_mapped_reads.txt.gz
Ean

value: adult

value: hamster

value: no

value: TAGGATCGTATGCCGTCTTCTGCTTG


title: NR-45102

description:
sha_mapped_reads.txt.gz
Ban

value: male

value: TAACGTCGTATGCCGTCTTCTGCTTG


title: Dam-EMD-SIRT7_KO_rep3

value: Mesenchymal stem cell

value: SIRT7 defecient hMSCs


title: Dam-SIRT7_KO_rep1

description:
DamID sequencing of SIRT7 deficient hMSCs.
DamID sequencing of SIRT7 deficient hMSCs.
SIRT7_KO_Dam-EMD_vs_Dam.bw


title: brain1_hc

description: gene expression library

tag: region

value: hippocampus

tag: age

value: barcoded

value: Chromium Single Cell 3' v2


title: NR-44216

description:
host: Bulinus spp. snails
sha_mapped_reads.txt.gz
dcn

value: Egyptian

value: not applicable

value: cercariae

value: Bulinus

value: TCCGTTCGTATGCCGTCTTCTGCTTG


title: breast tumour 94B

value: female

value: surgery(B)

value: breast tumour


title: brain1_cx

description: gene expression library

value: cortex

tag: replicate

tag: technology


title: Dam-EMD-WT_rep2

value: WT hMSCs


title: breast tumour 87B


title: NR-44215

description:
host: Bulinus spp. snails
sha_mapped_reads.txt.gz
bmn

tag: Stage

value: miracidia

tag: [rna], ng/µl

value: no

value: TCATCTCGTATGCCGTCTTCTGCTTG


title: Dam-EMD-SIRT7_KO_rep2

value: Mesenchymal stem cell

value: SIRT7 defecient hMSCs


title: SIM-A9_LPS_2h_rep3

city: Berkeley

first: Markita

last: Landry

address: 106 Gilman Hall

department: Chemical Engineering

institute: University of California, Berkeley

data_processing:
Sequenced reads were pre processed using HTStream v1.0.0 for adapter sequence, low quality scores, and rRNA.
Reads were mapped to the Gencode GRCm38.p6 genome assembly using STAR aligner v2.5.4b and gene counts ouput was selected
Genome_build: Gencode M20 (GRCm38.p6)
Supplementary_files_format_and_content: Tab delimited text file containing raw counts per gene annotation

source_name: SIM-A9 microglia

growth_protocol: SIM-A9 cells were cultured in a humidified incubator (37degC, 5% CO2) in T75 flasks in DMEM/F12 containing 10% FBS, 5% horse serum, and Pen-Strep-Glut. Cells were trypsinized and plated onto a 48-well plate in growth media. 2 hours prior to start of experiment, media was replaced with 270 uL sera free DMEM/F12

extract_protocol:
Total RNA was extracted from adherent cells using Zymo Quick-RNA microprep kits according to manufacturer instructions. Poly-A magnetic beads were used to enrich mRNA.
Libraries were constructed according to Kapa Biosystems protocols. Covaris/bioruptor shearing for gDNA and Unique Dual Indexes were used.

treatment_protocol: 30 uL of 10x sample was added to wells containing cells 2 h prior to RNA extraction. Cells were incubated at 37degC and 5% CO2.

tag: cell line

tag: time point

value: 2 h

value: LPS


title: breast tumour 201A

value: baseline(A)


title: Dam-EMD-SIRT7_KO_rep1


title: brain1_str

description: gene expression library

value: striatum

value: barcoded

value: Chromium Single Cell 3' v2


title: Dam-EMD-WT_rep1


title: UCD178

city: Aurora

first: Jessica

last: Finlay-Schultz

state: CO

department: Pathology

institute: University of Colorado Denver Anschutz Medical Campus

data_processing:
adaptrer trimming was done for raw fastq files cutadapt
Alignment to the reference genome was done using STAR
the aligned bam files were indexed and sorted using samtools
sorted bam files were used for gene expression quantification using cufflinks
Genome_build: GRCh38
Supplementary_files_format_and_content: gene expression quantification

source_name: Breast cancer cell line from PDX model

growth_protocol: Cells were grown in DMEM/F12 media supplemented with 10% FBS, 10^-9M insulin, and 100 ng/mL choleratoxin

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols at the University of Colorado Denver Genomics and Microarray Core facility.

value: cell line established from patient-derived luminal breast cancer xenografts


title: SIM-A9_LPS_2h_rep2


title: breast tumour 107A

value: female


title: breast tumour 94A


title: breast tumour 195B

value: surgery(B)


title: breast tumour 80A

value: breast tumour


title: breast tumour 127A


title: breast tumour 87A


title: breast tumour 136A


title: NR-45100_10_min_DSN

description:
sja_mapped_reads.txt.gz
Cat

organism: Schistosoma japonicum

value: Chinese

value: male

value: adult

tag: host

value: mouse

tag: barcode

tag: cdna cleavage by duplex specific nuclease?

value: 10 min

tag: 3' adapter sequence

value: TAATATCGTATGCTGTCCTCTGTGGAATTCT


title: UCD115

tag: cell type


title: SIM-A9_LPS_2h_rep1


title: NR-45101_10_min_DSN

description:
sja_mapped_reads.txt.gz
Dat

tag: strain

tag: Sex

value: TAGAGTCGTATGCTGTCCTCTGTGGAATTCT


title: SIM-A9_GT6-SWNT_2h_rep3

value: 2 h

tag: treatment

value: (GT)6 SWCNT


title: UCD65


title: SIM-A9_GT6-SWNT_2h_rep2


title: NR-31803_10_min_DSN

description:
sja_mapped_reads.txt.gz
ict

value: not applicable

value: cercariae

value: lab

value: TCTCCTCGTATGCTGTCCTCTGTGGAATTCT


title: UCD46

value: cell line established from patient-derived luminal breast cancer xenografts


title: UCD12


title: SIM-A9_GT6-SWNT_2h_rep1


title: NR-45101_5_min_DSN

description:
sja_mapped_reads.txt.gz
Daf

value: female

value: 5 min


title: SIM-A9_Fura2_2h_rep3


title: SIM-A9_Fura2_2h_rep2


title: NR-45100_5_min_DSN

description:
sja_mapped_reads.txt.gz
Caf


title: UCD4

value: cell line established from patient-derived luminal breast cancer xenografts (PDX)


title: breast tumour 127B

tag: timepoint

value: surgery(B)

tag: tissue

value: breast tumour


title: SPG cultured with AKT-I+FGF2 Rep2

city: La Jolla

first: Kun

last: Tan

address: 2880 Torrey Pines Scenic Dr. Room 4812

department: Department of Obstetrics, Gynecology, and Reproductive Sciences

institute: UCSD

description:
AKT-I+FGF2_Rep2_barcodes.tsv
AKT-I+FGF2_Rep2_features.tsv
AKT-I+FGF2_Rep2_matrix.mtx

data_processing:
For bulk RNA-Seq, Reads were filtered for quality and aligned with STAR (2.5.2b) against Homo sapiens, release-95, Ensembl genome (GRCh38). The exon counts were aggregated for each gene to build a read count table using SubRead function featureCounts. Differentially regulated genes were calculated using DESeq2. For differentially regulated genes a threshold (log2FC ≥ 1 or ≤ –1, q-val < 0.01) was followed. The R package pheatmap was used for clustering and heatmap plotting. The database for annotation, visualization and integrated discovery (DAVID) v6.8 was used for gene ontology analysis. The Ingenuity pathway analysis (IPA) was used for signaling pathway and genetic regulatory network analysis.
For single cell RNA-Seq, Demultiplexed raw sequencing reads were processed and mapped to the human genome (GRCh38) using Cell Ranger software (v3.0.2) with default parameters. Filtered count matrices for each library were tagged with a library batch ID and combined across independent experiments using the Seurat package (version 3.1.0) in R. To identify cell clusters, we employed Pathway and Geneset OverDispersion Analysis (PAGODA2). Single-cell pseudotime trajectories were constructed with the Monocle 2 package (v2.10.1).
Genome_build: GRCh38
Supplementary_files_format_and_content: For bulk RNA-Seq, processed data files are: fcounts.   For single cell RNA-Seq, processed data files are: matrix of genes, counts and cell barcodes.

source_name: human testicular cells

growth_protocol: For single cell RNA-Seq, Integrin-6 (ITGA6)+ SPG were purified from the isolated human testicular cells, and plated in 24-well plate pre-coated with laminin (20 μg/ml). The culture media are IMDM/SFM plus different growth factors or molecular inhibitor. Cells were passaged by incubation in StemPro accutase solution (Thermo Fisher Scientific) for 5 min.

extract_protocol:
For bulk RNA-Seq, total RNAs were extracted using the RNeasy Plus Micro Kit (Qiagen) according to the manufacturer’s protocol.   For single cell RNA-Seq, cells were incubated in StemPro accutase solution for 5 min. Single cell suspension were diluted for loading on Chromium chip for 10X Genomics library preparation and subsequent sequencing.
For bulk RNA-Seq, 10 ng of total RNA was subjected to prep the library using SMARTer® stranded total RNA-Seq kit v2 - pico input system (Takara Bio USA) per manufacturer's instructions.   For single cell RNA-Seq, Viable cells were washed once in PBS and resuspended in 0.04% BSA in PBS for loading on the 10x Chromium chip. Cell capturing, and library preparation was carried as per kit instructions (Chromium Single Cell 3′ Library Construction Kit v3).

treatment_protocol: For single cell RNA-Seq, cells were cultured under different conditions (FGF2 alone vs AKT-I+FGF2). Before loading for library prep, dead cells were removed using the ClioCell Dead Cell Removal kit (Amsbio) following the manufacturers’ instructions.

value: Testis biopsy

tag: age


title: breast tumour 39B


title: breast tumour 37A

value: baseline(A)


title: breast tumour 136B


title: breast tumour 39A


title: breast tumour 2A


title: SIM-A9_Fura2_2h_rep1


title: breast tumour 37B


title: SIM-A9_DiBASC2_2h_rep3


title: NR-31802_5_min_DSN

description:
sja_mapped_reads.txt.gz
Aef

value: eggs

value: mouse

value: TTAAGTCGTATGCTGTCCTCTGTGGAATTCT


title: NR-43232_10_min_DSN

description:
sja_mapped_reads.txt.gz
fat

value: Philippine

value: pooled male and female

value: adult

value: mouse?

value: 10 min

value: TCGATTCGTATGCTGTCCTCTGTGGAATTCT


title: SPG cultured with FGF2 alone Rep2

description:
FGF2_Rep2_barcodes.tsv
FGF2_Rep2_features.tsv
FGF2_Rep2_matrix.mtx


title: breast tumour 25B


title: SPG cultured with AKT-I+FGF2 Rep1

description:
AKT-I+FGF2_Rep1_barcodes.tsv
AKT-I+FGF2_Rep1_features.tsv
AKT-I+FGF2_Rep1_matrix.mtx


title: SIM-A9_DiBASC2_2h_rep2

value: 2 h


title: NR-43232_5_min_DSN

description:
sja_mapped_reads.txt.gz
faf


title: breast tumour 2B

value: female


title: SPG cultured with FGF2 alone Rep1

description:
FGF2_Rep1_barcodes.tsv
FGF2_Rep1_features.tsv
FGF2_Rep1_matrix.mtx


title: NR-45101

description:
sja_mapped_reads.txt.gz
Dan

value: Chinese

value: no

value: TAGAGTCGTATGCCGTCTTCTGCTTG


title: cloneIDs_from_10X_66

description: amplicon library

extract_protocol:
Targeted PCR for enrichment of cloneIDs on full length cDNA obtained from sample 10x66
Chromium: Brains were dissected and single cell dissociations prepared using the Papain dissociation system with manual trituration. Purified single cell suspensions were processed according to the manufacturer's instructions. Visium: Brains were fresh frozen, 10 µm cryosections mounted and fixed on a Visium glass slide +/- immunostaining and libraries prepared according to the manufacturer's instructions. Amplicon: full length cDNA obtained during Chromium or Visium library preparation.
10X Genomics Chromium Single Cell 3' v2 and v3; 10X Visium Spatial Gene Expression; Nested PCR

tag: region

value: hippocampus

value: barcoded

tag: replicate

value: Chromium Single Cell 3' v3


title: hMSCs NIR 2

city: Bryan

first: Irtisha

last: Singh

state: TX

address: 8447 Riverside Pkwy Medical Research and Education Building II

institute: Texas A&M Health Science Center

description: NIR treatment

data_processing:
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's NCS 1.0.2 and RFV 1.0.2 software with default parameter settings. Sequencer .cbcl basecall files were demultiplexed and formatted into .fastq files using bcl2fastq 2 2.19.0 script configureBclToFastq.pl.
Sequenced reads were trimmed for adaptor sequence and aligned by STAR aligner
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons (excluding 5UTR and 3UTR) of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library (only reads mapping to annotated regions of the genome were used for the total libraray size).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all samples

source_name: Mesenchymal stem cells

growth_protocol: hMSCs were cultured under normal media conditions consisting of α-minimal essential media (alpha-MEM, Hyclone, GE Sciences) with 16.5% fetal bovine serum (Atlanta Biologicals, USA) and 1% penicillin/streptomycin (100 U/100 µg/mL, Gibco). After every 2-3 days, half of culture media was exchanged for fresh media. Cells were passaged with 0.5% trypsin-EDTA upon reaching confluency of ~70% and seeded at ~2500 cells/cm2. All experiments were completed with cell populations under P5.

extract_protocol:
At the end of 7 days of culture, total RNA was extracted (High Pure RNA Isolation, Roche Life Sciences), and then converted into cDNA (>1 μg).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: hMSCs were cultured and treated with/without low-intensity NIR exposure and/or exfoliated MoS2 (25 µg/mL, 48 h).

value: Bone marrow derived mesenchymal stem cells


title: NR-31803_5_min_DSN

description:
sja_mapped_reads.txt.gz
icf

value: not applicable

tag: Stage

value: cercariae

value: lab

value: 5 min

value: TCTCCTCGTATGCTGTCCTCTGTGGAATTCT


title: hMSCs NIR 1

description: NIR treatment


title: cloneIDs_from_10X_67

description: amplicon library

extract_protocol:
Targeted PCR for enrichment of cloneIDs on full length cDNA obtained from sample 10x67
Chromium: Brains were dissected and single cell dissociations prepared using the Papain dissociation system with manual trituration. Purified single cell suspensions were processed according to the manufacturer's instructions. Visium: Brains were fresh frozen, 10 µm cryosections mounted and fixed on a Visium glass slide +/- immunostaining and libraries prepared according to the manufacturer's instructions. Amplicon: full length cDNA obtained during Chromium or Visium library preparation.
10X Genomics Chromium Single Cell 3' v2 and v3; 10X Visium Spatial Gene Expression; Nested PCR

value: striatum

tag: technology


title: NR-45100

description:
sja_mapped_reads.txt.gz
Can

value: male

value: adult

tag: [rna], ng/µl

value: mouse

value: TAATATCGTATGCCGTCTTCTGCTTG


title: NR-31802

description:
sja_mapped_reads.txt.gz
Aen

value: eggs

value: TTAAGTCGTATGCCGTCTTCTGCTTG


title: SIM-A9_Di2ANEQPEQ_2h_rep1

tag: cell line

tag: time point

value: 2 h


title: Sample_5.KO3_GCB

city: Farmington

first: Sheng

last: Li

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

data_processing:
Library strategy: DNA-Seq
Raw reads were trimmed using TrimGalore (version 0.4.0) (89), using settings: --stringency 3 -q 20
Trimmed reads were mapped to the GRCm38.p3 reference genome using BWA-Mem (version 0.7.9a) with the default parameters.
Variants were called  with LoFreq program (version 2.1.3.1).
Then, using bcftools (version 1.8), called variants were additionally filtered, excluding all known single-nucleotide polymorphisms (European Variation Archive accession GCA_000001635.6).
Separately, previously filtered reads for the analysis with the Immcantation pipeline. More specifically, the AssemblePairs.py, FilterSeq.py, CollapseSeq.py, and SplitSeq.py tools were used to construct clones of the JH4 and Sμ regions represented by at least two pairs of paired-end reads.
Genome_build: GRCm38
Supplementary_files_format_and_content: *.lofreq_vars.vcf.gz files contain the output calls from LoFreq program

source_name: Germinal Center B-cells

growth_protocol: GC B-cells (B220+Fas+GL7+) were isolated from mouse spleen

extract_protocol:
Genomic regions, JH4 (chr12:113,427,959-113,428,543) and Sμ (chr12:113,425,655-113,426,278), were PCR amplified, pooled and cleaned up using the MinElute PCR Purification Kit (Qiagen).
Illumina TruSeq DNA Sample Preparation Kit v2 (Illumina)

treatment_protocol: Not applicable

value: spleen

tag: genotype

value: TET2 Wild-Type


title: breast tumour 25A

value: female

value: baseline(A)

value: breast tumour


title: breast tumour 21B

value: surgery(B)


title: NR-31803

description:
sja_mapped_reads.txt.gz
icn

value: not applicable

value: cercariae

tag: host

value: lab

tag: barcode

tag: cdna cleavage by duplex specific nuclease?

value: no

value: TCTCCTCGTATGCCGTCTTCTGCTTG


title: hMSCs NIR MoS2 1

description: NIR MoS2 treatment

tag: cell type

value: Bone marrow derived mesenchymal stem cells


title: Sample_4.KO1_GCB

tag: strain


title: SIM-A9_DiBASC2_2h_rep1

tag: treatment


title: SIM-A9_COOH-SWNT_2h_rep3

value: Carboxylated SWCNT


title: hMSCs MoS2 2

description: MoS2 treatment


title: NR-43232

description:
sja_mapped_reads.txt.gz
fan

value: Philippine

tag: Sex

value: pooled male and female

value: adult

value: mouse?

tag: 3' adapter sequence

value: TCGATTCGTATGCCGTCTTCTGCTTG


title: hMSCs MoS2 1

description: MoS2 treatment


title: Sample_3.WT3_GCB

tag: tissue

value: spleen

value: TET2 Knock-Out


title: SIM-A9_COOH-SWNT_2h_rep2

value: 2 h


title: SIM-A9_COOH-SWNT_2h_rep1


title: Sample_2.WT2_GCB


title: SIM-A9_Di2ANEQPEQ_2h_rep3


title: hMSCs 2

description: Control


title: cloneIDs_from_10X_65

description: amplicon library

extract_protocol:
Targeted PCR for enrichment of cloneIDs on full length cDNA obtained from sample 10x65
Chromium: Brains were dissected and single cell dissociations prepared using the Papain dissociation system with manual trituration. Purified single cell suspensions were processed according to the manufacturer's instructions. Visium: Brains were fresh frozen, 10 µm cryosections mounted and fixed on a Visium glass slide +/- immunostaining and libraries prepared according to the manufacturer's instructions. Amplicon: full length cDNA obtained during Chromium or Visium library preparation.
10X Genomics Chromium Single Cell 3' v2 and v3; 10X Visium Spatial Gene Expression; Nested PCR

tag: region

value: cortex

tag: age

value: barcoded

value: Chromium Single Cell 3' v3


title: Sample_1.WT1_GCB


title: breast tumour 21A

value: female

tag: timepoint

value: baseline(A)

value: breast tumour


title: hMSCs NIR MoS2 2

description: NIR MoS2 treatment


title: SIM-A9_Di2ANEQPEQ_2h_rep2


title: neonatal Cardiomyocytes IP PE 2

city: Heidelberg

first: Mirko

last: Volkers

address: INF 410

institute: University Hospital Heidelberg

description: CPEB4 IP eluate

data_processing:
Reads were trimmed with Cutadapt (v2.5) and mapped to rat genome (Rnor_6.0) with STAR (v2.7) and summarized with featureCounts (v1.6.4)
DESeq2 (Love et al., 2014) with  IHW (Ignatiadis et al., 2016) for multiple hypothesis correction was used to determine significantly enriched RNAs in IP samples vs corresponding input controls (adjusted p-value < 0.1; log2 fold-change > 0.5).
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: heart

growth_protocol: Ventricular cardiomyocytes from 1 to 2 day old Wistar rats neonatal hearts (NRCMs) were prepared by trypsin digestion and percoll gradient separation. Myocytes were treated with phenylephrine for 24h and Cpeb4 was immunoprecipitated.

extract_protocol:
NRVCMs were harvested in polysomal lysis buffer  and sonicated for complete lysis. Lysate was incubated with Cpeb4 AB overnight at 4°C, then for 1h at RT with prepared dynabeads sheep anti rabbit IgG.  Coprecipiate was washed 3x with wash buffer (polysomal buffer, 10% Triton, DNase I), three times with high salt buffer (polysomal buffer + 1M KCl, 10% Triton, DNase I) and once with wash buffer. RNA was eluted by addition of Trizol and following RNA clean-up. Lexogen Quant-Seq kit was used for library generation following the manufactures instruction. Libraries were multiplexed and sequenced on a NextSeq550.
exogen Quant-Seq kit was used for library generation following the manufactures instruction using 200ng of isolated RNA. RT was performed with 15cycles.

treatment_protocol: Immunprecipiation against Cpeb4 overnight from 10million myocyters

value: Wistar

value: neonatal Cardiomyocytes

value: PE

tag: rip antibody

value: Cpeb4 Antibody (Sigma Aldrich, catalog# HPA038394, lot# A103984)

tag: sample type

value: Isolated RNA after CPEB4 IP


title: neonatal Cardiomyocytes IP PE 1

description: CPEB4 IP eluate


title: neonatal Cardiomyocytes IP PE 3

description: CPEB4 IP eluate


title: neonatal Cardiomyocytes IP3

description: CPEB4 IP eluate

value: mock


title: SIM-A9_Control_2h_rep2

tag: cell line

value: Untreated


title: a3V2

city: Nanjing

first: Peng

last: Hua

state: Jiangsu

address: 101 Longmiandadao

department: State Key Laboratory of Reproductive Medicine and Offspring Health

institute: Nanjing Medical University

description:
3V2
Vehicle/cytokines expanded
mRNA
processed data file: features_counts_ucsc.txt

data_processing:
Forty (40) million reads per sample were gained and raw files of the same sample from different lanes were merged into a single file using Samtools (1.3). Processed files were then aligned using STAR (2.4.2a) against the human genome (UCSC hg38) and the quality was also checked by fastQC (0.10.1). The non-adjusted read counts for each gene were assessed statistically for global differential expression between the specified populations using the edgeR package (3.22.2) on R (3.5.1). Genes that are significant at a 1% false discovery rate (calculated using a Benajmini-Hochberg adjusted p-value) were considered differentially expressed between populations as described 14. Gene ontology enrichment was assessed using the topGO package (2.32.0) and pathway enrichment was analysed on the ReactomePA package (1.24.0).
Genome_build: GRCh38-1.2.0
Supplementary_files_format_and_content: features_counts_ucsc.txt: Tab-delimited text file

source_name: cord blood

extract_protocol: RNA was isolated from 100,000 unexpanded, CPI203 (150nM) or vehicle (0.1% DMSO) expanded cord blood CD133 cells using RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer’s protocol. mRNA capture and cDNA synthesis was using KAPA mRNA Hyper Kit for Illumina platform (KAPA) according to the manufacturer’s protocol. After quality check using Qubit High-sensitivity kit (Life Technologies), 16 cycles of PCR was performed for amplifying each library. Each experiment starting from cell expansion was performed duplicately using cells from three different biological donors.

treatment_protocol: Cells were thawed and cultured overnight (20-24hs) in 24-well flat bottom plates at 50,000 cells/ml in serum-free Stem Span ACF media (Stem Cell Technologies) supplemented cytokines (SCF, FLT-3L (both at 100ng/ml) and TPO (20ng/ml) all from R&D Systems) at 37oC, 5% CO2, 95% humidity. On day 0, cells were harvested, counted using Countbright absolute counting beads (Molecular Probes) by flow cytometry and plated onto corning 24-well plates  at an optimised cell density of 5,000 cells/ml in Stem Span ACF supplemented with 3 cytokines as described. Cells were either treated with CPI203 at 150nM in DMSO or an equivalent amount of vehicle (0.1% DMSO, Sigma) then harvested for downstream assays on day 5.

value: Cord blood CD133+ cells

value: DMSO expanded

tag: donor


title: neonatal Cardiomyocytes IP2

description: CPEB4 IP eluate


title: SIM-A9_Control_2h_rep1

tag: time point


title: SIM-A9_AAV_2h_rep3

value: AAV


title: neonatal Cardiomyocytes IP1

description: CPEB4 IP eluate


title: neonatal Cardiomyocytes Input PE 3

description: Input total RNA

value: Input total RNA


title: a2V1

description:
2V1
Vehicle/cytokines expanded
mRNA
processed data file: features_counts_ucsc.txt


title: SIM-A9_AAV_2h_rep1

value: 2 h


title: SIM-A9_Control_2h_rep3


title: a2V2

description:
2V2
Vehicle/cytokines expanded
mRNA
processed data file: features_counts_ucsc.txt


title: a1V2

description:
1V2
Vehicle/cytokines expanded
mRNA
processed data file: features_counts_ucsc.txt


title: a1V1

description:
1V1
Vehicle/cytokines expanded
mRNA
processed data file: features_counts_ucsc.txt


title: hMSCs 1

description: Control

value: Bone marrow derived mesenchymal stem cells


title: adult T-cell lymphoblastic lymphoma specimens 6

city: Guangzhou

first: Xiao-Peng

last: Tian

address: 651 Dong Feng RD East

department: Department of Medical Oncology

institute: Sun Yat-sen University Cancer Center

description: lymph node biopsy or puncture

hyb_protocol: The labeled RNAs were then hybridized to Affymetrix Human Gene 2.0 ST GeneChips (Affymetrix, Santa Clara, CA, USA) under the support of Hybridization Oven 645 (Affymetrix) and Fluidics Station 450 (Affymetrix) following the manufacturer’s instructions.

scan_protocol: All slides were scanned with a GeneChip Scanner 3000 (Affymetrix) and Command Console Software 3.1(Affymetrix).

data_processing: The signal value which was normalized by gene level parameters in Console software was transformed to log2 formation. Significant analysis of microarray (SAM) was performed to identify differentially expressed mRNAs between progressive and progression-free tissues, with fold-change > 2.5 and associated p < 0.05 indicating significant differences.

label: Biotin

label_protocol: Encore Biotin Module (NuGEN) was used for fragmentation and labeling

extract_protocol: Total cellular RNA was extracted from 6 FFPE samples using the QIAGEN FFPE RNeasy kit (QIAGEN GmbH, Hilden, Germany) and amplified with the Ovation FFPE WTA system (NuGEN, San Carlos, CA, USA).

tag: phenotype

value: Drug resistance


title: RNA_Macrophages_HO1-KO2

city: Gosselies

first: Stanislas

last: Goriely

address: Rue Adrienne Bolland 8

institute: Université Libre de Bruxelles

description: ATAC-seq in mouse macrophages from HO1-KO sample

data_processing:
Adapters were removed with Trimmomatic-0.36 with the following parameters: Truseq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 HEADCROP:4
Reads were then mapped to the reference genome mm10 by using STAR_2.5.3 software with default parameters
Reads from the alignment were sorted and indexed according to chromosomes
Read counts in the alignment BAM-files that overlap with the gene features were obtained using HTSeq-0.9.1 with “--nonunique all” option
Raw read counts were normalized and a differential expression analysis was performed with DESeq2 by applying an adjusted p-value <0.05 and an absolute log2-ratio larger than 1
Genome_build: mm10
Supplementary_files_format_and_content: Excel file containing differential expression analysis results and csv file containing normalized read counts (such as total read count=20M) for each sample and gene

source_name: Peripheral blood

extract_protocol:
TAMs were isolated by FACS in RLT buffer and flash frozen. RNA extraction was performed using RNeasy kit (Qiagen) and sample quality was tested on a 2100 Bioanalyzer (Agilent)
Libraries were prepared using Ovation® SoLo RNA-Seq system (NuGEN Technologies) and underwent paired-end sequencing (25×106 paired-end reads/sample, Novaseq 6000 platform)

value: macrophages

tag: genotype


title: adult T-cell lymphoblastic lymphoma specimens 5

description: lymph node biopsy or puncture

value: male


title: adult T-cell lymphoblastic lymphoma specimens 2

description: lymph node biopsy or puncture

value: Drug Susceptibility


title: RNA_Macrophages_HO1-KO3


title: neonatal Cardiomyocytes Input PE 1

description: Input total RNA

value: Wistar


title: adult T-cell lymphoblastic lymphoma specimens 4

description: lymph node biopsy or puncture


title: Fibach_Scl_rep1

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

institute: The University of Oxford

data_processing:
Library Strategy: ChIP-seq
Mapping : bowtie -m 2 --maxIns 350, hg19
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks (ucsctools bedGraphToBigWig)
genome build: hg26
processed data files format and content: bigWig : DEEPtools bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above)from bam to bigwig,  (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30)

source_name: Erythroid culture

growth_protocol: Erythroid cells were differentiated in a two-phase liquid culture as described (Pope et al 2000 PMID 10863975; Fibach & Prus 2005 PMID 18432954). Briefly, peripheral blood mononuclear cells were isolated using Ficoll-Histopaque and cultured in phase I medium (Complete MEM, 10% (v/v) preselected FBS, 1µg/ml cyclosporin A, 10% (v/v) conditioned medium from 5637 human bladder carcinoma cell line) which lacks erythropoietin (EPO). After 7 days non-adherent cells were washed with MEM and transferred to Phase II media (Complete MEM, 30% (v/v) preselected FBS, 1% (w/v) demonised BSA, 0.1 mM 2-mercaptoethanol, 10µM dexamethasone, 0.3 mg/ml human holo-transferrin, 10 ng/ml human recombinant stem cell factor, 1 U/ml human EPO) for a further 6 days. Cells were fixed with formaldehyde for ChIP-seq (1% v/v) and NG CaptureC (2% v/v).

extract_protocol: ChIP-seq was carried out using ChIP Kit (17-295, Upstate Cell Signalling, now Millipore) following the manufacturers instructions. Briefly 10^7 cells and nuclei were lysed for 10 minutes before chromatin was sheared by sanitation in a Bioruptor (High: 10 min, 30sec on, 30 sec off). Insoluable material was pelleted and supernatant was incubated overnight with the relevant antibody. Antibodies were then conjugated to protein A-agarose and washed. DNA was extracted using phenol-chloroform followed by ethanol precipitation with yeast tRNA carrier. Samples were submitted to Oxford Genomics Center for indexing and sequencing (50 bp Illumina Genome Analyzer II).

value: Erythroid culture

tag: gender

value: Male

tag: antibody

value: SCL (C. Porcher - WIMM, Oxford University)


title: neonatal Cardiomyocytes Input 2

description: Input total RNA

tag: strain

tag: cell type

value: neonatal Cardiomyocytes


title: RNA_Macrophages_HO1-KO1


title: Fibach_Scl_rep2

data_processing:
Library Strategy: ChIP-seq
Mapping : bowtie -m 2 --maxIns 350, hg19
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks (ucsctools bedGraphToBigWig)
genome build: hg27
processed data files format and content: bigWig : DEEPtools bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above)from bam to bigwig,  (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30)


title: adult T-cell lymphoblastic lymphoma specimens 1

description: lymph node biopsy or puncture

tag: Sex

value: female


title: a3B2

description:
3B2
CPI203/cytokines expanded
mRNA
processed data file: features_counts_ucsc.txt

tag: treatment

value: CPI203 expanded


title: a3V1

description:
3V1
Vehicle/cytokines expanded
mRNA
processed data file: features_counts_ucsc.txt

value: Cord blood CD133+ cells


title: neonatal Cardiomyocytes Input PE 2

description: Input total RNA

value: PE


title: SIM-A9_AAV_2h_rep2

value: AAV


title: Fibach_Pol2

data_processing:
Library Strategy: ChIP-seq
Mapping : bowtie -m 2 --maxIns 350, hg19
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks (ucsctools bedGraphToBigWig)
genome build: hg25
processed data files format and content: bigWig : DEEPtools bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above)from bam to bigwig,  (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30)

tag: tissue

value: Pol2 (sc-9001; Santa Cruz)


title: a3B1

description:
3B1
CPI203/cytokines expanded
mRNA
processed data file: features_counts_ucsc.txt


title: RNA_Macrophages_WT2

description: ATAC-seq in mouse macrophages from HO1-wild type sample

value: Wild Type


title: RNA_Macrophages_WT3


title: Fibach_NFE2_rep2

data_processing:
Library Strategy: ChIP-seq
Mapping : bowtie -m 2 --maxIns 350, hg19
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks (ucsctools bedGraphToBigWig)
genome build: hg24
processed data files format and content: bigWig : DEEPtools bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above)from bam to bigwig,  (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30)

value: NF-E2 (sc-477; Santa Cruz)


title: Fibach_NFE2_rep1

data_processing:
Library Strategy: ChIP-seq
Mapping : bowtie -m 2 --maxIns 350, hg19
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks (ucsctools bedGraphToBigWig)
genome build: hg23
processed data files format and content: bigWig : DEEPtools bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above)from bam to bigwig,  (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30)


title: RNA_Macrophages_WT1


title: a1B2

description:
1B2
CPI203/cytokines expanded
mRNA
processed data file: features_counts_ucsc.txt


title: neonatal Cardiomyocytes Input 3

description: Input total RNA

value: mock

value: Input total RNA


title: adult T-cell lymphoblastic lymphoma specimens 3

description: lymph node biopsy or puncture

value: male


title: a2B2

description:
2B2
CPI203/cytokines expanded
mRNA
processed data file: features_counts_ucsc.txt


title: a1B1

description:
1B1
CPI203/cytokines expanded
mRNA
processed data file: features_counts_ucsc.txt


title: ATAC_Macrophages_WT2

data_processing:
Adapters were removed with TrimmomaticPE with the following parameters : LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Reads were aligned to mm10 by Bowtie2 with the following parameters: –X 2000 –fr –very-sensitive –no-discordant –no-mixed –non-deterministic
Reads from the alignment were sorted and indexed according to chromosomes
Duplicate reads were filtered out using MarkDuplicate tool from Picard suite
Reads mapping within the blacklist of the ENCODE project were removed with a custom script and samtools view
Peak calling was performed with MACS2 callpeak, using standard parameters for paired-end reads and q-value threshold=0.05
Genome_build: mm10
Supplementary_files_format_and_content: Bed: peaks ; bigwig: signal

source_name: Peripheral Blood

extract_protocol:
20 000 sorted TAMs were collected in 1mL of PBS + 3% FBS at 4°C.Cells were centrifuged, then cell pellets were resuspended in 50 μL of lysis buffer (Tris HCl 10 mM, NaCl 10 mM, MgCl2 3 mM, Igepal 0,1%) and centrifuged (500 g) for 10 minutes at 4°C. Supernatant was discarded and nuclei were resuspended in 50 μL of reaction buffer (Tn5 transposase 2,5 μL, TD buffer 22,5 μL and 25 μL H2O – Nextera DNA sample preparation kit, Illumina). Tagmentation was performed for 30 minutes at 37°C. DNA was purified using the MinElute purification kit (QIAGEN).
Purified DNA was amplified and indexed by PCR using NEBNext High-Fidelity 2× PCR Master Mix (New England Biolabs) with 10-12 cycles. Llibraries were purified using MinElute PCR Purification Kit (Qiagen) and quality controlled using a Bioanalyzer High-Sensitivity DNA Analysis kit (Agilent).

value: macrophages


title: Fibach_H3K27me3

data_processing:
Library Strategy: ChIP-seq
Mapping : bowtie -m 2 --maxIns 350, hg19
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks (ucsctools bedGraphToBigWig)
genome build: hg20
processed data files format and content: bigWig : DEEPtools bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above)from bam to bigwig,  (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30)

value: H3K27me3 (07-499; Millipore)


title: Fibach_H3K4me1

data_processing:
Library Strategy: ChIP-seq
Mapping : bowtie -m 2 --maxIns 350, hg19
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks (ucsctools bedGraphToBigWig)
genome build: hg21
processed data files format and content: bigWig : DEEPtools bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above)from bam to bigwig,  (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30)

value: Erythroid culture

value: H3K4me1 (07-436; Millipore)


title: Fibach_H3K4me3

data_processing:
Library Strategy: ChIP-seq
Mapping : bowtie -m 2 --maxIns 350, hg19
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks (ucsctools bedGraphToBigWig)
genome build: hg22
processed data files format and content: bigWig : DEEPtools bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above)from bam to bigwig,  (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30)

value: Male

value: H3K4me3 (07-473; Millipore)


title: Fibach_CTCF

data_processing:
Library Strategy: ChIP-seq
Mapping : bowtie -m 2 --maxIns 350, hg19
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks (ucsctools bedGraphToBigWig)
genome build: hg19
processed data files format and content: bigWig : DEEPtools bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above)from bam to bigwig,  (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30)

value: CTCF (07-729; Millipore)


title: Line 17 Input

city: Sacramento

first: Paul

last: Knoepfler

address: 2425 Stockton Blvd, Room 633

department: Cell Biology and Human Anatomy

institute: University of California Davis

data_processing:
Reads were called with illumina bclfastq
Reads were aligned to the hg19 genome with BWA (version 0.7.13-r1126 )
Peaks were called with MACS2 (version 2.1.0.20151222)
Differential peak occupancy analysis was performed with DiffBind (R version 3.5.2)
Downstream analysis was performed on the Galaxy webserver
Genome_build: hg19
Supplementary_files_format_and_content: bed files of peaks

source_name: Line XVII DIPG

growth_protocol: All DIPG cells were cultured in Tumor Stem Medium (Nagaraja et al, 2017), which contains DMEM/F12 1:1 (Invitrogen), Neurobasal-A (Invitrogen), 10mM HEPES (Invitrogen), 1X MEM sodium pyruvate (Invitrogen), 1X MEM nonessential amino acids (Invitrogen), 1% GlutaMax (Invitrogen), human-bFGF (20 ng/ml) (Shenandoah), human-EGF (20 ng/ml) (Shenandoah), human PDGF-A and PDGF-B (20ng/ml) (Shenandoah), heparin (10 ng/ml) (StemCell Technologies) and B27 without Vitamin A (Invitrogen).

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibodies to H3K27me3 (Cell Signaling C36B11) or H3.3  (Millipore #09-838).
Libraries were prepared with the Nextera library prep kit
Libraries were sequenced on the NovaSeq machine with 150 base paired-end sequencing

treatment_protocol: Single-stranded donor oligonucleotide (ssODN) templates were designed with the desired mutations to facilitate homology directed repair (HDR) after cleavage of H3F3A by Cas9n. cells were co-transfected with a combination of pSpCas9n(BB)-2A-GFP-guideA (0.5μg/well), pSpCas9n(BB)-2A-Puro-guideB (0.5μg/well), and ssODN HDR (1μg/well) template using XtremeGene-HP (Sigma).

tag: histone h3.3 status

value: mutant (K27M)


title: Line 13 WT_Input

source_name: Line XIII DIPG

value: WT


title: Line 17 WT


title: ATAC_Macrophages_KO2-HO1


title: ATAC_Macrophages_KO1-HO1


title: Line 13 Input


title: F9 differentiated [methylRAD]

city: West Lafayette

first: Humaira

last: Gowher

state: IN

address: 175 South University St.

department: Department of Biochemistry

institute: Purdue University

data_processing:
library strategy: MethylRAD seq
FastQC v.0.11.3 was used to observe read quality
Cutadaptversion 2.2 to trim data
Bowtie 2.3.3 to align data
Genome_build: GRCm38.93
Supplementary_files_format_and_content: BedGraph and TSV

growth_protocol: F9 embryonal carcinoma cells were cultured and maintained in gelatin-coated tissue culture plates. Differentiation was induced by plating 20X106 cells in low attachment 15 cm petri dishes and the addition of 1µM Retinoic acid

extract_protocol:
Genomic DNA was isolated using a standard phenol:chloroform extraction, followed by ethanol precipitation.
DNA from various samples was digested with FspEI overnight at 37°C and subjected to electrophoresis through a 2% agarose gel. 30 base pair fragments were cut out, purified, and adaptors were ligated at 4°C overnight (Wang et al., 2015b).

treatment_protocol: cell type

value: embryonal carcinoma cells

tag: cell state

value: differentiated


title: F9 differentiated ChIP

data_processing:
FastQC v.0.11.3 was used to observe read quality
TrimGalore for data trimming
Bowtie 2.3.3 to align data
Filter the BAM file to keep the reads with minimum MAPing Quality (MAPQ) 10.
Peak calling with epic2 using Input-ChIP pairs.
Peak annotations and visualizations through ChIPseeker R-package.
Genome_build: GRCm38.93
Supplementary_files_format_and_content: bedGraph and Excel

extract_protocol:
Genomic DNA was isolated from crosslined using a standard phenol:chloroform extraction, followed by ethanol precipitation.
NEXTflex® ChIP-Seq Kit from Bioo Scientific

tag: cell status

tag: chip antibody


title: neonatal Cardiomyocytes Input 1

description: Input total RNA

data_processing:
Reads were trimmed with Cutadapt (v2.5) and mapped to rat genome (Rnor_6.0) with STAR (v2.7) and summarized with featureCounts (v1.6.4)
DESeq2 (Love et al., 2014) with  IHW (Ignatiadis et al., 2016) for multiple hypothesis correction was used to determine significantly enriched RNAs in IP samples vs corresponding input controls (adjusted p-value < 0.1; log2 fold-change > 0.5).
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

value: Wistar

tag: age

value: neonatal Cardiomyocytes

tag: rip antibody

tag: sample type


title: a2B1

description:
2B1
CPI203/cytokines expanded
mRNA
processed data file: features_counts_ucsc.txt

data_processing:
Forty (40) million reads per sample were gained and raw files of the same sample from different lanes were merged into a single file using Samtools (1.3). Processed files were then aligned using STAR (2.4.2a) against the human genome (UCSC hg38) and the quality was also checked by fastQC (0.10.1). The non-adjusted read counts for each gene were assessed statistically for global differential expression between the specified populations using the edgeR package (3.22.2) on R (3.5.1). Genes that are significant at a 1% false discovery rate (calculated using a Benajmini-Hochberg adjusted p-value) were considered differentially expressed between populations as described 14. Gene ontology enrichment was assessed using the topGO package (2.32.0) and pathway enrichment was analysed on the ReactomePA package (1.24.0).
Genome_build: GRCh38-1.2.0
Supplementary_files_format_and_content: features_counts_ucsc.txt: Tab-delimited text file

value: Cord blood CD133+ cells

value: CPI203 expanded

tag: donor


title: LT_102e3

city: Harbin

first: Yu

last: Zhou

state: Heilongjiang

address: Changjiang Road,Xiangfang district

department: College of Agronomy

institute: Northeast Agricultural University

description: mRNA sequencing

data_processing:
Illumina Casava1.8 software used for basecalling.
A cDNA library constructed by technology from the total RNA was sequenced run with Illumina sequence platform. 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.
We aligned reads of samples to the reference genome using HISAT package.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM.
Genome_build: Zea mays NCBI B73 RefGen_v4
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Zea mays

source_name: Seed embryo

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.
Poly(A) RNA was purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Following purification, the mRNA was 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 TruSeq RNA Sample Preparation v2 (Cat. RS-122-2001,RS-122-2002) (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 ( 2 x 150 bp) on an Illumina Hiseq 4000 at the (LC Sceiences,USA) following the vendor’s recommended protocol.

value: low temperature


title: LT_102e2

description: mRNA sequencing


title: F9 undifferentiated [methylRAD]

tag: cell line

value: undifferentiated


title: LT_55e3

description: mRNA sequencing


title: LT_55e1

description: mRNA sequencing


title: LT_55e2

description: mRNA sequencing


title: LT_102e1

description: mRNA sequencing


title: CT_102e3

description: mRNA sequencing

value: normal control


title: CT_102e2

description: mRNA sequencing


title: F9 undifferentiated ChIP


title: F9 differentiated input

value: none (input)


title: F9 undifferentiated input


title: ATAC_Macrophages_WT1

value: macrophages

tag: genotype

value: Wild Type


title: CT_102e1

description: mRNA sequencing


title: CT_55e2

description: mRNA sequencing


title: CT_55e3

description: mRNA sequencing


title: NR-31802_10_min_DSN

description:
sja_mapped_reads.txt.gz
Aet

data_processing:
HiSeq 2500 standard base-calling
Mapping to Schistosoma sp. genomes using miRDeep2's mapper.pl
Genome_build: SchistoDB-38_SmansoniPuertoRico_Genome.fasta; SchistoDB-38_SjaponicumAnhui_Genome.fasta; SchistoDB-38_ShaematobiumEgypt_Genome.fasta
Supplementary_files_format_and_content: Compressed text files which are derived from miRDeep2's mapper.pl script output, using default parameters. Reads were mapped against the respective species genome.

extract_protocol:
TRIzol extraction followed by glycogen-fascilitated isopropanol precipitation
ligation & gel-based small RNA cDNA library (see PMID: 24489795)

value: not applicable

tag: Stage

value: eggs

tag: [rna], ng/µl

tag: host

value: mouse

tag: barcode

tag: cdna cleavage by duplex specific nuclease?

value: 10 min

tag: 3' adapter sequence

value: TTAAGTCGTATGCTGTCCTCTGTGGAATTCT


title: CT_55e1

description: mRNA sequencing

tag: treatment


title: Heads, Control A

city: Providence

first: Bess

last: Frost

state: RI

address: 185 Meeting St

institute: Center for Alzheimer’s Disease Research, Brown University

description: rRNA depleted

data_processing:
RNA-sequencing was performed by the Genome Sequencing Facility at Greehey Children’s Cancer Research Institute at the University of Texas Health San Antonio
Raw FASTQ files underwent quality control and were trimmed with Trimmomatic v.0.36
FastQC was used to evaluate the quality of the reads before and after trimming
Trimmed FASTQ files were mapped and aligned to the Drosophila melanogaster transcriptome (FlyBase (Thurmond et al., 2019) FB2018_6.27) using Salmon v.0.13.1
Differential expression analysis was performed using DESeq2 v1.24
Genome_build: dm6
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

organism: Drosophila melanogaster

source_name: 18 pooled Drosophila heads

growth_protocol: Heads of 10 day old control and tauR406W transgenic Drosophila were collected and frozen at -80C prior to RNA extraction.

extract_protocol:
Trizol extraction followed by RNeasy MinElute Column (Cat No./ID: 74204, Qiagen) clean up.
Extracted RNA was used for stranded library preparation using the Ovation RNA-Seq System for Drosophila (#0350, NuGen) according to the User Guide, including depletion of Drosophila rRNAs. RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: Head

value: day 10 of adulthood


title: Heads, Control E

description: rRNA depleted


title: Heads, Control B

description: rRNA depleted


title: Heads, Control D

description: rRNA depleted


title: Heads, Tau C

description: rRNA depleted


title: Heads, Control F

description: rRNA depleted


title: Heads, Tau E

description: rRNA depleted


title: Heads, Tau F

description: rRNA depleted


title: Heads, Control C

description: rRNA depleted


title: Heads, Tau B

description: rRNA depleted


title: LNCAP_ENZ.21d_3

city: Brisbane

first: Colleen

last: Nelson

state: Queensland

address: 199 Ipswich Road

department: Institute of Health and Biomedical Innovation; Vancouver Prostate Centre

country: Australia

institute: Queensland University of Technology; University of British Columbia

hyb_protocol: 1650 ng of the labeled cRNA were hybridised onto a custom Agilent oligo micrarray at 65⁰C for 17 hours.

scan_protocol: Arrays were scanned on an Agilent scanner (G2565CA) at 3 um resolution using the Agilent Scan Control Software (A.8.5.1) and feature extraction was performed using the Agilent Feature Extraction Software (10.7).

data_processing: A quantile between array normalization was applied and differential expression was determined using the Baysian adjusted t-statistic linear model of the ‘Linear Models for Microarray Data’ (LIMMA) package in R. Data was annotated using Ensembl 77 / Gencode v21 / GRCh38.

source_name: LNCaP prostate cancer cell line

label_protocol: 150 ng of total RNA was amplified and labelled using the Agilent Low Input Quick Amp Labeling Kit according to the manufacturer's protocol.

growth_protocol: LNCaP cells were seeded at 5.0 × 10^5 cells per T75 flask in phenol-red free RPMI-1640 medium + 5% FBS and cultured at 37°C in an atmosphere containing 5% CO2 for duration of treatment.

extract_protocol: Total cellular RNA was extracted using the Qiagen RNeasy Mini Kit including on-column DNAse-I treatment.

treatment_protocol: LNCaP cells were treated for up to 21 days with the Androgen-Receptor-antagonist Enzalutamide (ENZ, 10 µM) and samples were collected at days 0, 7, 14 and 21. Media +/- ENZ was replaced every 3 days, and cells were passaged at around 80% confluence by  trypsinization.

tag: time point

value: 21 days

tag: agent

value: Enzalutamide


title: LNCAP_ENZ.14d_3

value: 14 days


title: LNCAP_Control_3

value: untreated control


title: Upf2 WT Fore brain relicate 1

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

institute: Karolinska Institutet

description: Gene expression data from WT

hyb_protocol: The resulting labeled samples were hybridized to the Affymetrix Mouse Gene 1.0 ST Array from Affymetrix according the instructions of the manufacturer

scan_protocol: Arrays were scanned using the GeneArray Scanner 3000 according to the instructions from the manufacturer.

data_processing: Data were summarized and normalized using robust multiarray average (rma) using the rma function in affy 1.48.0 and R version 3.2.3 (www.r-project).

source_name: Fore brain

label_protocol: The Affymetrix kit for Affymetrix Mouse Gene 1.0 ST DNA micro arrays using conditions recommended by the manufacturer.

growth_protocol: All mice strains were maintained on a C57BL/6 background.

extract_protocol: Total RNA was isolated from the from fore brain of Upf2 WT and fore brain knock out animals using TRIzol as per the manufacturer’s instructions (Life Technologies).

tag: upf2 expression

value: WT

tag: replicate


title: LNCAP_ENZ.14d_2


title: Upf2 WT Fore brain relicate 3

description: Gene expression data from WT


title: LNCAP_ENZ.7d_2

value: 7 days


title: Heads, Tau A

description: rRNA depleted

tag: age


title: Heads, Tau D

description: rRNA depleted


title: LNCAP_ENZ.21d_1


title: Upf2 KO Fore brain relicate 3

description: Gene expression data from KO

value: KO


title: LNCAP_ENZ.7d_3


title: LNCAP_ENZ.14d_1


title: Upf2 WT Fore brain relicate 2

description: Gene expression data from WT


title: LNCAP_ENZ.21d_2


title: Upf2 KO Fore brain relicate 2

description: Gene expression data from KO


title: Upf2 KO Fore brain relicate 1

description: Gene expression data from KO


title: LNCAP_Control_2


title: D2_sperm_small RNA

status: Public on Jun 28 2020

first: Zhen

address: 22th,Hankou Road

department: School of Lifesciences

institute: Nanjing University

data_processing:
Precursor and mature miRNA sequences, tRNA sequences and piRNA sequences were obtained from miRBase v21(Kozomara and Griffiths-Jones, 2014), GtRNAdb (Chan and Lowe, 2016) and piRNA bank (Lakshmi and Agrawal, 2008), respectively. Bowtie was used to align clean reads to these reference sequences for annotation.
To annotate miRNA, only candidates with 1 mismatch and no more than 2 shifts were counted as miRNA matches. To annotate piRNA, only candidates with 1 mismatch were counted as piRNA matches. To annotate tsRNA, SPORTS 1.0(Shi et al., 2018) based on bowtie was used for tsRNA annotation.
For normalization, the total sequencing frequency of each type of sRNA in each sample was normalized to 1,000,000. Differential analysis was performed using Student’s t test. Significance was set at uncorrected P < 0.05 for broad pattern identification. A fold-change threshold was set at > 2. The average expression level threshold was set at > 500.
Genome_build: miRBase v21; GtRNAdb; piRNA bank
Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each Sample

source_name: Sperm

extract_protocol:
mature sperm were extracted from the cauda epididymis of male mice of the C57BL/6J backgrounds,and RNA was harvested using Trizol reagent.Illumina TruSeq RNA Sample Prep Kit  was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: sperm

value: 8 week

tag: strain

tag: disease state

value: Stress-induced depressed mice


title: C2_sperm_small RNA

value: Normal mice


title: D1_sperm_small RNA


title: C1_sperm_small RNA


title: D3_sperm_small RNA


title: LNCAP_ENZ.7d_1


title: WBP11si1 BT549 Rep1

city: Cleveland

first: Daniel

last: McGrail

state: Ohio

address: 9500 Euclid Avenue

department: Center for Immunotherapy and Precision Immuno-Oncology

institute: Cleveland Clinic

data_processing:
De-multiplex with bcl2fastq-1.8.4
Aligned/quantified with Tophat 2.1.1
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited counts tables

source_name: Cancer cells

extract_protocol:
Qiagen RNeasy Kit
Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit

tag: cell line

tag: sirna


title: WBP11si1 U2OS Rep1


title: WBP11si1 MDA231 Rep2


title: WBP11si2 BT549 Rep1


title: WBP11si1 BT549 Rep2


title: WBP11si2 BT549 Rep2


title: LNCAP_Control_1


title: WBP11si1 MDA231 Rep1


title: SONsi2 U2OS Rep2


title: SONsi2 BT549 Rep2


title: C3_sperm_small RNA


title: WBP11si1 U2OS Rep2


title: SONsi2 U2OS Rep1


title: SONsi2 MDA231 Rep1


title: SONsi1 BT549 Rep1


title: SONsi2 BT549 Rep1


title: SONsi2 MDA231 Rep2


title: SNRPEsi2 BT549 Rep1


title: SONsi1 BT549 Rep2


title: SNRPEsi1 U2OS Rep1


title: SNRPEsi2 BT549 Rep2


title: SNRPEsi1 BT549 Rep1


title: SNRPEsi1 U2OS Rep2


title: SNRPEsi1 MDA231 Rep2


title: SNRPEsi1 MDA231 Rep1


title: SNRPEsi1 BT549 Rep2


title: SNRPBsi2 BT549 Rep1


title: SNRPBsi1 U2OS Rep2


title: SNRPBsi2 BT549 Rep2


title: SNRPBsi1 MDA231 Rep2


title: SNRPBsi1 U2OS Rep1


title: SNRPBsi1 BT549 Rep1


title: SNRPBsi1 BT549 Rep2


title: SF3B5si2 U2OS Rep1


title: SNRPBsi1 MDA231 Rep1


title: SF3B5si2 MDA231 Rep1


title: SF3B5si2 BT549 Rep1


title: SF3B3si2 U2OS Rep2


title: SF3B5si2 MDA231 Rep2


title: SF3B5si1 BT549 Rep1


title: SF3B5si1 BT549 Rep2


title: SF3B3si2 MDA231 Rep1


title: SF3B3si1 BT549 Rep1


title: SF3B3si2 MDA231 Rep2


title: SF3B3si1 BT549 Rep2


title: SF3A1si2 BT549 Rep1


title: SF3A1si1 U2OS Rep2


title: SF3A1si1 BT549 Rep2


title: SF3A1si2 BT549 Rep2


title: SF3A1si1 MDA231 Rep1


title: RBMXsi2 U2OS Rep2


title: SF3A1si1 BT549 Rep1


title: RBMXsi2 BT549 Rep2


title: SF3A1si1 U2OS Rep1


title: SF3A1si1 MDA231 Rep2


title: SF3B3si2 U2OS Rep1


title: SF3B3si2 BT549 Rep1


title: SF3B5si2 BT549 Rep2


title: SF3B5si2 U2OS Rep2


title: RBMXsi2 MDA231 Rep2


title: RBMXsi2 BT549 Rep1


title: RBMXsi2 U2OS Rep1


title: RBMXsi1 BT549 Rep2


title: RBMXsi2 MDA231 Rep1


title: RBM15si2 BT549 Rep2


title: RBMXsi1 BT549 Rep1


title: RBM15si2 BT549 Rep1


title: RBM15si1 U2OS Rep2


title: RBM15si1 U2OS Rep1


title: RBM15si1 BT549 Rep1


title: RBM15si1 MDA231 Rep1


title: PRPF8si2 BT549 Rep1


title: RBM15si1 MDA231 Rep2


title: RBM15si1 BT549 Rep2


title: PRPF8si1 U2OS Rep2


title: PRPF8si1 BT549 Rep2


title: PRPF8si1 BT549 Rep1


title: PRPF8si2 BT549 Rep2


title: PRPF8si1 U2OS Rep1


title: PRPF8si1 MDA231 Rep1


title: PRPF31si2 BT549 Rep1


title: PRPF31si2 BT549 Rep2


title: PRPF31si1 U2OS Rep1


title: PRPF31si1 BT549 Rep2


title: PRPF8si1 MDA231 Rep2


title: PRPF31si1 U2OS Rep2


title: PRPF31si1 MDA231 Rep2


title: MED9si2 BT549 Rep1


title: PRPF31si1 MDA231 Rep1


title: MED9si1 U2OS Rep1


title: MED9si1 MDA231 Rep2


title: MED9si1 BT549 Rep2


title: MED9si1 BT549 Rep1


title: MED9si2 BT549 Rep2


title: LUC7L2si2 BT549 Rep1


title: LUC7L2si1 U2OS Rep2


title: LUC7L2si1 BT549 Rep2


title: MED9si1 MDA231 Rep1


title: LUC7L2si1 MDA231 Rep2


title: HNRNPCsi2 U2OS Rep2


title: LUC7L2si1 MDA231 Rep1


title: LUC7L2si1 BT549 Rep1


title: LUC7L2si1 U2OS Rep1


title: HNRNPCsi2 BT549 Rep1


title: HNRNPCsi2 U2OS Rep1


title: HNRNPCsi2 MDA231 Rep2


title: HNRNPCsi1 BT549 Rep2


title: DHX8si2 U2OS Rep1


title: HNRNPCsi2 BT549 Rep2


title: DHX8si2 U2OS Rep2


title: DHX8si2 BT549 Rep1


title: DHX8si2 BT549 Rep2


title: PRPF31si1 BT549 Rep1


title: MED9si1 U2OS Rep2


title: DHX8si2 MDA231 Rep1


title: LUC7L2si2 BT549 Rep2


title: DHX8si1 BT549 Rep1


title: DDX3Xsi2 BT549 Rep1


title: DDX3Xsi2 BT549 Rep2


title: DHX8si2 MDA231 Rep2


title: DHX8si1 BT549 Rep2


title: DDX3Xsi1 U2OS Rep2


title: DDX3Xsi1 U2OS Rep1


title: DDX3Xsi1 BT549 Rep2


title: DDX3Xsi1 BT549 Rep1


title: DDX3Xsi1 MDA231 Rep2


title: CTRLsi U2OS Rep1

value: CTRLsi


title: CTRLsi U2OS Rep4


title: CTRLsi BT549 Rep6


title: DDX3Xsi1 MDA231 Rep1


title: HNRNPCsi1 BT549 Rep1


title: CTRLsi U2OS Rep2


title: CTRLsi BT549 Rep5


title: CTRLsi U2OS Rep3


title: RG7834 replicate 2

city: Boulder

first: Siddharth

last: Shukla

address: 3415 Colorado Ave

institute: University of Colorado Boulder

data_processing:
Adapter trimmining using Trimmomatic
Alignemnt of genome using STAR
Compression to coordinate sorted BAM files using samtools
Raw count estimation for each gene using HTSeq
DESeq2 differential gene expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: Matrix containing read counts for every gene in each replicate of each condition.

source_name: stem cell

extract_protocol:
Cells were harvested using Trizol and total RNA was extracted.
Nextflex Rapid Directional RNA-seq kit 2.0

value: DKC1 A353V


title: RG7834 replicate 3


title: CTRLsi BT549 Rep3


title: CTRLsi BT549 Rep7


title: CTRLsi BT549 Rep4


title: CTRLsi BT549 Rep2


title: DMSO replicate 3

value: DMSO


title: CTRLsi BT549 Rep1


title: RG7834 replicate 1


title: DMSO replicate 2


title: CTRLsi MDA231 Rep3


title: CTRLsi MDA231 Rep4


title: DMSO replicate 1


title: CTRLsi MDA231 Rep1


title: CDC73si2 BT549 Rep1


title: CTRLsi BT549 Rep8


title: CDC73si2 BT549 Rep2


title: CDC73si1 U2OS Rep2


title: 4-hour C1QTNF5 treated WT cells sample 2

city: Milwaukee

first: Steven

last: Henle

state: WI

address: 8701, W Watertown Plank Rd

department: Cell Biology, Neurobiology, and Anatomy

institute: Medical College of Wisconsin

description:
C1QTNF5-MFRPKO_FPKM.txt
WT_T2_FPKM
C1QTNF5_treated_WT_2

data_processing:
Primary sequencing data was conducted with a Illumina Hi-Seq 2000 using 50SE reads at 20M reads per sample.
Raw reads are subjected to quality control (QC) to determine if a resequencing step is needed. After QC, raw reads are filtered into clean reads which are aligned to the reference sequences.
"Dirty" raw reads are reads which contain the sequence of adaptor, high content of unknown bases and low quality reads, and are removed before analysis.
Bowtie2 was used to map clean reads to reference gene, and HISAT used to reference genome.
The Fragments Per Kilobase of transcript per Million mapped reads (FPKM)  method is used to calculated expression level.
Genome_build: GRCh37
Supplementary_files_format_and_content: .txt files containing FPKM values for expression levels.

source_name: IMR90-4 cells differentiated into RPE

extract_protocol:
Trizol
RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low-input poly-A BGISEQ-500RSRNASeq (Transcriptome) protocol.

value: IMR90-4 cells differentiated into RPE

tag: genotype

value: 4 hours C1QTNF5


title: CDC73si1 BT549 Rep1


title: untreated WT cells from MFRP KO experiment sample 3

description:
C1QTNF5-MFRPKO_FPKM.txt
C3_FPKM
Untreated_WT_3

value: untreated


title: untreated WT cells from MFRP KO experiment sample 1

description:
C1QTNF5-MFRPKO_FPKM.txt
C1_FPKM
Untreated_WT_1


title: untreated MFRP KO cells sample 2

description:
C1QTNF5-MFRPKO_FPKM.txt
MFRP_C2_FPKM
Untreated_MFRPKO_2

source_name: IMR90-4 cells with a null mutation in MFRP  differentiated into RPE

value: MFRP -/-


title: untreated WT cells from MFRP KO experiment sample 2

description:
C1QTNF5-MFRPKO_FPKM.txt
C2_FPKM
Untreated_WT_2


title: 4-hour C1QTNF5 treated WT cells sample 3

description:
C1QTNF5-MFRPKO_FPKM.txt
WT_T3_FPKM
C1QTNF5_treated_WT_3


title: untreated MFRP KO cells sample 3

description:
C1QTNF5-MFRPKO_FPKM.txt
MFRP_C3_FPKM
Untreated_MFRPKO_3


title: CDC73si1 MDA231 Rep2


title: 4-hour C1QTNF5 treated WT cells sample 1

description:
C1QTNF5-MFRPKO_FPKM.txt
WT_T1_FPKM
C1QTNF5_treated_WT_1


title: 4-hour C1QTNF5 treated MFRP KO cells sample 3

description:
C1QTNF5-MFRPKO_FPKM.txt
MFRP_T3_FPKM
C1QTNF5_treated_MFRPKO_3


title: CDC73si1 MDA231 Rep1


title: CDC73si1 BT549 Rep2


title: BRCA2si2 BT549 Rep2


title: 4-hour C1QTNF5 treated MFRP KO cells sample 2

description:
C1QTNF5-MFRPKO_FPKM.txt
MFRP_T2_FPKM
C1QTNF5_treated_MFRPKO_2


title: BRCA2si2 BT549 Rep1


title: 4-hour C1QTNF5 treated MFRP KO cells sample 1

description:
C1QTNF5-MFRPKO_FPKM.txt
MFRP_T1_FPKM
C1QTNF5_treated_MFRPKO_1


title: CTRLsi MDA231 Rep2


title: BRCA2si1 U2OS Rep2


title: untreated WT cells sample 1

description:
C1QTNF5_timecourse_FPKM.txt
CTRP5_T0_S1_FPKM
C1QTNF5_T0_S1


title: untreated WT cells sample 2

description:
C1QTNF5_timecourse_FPKM.txt
CTRP5_T0_S2_FPKM
C1QTNF5_T0_S2


title: untreated WT cells sample 3

description:
C1QTNF5_timecourse_FPKM.txt
CTRP5_T0_S3_FPKM
C1QTNF5_T0_S3


title: BRCA2si1 U2OS Rep1


title: untreated MFRP KO cells sample 1

description:
C1QTNF5-MFRPKO_FPKM.txt
MFRP_C1_FPKM
Untreated_MFRPKO_1


title: CDC73si1 U2OS Rep1


title: Hi-C_donor_cumulus_cell_rep1

city: Beijing

first: Ke

last: Zhang

state: Beijing

address: Haidian District

department: School of Life Sciences

institute: Tsinghua university

description: Cumulus_cell_donor_rep12_allValidPairs.gz

data_processing:
Basecalls performed using CASAVA version 1.8
For Hi-C samples: sisHi-C sequencing reads were mapped, processed and iteratively corrected using HiC-Pro, a pipeline developed by Servant et al. Briefly, the read pairs were mapped to the mm9 reference genome in a two-step approach with bowtie2. Then the invalid read pairs including dangling end, self-circle ligation and duplicates were discarded. The genome was divided into bins of specific length to generate the contact maps. For global detection of contacts, a 100Kb bin size and 300Kb bin size wereused and a 40Kb bin size was used for examination of local domain level contacts. The raw contact counts are normalized with iterative correction.
Genome_build: mm9
Supplementary_files_format_and_content: The validpair txt file indicates the paired interaction reads for each sample.

source_name: Cumulus cell

extract_protocol:
The DNA extraction follows Hi-C protocol
Hi-C libraries were prepared using Hi-C protocal developed by Rao et al. with slightly modification

treatment_protocol: Cumulus cells were collected from cumulus-oocyte complexes of BDF1 female mouse, which was digested by hyaluronidase (Sigma, Cat # H3506).

value: Cumulus cell


title: BRCA2si1 BT549 Rep2


title: 2-hour C1QTNF5 treatment sample 1

description:
C1QTNF5_timecourse_FPKM.txt
CTRP5_T1_S1_FPKM
C1QTNF5_T1_S1

value: 2 hours C1QTNF5


title: 2-hour C1QTNF5 treatment sample 2

description:
C1QTNF5_timecourse_FPKM.txt
CTRP5_T1_S2_FPKM
C1QTNF5_T1_S2


title: Hi-C_SCNT_PCC_rep2

source_name: SCNT PCC

treatment_protocol: PCC SCNT embryos are collected one hour after the donor nucleus get injected into the enucleated MII oocytes. The reconstructed oocytes were incubated in CZB medium. The first polar body was removed by enucleation pipette on the micromanipulator, while the zona pellucida was gently removed by treatment with acid Tyrode’s solution (Sigma, Cat # T-1788) for several minutes.

value: SCNT PCC


title: Hi-C_SCNT_PCC_rep1


title: BRCA2si1 MDA231 Rep1


title: BRCA2si1 BT549 Rep1


title: 2-hour C1QTNF5 treatment sample 3

description:
C1QTNF5_timecourse_FPKM.txt
CTRP5_T1_S3_FPKM
C1QTNF5_T1_S3

value: WT


title: 4-hour C1QTNF5 treatment sample 1

description:
C1QTNF5_timecourse_FPKM.txt
CTRP5_T2_S1_FPKM
C1QTNF5_T2_S1


title: 4-hour C1QTNF5 treatment sample 2

description:
C1QTNF5_timecourse_FPKM.txt
CTRP5_T2_S2_FPKM
C1QTNF5_T2_S2


title: BRCA1si2 U2OS Rep2


title: Hi-C_donor_MEF_rep2

source_name: mouse embryonic fibroblast cell

treatment_protocol: MEF cells are derived from E13.5 mice. C57BL/6N (female) and PWK/PhJ (male) strain mice were used for mouse embryonic fibroblasts (MEFs) derivation. Embryos were processed by removing heads, limbs and internal organs, washing and cutting into smaller pieces in tubes, trypsinizing with 0.25% trypsin/EDTA (Gibco, Cat # 2530-0-056). The mixture of tissues was filtered and centrifuged at 2,000 rpm for five minutes. The supernatant was removed, the cell pellets were resuspended with DMEM (Gibco, Cat # 11965-092) supplemented with 10% fetal bovine serum (FBS) in the 100 mm Petri dish culture at 37 ℃, 5% CO2 incubator. Male MEF cells were used for donor cells of SCNT.

value: embryonic fibroblast cell


title: 6-hour C1QTNF5 treatment sample 1

description:
C1QTNF5_timecourse_FPKM.txt
CTRP5_T3_S1_FPKM
C1QTNF5_T3_S1

value: 6 hours C1QTNF5


title: 6-hour C1QTNF5 treatment sample 3

description:
C1QTNF5_timecourse_FPKM.txt
CTRP5_T3_S3_FPKM
C1QTNF5_T3_S3


title: Hi-C_donor_MEF_rep1


title: Hi-C_donor_cumulus_cell_rep2


title: 8-hour C1QTNF5 treatment sample 1

description:
C1QTNF5_timecourse_FPKM.txt
CTRP5_T4_S1_FPKM
C1QTNF5_T4_S1

value: 8 hours C1QTNF5


title: BRCA1si2 U2OS Rep1


title: CaIKK2EC_5

city: Vienna

first: Johannes

middle: A.

last: Schmid

address: Schwarzspanierstr. 17

department: Vascular Biology and Thrombosis Research

country: Austria

institute: Med. Univ. Wien

data_processing:
fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) (version 0.11.5) was used to check the quality of reads.
Sequence reads were aligned to UCSC mouse genome version mm10 using STAR version 2.7.0e.
Differential expression analysis was performed using DEseq2 version 1.22.2 package in R.
Gene annotation with biomaRt_2.40.5.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: caIKK2EC_vs_WT_DESeq2results.tsv: Tab-delimited text file containing differential expression (DE) analysis performed using DEseq2 version 1.22.2; Gene Symbol, ensembl gene ID, Entrez, gene_biotype;baseMean,log2FoldChange,lfcSE,stat,pvalue,padj, normalized counts for each sample.
Supplementary_files_format_and_content: caIKK2EC_vs_WT_DESeq2results_rlog_counts.tsv: Tab-delimited text file containing differential expression (DE) analysis performed using DEseq2 version 1.22.2; Gene Symbol, ensembl gene ID, Entrez, gene_biotype;baseMean,log2FoldChange,lfcSE,stat,pvalue,padj, rlog transformed counts for each sample.
Supplementary_files_format_and_content: all_samples_counts.txt: Tab-delimited text file containing gene counts for each sample obtained from the output of STAR aligner version 2.7.0e using the parameter --quantMode GeneCounts.

source_name: Aorta

growth_protocol: Mice with a constitutive active form of IKK2 (caIKK2(+/+)) and a co-translationally expressed EGFP downstream of a loxP-flanked STOP-cassette, were crossed with BMX-CreERT2(+/-) ApoE(-/-) mice, which express an inducible Cre recombinase only in arterial endothelial cells (obtained from Christian Weber, Munich, Germany) to generate caIKK2(+/+) BMXCreERT2(+/-) ApoE(-/-) mice (designated as caIKK2EC). BMX-Cre-negative, caIKK2(+/+) BMXCreERT2(-/-) ApoE(-/-) littermates were referred to as control (control) mice. MRNA profile of whole aortas was generated by deep sequencing, using Illumina HiSeq3000/4000 instrument.

extract_protocol:
For RNA isolation, aortas were homogenized in lysis buffer using a Precellys® homogenizer (VWR®, Randnor, Pennsylvania), RNA was isolated with the PeqGOLD total RNA isolation Kit (c-line, Thermo Fisher Scientific, Waltham, MA, US) according to the manufacture’s protocol and the RNA concentration was measured by NanoDrop (VWR®, Vienna, Austria).
Sequencing libraries were prepared at the Core Facility Genomics, Medical University of Vienna using the NEBNext Poly(A) mRNA MagneticIsolation Module and the NEBNext Ultra™ Directional RNA Library Prep Kitfor Illumina according to manufacturer's protocol (New EnglandBiolabs). Libraries were QC‑checked on a Bioanalyzer 2100 (Agilent) using a HighSensitivity DNA Kit for correct insert size and quantitated using QubitdsDNA HS Assay (Invitrogen). Pooled libraries had an average length of 330‑360 bp and were sequenced on a HiSeq3000/4000 instrument (Illumina) in 1x50bp sequencing mode.

treatment_protocol: Tamoxifen (1 mg/20 g mouse) was injected intraperitoneally (i.p.) at five consecutive days. Both experimental groups (Control and caIKK2EC mice) were injected to exclude potential off-target effects of the drug. To induce the development of atherosclerotic plaques, mice were fed a Western-type diet containing 21,2% fat and 2070 mg/kg cholesterol (TD88137 mod, ssniff, Germany) ad libitum for 12 weeks.

value: aorta

tag: Sex

value: Female

tag: age (weeks)


title: 8-hour C1QTNF5 treatment sample 2

description:
C1QTNF5_timecourse_FPKM.txt
CTRP5_T4_S2_FPKM
C1QTNF5_T4_S2


title: CaIKK2EC_4


title: CaIKK2EC_3


title: 8-hour C1QTNF5 treatment sample 3

description:
C1QTNF5_timecourse_FPKM.txt
CTRP5_T4_S3_FPKM
C1QTNF5_T4_S3


title: 6-hour C1QTNF5 treatment sample 2

description:
C1QTNF5_timecourse_FPKM.txt
CTRP5_T3_S2_FPKM
C1QTNF5_T3_S2


title: CaIKK2EC_2


title: BRCA1si2 BT549 Rep1


title: BRCA2si1 MDA231 Rep2


title: 4-hour C1QTNF5 treatment sample 3

description:
C1QTNF5_timecourse_FPKM.txt
CTRP5_T2_S3_FPKM
C1QTNF5_T2_S3


title: BRCA1si2 MDA231 Rep2


title: BRCA1si2 MDA231 Rep1


title: GBM_scRNAseq [PJ069]

city: New York

first: Peter

last: Sims

state: NY

address: 3960 Broadway

institute: Columbia University

data_processing:
Read 1 and read 2 fastq files were generated on basespace.
16-nt cell barcodes (CBs) were extracted from position 3-10 and 13-20, and 8-nt unique molecular identifiers (UMIs) were extracted from position 1-2, 11-12 and  21-24 of Read 1.
Read 2 were trimmed to remove poly(A) tails (> dA(7)) from the 3'-ends of each read.
Trimmed reads were then aligned to the reference human or(and) mouse genome using STAR v.2.7.0 with parameters "-- sjdbOverhang 65 --twopassMode Basic --outSAMtype BAM Unsorted". Only reads with unique, strand-specific alignments to exons were kept for further analysis.
All reads with the same CB, UMI, and gene mapping were collapsed to represent a single molecule. To correct for sequencing errors in UMIs, we further collapsed UMIs that were within Hamming distance 1 of another UMI with the same barcode and gene. A digital gene expression matrix was then generated from the corrected barcode-UMI-gene triplets.
Genome_build: GRCh38 and GRCm38 (sample 1)
Genome_build: GRCh38  (sample 2)
Supplementary_files_format_and_content: Tab-delimited text files that contain the gene expression level of each individual cell.

source_name: Brain

extract_protocol:
mRNA molecues were captured using bead-bound oligo dT(30).
Captured mRNA molecues were reverse transcriped to obtain cDNA which is then amplified by PCR reactions. The cDNA PCR reaction product was then purified with AMPure XP beads. The purified cDNA PCR product was used as the input for Nextera XT reactions to generate sequencing library.

value: human glioblastoma


title: CaIKK2EC_1


title: BRCA1si1 BT549 Rep2


title: Control_1

value: Control


title: AQRsi2 BT549 Rep2


title: BRCA1si2 BT549 Rep2


title: D4_depressed_Bisulfite-seq

data_processing:
All bisulfite sequencing reads were first trimmed to remove adaptors and lowquality bases using trim_galore (version 0.3.3) (parameters: --quality 20 --phred33 --length 50 --paired). Next, reads that passed quality control were mapped to the Mouse reference genome (mm10) using Bismark with paired-end alignment mode (parameters: --non-directional --fastq).
To recover additional sequencing reads, unmapped reads were realigned to the same reference genome in single-end alignment mode. Only reads with a unique mapping location in the genome were retained for further analysis.
All genomic DNA sequencing reads were also stripped of their adaptor sequences using the trim galore tool and then mapped to the mm10 reference genome using BWA31 with long-reads ‘Mem’ mode, resulting in an average of 14.98% mapping efficiency (7.07–28.48% range).
After alignment, reads were further deduplicated using the ‘samtools rmdup’ command (Borgel et al., 2010). For each cytosine site (or guanine corresponding to a cytosine on the opposite strand) in the reference genome sequence, the DNA methylation level was determined by the ratio of the number of reads supporting C (methylated) to that of total reads (methylated and unmethylated). Notably, in this study, the DNA methylation level of any given sample or region was referred to as the DNA methylation level of the CpG sites of this sample or region, unless specified elsewhere. A bin approach (10Kbp/bin) was used to estimate the methylation rate in consecutive regions.
We also estimated the DNA methylation level of different genomic regions that were annotated in the UCSC genome table and other databases, including CGIs, exons, introns, intergenic regions, intragenic regions, and repetitive regions (Bird, 2002). The DNA methylation level of these genomic regions was calculated on the basis of the average methylation level of all covered CpG sites within these regions.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include analysis resultf of differentially methylated regions for each group.

source_name: embryos

growth_protocol: sRNAs isolated from normal or depressed mice sperm with a concentration of 2 ng/μl were microinjected in to fertilized eggs of C57BL/6 background. The zygotes were then cultured in M16 medium (Sigma) at 37 °C in 5% CO2. At the second day, the 2-cell embryos were transferred to potassium-supplemented simplex optimized medium (KSOM, Millipore). Embryos at E4.5 stage were collected at approximately 108 h after microinjection, respectively.

extract_protocol:
Single E4.5-stage embryo was subjected to extraction of the genomic DNA using the Genomic DNA Clean and Concentrator kit (VisTech, Dayton, OH) according to the manufacturer’s instructions.
A single embryo was seeded into lysis buffer by mouth pipette. DNA was released after proteinase treatment at 50 °C and then subjected to bisulfite conversion. After column-based purification, DNA was complemented with the biotinylated random primer Bio-P5-N9 and 50 units of Klenow polymerase (3' to 5' exo–, New England BioLabs, Beverly, MA). This random priming was repeated five times in total. Second strands were synthesized using another random primer, P7-N9, and final libraries were generated after 8 to 12 cycles of PCR amplification with the Illumina universal PCR primer and Illumina indexed primer.Sequencing data were generated on the Illumina HiSeq 4000 platform (sequenced by Novogene).

value: embryos

tag: Stage

tag: injected with sperm srna from

value: Stress-induced depressed mice


title: WT-3

city: Albuquerque

first: Nora

last: Perrone-Bizzozero

state: NM

address: 1 University of New Mexico MSC08 4740

department: Neurosciences

institute: University of New Mexico

description: lncRNA-mRNAs

hyb_protocol: The labeled cRNAs were hybridized onto the Mouse LncRNA Array v3.0 (8 x 60K, Arraystar).

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: A series of data processing including quantile normalization were performed using the R software limma package.

source_name: striatum

label_protocol: Arraystar Flash RNA Labeling Kit was used for sample labeling.

growth_protocol: Adult mice

extract_protocol: Trizol. mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a mixture of oligo(dT) and random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).

treatment_protocol: HuD KO mice vs. WT

value: Adult striatum

tag: genotype/variation

value: wild type


title: D3_depressed_Bisulfite-seq

city: Nanjing

tag: tissue


title: AQRsi2 BT549 Rep1


title: AQRsi1 U2OS Rep2


title: HuD-KO-3

description: lncRNA-mRNAs

value: HuD KO (Elalvl4-/-)


title: D1_depressed_Bisulfite-seq


title: Control_3

value: Male


title: AQRsi1 U2OS Rep1