title: drerio_B15

description: drerio.loom

extract_protocol:
For zebrafish, cells were collected 3 days post fertilization. The head and tail were removed and the middle part of the larvae was collected for sequencing. The yolk was removed by gently pipetting up and down in 100 μL of calcium-free Ringer’s solution. Larvae (n=20) were transferred to a protease solution (0.25% trypsin, 1mM EDTA, pH 8.0, PBS, 50 ml) pre-warmed at 28°C and 27 μL collagenase P in HBSS was added to the samples for 15 minutes at 28°C with homogenizing every 5 minutes by gently pipetting up and down. Stop solution (6X, 30% calf serum, 6 mM CaCl2, PBS) was added to the tube and spun at 350 RCF for 5 minutes at 4°C. The resuspension was passed through a 20 μm cell strainer and the sample was placed on ice. Quality control was addressed by comparing live cells versus dead cells using a viability indicator for dead cells (NucRed™ Dead 647 ReadyProbes™ Reagent). For mice, the spinal cords from three E14.5 embryos were dissected in ice-cold 1X D-PBS (Thermofisher). Both the DRGs and vertebrae column were removed as much as possible. The spinal cords were pooled in one tube and dissociated using the adult brain dissociation kit (Milteny Biotec), adapted for spinal cord tissue. Briefly, 1 ml pre-heated (37ºC) enzyme solution 1 (50 µl enzyme P in 950ul buffer Z) was added to the spinal cords followed by 15ul enzyme solution 2 (5 µl enzyme A in 10 µl buffer Y). The tissue was incubated at 37ºC for 30 minutes. Every 10 minutes, the tissue was triturated 10 times with fire polished glass Pasteur pipettes pretreated in 0.5% BSA in 1X D-PBS. The pipets had a decreasing diameter staring with around 200% then 100% and finally around 20% of original opening diameter. Tissue was then transferred to 10 ml ice cold 1X D-PBS and filtered through a 40 µm cell strainer. The suspension was centrifuged at 300 RCF for 10 minutes at 4ºC and the supernatant was discarded. The cell pellet was resuspended in 900 µl 0.5% BSA in 1X D-PBS followed by 100 µl myelin removal beads (Milteny Biotec) and incubated for 15 min at 8ºC. 10 ml ice cold 1X D-PBS was added to the sample and centrifuged at 300 RCF for 10 minutes. Supernatant was discarded and the cell pellet was resuspended in 1 ml 0.5% BSA in 1X D-PBS. The sample was run through an LS-column (Milteny Biotec) on a magnetic stand and flushed with 2x1 ml 0.5% BSA in 1X D-PBS. Cell sorting was performed on a BD Melody cell sorter, and tomato positive cells were gated out in comparison to a non-fluorescent control.
cDNA synthesis and preamplification were performed using the SMART-seq2 method (Picelli et al., 2014). Briefly, cDNA was transcribed using SuperScript II reverse transcriptase, oligo(dT) primers and template switching oligonucleotides (TSO). Preamplification of the cDNA was facilitated by ISPCR primers that binds the TSO and oligo(dT). The cDNA was tagmented using the Tn5 transposase creating fragments of 200-600bp, followed by indexation using the Nextera XT sample preparation kits.


title: 4224T

status: Public on Jan 01 2022

type: RNA

city: Jacksonville

first: Tae Hyun

last: Hwang

state: FL

address: 4500 San Pablo Rd S.

country: USA

institute: Mayo Clinic

hyb_protocol: HumanHT-12 v3.0 Expression BeadChip array (Illumina) was used.

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with MATLAB. We then selected only the probs whose gene symbols are in our 32 gene list. Atter being transformed by logarithm base 2, for each gene symbol, we aggregate the expression values at the corresponding probs by taking their mean expression value.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Stomach

label_protocol: Illumina TotalPrep™ RNA Amplification Kit was used for synthesis of labeled cRNA.

extract_protocol: RecoverAll™ total nucleic acid isolation kit (Ambion) or the mirVana RNA Isolation Labeling Kit (Ambion) were used. Quality control was performed with NanoDrop 2000 (Thermo Fischer Scientific) and RNA Nano 6000 chip (Agilent).

tag: tumor stage

tag: age

tag: Sex

value: Female


title: drerio_B14

type: SRA

city: Uppsala

first: Henrik

last: Boije

address: Uppsala University, Dept. Of Neuroscience, Box 593, BMC

country: Sweden

institute: Uppsala University

description: drerio.loom

library_source: transcriptomic

data_processing:
Alignment and mapping: Genome indexing and read alignment was performed using STAR v.2.5.4b and Velocyto v0.17.17 (La Manno et al., 2018). Fasta files for extra genes were manually added for eGFP 146 (LC337138.1), tdTomato (GeneBank: AY678269.1) and ERCC genes (Thermofisher assets: https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip) and gene information was added to the species GTF file (Shaner et al., 2004; Nakajima et al., 2018). Reads were mapped to GRCm38.99 genome for mus musculus or GRCz11.98 genome for danio rerio. Genes were counted using featureCounts (subread V2.0.0) and Velocyto v0.17.17. Velocyto spliced and unspliced information was added to the final loom file as seperate layers. Full scripts are deposited at Github (http://github.com/jonetjakobsson/dmrt3-single-cell)
Genome_build: GRCm38.99
Genome_build: GRCz11.98
Supplementary_files_format_and_content: Loom file containing layers; reads, RPKM, spliced and unspliced meassures. Each row represents a well and each column represents one gene.

molecule: polyA RNA

organism: Danio rerio

source_name: Zebrafish spinal cord

tag: developmental stage

tag: tissue

value: spinal cord

tag: strain


title: 4173T

value: Male


title: drerio_B18

description: drerio.loom


title: methylation_sample_124

type: genomic

city: Heidelberg

first: David

last: Reuss

department: Neuropathology

country: Germany

institute: University Hospital Heidelberg

hyb_protocol: Illumina protocol

scan_protocol: Illumina scan protocol according to the manufacturer protocol

data_processing:
Bioconductor version 3.14 package minfi (Version 1.40.0) using processillumina
normalized data: Average Beta

molecule: genomic DNA

source_name: PMMRDIA

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

tag: material

value: Frozen


title: methylation_sample_123

value: FFPE


title: methylation_sample_122


title: drerio_B13

description: drerio.loom


title: 4171T


title: 4156T


title: 4078T


title: methylation_sample_126


title: CTR1_HiC_Lib3

city: Jinan

first: Yu

last: Xia

state: Shandong

address: 324 Jingwu Street

department: Department of Central Laboratory

country: China

institute: Shandong Provincial Hospital affiliated to Shandong University

description: HiC-seq of Homo sapiens, adult female monocytes, CTR1, library rep3

library_source: genomic

data_processing:
we used integrated pipeline of HiC-Pro (V2.7.8) to process from clean fastq to contact maps with default parameters. This pipeline mainly included two-step mapping using Bowtie2 and binned to generate genome-wide interaction map. The resulting contact matrices were normalized using iterative correction and eigenvector decomposition (ICED).
The loops were called by HiCCUPS with default parameters. HiCCUPS examines each pixel in a Hi-C contact matrix and identifies those with enriched contact frequencies relative to local neighborhoods (pixels to its lower-left, pixels to its left and right, pixels above and below, and pixels within a "donut" surrounding the pixel of interest).
The R packages GENOVA was used for future advanced analysis and visualization of contact matrix. Briefly, the heatmap of ICE-normalisation contact matrix were used for visualization; the relative contact probability (RCP) was computed for each chromosome; the insulation score was used to call TADs with parameters “--is 2000000 --ids 800000 --nt 0.3”. Package hicrep and multiHiCcompare were used to do comparison analysis.
Genome_build: hg19

source_name: primary monocyte

extract_protocol:
About one million monocytes were crosslinked by 40 ml 1% formaldehyde solution at room temperature for 10 min and 2.5 M Glycine was added to quench the crosslinking reaction. Supernatant was removed and the cells were washed three times by 1 X PBS. Crosslinked cells were resuspended in 500 µL of ice-cold Hi-C lysis buffer and rotated at 4 °C for 30 min.
in situ MboI Hi-C were assembled based on Illumina-compatible protocols.

value: peripheral blood

tag: cell type

value: CD14+ monocytes

tag: disease state

value: healthy

value: adult

tag: gender

value: female


title: methylation_sample_121


title: CD5high-CD5high.rep2

city: Beijing

first: Xiaoyang

last: Jin

state: -- Please, Select --

address: 15 Datun Road, Chaoyang District

institute: Institute of Biophysics, CAS

description: CD5high cDC2s are cultured with TGF-beta for 24 hours, and then sorted according to their CD5 expression level. The sample correspoonds to the CD5high part

data_processing:
Salmon (version: 0.8.2) was used to quantify the expression of each transcript.  The human transcript sequences were provided by GENCODE (release 26), and only protein-coding transcript sequences were considered. The transcript-level expression value was imported and summarized using tximport to estimate gene-level read counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw read counts and TPM (Transcripts Per Kilobase Million) value for each sample

source_name: CD5high cDC2s

extract_protocol:
According to the quality and RNA abundance of samples, construction of sequencing library takes a method suitable for single-cell RNA sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD5high to CD5high -TGF-beta cDC2


title: drerio_B12

description: drerio.loom


title: drerio_B11

description: drerio.loom


title: methylation_sample_120


title: drerio_B10

description: drerio.loom


title: methylation_sample_119


title: SLE2_HiC_Lib3

description: HiC-seq of Homo sapiens, adult female monocytes, SLE2, library rep3

value: Systemic Lupus Erythematosus (SLE) patient


title: CTR2_HiC_Lib1

description: HiC-seq of Homo sapiens, adult female monocytes, CTR2, library rep1


title: CTR1_HiC_Lib1

description: HiC-seq of Homo sapiens, adult female monocytes, CTR1, library rep1


title: 4066T


title: SLE2_HiC_Lib2

description: HiC-seq of Homo sapiens, adult female monocytes, SLE2, library rep2


title: drerio_A9

description: drerio.loom


title: drerio_B1

description: drerio.loom


title: 4030T


title: 3998T


title: methylation_sample_117


title: 3960T


title: 3972T


title: SLE2_HiC_Lib1

description: HiC-seq of Homo sapiens, adult female monocytes, SLE2, library rep1


title: methylation_sample_116


title: SLE1_HiC_Lib3

description: HiC-seq of Homo sapiens, adult female monocytes, SLE1, library rep3


title: CTR1_HiC_Lib2

description: HiC-seq of Homo sapiens, adult female monocytes, CTR1, library rep2


title: drerio_A8

description: drerio.loom


title: methylation_sample_114


title: methylation_sample_115


title: 3917T


title: drerio_A7

description: drerio.loom


title: SLE1_HiC_Lib1

description: HiC-seq of Homo sapiens, adult female monocytes, SLE1, library rep1


title: SLE1_HiC_Lib2

description: HiC-seq of Homo sapiens, adult female monocytes, SLE1, library rep2


title: drerio_A6

description: drerio.loom


title: methylation_sample_113


title: 3896T


title: drerio_A5

description: drerio.loom


title: methylation_sample_112


title: 3907T


title: CTR2Input

description: Input Control of Homo sapiens, adult female monocytes, CTR2

data_processing:
reads were quality-filtered according to the Illumina pipeline. The data was aligned to the human reference genome (ucsc.hg19) by bowtie2 (version 2.2.3) and binding sites were identified by MACS2 (version 2.1.1).
Genome_build: hg19
Supplementary_files_format_and_content: peaks file

extract_protocol:
Nuclear extracts from about one million cells and chromatin was sheared to an average size of 200 bp with asonicator (Bioruptor Pico, Diagenode).
ChIP libraries were prepared using standard Illumina protocols.

tag: chip antibody


title: drerio_A4

description: drerio.loom


title: methylation_sample_111

source_name: Oligosarcoma, IDH-mutant


title: CTR2H3K27me3

description: ChIP-seq of Homo sapiens, H3K27me3, adult female monocytes, CTR2

value: Histone H3K27me3 antibody (pAb)  (ActiveMotif, Catalog No:39155)


title: methylation_sample_110


title: drerio_A3

description: drerio.loom


title: CTR2H3K4me3

description: ChIP-seq of Homo sapiens, H3K4me3, adult female monocytes, CTR2

value: Histone H3K4me3 antibody (pAb)  (ActiveMotif, Catalog No:39915)


title: drerio_A24

description: drerio.loom


title: 3839T


title: drerio_A23

description: drerio.loom


title: EPCAM+/CD45- ECs, DKO4

city: Zwijnaarde

first: Jordy

last: De Coninck

address: Technologiepark 71

department: Department of Biomedical Molecular Biology

country: Belgium

institute: University Gent

data_processing:
Quality control was assesed with FASTQC (v0.11.9)
Reads were mapped to the mouse reference genome (mm10) via HiSat2
Counts were calculated using FeatureCounts (v2.0.0)
Genome_build: mm10
Supplementary_files_format_and_content: txt file containing counts for each sample

organism: Mus musculus

source_name: Ileum

extract_protocol: All Methods Listed in Ghazavi et al. The apoptotic executioner caspases-3 and -7 are dispensable during intestinal homeostasis. 2021.

value: Ileum

tag: genotype

value: Epithelial


title: methylation_sample_97


title: drerio_A22

description: drerio.loom


title: methylation_sample_95


title: 3849T


title: drerio_A21

description: drerio.loom


title: methylation_sample_94


title: EPCAM+/CD45- ECs, DKO2


title: CTR2H3K27ac

description: ChIP-seq of Homo sapiens, H3K27ac, adult female monocytes, CTR2

value: Histone H3K27ac antibody (pAb)  (ActiveMotif, Catalog No:39133)


title: methylation_sample_93


title: drerio_A20

description: drerio.loom


title: EPCAM+/CD45- ECs, DKO1


title: methylation_sample_92


title: drerio_A2

description: drerio.loom


title: EPCAM+/CD45- ECs, WT4


title: methylation_sample_96


title: methylation_sample_91


title: EPCAM+/CD45- ECs, WT3


title: EPCAM+/CD45- ECs, DKO3


title: drerio_A19

description: drerio.loom


title: 3318T


title: 3181T


title: 3108T


title: 3757T


title: 2553T


title: 2980T


title: 3810T


title: 2858T


title: EPCAM+/CD45- ECs, WT2


title: methylation_sample_89


title: drerio_A17

description: drerio.loom


title: EPCAM+/CD45- ECs, WT1


title: methylation_sample_88


title: 76T


title: Treg.PBS.Sp#9

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: Treg

extract_protocol:
1,000 Cells were double-sorted by FACS Aria 561 into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma).Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter)
total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 18 cycles using barcoded primers such that each sample carried a specific combination of eight-base Illumina P5 and P7 barcodes and were pooled together prior to Smart sequencing. Smart-seq paired-end sequencing was performed on an Illumina NextSeq500 using 2 x 38bp reads with no further trimming.

treatment_protocol: 5-8 week old C57Bl/6J mice shipped from the Jackson Laboratory, Bar Harbor. Mice were injected retro-orbitally with either a free cytokine or a cytokine-antibody complex with a 2 hour acute readout. Further, mice were injected with 10ug mIL2/110uL PBS,5 μg IL-4 with 25 μg 11B11 in 110 uL PBS, 0.75ug mIL-7 to 15ug anti-m/h IL-7 M25 mAb  in 110uL PBS, 5ug mIL9 in 110uL PBS, 2.5ug mIL-15 to 15ug mIL15Ra-Fc in 110uL PBS, or 20ug mIL-21 in 110uL PBS.

value: Spleen

value: Treg


title: drerio_A18

description: drerio.loom

value: spinal cord


title: drerio_A15

description: drerio.loom


title: drerio_A16

description: drerio.loom


title: methylation_sample_86

source_name: Oligodendroglioma, IDH-mutant and 1p/19q codeleted


title: 77T

value: Male


title: drerio_A14

description: drerio.loom


title: Treg.PBS.Sp#8


title: methylation_sample_87

value: FFPE


title: 74T


title: Treg.PBS.Sp#10


title: drerio_A13

description: drerio.loom


title: drerio_A12

description: drerio.loom


title: methylation_sample_85


title: Treg.PBS.Sp#7


title: Treg.PBS.Sp#6


title: Treg.PBS.Sp#5


title: 71T


title: drerio_A11

description: drerio.loom


title: methylation_sample_68


title: methylation_sample_67


title: methylation_sample_66

source_name: Astrocytoma, IDH-mutant, infratentorial, low grade


title: drerio_A10

description: drerio.loom


title: Treg.PBS.Sp#4


title: drerio_A1

description: drerio.loom


title: 70T


title: methylation_sample_59


title: methylation_sample_69


title: drerio_B21

description: drerio.loom


title: Treg.PBS.Sp#3


title: PBAT_sperm_hypoxia_3

city: Dunedin

first: Oscar

middle: Javier

last: Ortega-Recalde

state: Otago

address: 60 Hanover Street

department: Anatomy

country: New Zealand

institute: University of Otago

data_processing:
Trimming using TrimGalore ! (v0.6.4), quality threshold 20, hard trimming 10bp
Reads were aligned against Danio rerio genome GCRz11 using using HISAT2 v2.2.0 and Bismark v0.22.3 for RNA-seq and PBAT reads respectively
For RNA-seq analysis expression was summarized sample by sample at the gene level using featureCounts v2.0.0. For methylation analysis BAM files were deduplicated and CpG calls were extracted using bismark_methylation_extractor.
Genome_build: GCRz11
Supplementary_files_format_and_content: Processed files contain counts for gene expression analysis and individual CpG calls proccesed by Bismark for methylation analysis.

source_name: Sperm

growth_protocol: Breeding and husbandry took place within the Otago Zebrafish Facility (OZF), a temperature-controlled facility maintained at 25-27°C, pH 7-7.8 and conductivity 300-500 µS. Fish were maintained in a Tecniplast re-circulating system (Tecniplast, Varese, Italy) under a 14:10 light:dark photoperiodic cycle, with 30 minutes of simulated dawn and dusk at the start and end of each day.

extract_protocol:
Total RNA from 6 whole fry (3 control offspring, 3 treatment offspring) was extracted using a Zymo Duet extraction kit (Zymo, NZ). Total nucleic acids for methylation analysis were purified using the Bio-On-Magnetic-Beads (BOMB) approach (Oberacker et al., 2018).
Messenger RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA sample preparation kit (Illumina), as per the manufacturer's instructions. Bisulfite-coverted genomic libraries were prepared using a modified post-bisulfite adapter tagging method.

treatment_protocol: In November 2016, nine-month-old male zebrafish (AB wild-type; n=20/treatment) were exposed to hypoxic conditions (11-13 kPA oxygen; 53.1-60% air saturation) or control conditions (21 kPA), for two weeks.

tag: treatment

value: Hypoxia

value: sperm

tag: generation

value: parental


title: 73T

value: Female


title: methylation_sample_58


title: 68T


title: 66T


title: 72T


title: Treg.PBS.Sp#2


title: 69T


title: Treg.PBS.Sp#1


title: PBAT_sperm_hypoxia_1


title: PBAT_sperm_hypoxia_2


title: methylation_sample_57


title: Treg.IL9.Sp#2


title: methylation_sample_56


title: 64T


title: PBAT_sperm_no_treatment_3

value: No treatment


title: 63T


title: 62T


title: methylation_sample_55


title: PBAT_sperm_no_treatment_2


title: methylation_sample_54


title: Treg.IL7.Sp#1


title: Treg.IL9.Sp#1


title: 61T


title: methylation_sample_52


title: 65T


title: methylation_sample_51


title: Treg.IL4.Sp#2


title: methylation_sample_53


title: Treg.IL7.Sp#3


title: Treg.IL4.Sp#1


title: Treg.IL21.Sp#3


title: methylation_sample_49


title: Treg.IL4.Sp#3


title: RNA_seq_fry_hypoxia_3

source_name: Fry

value: whole organism


title: 58T


title: RNA_seq_fry_no_treatment_2


title: RNA_seq_fry_hypoxia_1


title: Treg.IL21.Sp#2


title: 60T


title: RNA_seq_fry_no_treatment_3


title: 59T


title: RNA_seq_fry_hypoxia_2


title: 56T


title: PBAT_sperm_no_treatment_1


title: 55T


title: methylation_sample_48


title: methylation_sample_40

source_name: Astrocytoma, IDH-mutant, infratentorial, high grade


title: 57T


title: methylation_sample_47


title: Treg.IL2.Sp#3


title: methylation_sample_50


title: RNA_seq_fry_no_treatment_1


title: methylation_sample_38


title: methylation_sample_37


title: Treg.IL21.Sp#1


title: Treg.IL2.Sp#2


title: Treg.IL2.Sp#1


title: methylation_sample_196

source_name: Astrocytoma, IDH-mutant, supratentorial, low


title: methylation_sample_197


title: Treg.IL15.Sp#2


title: Treg.IL15.Sp#3


title: 50T


title: 52T


title: methylation_sample_36


title: methylation_sample_195


title: methylation_sample_199


title: methylation_sample_35

value: Frozen


title: 49T


title: Treg.IL15.Sp#1


title: methylation_sample_194


title: 47T


title: 48T


title: methylation_sample_193


title: 45T


title: Tgd.PBS.Sp#10

source_name: Gamma-Delta T Cell

value: Gamma-Delta T Cell


title: Tgd.PBS.Sp#9


title: methylation_sample_191


title: methylation_sample_34


title: methylation_sample_39


title: methylation_sample_190


title: methylation_sample_31


title: methylation_sample_32


title: 42T


title: methylation_sample_33


title: 44T


title: 43T


title: methylation_sample_188


title: Tgd.PBS.Sp#5


title: Tgd.PBS.Sp#6


title: methylation_sample_187


title: Tgd.PBS.Sp#7


title: 41T


title: methylation_sample_27

source_name: GBM RTKII


title: methylation_sample_189


title: Tgd.PBS.Sp#4


title: methylation_sample_192


title: methylation_sample_186


title: methylation_sample_28


title: Tgd.PBS.Sp#8


title: Tgd.PBS.Sp#3


title: 4403T


title: methylation_sample_25


title: 39T


title: methylation_sample_198


title: 37T


title: methylation_sample_24


title: 40T


title: methylation_sample_184


title: methylation_sample_23


title: methylation_sample_185


title: Tgd.PBS.Sp#1


title: methylation_sample_22


title: methylation_sample_183


title: Tgd.IL9.Sp#2


title: methylation_sample_182


title: 38T


title: Tgd.IL9.Sp#1


title: methylation_sample_181


title: 36T


title: methylation_sample_19

source_name: GBM RTKI


title: methylation_sample_21


title: 35T

source_name: Stomach


title: Tgd.IL7.Sp#2


title: 46T


title: 34T


title: 33T


title: methylation_sample_180


title: 32T


title: Tgd.PBS.Sp#2


title: Tgd.IL7.Sp#1


title: methylation_sample_18


title: 31T


title: methylation_sample_179


title: Tgd.IL4.Sp#2


title: Tgd.IL4.Sp#3


title: Tgd.IL4.Sp#1


title: methylation_sample_16


title: methylation_sample_178


title: methylation_sample_17


title: methylation_sample_15


title: methylation_sample_176


title: methylation_sample_177


title: 28T


title: methylation_sample_14


title: 30T


title: methylation_sample_13


title: 29T


title: Tgd.IL21.Sp#2


title: methylation_sample_174


title: 27T


title: methylation_sample_12


title: 26T


title: Tgd.IL21.Sp#1


title: methylation_sample_172

source_name: Astrocytoma, IDH-mutant, supratentorial, high


title: 25T


title: methylation_sample_171


title: Tgd.IL2.Sp#2


title: methylation_sample_10

source_name: GBM MES


title: methylation_sample_9


title: Tgd.IL2.Sp#1


title: methylation_sample_175


title: Tgd.IL21.Sp#3


title: Tgd.IL15.Sp#3


title: methylation_sample_169


title: methylation_sample_8


title: methylation_sample_7


title: 23T


title: methylation_sample_167


title: Tgd.IL2.Sp#3


title: 22T


title: methylation_sample_11


title: methylation_sample_6


title: methylation_sample_166


title: T.8.PBS.Sp#11

source_name: Effector-Memory T Cell

value: Effector-Memory T Cell


title: Tgd.IL15.Sp#1


title: 21T


title: methylation_sample_5


title: 24T


title: 19T


title: 18T


title: 20T


title: methylation_sample_170


title: methylation_sample_4


title: T.8.PBS.Sp#10


title: methylation_sample_165


title: methylation_sample_164


title: methylation_sample_163


title: methylation_sample_168


title: Tgd.IL15.Sp#2


title: methylation_sample_3


title: methylation_sample_2


title: 16T


title: methylation_sample_162


title: methylation_sample_1


title: 17T


title: methylation_sample_161


title: T.8.PBS.Sp#7


title: T.8.PBS.Sp#8


title: T.8.PBS.Sp#6


title: T.8.PBS.Sp#5


title: 11T


title: T.8.PBS.Sp#9

source_name: Effector Memory T Cell

value: Effector Memory T Cell


title: 13T


title: methylation_sample_160


title: methylation_sample_159


title: methylation_sample_158


title: T.8.PBS.Sp#3


title: methylation_sample_157


title: T.8.PBS.Sp#2


title: 15T


title: T.8.PBS.Sp#1


title: methylation_sample_156


title: T.8.IL9.Sp#2


title: T.8.IL9.Sp#1


title: methylation_sample_152

source_name: Primary tumor of oligosarcoma


title: methylation_sample_151


title: methylation_sample_155


title: T.8.PBS.Sp#4


title: 9T


title: methylation_sample_150


title: T.8.IL7.Sp#1


title: methylation_sample_149


title: methylation_sample_26


title: methylation_sample_148


title: 6T


title: methylation_sample_147


title: 4T


title: 8T


title: 5T


title: 2T


title: T.8.IL4.Sp#3


title: 3T


title: w1118, rep3

city: Dalian

first: Ying

last: Ge

address: 9 Western Section, Lvshun South Street

institute: Dalian Medical University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 400.

scan_protocol: Gene chips were scaned using Affymetrix GeneChip Scanner 3000.

data_processing: Gene expression data was preprocessed using rma (R package affy)

label: biotin

organism: Drosophila melanogaster

source_name: Embryos of w1118 flies at 0 – 24 hr were collected

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: All flies were maintained at 25 °C on standard corn meal unless specified.

extract_protocol: RNA was extracted using RNeasy Lipid Tissue Mini Kit, Qiagen

tag: strain background

tag: genotype/variation

value: wild type

value: embryos at 0 - 24 hr


title: T.8.IL21.Sp#3

value: Spleen


title: w1118, rep2


title: clbn knock-out, rep1

source_name: Embryos of clbn knock-out flies at 0 – 24 hr were collected

value: clbn knock-out


title: T.8.IL4.Sp#2


title: T.8.IL7.Sp#3


title: methylation_sample_137

source_name: PMMRDIA


title: clbn knock-out, rep2


title: T.8.IL4.Sp#1


title: methylation_sample_136


title: T.8.IL21.Sp#1


title: XP-A-iMC Exp.2 UVB 150J 12hr

city: Kobe

first: Chihiro

last: Takemori

address: Kusunoki-cho 7-5-1

country: Japan

institute: Kobe University

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Gene Chip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed and normalized with GeneSpring 13.1.1 software program. Summarization algorithm is RMA.

source_name: XP-A-iMC Exp.2

label_protocol: Biotinylated cRNA were prepared usind GeneChip 3’IVT PLUS Reagent Kit from 250 ug total RNA.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: XP-A-iMC

tag: uv

value: UVB150J/m2 12hr


title: methylation_sample_141


title: clbn knock-out, rep3


title: w1118, rep1


title: methylation_sample_130

value: FFPE


title: XP-A-iMC Exp.2 UVB 30J 12hr

value: UVB30J/m2 12hr


title: T.8.IL21.Sp#2


title: XP-A-iMC Exp.2 UVB 150J 4hr

value: UVB150J/m2 4hr


title: methylation_sample_109

source_name: Oligosarcoma, IDH-mutant


title: methylation_sample_135


title: T.8.IL15.Sp#3


title: HC-iMC Exp.2 UVB 150J 12hr

source_name: HC-iMC Exp.2

value: HC-iMC


title: HC-iMC Exp.2 UVB 150J 4hr


title: XP-A-iMC Exp.2 UVB 30J 4hr

value: UVB30J/m2 4hr


title: T.8.IL2.Sp#3


title: T.8.IL2.Sp#2


title: genomic DNA from G_AML_424 leukemia

city: Setagaya

first: Tomoko

last: Kawai

state: Tokyo

department: Department of Maternal-Fetal Biology

institute: National Research Institute for Child Health and Development

description: Leukemia

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio software v1.9.0

label: Cy5 and Cy3

source_name: bone marrow

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from cord blood using QIAsymphony DNA Midi Kit (96) according to standard instructions

value: Leukemia

value: female


title: genomic DNA from G_AML_440 leukemia

description: Leukemia


title: T.8.IL2.Sp#1


title: genomic DNA from G_AML_434 leukemia

description: Leukemia

value: male


title: XP-A-iMC Exp.2 UVB pre

value: no UV


title: HC-iMC Exp.2 UVB 30J 12hr


title: genomic DNA from G_AML_432 leukemia

description: Leukemia


title: genomic DNA from G_AML_394 leukemia

description: Leukemia


title: genomic DNA from G_AML_398 leukemia

description: Leukemia


title: genomic DNA from G_AML_437 leukemia

description: Leukemia


title: T.8.IL15.Sp#1

value: Effector-Memory T Cell


title: genomic DNA from G_AML_373 leukemia

description: Leukemia


title: genomic DNA from G_AML_430 leukemia

description: Leukemia


title: methylation_sample_118

value: Frozen


title: methylation_sample_105


title: T.8.IL15.Sp#2


title: methylation_sample_107


title: methylation_sample_106


title: genomic DNA from G_AML_388 leukemia

description: Leukemia


title: T.4.PBS.Sp#7

source_name: Naïve T Cell

value: Naive T Cell


title: genomic DNA from G_AML_381 leukemia

description: Leukemia


title: T.4.PBS.Sp#9


title: genomic DNA from G_AML_352 leukemia

description: Leukemia


title: T.4.PBS.Sp#8


title: methylation_sample_104


title: HC-iMC Exp.2 UVB pre


title: methylation_sample_103


title: HC-iMC Exp.2 UVB 30J 4hr


title: NHEM Exp.2 UVB 150J 12hr

source_name: NHEM Exp.2

value: NHEM


title: genomic DNA from G_AML_347 leukemia

description: Leukemia


title: methylation_sample_108


title: T.4.PBS.Sp#5

value: Spleen


title: methylation_sample_101


title: T.4.PBS.Sp#6


title: NHEM Exp.2 UVB 150J 4hr


title: T.4.PBS.Sp#4


title: methylation_sample_100


title: T.4.PBS.Sp#3


title: methylation_sample_102


title: genomic DNA from G_AML_356 leukemia

description: Leukemia


title: genomic DNA from G_AML_357 leukemia

description: Leukemia


title: XP-A-iMC Exp.1 pre

source_name: XP-A-iMC Exp.1


title: NHEM Exp.2 UVB 30J 12hr


title: methylation_sample_99


title: NHEM Exp.2 UVB 30J 4hr


title: methylation_sample_98


title: T.4.PBS.Sp#1


title: T.4.PBS.Sp#2


title: NHEM Exp.2 UVB pre


title: HC-iMC Exp.1 pre

source_name: HC-iMC Exp.1


title: methylation_sample_90


title: T.4.IL9.Sp#2


title: genomic DNA from G_AML_329 leukemia

description: Leukemia


title: methylation_sample_84

source_name: Oligodendroglioma, IDH-mutant and 1p/19q codeleted


title: methylation_sample_83


title: genomic DNA from G_AML_324 leukemia

description: Leukemia


title: methylation_sample_82


title: WI38_2

city: Tampa

first: Eric

last: Welsh

address: 12902 Magnolia Dr

department: Biostatistics and Bioinformatics

institute: H Lee Moffitt Cancer Center

description: WI38 normal lung associated fibroblasts, biological replicate 2

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C to the Affymetrix U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scanner.

data_processing: The images were analyzed with the Affymetrix Command Console 4.0 software, then normalized using IRON against MRC5_2 as the reference sample

source_name: WI38 normal lung associated fibroblasts

label_protocol: Biotinylated cRNA was prepared according to the Ambion Message Amp Premier protocol using 100 ng of total RNA (Ambion).

growth_protocol: All cell lines were grown in RPMI-1640, supplemented with 10% fetal bovine serum. The cell lines were maintained in a humid incubator at 37°C and 5% CO2.

extract_protocol: Isolation of total RNA was performed using the Qiagen RNEasy column according to the manufacturer's instructions.

treatment_protocol: Cells were untreated and were harvested at 80-90% confluency over three consecutive passages for three biological replicates.

tag: cell line

value: normal lung associated fibroblasts

tag: cell type abbreviation

tag: biological replicate


title: WI38_1

description: WI38 normal lung associated fibroblasts, biological replicate 1


title: genomic DNA from G_AML_276 leukemia

description: Leukemia

tag: age


title: T.4.IL7.Sp#3

tag: tissue


title: WI38_3

description: WI38 normal lung associated fibroblasts, biological replicate 3


title: methylation_sample_81


title: T.4.IL9.Sp#1

tag: strain


title: PC9_GR_2

description: PC9_GR gefitinib resistant non-small cell lung cancer cells, biological replicate 2

tag: notes


title: genomic DNA from G_AML_269 leukemia

description: Leukemia


title: T.4.IL4.Sp#2

tag: cell type


title: methylation_sample_80

tag: material


title: genomic DNA from G_AML_319 leukemia

description: Leukemia

tag: disease state

tag: gender


title: T.4.IL4.Sp#3


title: PC9_3

description: PC9 non-small cell lung cancer cells, biological replicate 3

source_name: PC9 non-small cell lung cancer cells

value: non-small cell lung cancer

value: NSCLC


title: PC9_GR_1

description: PC9_GR gefitinib resistant non-small cell lung cancer cells, biological replicate 1


title: genomic DNA from G_AML_237 leukemia

description: Leukemia


title: T.4.IL4.Sp#1


title: PC9_GR_3

description: PC9_GR gefitinib resistant non-small cell lung cancer cells, biological replicate 3


title: methylation_sample_78

value: FFPE


title: PC9_2

description: PC9 non-small cell lung cancer cells, biological replicate 2


title: methylation_sample_77


title: genomic DNA from G_AML_259 leukemia

description: Leukemia


title: T.4.IL21.Sp#2


title: T.4.IL7.Sp#1


title: PC9_1

description: PC9 non-small cell lung cancer cells, biological replicate 1


title: genomic DNA from G_AML_228 leukemia

description: Leukemia


title: genomic DNA from G_AML_306 leukemia

description: Leukemia


title: MRC5_3

description: MRC5 normal lung associated fibroblasts, biological replicate 3

source_name: MRC5 normal lung associated fibroblasts


title: T.4.IL21.Sp#1


title: methylation_sample_75


title: methylation_sample_76


title: MRC5_2

description: MRC5 normal lung associated fibroblasts, biological replicate 2


title: genomic DNA from G_AML_188 leukemia

description: Leukemia


title: methylation_sample_74


title: T.4.IL2.Sp#2


title: genomic DNA from G_AML_222 leukemia

description: Leukemia


title: genomic DNA from G_AML_185 leukemia

description: Leukemia


title: T.4.IL2.Sp#1


title: IMR90_3

description: IMR90 normal lung associated fibroblasts, biological replicate 3


title: MRC5_1

description: MRC5 normal lung associated fibroblasts, biological replicate 1


title: genomic DNA from G_AML_223 leukemia

description: Leukemia


title: genomic DNA from G_AML_204 leukemia

description: Leukemia


title: genomic DNA from G_AML_187 leukemia

description: Leukemia


title: genomic DNA from G_AML_225 leukemia

description: Leukemia


title: methylation_sample_72


title: T.4.IL2.Sp#3


title: IMR90_2

description: IMR90 normal lung associated fibroblasts, biological replicate 2


title: T.4.IL15.Sp#3


title: genomic DNA from G_AML_175 leukemia

description: Leukemia


title: methylation_sample_71


title: T.4.IL15.Sp#2


title: IMR90_1

description: IMR90 normal lung associated fibroblasts, biological replicate 1


title: methylation_sample_70


title: T.4.IL15.Sp#1


title: methylation_sample_65

source_name: Astrocytoma, IDH-mutant, infratentorial, low grade


title: HS5_3

description: HS5 normal bone marrow associated fibroblasts, biological replicate 3


title: methylation_sample_64


title: methylation_sample_79


title: pDC.PBS.Sp#9

source_name: Plasmacytoid Dendritic Cell

value: Plasmacytoid Dendritic Cell


title: HS5_1

description: HS5 normal bone marrow associated fibroblasts, biological replicate 1


title: genomic DNA from G_AML_169 leukemia

description: Leukemia


title: pDC.PBS.Sp#8


title: methylation_sample_63


title: pDC.PBS.Sp#7


title: genomic DNA from G_AML_176 leukemia

description: Leukemia


title: T.4.IL21.Sp#3


title: methylation_sample_62


title: genomic DNA from G_AML_164 leukemia

description: Leukemia


title: methylation_sample_61


title: pDC.PBS.Sp#6


title: pDC.PBS.Sp#5


title: H3122_2

description: H3122 non-small cell lung cancer cells, biological replicate 2

source_name: H3122 non-small cell lung cancer cells


title: HS5_2

description: HS5 normal bone marrow associated fibroblasts, biological replicate 2


title: methylation_sample_60


title: H3122_3

description: H3122 non-small cell lung cancer cells, biological replicate 3


title: genomic DNA from G_AML_136 leukemia

description: Leukemia


title: CAF7_3

description: CAF7 lung cancer associated fibroblasts, biological replicate 3

source_name: CAF7 lung cancer associated fibroblasts

value: cancer associated fibroblasts


title: genomic DNA from G_AML_153 leukemia

description: Leukemia


title: CAF7_2

description: CAF7 lung cancer associated fibroblasts, biological replicate 2


title: pDC.PBS.Sp#3


title: genomic DNA from G_AML_156 leukemia

description: Leukemia


title: methylation_sample_73


title: methylation_sample_45

source_name: Astrocytoma, IDH-mutant, infratentorial, high grade


title: pDC.PBS.Sp#2


title: CAF7_1

description: CAF7 lung cancer associated fibroblasts, biological replicate 1


title: genomic DNA from G_AML_144 leukemia

description: Leukemia


title: methylation_sample_44


title: pDC.PBS.Sp#1


title: methylation_sample_46


title: genomic DNA from G_AML_128 leukemia

description: Leukemia


title: methylation_sample_43


title: genomic DNA from G_AML_129 leukemia

description: Leukemia


title: CAF12_2

description: CAF12 lung cancer associated fibroblasts, biological replicate 2


title: CAF12_3

description: CAF12 lung cancer associated fibroblasts, biological replicate 3


title: H3122_1

description: H3122 non-small cell lung cancer cells, biological replicate 1


title: genomic DNA from G_AML_109 leukemia

description: Leukemia


title: pDC.PBS.Sp#4


title: pDC.IL9.Sp#2


title: CAF12_1

description: CAF12 lung cancer associated fibroblasts, biological replicate 1


title: methylation_sample_42


title: genomic DNA from G_AML_108 leukemia

description: Leukemia


title: genomic DNA from G_AML_120 leukemia

description: Leukemia


title: methylation_sample_41


title: pDC.IL9.Sp#1


title: pDC.IL7.Sp#3


title: methylation_sample_30

source_name: GBM RTKII


title: genomic DNA from G_AML_125 leukemia

description: Leukemia


title: PAF #3, HGF neutralizing antibody

city: Tokyo

first: Akira

last: Saito

address: 7-31-, Hongo, Bunkyo

institute: Tokyo University

description: Gene expression data from PAF #3 containing collagen gels treated with HGF neutralizing antibody

hyb_protocol: Hybridization was processed according to the standard Affymetrix protocol.

scan_protocol: GeneChip® Scanner 3000 7G  (Affymetrix)

data_processing: Affymetrix® Expression Console™ Software  (Affymetrix)

growth_protocol: Gingival epithelial cells and periodontitis-associated fibroblasts (PAF) were co-cultured in collagen gels.

extract_protocol: RNeasy mini kit (Qiagen) was used for total RNA extraction.

treatment_protocol: Collagen gels were treated with HGF neutralizing antibody or control IgG.


title: pDC.IL7.Sp#2


title: methylation_sample_29


title: pDC.IL7.Sp#1


title: methylation_sample_20

source_name: GBM RTKI


title: PAF #2, HGF neutralizing antibody

description: Gene expression data from PAF #2 containing collagen gels treated with HGF neutralizing antibody


title: PAF #3, control IgG

description: Gene expression data from PAF #3 containing collagen gels treated with control IgG


title: pDC.IL4.Sp#3


title: genomic DNA from G_AML_101 leukemia

description: Leukemia


title: genomic DNA from G_AML_086 leukemia

description: Leukemia


title: genomic DNA from G_AML_105 leukemia

description: Leukemia


title: genomic DNA from G_AML_070 leukemia

description: Leukemia


title: pDC.IL4.Sp#2


title: PAF #1, HGF neutralizing antibody

description: Gene expression data from PAF #1 containing collagen gels treated with HGF neutralizing antibody


title: pDC.IL4.Sp#1


title: PAF #2, control IgG

description: Gene expression data from PAF #2 containing collagen gels treated with control IgG


title: PPE_week2_4

city: Munich

first: Bernd

middle: Henrik

last: Northoff

address: Marchioninistr. 15

department: Institute of Laboratory Medicine

institute: Ludwig-Maximilians-University Munich

description:
PPE infusion,  aorta was harvested after 2 weeks
DE_week2.csv

data_processing:
Fastq-files were generated using Illumina bcl2fastq.
Raw reads were mapped to the reference genome mm10 using split-read mapping algorithm implemented in segemhel.
Differential expression was analyzed using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: raw_counts: Raw gene counts given as comma-separated values.
Supplementary_files_format_and_content: DE_week1: Differential expression dataset given as comma-separated values.
Supplementary_files_format_and_content: DE_week2: Differential expression dataset given as comma-separated values.

source_name: Aorta

growth_protocol: Experiments were performed with 10-week-old male C57BL/6J mice.

extract_protocol:
Total RNA was extracted from murine aortic samples of the PPE mouse model using the TRIzol reagent and was purified using RNeasy Micro Kit.
500 ng of total RNA was used for library synthesis with the TrueSeq RNA Sample Prep Kit v2.

treatment_protocol: Mice were divided in 3 groups: 1) Control group (n = 4), where animals received saline infusion in the infrarenal aortic segment, and the aorta was harvested after 7 days. 2) Elastase 1 week (n = 4), where animals received PPE infusion in the infrarenal aortic segment, and the aorta was harvested after 7 days. 3) Elastase 2 week (n = 4), where animals received PPE infusion in the infrarenal aortic segment, and the aorta was harvested after 14 days.

value: PPE infusion

value: Aorta

tag: time

value: 2 weeks

tag: Sex


title: PPE_week2_3

tag: treatment


title: PAF #1, control IgG

description: Gene expression data from PAF #1 containing collagen gels treated with control IgG


title: pDC.IL21.Sp#3


title: pDC.IL21.Sp#1


title: BALBc2M_rep1

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description:
Biological replicate 2 of 2, Cy3 is mouse RNA and Cy5 is mouse reference
BALBCYoung_rep1

hyb_protocol: Slides were hybridized to Agilent-015087 arrays according to the manufacturer's protocol (Two-Color Microarray-Based Gene Expression Analysis Protocol, Product # G4140-90050, Version 5.0.1)

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

data_processing:
Data are extracted with Agilent Feature Extraction Software. The data were further processed with NIA ANOVA tool utilities. See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal, rDyeNormSignal in the raw files and log-transform them using: log10(max(x,10)). These values will be referenced below as Xgi and Xri, where i is array number.
(2) Take average of Xri's for the oligo among 28 arrays in the series: AverXr = average(Xri).
(3) For each array, estimate Yi = Xgi-Xri+AverXr (adjust to UMR).
(4) Remove outliers. Each cell/treatment type (CTT) is characterized by 2 replications, all are log-transformed (log10). Here we check if any of these values is an outlier.
First we estimate the average square difference (ASD) between replication pairs:
ASD = SUM[(x(i,1)-x(i,2))^2]/N/2
where x(i,j) is log intensities for i-th CTT and replication j, N = number of CTT. Then we estimate z-value for each CTT: z = (x(i,1)-x(i,2))/sqrt(ASD). If abs(z) > 4, then one of the replications is an outlier. The value that is farther away from the median expression value is considered an outlier and it is replaced with the value from another replication.
The result is used as the normalized VALUE. More detailed information with error correction can be found at: http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

label_protocol: Total RNA was labeled using the Agilent Low RNA Input Fluorescent Linear Amplification kit according to the manufacturer's instructions.

extract_protocol: 1ml of TRIzol reagent was added to each sample, and homogenized immediately. Trizol dissolved samples were then isolated with Purelink RNA mini kit (#121830A, Invitrogen) according to manufacturer's protocol. RNAs were subjected to on column DNase1 digestion, and transferred to -80C for storage.

treatment_protocol: Vastus intermedius muscles from 24M and 2M old BALB/c mice were collected under dissection microscope, and kept in -80C until use.

tag: development stage

value: Adult

value: vastus intermedius muscle

value: BALB/c

tag: individual identifier

source_name: Universal Mouse Reference

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts. The resulting UMR RNA was mixed with 129ES cell RNA (Lif+) at 2:1 ratio and 2.5ug of mixed RNA was used for labeling in each tube

tag: sample type

value: Reference


title: PPE_week2_2

value: male


title: BALBc2M_rep3

description:
Biological replicate 2 of 2, Cy3 is mouse RNA and Cy5 is mouse reference
BALBCYoung_rep3


title: genomic DNA from G_AML_067 leukemia

description: Leukemia

source_name: bone marrow

value: Leukemia


title: PPE_week2_1


title: RKO cells, shCHD7_2, rep2

city: Tianjin

first: Chenghao

last: Xuan

address: 22 Qixiangtai Road

institute: Tianjin Medical University

data_processing:
A propriety Sub-pixel Registration algorithm developed by MGI was used for base call.
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows:
1) Remove the reads containing the adaptor(adaptor pollution);
2) Remove reads whose N content is greater than 5%;
3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).
The filtered "Clean Reads" are saved in FASTQ format.
Bowtie2 was used to map the clean reads to the reference gene sequence (transcriptome), and then RSEM was used to calculate the gene expression level of each sample.
The DEseq2 was used to perform differential expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: RKO cells, shCHD7_2

growth_protocol: RKO cells were cultured in Eagle’s Minimum Essential Medium supplemented with 10% fetal bovine serum at 37 ℃ in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using oligo-dT beads

treatment_protocol: The lentiviruses expressing control or shCHD7 shRNA were employed to infect RKO cells to obtain stable expression cells.

tag: cell line

value: RKO

value: colon

value: colon cancer cell

value: CHD7 shRNA2

tag: genotype

value: CHD7 knockdown


title: pDC.IL2.Sp#3

value: Spleen


title: RKO cells, shCHD7_2, rep1


title: BALBc2M_rep2

description:
Biological replicate 1 of 2, Cy3 is mouse RNA and Cy5 is mouse reference
BALBCYoung_rep2


title: RKO cells, vector, rep2

source_name: RKO cells, vector

value: control


title: BALBc24M_rep2

description:
Biological replicate 2 of 2, Cy3 is mouse RNA and Cy5 is mouse reference
BALBCOld_rep2


title: PPE_week1_4

description:
PPE infusion,  aorta was harvested after 1 week
DE_week1.csv

value: 1 week


title: genomic DNA from G_AML_065 leukemia

description: Leukemia


title: PPE_week1_3

value: PPE infusion


title: pDC.IL2.Sp#2

value: Plasmacytoid Dendritic Cell


title: RKO cells, vector, rep1


title: pDC.IL15.Sp#3


title: PPE_week1_1

value: Aorta


title: pDC.IL2.Sp#1


title: MCF7_PacBio_Sequencing

city: Frederick

first: Lisheng

last: Dai

address: 1050 Boyles St.

institute: NCI-Frederick

description: wild type cells

data_processing:
PacBio sequencing was processed by the Iso-Seq standard pipeline.
Small RNA sequencing was processed by customized scripts. Reads without the 3′ adaptor sequences or shorter than 18 nt were discarded
Genome_build: GRCH38 or miRBase21
Supplementary_files_format_and_content: BED files or TXT files

source_name: cell line

growth_protocol: Cells were maintained in DMEM (high glucose) (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Hyclone), 100 U/ml penicillin and 100 μg/ml streptomycin (Gibco).

extract_protocol:
RNA was extracted from cell lines using Trizol
Sequencing libraries were prepared using standard protocols. Samll RNA library was constructed by NEBNext® Multiplex Small RNA Library Prep Set according to the manufacturer's’ protocol
PacBio Sequencing or MiSeq

treatment_protocol: No treatment or Transfection

tag: passage


title: genomic DNA from G_AML_051 leukemia

description: Leukemia

value: female

tag: age


title: BALBc24M_rep1

description:
Biological replicate 1 of 2, Cy3 is mouse RNA and Cy5 is mouse reference
BALBCOld_rep1

value: Adult

tag: tissue

value: vastus intermedius muscle


title: KO_00_rep2

city: Freiburg

first: Yoko

middle: Fukuda

last: Yuzawa

address: Stübeweg 51

institute: Max-Planck Institute of Immunobiology

description: Gene expression of macrophages

hyb_protocol: Hybridization and washing were done using Agilent Gene Expression Hybridization Kit (Agilent, 5188-5242) and Agilent Wash Buffer Kit (Agilent, 5188-5327) according to manufacturer’s protocols (One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.5, May 2012).

scan_protocol: Slides were scanned (after washing) on the Agilent Microarray Scanner (G2565CA) using one color scan setting for 4x 44k array slides (Profile: AgilentHD_GX1col, resolution: 5 μm).

data_processing: The scanned images were analyzed with Feature Extraction Software using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Further data processing was done using GeneSpring GX Software v12.0

source_name: miR-155 KO macrophages in steady state replicate2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using Low Input Quick Amp Labeling Kit, One-Color (Agilent, 5190-2305) according to manufacturer’s instructions (One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.5, May 2012), followed by RNAeasy column purification (Qiagen, 4106).

growth_protocol: Bone marrow cells were cultured in 10 ng/mL M-CSF enriched media for 9 days.

extract_protocol: RNA was extracted by using the miRMeasy kit (Qiagen, 217004), following the manufacturer’s protocol. Additional on-column DNase digestion was performed. The total RNA was quatified by a NanoDrop-1000 spectrophotometer and RNA quality was established by an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: On day 9, adherent macrophages were either kept unstimulated and lysed directly in RNA lysis buffer, or the macrophages were stimulated in 100 ng/mL LPS. After 6-, 12- and 24 h of stimulation, the samples were also lysed in RNA lysis buffer and the total RNA from the WT- and miR-155 KO MΦ samples were sent for agilent microarray analysis (Source BioScience).

value: Cultured bone marrow cells

tag: strain

tag: genotype/variation

value: miR-155 KO


title: genomic DNA from G_AML_049 leukemia

description: Leukemia

value: Leukemia


title: KO_24_rep2

description: Gene expression of LPS treated macrophages

source_name: miR-155 KO macrophages after 24h of LPS stimulation replicate2

tag: cell type

value: male


title: genomic DNA from G_AML_040 leukemia

description: Leukemia


title: genomic DNA from G_AML_048 leukemia

description: Leukemia


title: genomic DNA from G_AML_068 leukemia

description: Leukemia


title: pDC.IL15.Sp#1


title: PPE_week1_2


title: pDC.IL15.Sp#2


title: Sham_3

description: Control group with saline infusion

value: Saline infusion


title: HeLa_PacBio_Sequencing

description: wild type cells

value: HeLa


title: genomic DNA from G_AML_061 leukemia

description: Leukemia


title: BALBc24M_rep3

description:
Biological replicate 1 of 2, Cy3 is mouse RNA and Cy5 is mouse reference
BALBCOld_rep3

value: BALB/c

value: Reference


title: Sham_2

description: Control group with saline infusion


title: No40_eps_3

city: Shinjuku

first: Sho

last: Yoshimatsu

address: 35 Shinanomachi

department: Physiology

institute: Keio University School of Medicine

data_processing:
Data of RNA-seq (fastq file format) were quality-checked, and low-quality reads (score < 30), adapter sequences, and overrepresented sequences such as poly-A chain were trimmed using the Trim Galore! (ver.0.4.0).
The remaining reads were mapped to the Callithrix jacchus genome (cj3.2.1.86) using the STAR (ver.2.5.3a), and the output file (BAM file format) were summarized using the featureCounts (1.5.2).
Genome_build: cj3.2.1.86
Supplementary_files_format_and_content: raw counts

organism: Callithrix jacchus

source_name: Extended pluripotent stem cell

extract_protocol:
RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Extended pluripotent stem cell


title: KO_06_rep2

source_name: miR-155 KO macrophages after 6h of LPS stimulation replicate2


title: 293T_PacBio_Sequencing

description: wild type cells


title: genomic DNA from G_AML_018 leukemia

description: Leukemia


title: NK.PBS.Sp#9

source_name: Natural Killer Cell

value: Spleen

value: Natural Killer Cell


title: genomic DNA from G_AML_006 leukemia

description: Leukemia


title: genomic DNA from G_AML_014 leukemia

description: Leukemia


title: WT_12_rep2

source_name: WT macrophages after 12h of LPS stimulation replicate2

value: WT


title: genomic DNA from G_AML_021 leukemia

description: Leukemia


title: R28_LCORL KD HEK293T #2 RNA-seq replicate 4

city: Chikusa-ku, Nagoya, Aichi

first: Kazuya

last: Ichihara

address: Furo-cho

institute: Nagoya University

data_processing:
Reads of low quality were discarded with the use of fastq_quality_trimmer and fastq_quality_filter of the FASTX-Toolkit.
Ribosomal RNA reads were removed by alignment with human rRNA sequences with the use of STAR, and the remaining reads were aligned with the human transcriptome (GRCh38.p13) and human genome (hg38) also with the use of STAR.
Read counting was performed with the use of featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: Counts per transcript

source_name: HEK293T cells

growth_protocol: The cells were cultured under an atmosphere of 5% CO2 at 37°C in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (Life Technologies) and antibiotics.

extract_protocol:
Total RNA was extracted from cell lysates with the use of a PureLink RNA Mini kit (Thermo Fisher Scientific). The quality of the purified RNA was assessed with a 2100 Bioanalyzer (Agilent).
After mRNA selection with the use of a NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), libraries were prepared with the use of a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: HEK293T cells were transfected with 10 nM small interfering RNAs (siRNAs) with the use of Lipofectamine RNAiMAX (Invitrogen).

value: LCORL KD


title: NK.PBS.Sp#6


title: NK.PBS.Sp#7


title: serritia1_1

city: qingdao

first: ZIPENG

last: YU

state: China

address: No.72 Binhai Road,

institute: shandong university

data_processing:
The RNA was purified by electrophoresis through a TBE-urea polyacrylamide gel. The gel regions harboring 18-30 nt fragments were excised and the RNA recovered. The resulting population of sRNAs was 5' and 3' RNA adapter-ligated using T4 RNA ligase, and amplified for 18 PCR cycles
The amplicons were purified and sequenced using an Illumina/Solexa Genome Analyzer (Beijing Genomics Institute, Shenzhen, China).
Raw reads were trimmed by removing low-quality and adaptor sequences, then aligned to the A. thaliana genome using SOAP2 software.
Transcript frequency was calculated using the reads per kilobase per million reads method. Differentially transcribed genes were identified using a method modified from Audic and Claverie (1997). Significance was based on the P value and the false discovery rate (FDR) (Audic and Claverie, 1997).
Supplementary_files_format_and_content: The DEGs in RNA-seq.xlsx

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Five-day-old Arabidopsis seedlings treated with or without PLR for another two days

extract_protocol:
Total RNA was isolated with Trizol reagent (Invitrogen, Carlsbad, CA, USA)
First strand cDNA was generated using reverse transcriptase and random primers. The constructed cDNA libraries was qualified and quantified with Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System, and then sequenced via Illumina HiSeqTM 2000 or other sequencer when necessary at the Beijing Genomics Institute, Shenzhen, China.

tag: seedling age

value: seedlings

value: wild type

tag: agent

value: Serratia marcescens


title: genomic DNA from G_AML_012 leukemia

description: Leukemia

tag: disease state

tag: gender

value: female


title: serritia1_3


title: NK.PBS.Sp#8


title: No40_eps_1


title: WT_06_rep2

source_name: WT macrophages after 6h of LPS stimulation replicate2

value: Cultured bone marrow cells


title: KO_12_rep2

source_name: miR-155 KO macrophages after 12h of LPS stimulation replicate2

value: miR-155 KO


title: WT_24_rep2

source_name: WT macrophages after 24h of LPS stimulation replicate2


title: KO_24_rep1

source_name: miR-155 KO macrophages after 24h of LPS stimulation replicate1


title: No40_eps_2


title: NK.PBS.Sp#5


title: KO_12_rep1

source_name: miR-155 KO macrophages after 12h of LPS stimulation replicate1


title: WT_00_rep2

description: Gene expression of macrophages

source_name: WT macrophages in steady state replicate2


title: Sham_1

description: Control group with saline infusion

source_name: Aorta

value: Aorta

tag: time

value: 1 week

tag: Sex


title: R27_LCORL KD HEK293T #2 RNA-seq replicate 3

tag: treatment


title: serritia1_2


title: R24_LCORL KD HEK293T #1 RNA-seq replicate 4


title: genomic DNA from G_AML_013 leukemia

description: Leukemia

source_name: bone marrow

value: Leukemia


title: NK.PBS.Sp#2


title: U2OS_PacBio_Sequencing

description: wild type cells

source_name: cell line


title: NK.PBS.Sp#4


title: control1_3


title: R26_LCORL KD HEK293T #2 RNA-seq replicate 2


title: genomic DNA from G_AML_038 leukemia

description: Leukemia


title: R25_LCORL KD HEK293T #2 RNA-seq replicate 1


title: NK.PBS.Sp#3


title: control1_2


title: R23_LCORL KD HEK293T #1 RNA-seq replicate 3


title: R49bAG_s2_T1_N4

city: Beijing

first: shaofang

last: Li

state: Beijing

address: No 50, ZhanghuaLu, HAIDIAN

department: Beijing Vegetable Research Center

institute: Beijing Academy of Agriculture and Forestry Science

data_processing:
All sequenced reads were and mapped back toKittaake V3 genome using STAR with maximum 8 mismatches.
SNVs  and indels were called on each genome data using GATK, Strelka, LoFreq, separately
Genome_build: Kittaake V3
Supplementary_files_format_and_content: GATK.vcf.gz are mutations files called by GATK,Strelka.vcf.gz are mutations called by Strelka, LoFreq.vcf are mutations called by LoFreq. Wiggle format files with normalized read densities for each nucleotide. The normalized reads were calculated as RPM(reads per million).

organism: Oryza sativa

source_name: four-week plants

growth_protocol: Plants were grown with 16hr of light at  28 °C daytime,  25°C  night

extract_protocol:
RNA was extracted using using TRIzol™ Reagent
All libraryies were built using NEB Next® UltraTM RNA Library Prep Kit for Illumina

tag: cultivar

value: Kitaake

tag: age/tissue

value: four-week plants


title: NK.IL7.Sp#3

extract_protocol:
1,000 Cells were double-sorted by FACS Aria 561 into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma).Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter)
total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 18 cycles using barcoded primers such that each sample carried a specific combination of eight-base Illumina P5 and P7 barcodes and were pooled together prior to Smart sequencing. Smart-seq paired-end sequencing was performed on an Illumina NextSeq500 using 2 x 38bp reads with no further trimming.


title: R20_NOL4L KD HEK293T #2 RNA-seq replicate 4

tag: cell line

value: NOL4L KD


title: R22_LCORL KD HEK293T #1 RNA-seq replicate 2

tag: genotype


title: NK.IL7.Sp#2


title: NK.IL7.Sp#1


title: R21_LCORL KD HEK293T #1 RNA-seq replicate 1


title: R49bAG_s2_T1_N3


title: control1_1


title: NK.IL4.Sp#3


title: WT_06_rep1

source_name: WT macrophages after 6h of LPS stimulation replicate1

value: male


title: R49bAG_s2_T1_N2


title: NK.IL4.Sp#2

value: Spleen


title: WT_24_rep1

source_name: WT macrophages after 24h of LPS stimulation replicate1


title: WT_00_rep1

description: Gene expression of macrophages

source_name: WT macrophages in steady state replicate1


title: KO_06_rep1

source_name: miR-155 KO macrophages after 6h of LPS stimulation replicate1


title: NK.PBS.Sp#1

source_name: Natural Killer Cell

value: Natural Killer Cell


title: KO_s_rep1

description: Gene expression of GM-CSF cultured and LPS treated DC cells

source_name: LPS stimulated miR-155 KO DC cells replicate1

growth_protocol: Bone marrow cells were cultured in 40 ng/mL GM-CSF enriched media for 7 days.

treatment_protocol: On day 7, cells were stimulated in 100 ng/mL LPS and after 16 h, DC from both unstimulated samples and stimulated samples were sorted by FACS also verifying their inflammatory status by CD86 expression. RNA from WT- and miR-155 KO DC, either unstimulated (CD86-) or LPS-stimulated (CD86+) was isolated and used for agilent microarray analysis.


title: KO_00_rep1

description: Gene expression of macrophages

source_name: miR-155 KO macrophages in steady state replicate1


title: NK.IL4.Sp#1


title: WT_12_rep1

source_name: WT macrophages after 12h of LPS stimulation replicate1

value: WT


title: RC2_s3

data_processing:
All sequenced reads were and mapped back toKittaake V3 genome using STAR with maximum 8 mismatches.
SNVs  and indels were called on each genome data using GATK, Strelka, LoFreq, separately
Genome_build: Kittaake V3; https://phytozome-next.jgi.doe.gov/info/OsativaKitaake_v3_1
Supplementary_files_format_and_content: GATK.vcf.gz are mutations files called by GATK,Strelka.vcf.gz are mutations called by Strelka, LoFreq.vcf are mutations called by LoFreq. Wiggle format files with normalized read densities for each nucleotide. The normalized reads were calculated as RPM(reads per million).

source_name: RC2_four-week plants


title: R18_NOL4L KD HEK293T #2 RNA-seq replicate 2

source_name: HEK293T cells


title: RC2_s2


title: R17_NOL4L KD HEK293T #2 RNA-seq replicate 1


title: KO_s_rep2

source_name: LPS stimulated miR-155 KO DC cells replicate2


title: R49bAG_s2_T1_N1


title: NK.IL21.Sp#2

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts


title: R16_NOL4L KD HEK293T #1 RNA-seq replicate 4


title: RC2_s1


title: WT_s_rep1

source_name: LPS stimulated WT DC cells replicate1


title: R15_NOL4L KD HEK293T #1 RNA-seq replicate 3


title: R19_NOL4L KD HEK293T #2 RNA-seq replicate 3


title: RCas_s3

source_name: RCas_four-week plants

value: RCas


title: RCas_s2


title: R14_NOL4L KD HEK293T #1 RNA-seq replicate 2


title: NK.IL2.Sp#2


title: RCas_s1


title: KO_u_rep2

source_name: LPS unstimulated miR-155 KO DC cells replicate2


title: R13_NOL4L KD HEK293T #1 RNA-seq replicate 1


title: R49bg_s3

source_name: R49bg_four-week plants


title: R12_CHD4 KD HEK293T #2 RNA-seq replicate 4

value: CHD4 KD


title: R49bg_s2


title: NK.IL2.Sp#3


title: NK.IL2.Sp#1


title: NK.IL15.Sp#3


title: R11_CHD4 KD HEK293T #2 RNA-seq replicate 3


title: NK.IL21.Sp#1


title: WT_u_rep2

source_name: LPS unstimulated WT DC cells replicate2


title: R49bg_s1


title: NK.IL15.Sp#2


title: WT_u_rep1

source_name: LPS unstimulated WT DC cells repicate1


title: R9_CHD4 KD HEK293T #2 RNA-seq replicate 1


title: WT_s_rep2

source_name: LPS stimulated WT DC cells replicate2


title: R10_CHD4 KD HEK293T #2 RNA-seq replicate 2


title: R49bTm_s3

source_name: R49bTm_four-week plants


title: Sham_4

description: Control group with saline infusion

source_name: Aorta

value: Saline infusion


title: KO_u_rep1

source_name: LPS unstimulated miR-155 KO DC cells replicate1


title: R49bM_s3

source_name: R49bM_four-week plants


title: R49bTm_s1


title: R49bTm_s2


title: NK.IL15.Sp#1

source_name: Natural Killer Cell


title: MZB.PBS.Sp#12

source_name: Marginal Zone B Cell

value: Marginal Zone B Cell


title: MZB.PBS.Sp#8


title: R49bM_s1


title: Monocyte

description: Monocytes were sorted from bone marrow cells and analyzed.

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 1.65 μg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Mouse Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with 6x SSPE buffer containing 0.005% Nlauroylsarcosine for 1 min at room temperature followed by a second wash with preheated 0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. Further data processing was done using GeneSpring GX Software v11.0.

source_name: Monocyte cells

label_protocol:
For the linear T7-based amplification step, 0.5 μg of each total RNA sample was used. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) following the manufacturer’s protocol.
Yields of cRNA and the dye-incorporation rate were measured with the ND-1000
Spectrophotometer (NanoDrop Technologies).

extract_protocol: RNA was prepared using the miRNeasy Kit (Qiagen, 217004) following the manufacturer's recommendations. The protocol includes on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

value: monoctye

value: wild type


title: R7_CHD4 KD HEK293T #1 RNA-seq replicate 3


title: MZB.PBS.Sp#11


title: Granulocyte

description: Granulocytes were sorted from bone marrow cells and analyzed.

source_name: Granulocyte cells

value: granulocyte


title: R49bM_s2


title: MZB.PBS.Sp#9


title: R5_CHD4 KD HEK293T #1 RNA-seq replicate 1

source_name: HEK293T cells


title: R6_CHD4 KD HEK293T #1 RNA-seq replicate 2


title: Immature granulocyte WT rep2

description: Immature granulocytes were sorted from bone marrow cells and analyzed.

hyb_protocol: Hybridization and washing were done using Agilent Gene Expression Hybridization Kit (Agilent, 5188-5242) and Agilent Wash Buffer Kit (Agilent, 5188-5327) according to manufacturer's protocols (One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling, v6.5 May 2010).

scan_protocol: Slides were scanned after washing on the Agilent Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides (Profile: AgilentHD_GX1col, Resolution: 5 μm).

data_processing: The scanned images were analyzed with Feature Extraction Software using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Further data processing was done using GeneSpring GX Software v11.0.

source_name: Immature granulocyte in wild-type bone marrow replicate2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using Low Input Quick Amp Labeling Kit, One-Color (Agilent, 5190-2305) according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling, v6.5, May 2010), followed by RNAeasy column purification (Qiagen, 4106).

value: Immature granulocyte


title: GMCSF KO rep2

description: Expanding immature granulocytes were sorted for analysis.

source_name: GM-CSF cultured miR-223 KO bone marrow replicate2

growth_protocol: Bone marrow cells were cultured with 40ng/ml GM-CSF for 4 days.

value: bone marrow cells

value: miR-223 KO


title: Immature granulocyte KO rep2

source_name: Immature granulocyte in miR-223 KO bone marrow replicate2


title: R4_siControl HEK293T RNA-seq replicate 4

value: siControl


title: R49bAG_s3

source_name: R49bAG_four-week plants

value: Kitaake

value: four-week plants


title: Immature granulocyte KO rep1

source_name: Immature granulocyte in miR-223 KO bone marrow replicate1

value: male


title: MZB.PBS.Sp#7

value: Spleen


title: R8_CHD4 KD HEK293T #1 RNA-seq replicate 4


title: R3_siControl HEK293T RNA-seq replicate 3


title: R49bAG_s2


title: R1_siControl HEK293T RNA-seq replicate 1


title: MZB.PBS.Sp#10


title: MZB.PBS.Sp#6


title: R49bAG_s1


title: Saos-2_AIL_rep3

city: Shanghai

first: Jianjun

last: Zhang

address: 600 Yishan R.

institute: Shanghai Jiao Tong University Affiliated Sixth People’s Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
RSEM can accurately quantify gene or transcript expression levels from RNA-seq data. In the analysis of this project, expression estimation of gene and transcript was performed by using RSEM with setting --estimate-rspd parameter to estimate the distribution of the starting position of the sequence (RSPD) and other parameters were set as defalut.
Then edgeR (v3.8.5) package in R was used to perform TMM (trimmed mean of M values) and CPM (count per million) normalization for the the gene expression.
Genome_build: human genome build 38
Supplementary_files_format_and_content: tab-delimited text file with TMM normalized expression for every gene and every sample

source_name: Saos-2 cell line

growth_protocol: The cell lines were routinely cultured in DMEM supplemented with 10% fetal bovine serum, 100 μg/mL strep-tomycin, and 100 U/mL penicillin at 37℃ in an incubator with a constant airflow of 5% CO2 and 95% O2.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific,15596026), 1 μg of qualified RNA (RIN > 8.0) was used as input for library construction following the Illumina TruSeq RNA Sample Preparation protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Saos-2 cells were treated with IC50 (0.20 μM) of AIL or DMSO for 24 h (3 biological replicates each group).

value: Saos-2 cell line

value: AIL


title: Saos-2_AIL_rep2


title: R2_siControl HEK293T RNA-seq replicate 2

value: WT


title: MZB.PBS.Sp#5

city: Boston

first: Liang

last: Yang

institute: Harvard Medical School


title: Saos-2_AIL_rep1


title: GMCSF KO rep1

source_name: GM-CSF cultured miR-223 KO bone marrow replicate1


title: MZB.PBS.Sp#4


title: R46bg_s1

source_name: R46bg_four-week plants


title: R46bM_s2

source_name: R46bM_four-week plants


title: MZB.PBS.Sp#3


title: embryos_totalRNA_WT_5

city: Grand Rapids

first: Ian

last: Beddows

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Institute

description: mRNA

data_processing:
QC and read mapping. Small RNA reads were trimmed for sequencing adapters using Trim Galore v0.5.0 (https://github.com/FelixKrueger/TrimGalore) in conjunction with Cutadapt v1.1135. Low-quality (Q<20) bases were also trimmed from the ends of reads, and reads were discarded if their length was then less than 20 nucleotides following trimming. Trimmed reads greater than 20 nucleotides in length were then mapped to dm6 genome (FlyBase BDGP6.22 release) using the short-read aligner bowtie v1.2.3 36, allowing for one mismatch. If there were multiple alignments, then only the highest quality alignment was retained (bowtie options -M 1 --best --strata). Alignment files were sorted and indexed using SAMtools v1.8.
Hierarchical Feature Counting. Annotation data was downloaded from FlyBase, release BDGP6.22. The annotations were stratified into 14 ordered feature categories: rRNA, tRNA, snRNA, snoRNA, pre miRNA, simple repeats, complex repeats, Piwi RNA, 5’ UTR, 3’ UTR, protein coding exon, pseudogene, ncRNA, and mitochondrial genome. The Piwi RNA cluster (n=114) annotations were from piPipes. Next, using featureCounts (subread v2.0.0), mapped reads were counted for each of the 13 categories independently. A minimum overlap of 15 nucleotides was required, with the fractional counts option was on. This counting was strand-specific and was done for both forward (sense) and reverse (antisense) strands independently. Finally, using a custom script (https://github.com/vari-bbc/Piwi_RNA_pipeline), we did a hierarchical counting for the 13 categories. That is, for any read annotated to multiple features, it was counted only for the feature highest in the category. So, reads mapped to a Piwi RNA cluster within an exon were counted towards the Piwi RNA cluster not the exonic feature. This approach assured that reads were assigned correctly, and ambiguities from reads mapping to rRNA and other small RNA features were not included as Piwi RNAs. This resulted in a counts file for sense and antisense features.
Genome_build: dm6
Supplementary_files_format_and_content: Tab-delimited files with raw feature counts

source_name: Embryo

extract_protocol:
Samples prepared in Linkoping: Frozen samples were homogenized in Qiazol with 0.15 g 0.2 mm steel beads, Tissue Lyser 2 min 40 osc. RNA extraction was done using miRNeasy Micro kit (Qiagen, Venlo, the Netherlands) and performed according to the manufacturer instructions, RNA was eluted in 14 μl of water and stored at −70 °C until library preparation. Samples prepared in Freiburg: Dried RNA were shipped on dry ice and kept in -70 °C. Dried and washed once with 80% ethanol and dried, dissolved in 20 ul water, extraction was done using miRNeasy Micro kit (Qiagen, Venlo, the Netherlands) and performed according to the manufacturer instructions. RNA was eluted in 14 μl of water and stored at −70 °C until library preparation. Bioanalyzer confirmed the quality of the RNA.
Library preparation was done with NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA) according to the manufacturer instructions with the following minor customizations.  All testicle samples, but not sperm samples, were downscaled to half volume, using 3 μl of input RNA instead of 6 ul as recommended. In all steps the primers in the kit were diluted 1:3 prior to use. 2S rRNA was blocked by adding anti-sense oligos (5´-TAC AAC CCT CAA CCA TAT GTA GTC CAA GCA372 SpcC3 3´; 10 µM) and set to hybridized in the same step as NEBNext SR RT primer (pink). Amplification was made during 16 cycles and amplified libraries were cleaned using Agencourt AMPure XP (Beckman Coulter, Brea, CA) and size selected for 130 to 165 nt fragments on a pre-casted 6% polyacrylamide Novex TBE gel (Invitrogen, Waltham, MA). Gel extraction was done using Gel breaker tubes (IST Engineering, Milpitas, CA) in the buffer provided in the NEBNext kit. Disintegrated gels were incubated at 37 °C for 1 hour on a shaker, quickly frozen for 15 minutes at −80 °C, followed by another incubation for 1 hour. Any remaining gel debris was removed by Spin-X 0.45 μm centrifuge tubes (Corning Inc., Corning, NY) as recommended by the NEBnext protocol. The libraries were precipitated overnight at −80 °C by adding 1 μl of GlycoBlue (Invitrogen) as co-precipitant, 0.1 times the volume of Acetate 3M (pH 5.5), and 3 times the volume of 100% ethanol. Library concentrations were estimated using QuantiFluor ONE ds DNAsystem on a Quantus fluorometer (Promega, Madison, WI). Pooled libraries were sequenced on NextSeq 500 with NextSeq 500/550 High Output Kit version 2, 75 cycles (Illumina, San Diego, CA). All pooled libraries passed Illumina’s default quality control.

value: mRNA

tag: mutation

value: wt


title: R46bM_s3


title: R46bg_s2


title: GMCSF WT rep2

source_name: GM-CSF cultured wild-type bone marrow replicate2


title: R46bM_s1


title: embryos_totalRNA_WT_3

description: mRNA


title: Immature granulocyte WT rep1

source_name: Immature granulocyte in wild-type bone marrow replicate1


title: MZB.IL9.Sp#1

address: 77 Avenue Louis Pasteur

value: Marginal Zone B Cell


title: GMCSF WT rep1

source_name: GM-CSF cultured wild-type bone marrow replicate1


title: MZB.PBS.Sp#1

source_name: Marginal Zone B Cell


title: Saos-2_Control_rep3

value: DMSO


title: Saos-2_Control_rep1


title: embryos_totalRNA_WT_2

description: mRNA


title: MZB.IL7.Sp#3


title: R46bg_s3


title: Lmajor_KO_rep1

description: Mac1+ cells were sorted from bone marrow cells and analyzed.

source_name: Leishmania major infected miR-223 KO mice replicate1

treatment_protocol: Mice were subcutaneously inoculated with Leishmania major promastigotes at right hind foot pad for 4 weeks.

value: Balb/c


title: Lmajor_KO_rep2

source_name: Leishmania major infected miR-223 KO mice replicate2


title: R46bGG_s2

source_name: R46bGG_four-week plants


title: Lmajor_WT_rep2

source_name: Leishmania major infected wild-type mice replicate2

value: wild type


title: embryos_totalRNA_WT_1

description: mRNA


title: Saos-2_Control_rep2


title: MZB.PBS.Sp#2


title: R46bGG_s3


title: embryos_totalRNA_WT_4

description: mRNA


title: MZB.IL7.Sp#2


title: PANC-1 shCtrl

first: Hua

last: Huang

address: 100 Pingleyuan,  Chaoyang District

institute: Beijing university of technology

data_processing:
bcl2fastq software used for basecalling and sequenced reads
FastQC software used for filtering.Primer/Adaptor contaminated reads, Low quality reads and N overtop reads were filtered.
hisat2 used for comparing clean reads with reference genome sequences
RseQC used for homogeneity analysis of Clean Read
Stringtie used for reconstructing the gene and transcript based on reads comparison results
Feature Recounts and StringTie software used for calculating readcount of gene and transcript expression and getting the FPKM of genes and transcripts
DESeq software used for difference analysis
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table of FPKM values for every gene
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: pancreatic cancer

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle medium (DMEM, Gibco:11995040) supplemented with 10% FBS, 100 ng/ml streptomycin reagent (Hyclone, Logan, UT, USA) and 100 U/ml penicillin (Hyclone, Logan, UT, USA). The culture conditions were maintained in a humidified incubator with 5% CO2 level at 37 °C.

extract_protocol:
Cells were harvested, and total RNA was extracted with Trizol (Invitrogen) and assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and Qubit Fluorometer (Invitrogen).  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: pancreatic cancer

value: shCtrl


title: MZB.IL9.Sp#2


title: PANC-1 shWBSCR22


title: MZB.IL7.Sp#1


title: embryos_totalRNA_AUB_paternal_5

description: mRNA

value: paternal aub


title: Control0004

city: New York

first: Bettina

last: Nadorp

state: NY

address: 500 1st Ave

department: Medicine/Pathology

institute: NYU Langone Health

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment to GRCh38 (version 3.0.0) was performed with 10x Genomics Cell Ranger Single Cell Gene Expression Software (version 3.1.0).
HTOs for each cell were normalized using a centered log ratio (CLR) transformation across cells.
Samples were demultiplexed based on HTOs using the HTODemux function in Seurat.
Genome_build: hg38
Supplementary_files_format_and_content: Indexed BAM files containing position-sorted reads aligned to the genome.

source_name: bone marrow

extract_protocol:
Bone marrow cells were isolated from the spine, hips, femur and tibia of mice. A single-cell suspension was generated after red blood cell lysis ACK buffer. Cells were tagged with cell hashing (Stoeckius et al, 2018) oligo-tagged antibodies (BioLegend) according to manufacturer’s instructions and pooled on a 10x Chromium instrument (10x Genomics) to generate barcoded single-cell beads-in emulsion (GEM) according to the manufacturer’s protocol. scRNA-seq libraries were prepared using the Chromium Single-Cell’ v3 Reagent Kit (10x Genomics) following the direction of the manufacturer. The libraries were quantified using Qubit fluorometric quantification (Thermo Fisher Scientific). The quality was assessed on an Agilent Bioanalyzer 2000, obtaining an average library size of 455 bp. Libraries were pooled and normalized to 2 nmol/L and clustered on a HiSeq4000 high output mode on a paired-end read flow cell and sequenced for 28 cycles on R1 (10x barcode and the UMIs). Followed by 8 cycles of i7 index (sample index), and 98 bases on R2 (transcript), with a coverage around 130M reads per sample.
Chromium Single Cell 3’ Reagent Kits (v3 )
Single Cell RNAseq

value: bone marrow cells


title: embryos_totalRNA_AUB_paternal_4

description: mRNA


title: MZB.IL4.Sp#3


title: Control5b


title: Lmajor_WT_rep1

source_name: Leishmania major infected wild-type mice replicate1


title: R46bAG_s3

source_name: R46bAG_four-week plants

value: Kitaake


title: Control5a


title: R46bAG_s2

value: four-week plants


title: R46bAG_s1


title: embryos_totalRNA_AUB_maternal_1

description: mRNA

value: maternal aub


title: embryos_totalRNA_AUB_maternal_2

description: mRNA


title: Control1_2_3c


title: MZB.IL4.Sp#1

value: Spleen


title: kit_s10

data_processing:
library strategy: Whole genome sequencing
All sequenced reads were and mapped back toKittaake V3 genome using BWA mem
SNVs  and indels were called on each genome data using GATK, Strelka, LoFreq, separately
Genome_build: Kittaake V3; https://phytozome-next.jgi.doe.gov/info/OsativaKitaake_v3_1
Supplementary_files_format_and_content: GATK.vcf.gz are mutations files called by GATK,Strelka.vcf.gz are mutations called by Strelka, LoFreq.vcf are mutations called by LoFreq

source_name: kit_four-week plants

extract_protocol:
Genomic DNA was extracted using CTAB methods and treated with RNase I
All libraryies were built using NEB Next® UltraTM DNA Library Prep Kit

value: kit


title: MZB.IL21.Sp#3


title: Control1_2_3b


title: embryos_totalRNA_AUB_paternal_2

description: mRNA


title: MZB.IL21.Sp#2


title: R46bGG_s1


title: Control1_2_3a


title: embryos_totalRNA_AUB_paternal_1

description: mRNA


title: PANC-1-CGAOE

source_name: pancreatic cancer

tag: transfection

value: CGAOE


title: MZB.IL21.Sp#1

tag: tissue


title: kit_s7


title: kit_s9


title: aub_Sperm_rep3

description: small RNA

source_name: Sperm

value: small RNA

value: aub


title: PANC-1-Vector

value: vector


title: MZB.IL4.Sp#2

tag: strain

value: Marginal Zone B Cell


title: kit_s8


title: MZB.IL2.Sp#3


title: kit_s6


title: piwi_Sperm_rep3

description: small RNA

value: piwi


title: MZB.IL2.Sp#2


title: MZB.IL2.Sp#1


title: WT_Sperm_rep3

description: small RNA

value: wt


title: PANC-1-shCtrl


title: aub_Sperm_rep2

description: small RNA


title: kit_s5


title: kit_s4


title: PANC-1-shL3MBTL2


title: embryos_totalRNA_AUB_paternal_3

description: mRNA

value: mRNA


title: MZB.IL15.Sp#3


title: MZB.IL15.Sp#2


title: kit_s3


title: kit_s2


title: WT_Sperm_rep2

description: small RNA


title: piwi_Sperm_rep2

description: small RNA


title: Vulvar tissue , HPV_positive, 30

city: Dallas

first: Richard

middle: C

last: Wang

state: TX

address: 5323 Harry Hines Blvd

department: Dermatology

institute: UT Southwestern

data_processing:
Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used for quality and adapter trimming. The human reference genome sequence and gene annotation data, hg38, were downloaded from Illumina iGenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html). STAR (v2.7.2b) (Dobin et al., 2013) was employed to align the reads onto the human genome, SAMtools (v1.9) (Li et al., 2009) was employed to sort the alignments, and HTSeq Python package (Anders et al., 2015) was employed to count reads per gene.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Vulvar tissue

extract_protocol:
tissue curls cut from formalin fixed paraffin embedded tumor blocks
KAPA RNA HyperPrep with RiboErase (HMR)

value: Vulvar tissue

tag: hpv status

value: positive


title: MZB.IL15.Sp#1

tag: cell type


title: Vulvar tissue , HPV_positive, 23


title: aub_Sperm_rep1

description: small RNA


title: kit_s1


title: Vulvar tissue , HPV_positive, 15


title: Mo.6C+.PBS.Sp#12

source_name: Monocyte

value: Monocyte


title: Vulvar tissue , HPV_positive, 19


title: Vulvar tissue , HPV_positive, 31


title: Mo.6C+.PBS.Sp#13


title: Vulvar tissue , HPV_positive, 13


title: Mo.6C+.PBS.Sp#11


title: WT_Sperm_rep1

description: small RNA


title: piwi_Sperm_rep1

description: small RNA


title: C1_s1

source_name: C1_four-week plants


title: C2_s6

source_name: C2_four-week plants


title: WT_Testis_T2_rep2

description: small RNA

source_name: Testicle


title: Vulvar tissue , HPV_positive, 11


title: Vulvar tissue , HPV_positive, 10


title: C2_s5


title: WT_Testis_T1_rep2

description: small RNA


title: Vulvar tissue , HPV_positive, 7


title: C1_s3


title: Vulvar tissue , HPV_positive, 6


title: WT_Testis_T2_rep1

description: small RNA


title: WT_Testis_T1_rep1

description: small RNA


title: Mo.6C+.PBS.Sp#7


title: C1_s2


title: Mo.6C+.PBS.Sp#6


title: C2_s3


title: C2_s4


title: Mo.6C+.PBS.Sp#5


title: Vulvar tissue , HPV_positive, 1


title: Vulvar tissue , HPV_positive, 4


title: WT_Testis_T3_rep2

description: small RNA


title: WT_Testis_T3_rep1

description: small RNA


title: C2_s2


title: Mo.6C+.PBS.Sp#10


title: Mo.6C+.PBS.Sp#4


title: 53bg_s3

source_name: 53bg_four-week plants


title: C2_s1


title: SV_Total_RNA_2

description: small RNA


title: Vulvar tissue , HPV_negative, 35

value: negative


title: Mo.6C+.PBS.Sp#9


title: Mo.6C+.PBS.Sp#8


title: 53bg_s2

value: Kitaake


title: Mo.6C+.PBS.Sp#3


title: Vulvar tissue , HPV_negative, 36


title: SV_Total_RNA_1

description: small RNA


title: Vulvar tissue , HPV_negative, 33


title: Mo.6C+.PBS.Sp#2


title: Mo.6C+.PBS.Sp#1


title: Vulvar tissue , HPV_negative, 28


title: SV_PIWI_IP_4

description: small RNA


title: Mo.6C+.IL9.Sp#2


title: 53bg_s1

value: four-week plants


title: Vulvar tissue , HPV_negative, 27


title: SV_PIWI_IP_3

description: small RNA


title: SV_Total_RNA_3

description: small RNA


title: 53DEP_s2

source_name: 53DEP_four-week plants


title: Vulvar tissue , HPV_negative, 26


title: 53DEP_s3


title: SV_PIWI_IP_2

description: small RNA


title: 53DEP_s1


title: Mo.6C+.IL9.Sp#1


title: 53G_s3

source_name: 53G_four-week plants


title: Vulvar tissue , HPV_negative, 20


title: Vulvar tissue , HPV_negative, 24


title: WT2U_old_ZT44

first: Zikun

state: New York

address: 1230 York Av

institute: The Rockefeller University

data_processing:
bcl2fastq v2.20 was used for basecalling.
STAR v2.4.2a was used for alignment.
featureCounts was used for generate counts matrix.
Genome_build: FlyBase release 6.13 (May 2016)
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each aligned gene for each sample

source_name: fly heads

extract_protocol:
Total RNA was extracted using TRIzol reagents and homogenized using a BeadBug microtube homogenizer (Benchmark Scientific). Samples were further extracted using chloroform and the aqueous phase containing nucleic acid was collected. RNeasy Mini Kit (Qiagen) was then used to remove DNA with DNase and further purify the samples, following the manufacturer's protocol.
Sequencing libraries were prepared with the Illumina TruSeq stranded mRNA LT kit

value: Canton-S w1118 (iso1CJ)

tag: age

value: 49 days old

tag: timepoint

value: Zeitgeber time 44


title: Mo.6C+.IL7.Sp#2

value: Spleen


title: 53G_s2


title: Mo.6C+.IL7.Sp#3


title: INC1_ZT44

value: 27 days old


title: Vulvar tissue , HPV_negative, 14


title: Mo.6C+.IL7.Sp#1


title: 53G_s1


title: WAKED2_ZT44


title: Mo.6C+.IL4.Sp#3


title: Vulvar tissue , HPV_negative, 8


title: 53SE_s3

source_name: 53SE_four-week plants


title: Vulvar tissue , HPV_negative, 5