title: 5820: Nextflex_v2_MA_TR1000_3

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using Nextflex_v2 method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2523

value: Meiotic Anthers (MA)


title: F102C-4

status: Public on Aug 01 2021

type: genomic

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

country: USA

institute: Mayo Clinic

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium 850K Infinium® MethylationEPIC Beadchip using standard Illumina protocol at the University of Minnesota Genomics Center.

scan_protocol: Arrays were imaged using BeadArray Reader Hi-Scan system.

data_processing:
Resultant IDAT files were processed and normalized using Illumina's GenomeStudio software (version 2011.1).
value definition: Average Beta

label: cy3, cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Prostate

label_protocol: Standard Illumina Protocol

growth_protocol: Cells were maintained at 37°C and 5% CO2 in RPMI 1640 containing 10% fetal bovine serum (FBS) and 1% antibiotic/antimycotic (Thermo Fisher Scientific).FGF-2 (NS expansion medium).

extract_protocol: Genomic DNA were extracted using standard DNA extraction method

treatment_protocol: 22Rv1 cells were infected with lentivirus expressiong empty vector or SPOP F102C construct and cultured for 1 week to stably express SPOP F102C protein.

tag: cell type

value: Pca cell line

tag: passage

tag: genotype/variation

value: SPOP F102C


title: CR463 Line Recovery Nuclear Fraction Replicate 1

type: SRA

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description:
nuc_CR463_rec_rep1
deseq2_normalized_counts.txt

library_source: transcriptomic

data_processing:
Fastq files were trimmed for adapters using cutadapt
Trimmed reads were aligned to the human genome build hg19 using STAR aligner
seCLIP : Binding region peaks were identified based on read pileup densities (Clipper)
seCLIP : Reproducible peaks were identified by comparing replicate read pileups along binding regions
Genome_build: hg19
Supplementary_files_format_and_content: normalized read counts text file
wiggle files
peak text files

molecule: total RNA

source_name: motor neurons

growth_protocol: stem cells were grown in feeder-free conditions using mTeSR on matrigel-coated plates. Stem cell-derived motor neurons were generated using a widely published dual-smad inhibition-based protocol, including intermittent expansion of motor neuron progenitor (MNP) cells in DMEM/F12 medium supplemented with N2 and B27 supplements plus ascorbic acid, CHIR99021, DMH1, SB431542, retinoic acid, purmorphamine and valproic acid.

extract_protocol:
for ceFRA-seq samples, RNA was extracted using either Trizol (total, nuclear, insoluble) or Trizol LS (cytoplasm) following manufacturer's standard protocol
libraries for ceFRA-seq were generated using Illumina Truseq stranded mRNA library prep kits, eCLIP libraries using in-house seCLIP library prep protocol
RNAseq (polyA), seCLIP-seq

treatment_protocol: "stress" samples were treated with puromuycin at 10ug/ml for 24h. "recovery" samples were treated with puromycin at 10ug/ml for 24h, followed by a washout and allowed to recover in puromycin-free medium for 72h

value: iPSC-derived motor neurons

tag: cell line

value: CR463.4 hiPSC line

tag: treatment

value: Recovery

tag: fraction

value: Nucleus


title: F102C-1


title: EV-4

value: SPOP WT


title: 5819: Nextflex_v2_MA_TR1000_2

city: Davis

first: Patricia

last: Baldrich Gonzalez

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using Nextflex_v2 method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2522

data_processing:
The sRNA sequencing libraries were trimmed for adaptors using Trimmomatic v0.32(15) with the following options -phred33; -threads 10; ILLUMINACLIP:4:30:10; LEADING:3; TRAILING:3; SLIDINGWINDOW:4:10; MINLEN: 18.
Sequence quality was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Clean reads were aligned to the B73 Maize genome version 4(16) using the software Bowtie2 (Langmead and Salzberg, 2012).
Genome_build: B73 Maize genome version 4
Supplementary_files_format_and_content: Count format

organism: Zea mays

source_name: Maize anthers

growth_protocol: Anther samples were collected from 4- to 5-week-old W23 maize plants grown controlled conditions in greenhouses with temperatures of 28°C/22°C, relative humidity of 50%/60%, and a photoperiod of 16 h/8 h (day/night)

extract_protocol:
Total RNA was isolated using the Plant RNA Reagent (Thermo Fisher, cat #12322012). Briefly, samples were ground in a liquid nitrogen-frozen mortar and pestle. Then, the cold mortar with the powdered tissue was transferred to a chemical safe hood and 1 ml of Plant RNA Reagent was added directly in the mortar. The sample was ground with the reagent for another 20 sec and then collected with a 1ml micropipette and transferred to a 2 ml nuclease-free microcentrifuge tube. The remaining steps for the RNA extraction were followed as described previously (14).
All sRNA libraries were generated following the manufacturers’ instructions. A summarized workflow can be seen in Figure 1. Additionally, we performed a final step of size selection using 6% polyacrylamide gels as described in Mathioni et al., 2017

treatment_protocol: Two developmental stages were dissected, the premeiotic anther stage consisting of spikelets with 0.2 to 0.7 mm anthers, and the meiotic anther stage consisting of 1.5 mm anthers. Samples were flash frozen in liquid nitrogen and kept at -80°C until further processing.

tag: tissue

tag: construction method

tag: molecule

value: Total RNA


title: CR463 Line Puromycin Treatment Nuclear Fraction Replicate 2

description:
nuc_CR463_puro_rep2
deseq2_normalized_counts.txt

value: Puromycin


title: CR463 Line Puromycin Treatment Nuclear Fraction Replicate 1

description:
nuc_CR463_puro_rep1
deseq2_normalized_counts.txt


title: EV-2


title: PC3_2

city: Jinan

first: Jiajun

last: Du

address: 324 Jingwu Road

country: China

institute: Provincial Hospital Affiliated to Shandong University

description: control group

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In  this step, clean data (clean reads) were obtained by removing reads containing adapter, reads1  containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC  content the clean data were calculated. All the downstream analyses were based on the clean  data with high quality.
Reference genome and gene model annotation files were downloaded from genome website  directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean  reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the  mapping tool for that Hisat2 can generate a database of splice junctions based on the gene  model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then  FPKM of each gene was calculated based on the length of the gene and reads count mapped  to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per  Millions base pairs sequenced, considers the effect of sequencing depth and gene length for  the reads count at the same time, and is currently the most commonly used method for  estimating gene expression levels.
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the DESeq2  R package (1.20.0). DESeq2 provide statistical routines for determining differential expression  in digital gene expression data using a model based on the negative binomial distribution. The  resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling  the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were  assigned as differentially expressed
Prior to differential gene expression analysis, for  each sequenced library, the read counts were adjusted by edgeR program package through one  scaling normalized factor. Differential expression analysis of two conditions was performed  using the edgeR R package (3.22.5). The P values were adjusted using the Benjamini &  Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the2  threshold for significantly differential expression.
Genome_build: Homo Sapiens(GRCh38/hg38)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: A549 cell

extract_protocol:
The total RNA of A549 was extracted via Trizol and samples were sent to Novogene Co., LTD beijing）for RNA-seq analysis. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer  2100 system (Agilent Technologies, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: transfected PC3.2 plasmid


title: 5818: Nextflex_v2_MA_TR1000_1

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using Nextflex_v2 method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2521


title: Kin 2-4 Motor Neuron Untreated Total RNA Replicate 2

description:
Kin2-4_ut_total_rep2
deseq2_normalized_counts.txt

value: Kin2ALS4 hiPSC line

value: Untreated

value: Total


title: Kin 2-4 Motor Neuron Untreated Nuclear Fraction Replicate 1

description:
Kin2-4_ut_nucl_rep1
deseq2_normalized_counts.txt


title: Kin 2-4 Motor Neuron Untreated Total RNA Replicate 1

description:
Kin2-4_ut_total_rep1
deseq2_normalized_counts.txt


title: 5817: Nextflex_v2_MA_SS1000_3

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using Nextflex_v2 method with 1000ng of Size selected RNA as starting material. Library was sequenced using HiSeq 2520

value: Size selected RNA


title: PC3_1

description: control group

value: transfected PC3.1 plasmid


title: EV-3


title: 2102EP-dCD24 3

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Moorenstr. 5

department: Dep. of Urology

country: Germany

institute: Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University

description: CD24 deficient clone

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Bead array (850k) using standard Illumina protocol

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

data_processing:
Data and bioinformatic analyses were carried out using ‘GenomeStudio’ software (version 2011.1, Methylation Module v1.9) (Illumina) and. A detailed report on quality controls and internal control measurements provided by Diagenode is available upon request.
data processing and QC according to the in-house analysis pipeline of Diagenode and calculation beta-values and M-values

source_name: non-seminoma germ cell tumor, embryonal carcinoma

label_protocol: The Infinium MethylationEPIC array BeadChip (Illumina, San Diego, CA, USA) was carried out by the Epigenomic Services from Diagenode (Liege, Belgium, Cat. nr. G02090000) following an established in-house analysis pipeline. For each sample, 500 ng of DNA were used for sodium-bisulfite conversion using the EZ-96 DNA Methylation Kit (Zymo Research, Freiburg im Breisgau, Germany). Bisulfite conversion was controlled by qPCR. One assay targeting a methylated region of DNAJC15 and two assays targeting the GNAS locus (one assay for the unmethylated allele and one assay for the methylated allele) was used for quality control. Deaminated DNA derived from blood was amplified in parallel and served as positive control. A sample passed the quality control when the received Ct-value either for the two GNAS loci or the DNAJC15 locus reaches the threshold not later than five cycles compared to the positive control.

growth_protocol: NCCIT / 2102EP cells were cultivated in DMEM medium (10% FCS, 1% Penicillin / Streptomycin)

extract_protocol: Genomic DNA used for the Infinium MethylationEPIC BeadChip array (850k) was isolated and purified by two rounds of PCI precipitation including a RNaseA treatment. DNA concentrations were measured by the ‘Qubit 4 Fluorometer’ (Thermo Fisher Scientific).

treatment_protocol: CD24 deficiency was generated by CRISPR/Cas9 method

tag: genotype

value: CD24 deficient clone


title: 5815: Nextflex_v2_MA_SS1000_1

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using Nextflex_v2 method with 1000ng of Size selected RNA as starting material. Library was sequenced using HiSeq 2518

value: Meiotic Anthers (MA)


title: 2102EP-dCD24 2

description: CD24 deficient clone


title: EV-1

value: Pca cell line


title: Kin 2-4 Motor Neuron Untreated Nuclear Fraction Replicate 2

description:
Kin2-4_ut_nucl_rep2
deseq2_normalized_counts.txt


title: 5816: Nextflex_v2_MA_SS1000_2

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using Nextflex_v2 method with 1000ng of Size selected RNA as starting material. Library was sequenced using HiSeq 2519


title: 2102EP-dCD24 1

description: CD24 deficient clone


title: Kin 2-4 Motor Neuron Untreated Cytoplasm Fraction Replicate 2

description:
Kin2-4_ut_cyto_rep2
deseq2_normalized_counts.txt

value: Cytoplasm


title: Kin 2-4 Motor Neuron Untreated Insoluble Fraction Replicate 2

description:
Kin2-4_ut_insol_rep2
deseq2_normalized_counts.txt

value: iPSC-derived motor neurons

value: Insoluble


title: Mouse_Femur_Endosteal_A

type: RNA

city: Brisbane

first: Gareth

last: Price

state: Queensland

address: Carmody Road

country: Australia

institute: Queensland Facility for Advanced Bioinformatics

hyb_protocol: 10ug of fragmented biotin labelled cRNA was hybridised to a Mouse Genome 430 2.0 Array GeneChip, according to manufacturer’s instructions. GeneChip was incubated for 16hrs at 45oC in a rotating hybridisation oven at 60rpm. GeneChip was washed using Affymetrix washing script EukGE-WS2v5_450 on a Affymetrix Fluidics Station 450

scan_protocol: GeneChip was scanned on a Affymetrix GeneSchip Scanner 3000.

data_processing: The data was extracted from the CEL files using Affymetrix GeneChip Operating Software (1.4) using Affymetrix default analysis settings. Tabulated data (CHP) was generated with global scaing trimmed mean target intensity of 500.

label: Biotin

organism: Mus musculus

source_name: Endosteal

label_protocol: cRNA was prepared using the Affymetrix One-Cycle Labelling Kit, using 2ug total RNA as starting material.

extract_protocol: Femur was removed from the mouse, cleaned with a scalpel blade and then vigorously rubbed with coarse paper towel to remove traces of muscle and periosteum. Metaphyseal zones of the bones were carefully removed using a scalpel blade. Remaining femoral diaphyses were flushed with 1 mL Phosphate Buffered Saline (PBS) plus 2% new born calf serum (NCS) (Invitrogen) using a 1mL syringe mounted with a 23-gauge needle, and reflushed up and down five times. Cells extracted into this 1mL volume of PBS were defined as the central BM fraction. These central BM cells were then pelleted via centrifugation (370g for 5 minutes) before lysis in Trizol (Invitrogen) to extract the RNA. 1mL of Trizol was flushed through each remaining empty femoral diaphysis and collected in separate tubes and defined as the endosteal RNA fraction.

treatment_protocol: Injected with Saline (Intraperitoneal)

tag: strain

tag: gender

value: Male

tag: age

value: 8 weeks

value: Femur (Endosteal)


title: Mouse_Femur_Endosteal_C


title: Mouse_Femur_Endosteal_B


title: NCCIT-dCD24 3

description: CD24 deficient clone


title: Kin 2-4 Motor Neuron Untreated Cytoplasm Fraction Replicate 1

description:
Kin2-4_ut_cyto_rep1
deseq2_normalized_counts.txt


title: Kin 2-4 Motor Neuron Untreated Insoluble Fraction Replicate 1

description:
Kin2-4_ut_insol_rep1
deseq2_normalized_counts.txt


title: 5993: Nextflex_v3_MA_1000_3

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using Nextflex_v3 method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2535

value: Total RNA


title: 5814: Illumina_MA_SS_3

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using Illumina method with 1000ng of Size selected RNA as starting material. Library was sequenced using HiSeq 2517

value: Illumina


title: 5812: Illumina_MA_SS_1

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using Illumina method with 1000ng of Size selected RNA as starting material. Library was sequenced using HiSeq 2515


title: SAMPLE 1: hippocampus_wild-type_3-month-old_replicate1

city: Kyoto

first: Keiichi

last: Ishihara

state: Kyoto

address: 5 Misasagi Nakauchi-cho, Yamashina-ku

department: Department of Pathological Biochemistry

country: Japan

institute: Kyoto Pharmaceutical University

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity > 8 pmol Cy3/ug cRNA) was fragmented at 60ﾂｰC for 30 minutes. On completion of the fragmentation reaction, hybridized to SurePrint G3 Mouse GE 8x60 K microarray (G4851A) for 17 hours at 65ﾂｰC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37ﾂｰC GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting. (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: The scanned images were analyzed with GeneSpring GX (ver 12.0.0) (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: wild-type, hippocampus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the The Low Input Quick Amp Labeling kit, one color (Agilent) according to the manufacturer's instructions, followed by RNAeasy mini kit (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using RNAiso (Takara) according to the manufacturer's instructions, followed by treatment with DNase I.

value: wild-type

value: hippocampus


title: NCCIT-dCD24 2

description: CD24 deficient clone


title: Mouse_Femur_Central_Bone_Marrow_C

source_name: Central Bone Marrow

extract_protocol: Femur was removed from the mouse, cleaned with a scalpel blade and then vigorously rubbed with coarse paper towel to remove traces of muscle and periosteum. Metaphyseal zones of the bones were carefully removed using a scalpel blade. Remaining femoral diaphyses were flushed with 1 mL Phosphate Buffered Saline (PBS) plus 2% new born calf serum (NCS) (Invitrogen) using a 1mL syringe mounted with a 23-gauge needle, and reflushed up and down five times. Cells extracted into this 1mL volume of PBS were defined as the central BM fraction. These central BM cells were then pelleted via centrifugation (370g for 5 minutes) before lysis in Trizol (Invitrogen) to extract the RNA.

value: Femur (Central Bone Marrow)


title: 5810: Illumina_MA_TR_2

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using Illumina method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2513


title: 5811: Illumina_MA_TR_3

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using Illumina method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2514


title: NCCIT-dCD24 1

description: CD24 deficient clone


title: Ileum-NaCl_WT-rep4

city: Ulm

first: Hans

middle: A

last: Kestler

address: Albert-Einstein-Allee 11

department: Research Group Bioinformatics and Systems Biology

institute: University of Ulm

hyb_protocol: Cy3-labelled cRNA was fragmented and blocked following manufacturer's instructions.

scan_protocol: Slides were scanned using one color scan setting for GE 8x60K slides with the scanner (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent). Further processing (background correction, percentile shift normalization, summarization, log2 transformation) was done following Agilent's quickstart guided workflow.

source_name: Ileum, NaCl-treatment, WT

label_protocol: 200ng of each sample was labeled with the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to manufacturer's instructions.

extract_protocol: RNA was prepared using the RNeasy Mini Kit  RNA Isolation kit (Quagen) following manfacturer's instructions.

treatment_protocol: Inducible TNK-knockin mice (Rosa26rtTA/+, Hprt Myc-Tnk1tg)  were treated with doxycycline (I.P injection 50µg/g of the mouse weight, 100µl) or saline solution (I.P injection of 0.9% NaCl 100µl). Mice were analysed 24 hours upon drug exposure.

value: Rosa26rtTA/+, Hprt Myc-Tnk1tg

value: female


title: 2102EP-CD24 wt

description: parental control, CD24 'wildtype'

value: parental control, CD24 'wildtype'


title: Kin 2-4 Motor Neuron Puromycin Treatment Total RNA Replicate 1

description:
Kin2-4_puro_total_rep1
deseq2_normalized_counts.txt

value: Kin2ALS4 hiPSC line

value: Puromycin

value: Total


title: Kin 2-4 Motor Neuron Puromycin Treatment Nuclear Fraction Replicate 2

description:
Kin2-4_puro_nucl_rep2
deseq2_normalized_counts.txt

value: Nucleus


title: 5813: Illumina_MA_SS_2

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using Illumina method with 1000ng of Size selected RNA as starting material. Library was sequenced using HiSeq 2516

value: Meiotic Anthers (MA)

value: Size selected RNA


title: Mammary carcinoma, #5

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

institute: National Institutes for Quantum and Radiological Science and Technology

hyb_protocol: Slides were hybridised in 1X Agilent Blocking Agent/Hi-RPM Buffer for 40 hours at 65°C in a rotating hybridization oven, then washed with the Agilent Oligo aCGH Buffer 1 and Buffer 2 in an ozone-depleted hood.

scan_protocol: Scanned on an Agilent microarray scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

organism: Rattus norvegicus

source_name: Mammary carcinoma induced by radiation

label_protocol: Labeling reactions with cyanine 5-UTP and cyanine 3-UTP were performed according to the Agilent SureTag DNA labeling kit (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: Rats were housed in autoclaved cages and maintained in a room with a controlled temperature (23 ± 1°C) and humidity (50 ± 5%) under a regular 12-hours light, 12-hours dark cycle. They were fed a standard laboratory animal diet (CE-2; Clea Japan, Tokyo, Japan) and sterilized water ad libitum.

extract_protocol: Genomic DNA was isolated by proteinase K digestion, followed by phenol/chloroform extraction.

treatment_protocol: Rats were left untreated or were subjected to whole-body 137Cs gamma-irradiation (4 Gy, 0.5 Gy/min) at 7 weeks of age.

value: Carcinoma

value: Female

value: F1 hybrid of Sprague-Dawley and Copenhagen rats

source_name: Normal ear

value: Ear skin


title: NCCIT-CD24 wt

description: parental control, CD24 'wildtype'


title: 5806: Nextflex_v2_PMA_TR1000_1

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using Nextflex_v2 method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2509

value: Pre-meiotic Anthers (PMA)

value: Total RNA


title: Ileum-NaCl_WT-rep2

source_name: Ileum NaCl-treatment, WT

value: saline solution (I.P injection of 0.9% NaCl 100µl)


title: Ileum-Dox_TNK1-rep4

source_name: Ileum, Doxicyclin-treatment, TNK1 knock-in

value: doxycycline (I.P injection 50µg/g of the mouse weight, 100µl)


title: Mouse_Femur_Central_Bone_Marrow_B

value: Male

value: 8 weeks

value: Femur (Central Bone Marrow)


title: 5807: Nextflex_v2_PMA_TR1000_2

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using Nextflex_v2 method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2510


title: Ileum-NaCl_WT-rep1

value: Rosa26rtTA/+, Hprt Myc-Tnk1tg

value: female


title: 5805: Nextflex_v2_PMA_SS1000_3

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using Nextflex_v2 method with 1000ng of Size selected RNA as starting material. Library was sequenced using HiSeq 2508


title: Mouse_Femur_Central_Bone_Marrow_A


title: Kin 2-4 Motor Neuron Puromycin Treatment Total RNA Replicate 2

description:
Kin2-4_puro_total_rep2
deseq2_normalized_counts.txt

value: iPSC-derived motor neurons

value: Kin2ALS4 hiPSC line

value: Puromycin

value: Total


title: Ileum-Dox_TNK1-rep3


title: 5804: Nextflex_v2_PMA_SS1000_2

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using Nextflex_v2 method with 1000ng of Size selected RNA as starting material. Library was sequenced using HiSeq 2507

value: Size selected RNA


title: SGBS_day14_batch1_rep1 [RNA-seq]

city: Chapel Hill

first: Karen

middle: L

last: Mohlke

state: NC

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

description:
processed data file:
DESeq2Datasets_forGEO_RNA_SGBS-days0-2-4-14.RData

data_processing:
Sequencing adapters and low quality base calls were trimmed from the 3’ ends of reads using cutadapt with parameters -q 20 –minimum-length 36.
We aligned reads to the hg19 human genome using STAR with parameters --sjdbOverhang 149 --twopassMode Basic --quantMode TranscriptomeSAM --outFilterMultimapNmax 20 --alignSJoverhangMin  8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin  20 --alignIntronMax 1000000 --alignMatesGapMax 1000000.
We quantified expression of genes from GENCODE v29 lift37 and corrected for GC bias using salmon with parameters –seqBias –gcBias –gencode.
We generated RNA-seq quality metrics using the CollectRnaSeqMetrics tool from Picard.
We imported salmon transcript quantifications and collapsed to the gene level using tximport and made DESeq2 datasets.
Genome_build: hg19
Supplementary_files_format_and_content: The file "DESeq2Datasets_forGEO_RNA_SGBS-days0-2-4-14.RData" contains two DESeq2 datasets. The "dds" dataset contains the discrete gene counts across each sample. The "dds.rlog" dataset contains variance-stabilized gene expression using the DESeq2 rlog function. Both datasets contain all genes from GENCODE v29lift37, but we restricted to the 18,299 genes with median size factor-normalized count >=1 across libraries.

molecule: polyA RNA

growth_protocol: We cultured SGBS preadipocytes in serum-containing basal medium (DMEM:F12 + 33uM biotin + 17uM pantothenate) with 10% FBS.

extract_protocol:
We isolated total RNA from SGBS cells at D0, D2, D4, and D14 of differentiation using the Total RNA Purification Kit (product #17200) from Norgen Biotek (Ontario, Canada).
Novogene (Beijing, China) generated poly-A RNA libraries.

treatment_protocol: We cultured SGBS preadipocytes using the growth protocol until confluent, then rinsed in phosphate-buffered-saline (PBS) and differentiated for four days in medium supplemented with 0.01 mg/mL transferrin, 20 nM insulin, 200 nM cortisol, 0.4 nM triiodothyronine, 50 nM dexamethasone, 500 uM IBMX, and 2 uM rosiglitazone. After four days, we maintained differentiated SGBS cells in basal medium supplemented with 0.01 mg/mL transferrin, 20 nM insulin, 200 nM cortisol, 0.4 nM triiodothyronine until harvested at the specified differentiation timepoint.

value: adipocyte


title: SGBS_day14_batch3_rep1 [RNA-seq]


title: SGBS_day4_batch3_rep2 [RNA-seq]

value: immature adipocyte


title: Ileum-NaCl_WT-rep3


title: CR464 Line Untreated Insoluble Fraction Replicate 2

description:
insol_CR464_ut_rep2
deseq2_normalized_counts.txt

value: CR464.2 hiPSC line

value: Untreated

value: Insoluble


title: Kin 2-4 Motor Neuron Puromycin Treatment Cytoplasm Fraction Replicate 1

description:
Kin2-4_puro_cyto_rep1
deseq2_normalized_counts.txt

value: Cytoplasm


title: cDNA7044

city: Dallas

first: Uthra

last: Balaji

state: Texas

address: 3434 Live Oak St

department: Biostatistics Core

institute: Baylor Scott & White Research Institute

description: Mito+ RBCs : Ops IgG- group are PBMCs from SLE patients that carry mitochondria inside their RBCs (Red blood cells) and they don' t have opsonizing anti-RBCs IgG in their plasma

data_processing:
RNAseq reads were trimmed and aligned to human genome using hisat2 and counted using featurecounts
Normalization and differential gene  expression (DGE) analysis was performed using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file includes raw counts

source_name: PBMCs isolated from SLE patients

growth_protocol: Samples 14-27: SLE blood was subjected to Ficcol separation and then RNA was extracted form the PBMCs fraction.

extract_protocol:
Total RNA was isolated from cell lysates using the RNeasy Micro Kit (Qiagen), including on-column deoxyribonuclease digestion, and was analyzed for quality using the RNA 6000 Pico Kit (Agilent Technologies).
Poly(A)-enriched next-generation sequencing library construction was performed using the KAPA mRNA Hyper Prep Kit (KAPA Biosystems) with 100  ng of input total RNA and 15 amplification cycles according to the manufacturer’s protocol. The quality and quantity of the individual libraries was assessed using the High Sensitivity DNA Kit (Agilent).  The libraries were equimolar pooled and an additional 1X bead clean-up was used to remove adapter dimer. The pooled libraries were quantitated using the KAPA Library Quantification Kit, Universal (KAPA Biosystems) and sequenced on an Illumina NextSeq 500 with paired-end 75-base-pair (bp) read lengths.

tag: patient diagnosis

value: SLE

value: PBMC

tag: condition

value: Mito+ RBCs :Ops IgG- group


title: SGBS_day14_batch3_rep2 [RNA-seq]


title: Ileum-Dox_TNK1-rep1

value: doxycycline (I.P injection 50µg/g of the mouse weight, 100µl)


title: 5800: Illumina_PMA_SS_1

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using Illumina method with 1000ng of Size selected RNA as starting material. Library was sequenced using HiSeq 2503

value: Pre-meiotic Anthers (PMA)

value: Illumina


title: 5809: Illumina_MA_TR_1

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using Illumina method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2512

value: Meiotic Anthers (MA)

value: Total RNA


title: CR464 Line Untreated Insoluble Fraction Replicate 1

description:
insol_CR464_ut_rep1
deseq2_normalized_counts.txt

value: iPSC-derived motor neurons


title: 5799: Illumina_PMA_TR_3

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using Illumina method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2502


title: SGBS_day14_batch1_rep2 [RNA-seq]


title: Kin 2-4 Motor Neuron Puromycin Treatment Insoluble Fraction Replicate 2

description:
Kin2-4_puro_insol_rep2
deseq2_normalized_counts.txt

value: Kin2ALS4 hiPSC line

value: Puromycin


title: Kin 2-4 Motor Neuron Puromycin Treatment Cytoplasm Fraction Replicate 2

description:
Kin2-4_puro_cyto_rep2
deseq2_normalized_counts.txt


title: 5803: Nextflex_v2_PMA_SS1000_1

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using Nextflex_v2 method with 1000ng of Size selected RNA as starting material. Library was sequenced using HiSeq 2506

value: Size selected RNA


title: cDNA7048

description: Mito- RBCs group are PBMCs from SLE patients that do not carry mitochondria inside their RBCs (Red blood cells)

value: Mito- RBCs group


title: cDNA7047


title: Kin 2-4 Motor Neuron Puromycin Treatment Insoluble Fraction Replicate 1

description:
Kin2-4_puro_insol_rep1
deseq2_normalized_counts.txt


title: SGBS_day4_batch2_rep2 [RNA-seq]

value: immature adipocyte


title: 5797: Illumina_PMA_TR_1

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using Illumina method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2500


title: CR464 Line Puromycin Treatment Insoluble Fraction Replicate 2

description:
insol_CR464_puro_rep2
deseq2_normalized_counts.txt

value: CR464.2 hiPSC line


title: cDNA7039

description: Mito+ RBCs : Ops IgG+ group are PBMCs from SLE patients that carry mitochondria inside their RBCs (Red blood cells) and they have opsonizing anti-RBCs IgG in their plasma

value: Mito+ RBCs :Ops IgG+ group


title: CR464 Line Puromycin Treatment Insoluble Fraction Replicate 1

description:
insol_CR464_puro_rep1
deseq2_normalized_counts.txt

value: Insoluble


title: SGBS_day2_batch1_rep2 [RNA-seq]

description:
processed data file:
DESeq2Datasets_forGEO_RNA_SGBS-days0-2-4-14.RData


title: Kin 2-4 Motor Neuron Puromycin Treatment Nuclear Fraction Replicate 1

description:
Kin2-4_puro_nucl_rep1
deseq2_normalized_counts.txt

value: Nucleus


title: SGBS_day4_batch1_rep1 [RNA-seq]


title: SGBS_day4_batch2_rep1 [RNA-seq]


title: WT CD4 T cell Post-transplant Day 7 Rep3

city: Syracuse

first: Mobin

last: Karimi

state: NY

address: 766 Irving Ave Suite 2281

department: Microbiology/Immunology

institute: Suny Upstate Medical University

data_processing:
All data were processed and analyzed using the R programming language (Version 4.0.4), the RStudio interface (Version 1.4.1106), and Bioconductor
Transcript abundance of samples was computed by pseudoalignment with Kallisto (version 0.46.2). Transcript per million (TPM) values were then normalized for each CD4 and CD8 samples separately and fitted to a linear model by empirical Bayes method with the Voom and Limma R packages
Differential gene expression was defined as a ≥2 fold, FDR£5%; after controlling for multiple testing using the Benjamini-Hochberg method  were used for hierarchical clustering and heatmap generation in R.
For GO enrichment analysis, the g: Profiler toolset, g:GOSt tool was utilized. Gene Set Enrichment Analysis (GSEA) was performed using clusterProfiler and the Molecular Signatures Database (MSigDB) using the Hallmark pathways collection
Genome_build: mm9
Supplementary_files_format_and_content: .tsv file

source_name: sorted CD4 T cell

extract_protocol:
Total RNA was extracted with the Qiagen miRNeasy Mini kit. RNA quality and quantity were assessed with the Agilent 2100 Bioanalyzer. cDNA was prepared with the SMARTseq HT Kit (Takara Bio), using 1ng total RNA. Dual indexed sequencing libraries were prepared using the Nextera XT DNA Library Prep kit (Illumina), using 250pg cDNA.
Illumina TruSeq

tag: background strain

value: Wild type

tag: organ obtained

value: spleen

tag: day transplantation

value: Post transplanted Day 7


title: 5801: Illumina_PMA_SS_2

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using Illumina method with 1000ng of Size selected RNA as starting material. Library was sequenced using HiSeq 2504

value: Pre-meiotic Anthers (PMA)


title: cDNA7042

value: SLE

tag: cell type

value: PBMC


title: 5802: Illumina_PMA_SS_3

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using Illumina method with 1000ng of Size selected RNA as starting material. Library was sequenced using HiSeq 2505

value: Illumina


title: Ileum-Dox_TNK1-rep2

value: Rosa26rtTA/+, Hprt Myc-Tnk1tg

value: female

value: doxycycline (I.P injection 50µg/g of the mouse weight, 100µl)


title: SGBS_day2_batch1_rep1 [RNA-seq]


title: WT CD8 T cell Post-transplant Day 7 Rep3

source_name: sorted CD8 T cell


title: CR463 Line Untreated Insoluble Fraction Replicate 1

description:
insol_CR463_ut_rep1
deseq2_normalized_counts.txt

value: iPSC-derived motor neurons

value: CR463.4 hiPSC line

value: Untreated


title: CR463 Line Untreated Insoluble Fraction Replicate 2

description:
insol_CR463_ut_rep2
deseq2_normalized_counts.txt


title: cDNA7043

value: Mito- RBCs group


title: SGBS_day0_batch3_rep2 [RNA-seq]

value: preadipocyte


title: CR463 Line Recovery Insoluble Fraction Replicate 2

description:
insol_CR463_rec_rep2
deseq2_normalized_counts.txt

value: Recovery

value: Insoluble


title: WT CD8 T cell Post-transplant Day 7 Rep2

value: Wild type


title: CR464 Line Recovery Insoluble Fraction Replicate 1

description:
insol_CR464_rec_rep1
deseq2_normalized_counts.txt

value: CR464.2 hiPSC line


title: SGBS_day4_batch1_rep2 [RNA-seq]

value: immature adipocyte


title: cDNA7034

description: Mito+ RBCs : Ops IgG- group are PBMCs from SLE patients that carry mitochondria inside their RBCs (Red blood cells) and they don' t have opsonizing anti-RBCs IgG in their plasma

value: Mito+ RBCs :Ops IgG- group


title: cDNA7035

value: SLE


title: SGBS_day4_batch3_rep1 [RNA-seq]


title: SGBS_day0_batch2_rep1 [RNA-seq]


title: 5798: Illumina_PMA_TR_2

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using Illumina method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2501

value: Pre-meiotic Anthers (PMA)

value: Total RNA


title: CR463 Line Puromycin Treatment Insoluble Fraction Replicate 2

description:
insol_CR463_puro_rep2
deseq2_normalized_counts.txt

value: Puromycin


title: cDNA7045

description: Mito- RBCs group are PBMCs from SLE patients that do not carry mitochondria inside their RBCs (Red blood cells)

value: PBMC


title: SGBS_day0_batch2_rep2 [RNA-seq]


title: cDNA7036

value: Mito+ RBCs :Ops IgG+ group


title: cDNA7032


title: SGBS_day0_batch3_rep1 [RNA-seq]


title: CR463 Line Puromycin Treatment Insoluble Fraction Replicate 1

description:
insol_CR463_puro_rep1
deseq2_normalized_counts.txt

value: iPSC-derived motor neurons


title: WT CD8 T cell Post-transplant Day 7  Rep1

value: spleen

value: Post transplanted Day 7


title: CR464 Line Recovery Insoluble Fraction Replicate 2

description:
insol_CR464_rec_rep2
deseq2_normalized_counts.txt


title: WT CD4 T cell Post-transplant Day 7 Rep2


title: cDNA7030

growth_protocol: Samples 11-13: RBCs were generated from HD PBMCs and collected for RNA extraction 0, 24 and 48 h post-differentiation

value: healthy

value: RBC generated from PBMC

value: RBCs generated from Healthy Donors PBMCs (48 h post-differentiation)


title: WT CD4 T cell Post-transplant Day 7 Rep1


title: H9 Stem Cell Total RNA Replicate 1

description:
H9_ESC_total_rep1
deseq2_normalized_counts.txt

source_name: stem cells

value: hESCs

value: H9 ESC line

value: Untreated

value: Total


title: WT CD4 T cell Pre-transplant Rep3

value: Wild type

value: Pre transplanted


title: cDNA7038

description: Mito+ RBCs : Ops IgG+ group are PBMCs from SLE patients that carry mitochondria inside their RBCs (Red blood cells) and they have opsonizing anti-RBCs IgG in their plasma

value: SLE


title: SGBS_day0_batch1_rep1 [RNA-seq]

value: preadipocyte


title: SGBS_day0_batch1_rep2 [RNA-seq]


title: cDNA7033

value: Mito+ RBCs :Ops IgG- group


title: H9 Stem Cell Nuclear Fraction Replicate 1

description:
H9_ESC_nuclei_rep1
deseq2_normalized_counts.txt

value: Nucleus


title: SGBS_day14_batch3_rep2

description:
processed data file:
mergedConsensusPeaks_forDifferentialTesting_SGBS-days0-2-4-14.bed.gz
DESeq2Datasets_forGEO_ATAC_SGBS-days0-2-4-14.RData
SGBS-day14_consensusPeaks-fromUnionRepPeaks_top100k-byMedianPval.bed.gz

library_source: genomic

data_processing:
We trimmed sequencing adapters and low quality base calls from the 3’ ends of reads using cutadapt with parameters -q 20 –minimum-length 36.
We aligned trimmed reads to the hg19 human genome using bowtie2 with parameters –minins 36 –maxins 1000 –no-mixed –no-discordant –no-unal
We selected nuclear chromosomal alignments with mapq>20 using samtools, removed alignments overlapping high-signal regions (Duke excluded and ENCODE/DAC exclusion list regions) using BEDTools pairToBed with the parameter -type notospan, and removed duplicate alignments using Picard MarkDuplicates.
We generated ATAC-seq quality metrics using ataqv. Ataqv is only designed for paired-end reads, so we wrote a customized script to calculate TSS enrichment for the single-end METSIM libraries.
Prior to peak calling, we trimmed alignments so their 5’ ends corresponded to the Tn5 binding site (+4 for + strand alignments and -5 for – strand alignments) and smoothed signal by extending alignments 100 bp on either side of the Tn5 binding sites using BEDTools slop. We called peaks (FDR<5%) with MACS2 with parameters -q 0.05 –nomodel –bdg.
For each analyzed day of SGBS differentiation, we generated a set of consensus ATAC peaks using the following method. First, we merged peak genomic coordinates across replicates for a given day using BEDTools merge. Second, we defined consensus peaks as merged peaks that overlapped individual replicate peaks in greater than 50% of replicates (at least 3 out of 5 replicates for D14 and 6 out of 10 replicates for D0 and D4). For each sample of METSIM adipose tissue, we generated a set of consensus ATAC peaks using the following method. First, we merged peak genomic coordinates across replicates for a given day using BEDTools merge. Second, we defined consensus peaks as merged peaks that overlapped individual replicate peaks in at least three individuals.
For SGBS, we generated a set of merged peaks to test for differential chromatin accessibility by merging the top 100,000 consensus peaks in each day (ranked by median peak p-value across replicates). We quantified the accessibility of these merged peaks in each library using featureCounts. We computed the GC percent of each peak using BEDTools nuc and generated within-library GC bias normalization factors using full quantile normalization with EDASeq. We then used EDASeq GC bias normalization factors within DESeq2 and used DESeq2 size factors to control for differences in sequencing depth between libraries. We tested for differential chromatin accessibility using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: The files SGBS-day<day>_consensusPeaks-fromUnionRepPeaks_top100k-byMedianPval.bed.gz contain bed coordinates of the top 100,000 consensus ATAC peaks in each SGBS differentiation day ranked by median MACS2 p-value. The first three columns have peak genomic coordinates, the 4th column contains an arbitrary peak ID, columns 5-7 contain median MACS2 fold enrichment, p-value, and q-value across replicates that contributed to the peak, and column 8 lists the number of samples contributing to the peak.
Supplementary_files_format_and_content: The file mergedConsensusPeaks_forDifferentialTesting_SGBS-days0-2-4-14.bed.gz contains bed coordinates of the peaks used for differential chromatin accessibility testing. These are the union of the top 100,000 consensus peaks in each SGBS differentiation day. Columns 1-3 are peak bed coordinates, column 4 is an arbitrary peak ID, and column 5 contains the GC content of the peak calculated with BEDTools nuc.
Supplementary_files_format_and_content: The file DESeq2Datasets_forGEO_ATAC_SGBS-days0-2-4-14.Rdata contains DESeq2 datasets of peak counts across samples in Rdata format and can be read directly into the R statistical software package. The file contains two DESeq2 datasets (1) peaks.gc.dds: raw peak counts by sample with EDASeq GC normalization and DESeq2 size factors and (2) peaks.gc.rlog: variance-stabilized peak counts using the DESeq2 rlog function. Sample information can be obtained using colData(peaks.gc.dds) or colData(peaks.gc.rlog).
Supplementary_files_format_and_content: The files "adiposeTissue<sampleNumber>_peaks.narrowPeak.gz" contain peaks called on individual adipose tissue samples using MACS2 and are in standard narrowPeak format.
Supplementary_files_format_and_content: The files "adiposeTissue_consensusPeaks-from11samples_unionPeaksInAtLeast3samples.bed.gz" and "adiposeTissue_consensusPeaks-from17samples_unionPeaksInAtLeast3samples.bed.gz" contain consensus peaks obtained using either all 17 adipose tissue samples or a subset of 11 samples after removing outliers. These files are in modified BED format with the first 3 columns representing peak genomic coordinates, column 4 containing an arbitrary peak ID, and column 5 listing the number of samples the peak was found in.

extract_protocol:
All extraction steps were performed at 4C. For SGBS, nuclei were extracted by pelleting 50,000 cells at 500 RCF, resuspended and incubated on ice 3 minutes in 50 ul buffer containing 10 mM Tris-HCL, 10 mM NaCL, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin. 1 mL buffer containing 10 mM Tris-HCL, 10 mM NaCL, 3 mM MgCl2, and 0.1% Tween-20 was added. Nuclei were pelleted at 500 RCF for 10 minutes. For adipose tissue, 50 mg of frozen tissue was crushed and then homogenized in a dounce with 1 mL buffer containing 20mM Tris-HCl, 50mM EDTA, 5mM Spermidine, 0.15mM Spermine, 0.1% mercaptoethanol, and 40% Glycerol, pH 7.5. The homogenized sample was added to 9 mL of the same buffer and incubated on ice for 5 minutes and filtered through a Miracloth before pelleting at 1100xg for 10 minutes. The pellet was resuspended in 200 uL of the same buffer with an addition of 0.5% Triton X-100 and centrifuged at 500xg for 5 minutes. The pellet was resuspended in 250 uL of a wash buffer containing 10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, pH 7.4.
For both SGBS and adipose tissue, nuclei were suspended in 25 μl transposase buffer from the Nextera kit, 5 μl TDE1 Transposase enzyme, and 20 μl water for 30 minutes at 37C. Transposition reaction was cleaned with a Zymo DNA Clean and Concentrator kit. Libraries were amplified with 10 μl transposed DNA, 10 μl nuclease-free H2O, 2.5 μl 25 μM PCR Primer 1, 2.5 μl 25 μM Barcoded PCR Primer 2, and 25 μl NEBNext High-Fidelity 2X PCR Master Mix. Final PCR product was cleaned again with Zymo DNA Clean and Concentrator kit.

value: adipocyte


title: WT CD8 T cell Pre-transplant Rep2


title: CR463 Line Recovery Insoluble Fraction Replicate 1

description:
insol_CR463_rec_rep1
deseq2_normalized_counts.txt

value: iPSC-derived motor neurons

value: CR463.4 hiPSC line

value: Recovery

value: Insoluble


title: WT CD8 T cell Pre-transplant Rep3

value: spleen


title: SGBS_day14_batch3_rep1


title: cDNA7025

source_name: Monocytes-derived macrophages

growth_protocol: Samples 7-10; monocytes were differentiated into macrophages with GMCSF. Macrophages were then treated as described and collected for RNA extraction 24 h later.

treatment_protocol: Monocyte enrichment and differentiation into macrophages (M): PBMCs were isolated from healthy human donor buffy coats (obtained from the New York Blood Center) through Lymphoprep    (Stem Cell Technologies) gradient centrifugation. Monocytes were then isolated with EasySep    Human Monocyte Enrichment Kit (Stem Cell Technologies) following the manufacturer protocol and then differentiated into macrophages in macrophages-SFM medium (Thermo-Fisher) supplemented with GM-CSF (50 ng/mL; Sargramostim, Sanofi-Avantis-Montrouge). At day 3, non-adherent cells were removed by replacing the culture media. Cells were used for co-culture experiments at day 5.

value: healthy

value: Monocytes-derived macrophages

value: macrophages treated with mito- RBCs


title: WT CD8 T cell Pre-transplant Rep1


title: SGBS_day2_batch3_rep2

description:
processed data file:
mergedConsensusPeaks_forDifferentialTesting_SGBS-days0-2-4-14.bed.gz
DESeq2Datasets_forGEO_ATAC_SGBS-days0-2-4-14.RData
SGBS-day2_consensusPeaks-fromUnionRepPeaks_top100k-byMedianPval.bed.gz

value: immature adipocyte


title: H1 Motor Neuron Untreated Total RNA Replicate 1

description:
H1_ut_total_rep1
deseq2_normalized_counts.txt

source_name: motor neurons

value: hESC-derived motor neurons

value: H1 ESC line

value: Untreated

value: Total


title: cDNA7028

value: RBC generated from PBMC

value: RBCs generated from Healthy Donors PBMCs (0 h post-differentiation)


title: H1 Motor Neuron Untreated Nuclear Fraction Replicate 2

description:
H1_ut_nucl_rep2
deseq2_normalized_counts.txt

value: Nucleus


title: WT CD4 T cell Pre-transplant Rep2

value: Wild type

value: Pre transplanted


title: 5808: Nextflex_v2_PMA_TR1000_3

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using Nextflex_v2 method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2511

source_name: Maize anthers

value: Pre-meiotic Anthers (PMA)

value: Total RNA


title: cDNA7029

value: RBCs generated from Healthy Donors PBMCs (24 h post-differentiation)


title: H1 Motor Neuron Untreated Insoluble Fraction Replicate 2

description:
H1_ut_insol_rep2
deseq2_normalized_counts.txt

value: Insoluble


title: Cat-Tg CD4 Tcell Post-transplant Day 7 Rep2

value: Cat-Tg

value: spleen

value: Post transplanted Day 7


title: cDNA7026

value: healthy

value: Monocytes-derived macrophages

value: macrophages treated with mito+ RBCs


title: WT CD4 T cell Pre-transplant Rep1


title: H9 Stem Cell Cytoplasm Fraction Replicate 1

description:
H9_ESC_cyto_rep1
deseq2_normalized_counts.txt

value: hESCs

value: H9 ESC line

value: Untreated

value: Cytoplasm


title: H9 Stem Cell Insoluble Fraction Replicate 1

description:
H9_ESC_insol_rep1
deseq2_normalized_counts.txt


title: H1 Motor Neuron Untreated Total RNA Replicate 2

description:
H1_ut_total_rep2
deseq2_normalized_counts.txt

value: hESC-derived motor neurons

value: H1 ESC line

value: Total


title: H1 Motor Neuron Untreated Insoluble Fraction Replicate 1

description:
H1_ut_insol_rep1
deseq2_normalized_counts.txt


title: cDNA6818

description: RBCs (Red blood cells) from SLE patients that do not remove their mitochondria during the differentiation process

source_name: RBCs generated from SLE PBMCs (24 hr post-differentiation)

growth_protocol: Samples 1-6: RBCs were generated from SLE PBMCs and collected for RNA extraction 24 h post-differentiation

value: SLE

value: RBC generated from PBMC

value: SLE Non Remover


title: Cat-Tg CD4 Tcell Post-transplant Day 7 Rep3


title: cDNA6817

description: RBCs (Red blood cells) from SLE patients that remove their mitochondria during the differentiation process

value: SLE Remover


title: cDNA7024

value: macrophages treated with media


title: SGBS_day2_batch3_rep1

value: immature adipocyte


title: SGBS_day4_batch4_rep2

description:
processed data file:
mergedConsensusPeaks_forDifferentialTesting_SGBS-days0-2-4-14.bed.gz
DESeq2Datasets_forGEO_ATAC_SGBS-days0-2-4-14.RData
SGBS-day4_consensusPeaks-fromUnionRepPeaks_top100k-byMedianPval.bed.gz


title: cDNA6820


title: cDNA6811


title: cDNA7027

value: macrophages treated with Poly dA:dT


title: Cat-Tg CD8 Tcell Post-transplant Day 7 Rep1

value: Cat-Tg

value: spleen

value: Post transplanted Day 7


title: H1 Motor Neuron Untreated Nuclear Fraction Replicate 1

description:
H1_ut_nucl_rep1
deseq2_normalized_counts.txt

value: Nucleus


title: SGBS_day4_batch4_rep1


title: H1 Motor Neuron Untreated Cytoplasm Fraction Replicate 1

description:
H1_ut_cyto_rep1
deseq2_normalized_counts.txt


title: SGBS_day4_batch3_rep2


title: Cat-Tg CD8 Tcell Post-transplant Day 7 Rep3


title: SGBS_day4_batch2_rep3


title: SGBS_day4_batch2_rep4


title: Cat-Tg CD8 Tcell Pre-transplant Rep3

value: Pre transplanted


title: cDNA6819


title: Cat-Tg CD8 Tcell Post-transplant Day 7  Rep2


title: Cat-Tg CD4 Tcell Pre-transplant Rep2


title: SGBS_day4_batch2_rep6


title: Cat-Tg CD4 Tcell Post-transplant Day 7 Rep1


title: cDNA7041

description: Mito+ RBCs : Ops IgG- group are PBMCs from SLE patients that carry mitochondria inside their RBCs (Red blood cells) and they don' t have opsonizing anti-RBCs IgG in their plasma

value: PBMC

value: Mito+ RBCs :Ops IgG- group


title: SGBS_day4_batch2_rep1


title: A549 MS023 7 days Rep2

city: Bronx

first: Thomas

last: Meier

state: New York

address: 1300 Morris Park Avenue

department: Department of Anatomy & Structural Biology

institute: Albert Einstein College of Medicine, INC

data_processing:
adapter trimming performed with Cutadapt
RNA-seq reads where aligned with STAR
Differential gene expression was determined using featureCounts and DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: fpkm measurements
Supplementary_files_format_and_content: raw counts

growth_protocol: A549 cells (freshly purchased for this study from ATCC) were cultured in DMEM medium (FBS and Penicillin/Streptomycin at 10% and 1X final concentration, respectively). Incubator maintained temperature and CO2 concentration at 37 °C and 5%, respectively.

extract_protocol:
For each condition, triplicate total RNA was extracted with mRNeasy kits (Qiagen)
rRNA removed with Riboerase (Kapa Biosystems) and paired-end libraries were prepared with random hexamers (Kapa)
Each library was sequenced to attain approximately 40M paired-end 150bp reads on a NextSeq 500

treatment_protocol: MS023 Type-I PRMT inhibitor or GSK591 PRMT5 specific inhibitor (1 µM final concentration) for seven days; both compounds were obtained from Cayman Chemicals. 150 mm plates (30 mL medium) were seeded with 0.2 x 105 and 0.4 x 105 cells for the control and drug-treated groups, respectively.

value: epithelial


title: SGBS_day4_batch2_rep5


title: H1 Motor Neuron Untreated Cytoplasm Fraction Replicate 2

description:
H1_ut_cyto_rep2
deseq2_normalized_counts.txt

value: hESC-derived motor neurons

value: H1 ESC line

value: Untreated

value: Cytoplasm


title: H1 Motor Neuron Recovery Insoluble Fraction Replicate 2

description:
H1_rec_insol_rep2
deseq2_normalized_counts.txt

value: Recovery

value: Insoluble


title: SGBS_day4_batch3_rep1


title: Cat-Tg CD8 Tcell Pre-transplant Rep1


title: SGBS_day0_batch2_rep6

description:
processed data file:
mergedConsensusPeaks_forDifferentialTesting_SGBS-days0-2-4-14.bed.gz
DESeq2Datasets_forGEO_ATAC_SGBS-days0-2-4-14.RData
SGBS-day0_consensusPeaks-fromUnionRepPeaks_top100k-byMedianPval.bed.gz

value: preadipocyte


title: A549 GSK591 7 days Rep1


title: Cat-Tg CD4 Tcell Pre-transplant Rep3


title: Cat-Tg CD8 Tcell Pre-transplant Rep2


title: Sequence Pool 2, RNA

city: Minneapolis

first: Adam

last: Herman

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

description:
vanBerlo-010-features.csv
pool2_barcodes.tsv.gz
pool2_features.tsv.gz
pool2_matrix.mtx.gz

data_processing:
GEX, HTO, and ADT quantification with cellranger 3.1.0
Data QC and processing in Seurat 3.1.1 including multiplet calling with HTOdemux
Normalization and variance stabilization with scTransform followed by integration.
DE testing using Wilcox method (default in Seurat)
Genome_build: mm10
Supplementary_files_format_and_content: raw counts matrices for GEX, HTO, and ADT for pool1 and pool2
Supplementary_files_format_and_content: csv file describing ADT and HTO barcodes, position in read, TotalSeq ID, and name

source_name: heart tissue

growth_protocol: C57Bl/6j mice were kept in SPF cages with free access to water and food

extract_protocol:
Cardiac cells were extracted using Collagenase B and Dispase II digestion, followed by magnetic selection of CD45 positive cells
Capture of cells was performed on 10X Chromium with 3' GEX. Hashtag and mRNA libraries were generated separately and sequenced together

treatment_protocol: Mice were subjected to sham or TAC surgeries at 8 weeks of age

tag: antibodies

tag: hashtags


title: H1 Motor Neuron Recovery Total RNA Replicate 2

description:
H1_rec_total_rep2
deseq2_normalized_counts.txt

tag: cell line

tag: treatment

value: Total


title: H1 Motor Neuron Recovery Nuclear Fraction Replicate 2

description:
H1_rec_nucl_rep2
deseq2_normalized_counts.txt

tag: fraction


title: Sequence Pool 2, Epitope tags


title: H1 Motor Neuron Recovery Nuclear Fraction Replicate 1

description:
H1_rec_nucl_rep1
deseq2_normalized_counts.txt


title: A549 MS023 7 days Rep3


title: SGBS_day0_batch2_rep4


title: SGBS_day0_batch4_rep1


title: Sequence Pool 2, Hashtags


title: SGBS_day0_batch4_rep2


title: Cat-Tg CD4 Tcell Pre-transplant Rep1


title: cDNA6810

value: SLE

value: RBC generated from PBMC

value: SLE Remover


title: SGBS_day0_batch2_rep2


title: H1 Motor Neuron Recovery Insoluble Fraction Replicate 1

description:
H1_rec_insol_rep1
deseq2_normalized_counts.txt


title: Sequence Pool 1, Epitope tags

description:
vanBerlo-010-features.csv
pool1_barcodes.tsv.gz
pool1_features.tsv.gz
pool1_matrix.mtx.gz


title: SGBS_day0_batch2_rep1


title: A549 MS023 7 days Rep1


title: P401_Tami_3

city: Houston

first: Charles

middle: Yang

last: Lin

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: RNA-Seq for primary patient samples treated with DMSO

data_processing:
The RNA-Seq data was first preprocessed with BBDuk for paired end samples
All RNA-seq datasets were aligned with STAR and quantified via Cuffquant 2.2 with the hg19 ERCC annotation
Cuffnorm was utilized to normalize data
Top 3 replicates (based on correlation) were used
Inactive genes (no samples with FPKM > 10) were filtered out prior to additional analysis
Genome_build: hg19 ERCC
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Human primary leukopheresis sample

growth_protocol: Cells were rapidly defrosted in a 37deg C water bath, mixed with RPMI+10% FBS+1% Pen/Strep (R10) media. After centrifuging, aspiration, and resuspension into fresh R10 media, cells were counted and suspended into max 2-3million cells/ml of R10+conditioned media overnight. The following day, cells were counted, dead cells were centrifuged off, and then remaining viable cells were resuspended at 1 million/ml of R10+conditioned media.

extract_protocol:
Samples (~1-2 million cells) were flash frozen in trizol and RNA was extracted via the Zymo Direct-zol RNA miniprep kit
RNA-Seq libraries were prepared for sequencing using standard NEB protocols

treatment_protocol: Resuspended cells were treated with either 100nM of tamibarotene or equal volume of DMSO in biologic quadruplicates, not to exceed 0.1% DMSO. After 24 hours of treatment cells were harvested for RNA.

value: Human primary leukopheresis sample

value: Tamibarotene


title: H1 Motor Neuron Puromycin Treatment Insoluble Fraction Replicate 2

description:
H1_puro2_insol_rep2
deseq2_normalized_counts.txt

value: Puromycin


title: SGBS_day0_batch2_rep5


title: A549 GSK591 7 days Rep2


title: H1 Motor Neuron Puromycin Treatment Cytoplasm Fraction Replicate 2

description:
H1_puro2_cyto_rep2
deseq2_normalized_counts.txt


title: SGBS_day4_batch2_rep2

value: immature adipocyte


title: A549 GSK591 7 days Rep3


title: A549 DMSO 7 days Rep2

value: DMSO


title: H1 Motor Neuron Recovery Total RNA Replicate 1

description:
H1_rec_total_rep1
deseq2_normalized_counts.txt


title: SGBS_day0_batch2_rep3


title: p400_2 RNA-seq

source_name: Human primary leukophereses sample

growth_protocol: Cells were rapidly defrosted in a 37deg C water bath, mixed with RPMI+10% FBS+1% Pen/Strep (R10) media. After centrifuging, aspiration, and resuspension into fresh R10 media, cells were counted and suspended into max 2-3million cells/ml of R10+conditioned media overnight (see supplemental methods for details). The following day, cells were fixed for ChIP

extract_protocol:
Samples (~1-2 million cells) were flash frozen in trizol and RNA was extracted via the qiagen RNA extraction kit
RNA-Seq libraries were prepared for sequencing using standard NEB protocols
Paired-End RNA-Seq

treatment_protocol: n/a except sample p401; cells were plated at 1 million cells/mL media and treated with Tamibarotene (100nM) or DMSO for 24 hours prior to RNA extraction

value: Human primary leukophereses sample


title: A549 DMSO 7 days Rep3

value: epithelial


title: H1 Motor Neuron Puromycin Treatment Total RNA Replicate 1

description:
H1_puro1_total_rep1
deseq2_normalized_counts.txt

extract_protocol:
for ceFRA-seq samples, RNA was extracted using either Trizol (total, nuclear, insoluble) or Trizol LS (cytoplasm) following manufacturer's standard protocol
libraries for ceFRA-seq were generated using Illumina Truseq stranded mRNA library prep kits, eCLIP libraries using in-house seCLIP library prep protocol
RNAseq (polyA), seCLIP-seq

value: hESC-derived motor neurons

value: H1 ESC line


title: P401_DMSO_4


title: H1 Motor Neuron Puromycin Treatment Total RNA Replicate 2

description:
H1_puro2_total_rep2
deseq2_normalized_counts.txt


title: P401_Tami_1


title: H1 Motor Neuron Puromycin Treatment Insoluble Fraction Replicate 1

description:
H1_puro1_insol_rep1
deseq2_normalized_counts.txt


title: Macrophage_young_1wk_ECM

city: Baltimore

first: Christopher

last: Cherry

state: MD

address: 1800 Orleans St

institute: Johns Hopkins University

data_processing:
Generation of counts with CellRanger or Drop-seq cookbook as applicable. Alignment with STAR
Genome_build: GENCODE Release 23
Supplementary_files_format_and_content: Individual samples are provided as raw counts. A processed Seurat object is provided with annotations, UMAP, etc.

source_name: Macrophage sort from quadriceps

extract_protocol:
Tissue samples were obtained by cutting the quadriceps femoris muscle from the hip to just above the knee. Tissues were finely diced manually with standard razor blades and digested for 45 min at 37oC with 1.67 Wünsch U/mL (0.5 mg/mL) Liberase TL (Roche Diagnostics, Sigma Aldrich) and 0.2 mg/mL DNase I (Roche Diagnostics, Sigma Aldrich) in RPMI-1640 medium supplemented with L-Glutamine and 15 mM HEPES (Gibco). The digested tissues were then pestled through 70 μm cell strainers (ThermoFisher Scientific) with RPMI-1640 (supplemented as before), and then washed twice with 1X DPBS. A Percoll (GE Healthcare) density gradient centrifugation was used to enrich the leukocyte fraction and remove blood and debris from the muscle samples and centrifuged at 2100 x g for 30 min with the lowest acceleration and no brake. Cells were washed 1X DPBS, stained with a viability live/dead amine reactive dye, washed with 1X DPS, blocked with anti-mouse TruStain FcX (BioLegend), and surface stained (Supplementary Table 6). Flow cytometry was performed using an Attune NxT Flow Cytometer (ThermoFisher Scientific) with a Violet, Blue, Green, and Red laser configuration. All subsequent analyses were performed on Live singlet cells using Windows based FlowJoTM software v10 (Benton Dickinson), license supplemented courtesy of the Johns Hopkins Bloomberg Flow Cytometry and Immunology Core.
According to Dropseq and 10X respectively

tag: material

value: ECM

tag: time of harvest

tag: tissue

value: muscle

tag: cell tpye

value: macrophage


title: P401_DMSO_2


title: p195_2 RNA-seq


title: A549 DMSO 7 days Rep1


title: P401_Tami_4


title: Sequence Pool 1, RNA

tag: genotype


title: Sequence Pool 1, Hashtags


title: Macrophage_young_1wk_PCL

tag: strain

value: PCL

tag: age


title: p217 RNA-seq


title: BM106029 RNA-seq


title: Fibroblast_young_6wk_Saline

source_name: Fibroblast sort from quadriceps

value: Saline

value: fibroblast


title: P401_DMSO_3


title: P401_Tami_2


title: H1 Motor Neuron Puromycin Treatment Cytoplasm Fraction Replicate 1

description:
H1_puro1_cyto_rep1
deseq2_normalized_counts.txt

value: Cytoplasm


title: H1 Motor Neuron Puromycin Treatment Nuclear Fraction Replicate 1

description:
H1_puro1_nucl_rep1
deseq2_normalized_counts.txt

value: Nucleus


title: p400_1 RNA-seq


title: Macrophage_young_1wk_Saline


title: H1 Motor Neuron Recovery Cytoplasm Fraction Replicate 1

description:
H1_rec_cyto_rep1
deseq2_normalized_counts.txt

value: Recovery


title: H1 Motor Neuron Puromycin Treatment Nuclear Fraction Replicate 2

description:
H1_puro2_nucl_rep2
deseq2_normalized_counts.txt


title: H1 Stem Cell Total RNA Replicate 2

description:
H1_ESC_total_rep2
deseq2_normalized_counts.txt

value: hESCs

value: Untreated

value: Total


title: H1 Motor Neuron Recovery Cytoplasm Fraction Replicate 2

description:
H1_rec_cyto_rep2
deseq2_normalized_counts.txt


title: Fibroblast_young_6wk_Naive

value: Naive


title: THP1_Input

description: Whole cell extract input control from H3K27ac in THP1 cell line

data_processing:
The H3K27ac ChIP-seq data was processed using the AQUAS pipeline (https://github.com/kundajelab/chipseq_pipeline) followibng the phase-3 ENCODE guidelines.
All ChIP-Seq datasets were aligned with BWA to human reference genome hg19/GRCh37.
Low-quality, duplicate, multimapping, and unmapped reads were filtered out. Reads mapping to the mitochondrial genome were also filtered out.
Peaks were called using MACS2 with a p-value threshold of 1e-5.
The H3K27ac ChIP-seq experiments with PBC1 > 0.5 with total mapped reads > 5M and MACS2 peaks (pvalue < 1e-5) > 5,000 were utilized for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Prcoessed ChIP-Seq data files are in bedgraph format

source_name: THP1 cell line

extract_protocol:
See Schmidl, et al, Nature Methods, 2015. In brief, lysates were clarified from fixed, sonicated nuclei and histone-DNA complexes were isolated with H3K27ac antibody.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75nt reads, single end).

tag: input

tag: chip antibody


title: H1 Stem Cell Nuclear Fraction Replicate 2

description:
H1_ESC_nuclei_rep2
deseq2_normalized_counts.txt

data_processing:
Fastq files were trimmed for adapters using cutadapt
Trimmed reads were aligned to the human genome build hg19 using STAR aligner
seCLIP : Binding region peaks were identified based on read pileup densities (Clipper)
seCLIP : Reproducible peaks were identified by comparing replicate read pileups along binding regions
Genome_build: hg19
Supplementary_files_format_and_content: normalized read counts text file
wiggle files
peak text files


title: Fibroblast_young_6wk_PCL


title: PT408 RNA-seq

value: Human primary leukophereses sample

value: DMSO


title: Fibroblast_young_6wk_ECM


title: THP1_H3K2ac

description: ChIP-Seq for H3K27ac in THP-1 cell line

value: H3K27ac (8173S, Cell Signaling Technology)


title: p456_Input

description: Whole cell extract input control from H3K27ac primary patient samples


title: H1 Stem Cell Insoluble Fraction Replicate 2

description:
H1_ESC_insol_rep2
deseq2_normalized_counts.txt

value: H1 ESC line

value: Insoluble


title: Fibroblast_young_1wk_Naive

value: muscle


title: MDA-MB-231 EV treatment_rep1 [D1]

city: San Diego

first: Minghui

last: Cao

state: California

address: 9500 Gilman Dr

department: Pathology

institute: UC San Diego

data_processing:
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by Trim Galore, then sequence reads were mapped to hg38 genome using Hisat2 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Normalized count were calculated using a protocol from Davide Risso et al., Nature biotechnology, 2014.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file include Normalized count values for each Sample.

source_name: MDA-MB-231 EV treatment_pancreatic islets

growth_protocol: High glucose DMEM supplemented with 10% FBS and 1% GlutaMAX

extract_protocol:
Total RNA was extracted with Trizon Reagen (CWBIO) and was subjected to DNase Ｉ(Thermo Scientific) for 30min
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (VAHTS mRNA-seq V2 Library Prep Kit for Illumina). The mRNA fragmentation and priming was performed using VAHTSFirst Strand Synthesis Reaction Buffer and VAHTS Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA（byAxyPrep Mag PCR Clean-up (Axygen)was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: Extracellular vesicles (EVs) were purified from culture medium from MDA-MB-231 and MCF-10A cells. And Evs or PBS were added into isolated human pancreatic islets cultured in 24 well plates. The treatment was done twice in 48 hours.

value: pancreatic islets

tag: disease state

value: non-diabetic

value: MDA-MB-231 EV


title: p411_Input


title: PT358 RNA-seq

description: RNA-Seq for primary patient samples treated with DMSO


title: Fibroblast_young_1wk_Saline

value: Saline

value: fibroblast


title: H1 Stem Cell Nuclear Fraction Replicate 1

description:
H1_ESC_nuclei_rep1
deseq2_normalized_counts.txt

value: Nucleus


title: H1 Stem Cell Total RNA Replicate 1

description:
H1_ESC_total_rep1
deseq2_normalized_counts.txt


title: P401_DMSO_1

value: Human primary leukopheresis sample


title: MCF-10A EV treatment_rep1 [B1]

source_name: MCF-10A EV treatment_pancreatic islets

value: MCF-10A EV


title: p195_1 RNA-seq


title: H1 Stem Cell Cytoplasm Fraction Replicate 2

description:
H1_ESC_cyto_rep2
deseq2_normalized_counts.txt

value: hESCs

value: Untreated

value: Cytoplasm


title: p411_H3K27ac

description: ChIP-seq for H3K27ac in primary patient samples

value: Human primary leukophereses sample


title: PT411 RNA-seq

value: DMSO


title: H1 Stem Cell Cytoplasm Fraction Replicate 1

description:
H1_ESC_cyto_rep1
deseq2_normalized_counts.txt


title: MDA-MB-231 EV treatment_rep2 [D2]


title: Fibroblast_young_1wk_PCL

value: PCL


title: CR464 Line Untreated Cytoplasm Fraction Replicate 2

description:
cyto_CR464_ut_rep2
deseq2_normalized_counts.txt

value: iPSC-derived motor neurons

value: CR464.2 hiPSC line


title: p408_Input


title: CD45e_young_1wk_Naive

source_name: CD45 enriched from quadriceps

value: Naive

value: muscle


title: CR464 Line Untreated Cytoplasm Fraction Replicate 1

description:
cyto_CR464_ut_rep1
deseq2_normalized_counts.txt


title: MCF-10A EV treatment_rep2 [B2]

value: pancreatic islets

value: non-diabetic


title: PBS treatment_rep2 [A2]

source_name: PBS treatment_pancreatic islets

value: PBS


title: CD45e_young_1wk_PCL


title: CR464 Line Recovery Cytoplasm Fraction Replicate 2

description:
cyto_CR464_rec_rep2
deseq2_normalized_counts.txt

value: Recovery


title: Fibroblast_young_1wk_ECM

value: ECM

value: fibroblast


title: CD45e_young_1wk_ECM


title: p401_H3K27ac

value: H3K27ac (8173S, Cell Signaling Technology)


title: H1 Stem Cell Insoluble Fraction Replicate 1

description:
H1_ESC_insol_rep1
deseq2_normalized_counts.txt

value: hESCs

value: H1 ESC line

value: Insoluble


title: CD45e_young_1wk_Saline

value: Saline


title: HD_2

city: Los Angeles

first: Matteo

last: Pellegrini

address: 405 Hilgard Avenue

institute: UCLA

description: RNA

data_processing:
Reads from FASTQ files were aligned against the GRCh38 human reference genome and quantified using the Cell Ranger pipeline version 3.0 (10x Genomics) with default parameters.
Data processing and analysis were performed using Seurat 4.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene expression matrices (mtx). The files barcodes.tsv and features.tsv are also included.

source_name: HD

extract_protocol:
Myeloid cells were sorted (CD11c+ MHCII+) from 3 COVID-19 patients and 2 healthy donors using a MACSQuant Tyto (Miltenyi).
10,000 cells per sample were loaded on a Chromium Next GEM Chip G (10x Genomics). A Chromium controller (10x Genomics, Pleasanton, CA, USA) was used to generate single-cell GEMs, according to Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1 protocol (PN-1000165; 10x Genomics). Full-length cDNA amplification and 5’ gene expression library construction were performed according to manufacturers’ instructions in a Veriti 96-well Thermal Cycler (Thermo Fisher Scientific).
scRNA-seq

value: CD11c+ MHCII+ cells

value: Healthy


title: p400_Input

value: Human primary leukophereses sample


title: p408_H3K27ac


title: p401_Input


title: PBS treatment_rep1 [A1]


title: HD_1

description: RNA


title: CD45e_old_1wk_Naive


title: CD45e_old_1wk_Saline


title: Covid19_3

description: RNA


title: Covid19_1

description: RNA


title: CR463 Line Untreated Cytoplasm Fraction Replicate 2

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description:
cyto_CR463_ut_rep2
deseq2_normalized_counts.txt

value: iPSC-derived motor neurons

value: CR463.4 hiPSC line

value: Untreated

value: Cytoplasm


title: IL17ra-/- 5

data_processing:
After demultiplexing, paired read alignment and counting was performed using STAR against the GENCODE release 23 annotations and genome.
Genome_build: GENCODE release 23
Supplementary_files_format_and_content: counts

source_name: Quadriceps

extract_protocol:
Muscles from Il17ra-/- or wild type mice treated with VML and PCL were collected 6 week after surgery, submerged in Trizol reagent, and minced and grinded in Trizol. Qiagen RNeasy Mini Kits were used to purify RNA following TRIzol RNA extraction. Purified RNA was quantified using an Agilent 2100 Bioanalyzer RNA 6000 Nano Kit according to manufacturer’s protocol. All RNA samples had RNA integrity score (RIN score) greater than 8.0. Libraries were then prepared with the Illumina TruSeq RNA Library Prep Kit V2 and sequencing at a depth of 30M unique reads per sample using an Illumina NovaSeq S2.
TruSeq v2

value: muscle

value: 6 weeks

value: 1 week post surgery


title: CD45e_old_1wk_PCL

value: PCL


title: CD45e_old_1wk_ECM

value: ECM


title: CR463 Line Untreated Cytoplasm Fraction Replicate 1

description:
cyto_CR463_ut_rep1
deseq2_normalized_counts.txt


title: CR464 Line Puromycin Treatment Cytoplasm Fraction Replicate 2

description:
cyto_CR464_puro_rep2
deseq2_normalized_counts.txt

value: CR464.2 hiPSC line

value: Puromycin


title: CR464 Line Recovery Cytoplasm Fraction Replicate 1

description:
cyto_CR464_rec_rep1
deseq2_normalized_counts.txt

value: Recovery


title: p358_H3K27ac

value: H3K27ac (8173S, Cell Signaling Technology)


title: CR464 Line Puromycin Treatment Cytoplasm Fraction Replicate 1

description:
cyto_CR464_puro_rep1
deseq2_normalized_counts.txt


title: p217_H3K27ac


title: IL17ra-/- 4

value: Saline


title: Covid19_2

description: RNA

value: CD11c+ MHCII+ cells


title: CR463 Line Recovery Cytoplasm Fraction Replicate 1

description:
cyto_CR463_rec_rep1
deseq2_normalized_counts.txt


title: CR463 Line Recovery Cytoplasm Fraction Replicate 2

description:
cyto_CR463_rec_rep2
deseq2_normalized_counts.txt


title: p217_Input

description: Whole cell extract input control from H3K27ac primary patient samples


title: COVID-19 Positive samples rep 34

city: Hyderabad

first: Nitesh

middle: Kumar

last: Singh

state: Telangana

address: Habsiguda

department: Bioinformatics

country: India

institute: Center for Cellular and Molecular Biology

data_processing:
illumina universal adapters and low quality reads were removed using cutadapt 2.8. We removed reads with quality scores less than 20 and discarded reads smaller than 36 bp.
The processed reads were then mapped to the human genome GRCh38 using STAR 2.7.3a with default parameters 88. The STAR index was generated using the GRCh38 genome and annotation gtf file downloaded from ENSEMBL 89. BAM files generated were then sorted according to position using Samtools 1.10 90.
Uniquely aligned reads were counted using HTSeq 93. Genes with read count 0 across all the samples were removed from further analysis.
Differential gene expression analysis was performed using DESeq2_1.24.0 94. Genes with adjusted p-value < 0.05 and absolute log2 Fold change > 1 were considered significantly differentially expressed.
Genome_build: GrCh38
Supplementary_files_format_and_content: count Data from BAM using htseqcount in text file

source_name: COVID-19 positive samples

extract_protocol:
Total RNA was extracted from 1ml of VTM using TRIzol reagent (Thermo Fisher Scientific, USA) or TRIzol in combination with Direct-zol RNA Microprep Kits (Zymo, USA) according to the manufacturerâ€™s protocol. RNA was quantified using Qubit RNA HS Assay Kit (Thermo Fisher Scientific, USA) and 1 Âµg total RNA was used for library preparation. Ribosomal RNA was removed using the RiboCop rRNA Depletion Kit (Lexogen, Austria).
RNA-Seq libraries were made using the CORALL Total RNA-Seq Library Prep Kit (Lexogen, Austria) according to the manufacturerâ€™s protocol. Briefly, rRNA depleted RNA was reverse transcribed using displacement stop primers which contain partial Illumina-compatible P7 sequences. Linkers containing partial Illumina-compatible P5 sequences and Unique Molecular Identifiers were ligated to the 3â€™ end of cDNA fragments. The library was PCR amplified to add the remaining adapter sequences and 12 nucleotide unique indices for multiplexing. Samples were sequenced at PE150 using the Illumina NovaSeq 6000.

tag: subject status

value: COVID-19 Positive

tag: sample type

value: nasopharyngeal or oropharyngeal swabs

tag: molecule subtype

value: ribodepleted RNA


title: IL17ra-/- 2


title: IL17ra-/- 3


title: p400_H3K27ac

tag: cell type

value: Human primary leukophereses sample


title: p195_Input


title: p358_Input


title: COVID-19 Positive samples rep 35


title: IL17ra-/- 1


title: COVID-19 Positive samples rep 36


title: CR463 Line Puromycin Treatment Cytoplasm Fraction Replicate 2

description:
cyto_CR463_puro_rep2
deseq2_normalized_counts.txt

value: iPSC-derived motor neurons

tag: cell line

value: CR463.4 hiPSC line


title: p456_H3K27ac


title: p195_H3K27ac


title: COVID-19 Positive samples rep 31


title: COVID-19 Positive samples rep 32


title: COVID-19 Positive samples rep 33


title: CR463 Line Puromycin Treatment Cytoplasm Fraction Replicate 1

description:
cyto_CR463_puro_rep1
deseq2_normalized_counts.txt

tag: treatment

value: Cytoplasm


title: CVB Stem Cell Total RNA Replicate 1

description:
CVB_iPSC_total_rep1
deseq2_normalized_counts.txt

source_name: stem cells

value: hiPSCs

value: CV-B hiPSC line

value: Untreated

tag: fraction

value: Total


title: COVID-19 Positive samples rep 30


title: CVB Stem Cell Total RNA Replicate 2

description:
CVB_iPSC_total_rep2
deseq2_normalized_counts.txt


title: WT3

value: wild type

value: muscle

tag: material

value: 6 weeks

value: 1 week post surgery


title: NB4_Input

description: Whole cell extract input control from H3K27ac in NB4 cell line

source_name: NB4 cell line


title: CVB Stem Cell Nuclear Fraction Replicate 2

description:
CVB_iPSC_nuclei_rep2
deseq2_normalized_counts.txt

value: Nucleus


title: CVWTA2

city: Fukuoka-city

first: Shingo

last: Takai

state: Fukuoka

address: 3-1-1, Maidashi, Higashi-ku,

department: Graduate School of Dental Science

institute: Kyushu University

description: cDNA read data

data_processing:
For mouse data, after adapter removal by using Cutadapt-2.10, gene-expression libraries were aligned to the mm10 reference transcriptome by using Bowtie2-2.3.4.1, and count matrices were generated using home-built shell scripts and the modified python script of BD Rhapsody workflow. Valid cell barcodes were identified as cell barcodes above inflection threshold of knee-plot of total read counts of each cell barcode identified by DropletUtils package (Griffiths JA et al. Nat. Commun. 2018). Each sample origin and doublets were identified based on fold-change of the normalized read counts of Hashtag antibodies. Data were log-transformed [log(TPM + 1)] for all downstream analyses, most of which were performed using the R software package Seurat v2.3.4 (http://satijalab.org/seurat) to analyze immune cell populations.
For each cell, three quality control metrics were calculated: (1) the total detected number of genes; (2) the proportion of ribosome encoded transcripts; and (3) the proportion of mitochondrially encoded transcripts. Cells were excluded from downstream analysis if fewer than 500 genes were detected. Each gene expression measurement was normalized by total expression within the corresponding cell and multiplied by a scaling factor of 1,000,000. Highly-variable genes identified by Seurat package were used for principal components analysis. Principal components were determined to be significant (P < 0.05) using the jackstraw method and FIt-SNE (https://www.nature.com/articles/s41592-018-0308-4) was performed on these key principal components. Unsupervised clustering was performed using a shared nearest neighbor modularity optimization-based algorithm
Genome_build: mm10
Supplementary_files_format_and_content: .txt

source_name: Taste buds from circumvallatae papillae of α-gustducin-GFP mice

extract_protocol:
The tongues dissected from α-gustducin-GFP mice were parted into anterior and posterior. Both anterior and posterior parts were injected with 0.3 mL and 0.1 mL of dispase II  (0.1 U/mL, Sigma-Aldrich) and incubated for 10 min. at 37 ℃, then epithelia surrounding papillae were peeled and incubated in the enzyme mixture containing elastase (0.28 U/mL, Elastin Product) and TrypLE (Sigma-Aldrich) for 15 min. at 37 ℃. The cells were mechanically separated into single cells by glass pipettes (diameter: 100 μm) after filtration using 70 μm cell strainer (Corning). To collect the GFP-positive cells from cell suspensions after cell isolation, FACS was performed using BD FACSAria™ III (BD). Cells were sorted according to cell size (FSC), cell granularity (SSC), 7-AAD (Thermo Fisher Scientific) signals (excitation, 488 nm; emission, 695 nm) for dead cells, FSC pulse-width and SSC pulse-width for singlets, GFP signals (excitation, 488 nm; emission, 530 nm) for GFP-positive cells.
For scRNA-seq, cDNA libraries and hashtag libraries were prepared and combined by an BD Rhapsody system and an optimized process similar to our magnetic bead-based bulk RNA-seq method (Shichino et al. JCI insight 2019). Sequencing libraries were generated by using NEBNext UltraII FS library prep kit (New England Biolabs), and QC of cDNA/Hashtag libraries was performed by MultiNA (Shimazu) and qPCR library quantification assay (KAPA).
BD Rhapsody WTA

value: CV

tag: developmental stage

value: adult


title: CVB Stem Cell Insoluble Fraction Replicate 2

description:
CVB_iPSC_insol_rep2
deseq2_normalized_counts.txt

value: Insoluble


title: COVID-19 Positive samples rep 28

value: COVID-19 Positive

value: nasopharyngeal or oropharyngeal swabs

value: ribodepleted RNA


title: COVID-19 Positive samples rep 27


title: WT4

tag: tissue

value: Saline

tag: time of harvest


title: FPWTA1

description: cDNA read data

source_name: Taste buds from fungiform papillae of α-gustducin-GFP mice

value: FP


title: WT2

tag: genotype


title: COVID-19 Positive samples rep 29


title: COVID-19 Positive samples rep 26


title: NB4_H3K27ac

description: ChIP-Seq for H3K27ac in NB4 cell line

value: H3K27ac (8173S, Cell Signaling Technology)


title: CVB Stem Cell Insoluble Fraction Replicate 1

description:
CVB_iPSC_insol_rep1
deseq2_normalized_counts.txt

value: hiPSCs

value: CV-B hiPSC line


title: WT1

tag: strain


title: MCD2

city: HangZhou

first: jingyang

last: qian

address: No. 886, Yuhangtang Road

institute: Zhejiang University

data_processing:
The raw sequencing data from 10X Genomics were aligned and quantified using the CellRanger (10X Genomics) suite (version 3.0.2). The mouse genome mm10 was used as the reference genome and the CellRanger count module was used to map reads.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx files. Matrix table with raw gene counts for every gene and every cell.

source_name: Liver, MCD

extract_protocol:
Liver NPCs were isolated from mice according to a two-step collagenase method. In detail, murine livers were perfused in situ via the inferior vana cava with calcium-free Hank’s Balanced Salt Solution (HBSS, Gibco, Cat#14170112) containing 0.2 mg/mL EDTA (Sigma, Cat#E6758), followed by 0.4 mg/mL pronase (Sigma, Cat#P5147-1G) and 0.2% collagenase type II (Worthington, Cat#LS004176) at a perfusion rate of 8 mL/minute. Then livers were surgically removed and cut into small pieces. Tissues were transferred in HBSS containing 0.2% collagenase type II, 0.4 mg/mL pronase and 0.1 mg/mL DNase I (Roche, Cat#10104159001), and then incubated for digestion at 37℃ in a water bath for 20 minutes. DMEM (Mediatech, Cat#10-013-CV) containing 10% serum (FBS, Gibco, Cat#10099-141C) was added at the end of the incubation. Sequentially, hepatocytes removal was achieved by centrifugation for 3 minutes at 50 g. Then cell suspension was filtered using a 40 μm nylon cell strainer (Falcon, Cat#352340). Erythrocytes were lysed by treatment with 3-5 mL ACK lysing buffer (Gibco, Cat#A1049201) for 5 minutes after which PBS (Beyotime Biotec, Cat#C0221A) was added to terminate the lysis. The resulting suspension was subjected to Dead Cell Removal Kit (Miltenyi Biotec, Cat#130090101) to remove dead cells according to the manufacturer’s recommendations. The obtained cell pellet was washed twice and suspended in PBS. Cell viability was assessed by Trypan Blue (Gibco, Cat#15250-061).
Liver NPCs single cell suspensions were loaded onto the 10x Genomics Chromium chip (10x Genomics; Pleasanton, CA, USA) to generate droplets. Then the obtained Gel Beads-in-emulsion (GEMs) were transferred into a PCR tube strip, followed by reverse transcription using ProFlex PCR System (Thermo Fisher, MA, USA). The resulting cDNA was purified and amplified for 12 cycles before cleanup with SPRIselect beads (Beckman, Cat#B23318). Based on the cDNA concentration determined by Qubit (Thermo Fisher, MA, USA), libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (10x Genomics; Pleasanton, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Model of alcoholic liver disease was constructed by two weeks of chronic ethanol feeding plus a single binge ethanol feeding. Model of non-alcoholic steatohepatitis was built by a long-term feeding of methionine/choline deficient diet (MCD) containing 45 kcal% fat. Model of liver ischemia-reperfusion injury was established by the surgery that 70% warm hepatic ischemia for 45 min and reperfusion for 24 h. Model of drug-induced liver injury was constructed by once intraperitoneal injection of 300 mg/kg acetaminophen for 24 h. Model of cholestatic liver injury was established by bile duct ligation for 10 days. Subsequently, unbiased scRNA-seq analysis and validation experiments were performed.

tag: disease model

value: Nonalcoholic steatohepatitis

value: Liver non-parenchymal cells (NPCs)


title: MCD3


title: COVID-19 Positive samples rep 24


title: COVID-19 Positive samples rep 23


title: IR3

source_name: Liver, IR

value: Liver ischemia-reperfusion injury


title: CVB Stem Cell Nuclear Fraction Replicate 1

description:
CVB_iPSC_nuclei_rep1
deseq2_normalized_counts.txt

value: Untreated


title: s_22rv1_ev_nc1_rep2

city: Rochester

first: Ting

last: Wei

address: 507 3rd St SW

institute: Mayo Clinic

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Clinic sequence core using the pipeline Cassava 1.7.
Low quality bases and adapter sequences were trimmed using Trim_Galore.
Alignment to reference genome (hg19/GRCh37) was performed using BSMAP built in the SAAP_BS workflow (v1.1).
"Methy read count" and "Total read count" were calculated by SAAP_BS workflow (v1.1).
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: The processed file is tab-separated plain text file containing 17 columns: IGV_Link, Chromosome ID, Chromosome position, Strand, Number of methylated reads, Number of total reads, Ratio, dbSNP135, dbSNP135Alleles, Gene, Transcript, Strand, InExon, TssDistance, InCpGIsland, Entrez_id, Gene_title.

source_name: Prostate

extract_protocol:
Genomic DNA were extracted using standard DNA extraction method.
Libraries were generated as previously described (Boyle, P., et al. 2012; Gu, H., et al. 2011). Briefly, genomic DNA was digested with MspI and purified with a QIAquick PCR purification kit (QIAGEN, Hilden, Germany) was used for library preparation, which was done using a TruSeq Nano DNA Library Prep Kit (Illumina, San Diego, USA).

treatment_protocol: 22Rv1 cells were infected with lentivirus expressing empty vector or SPOP F133V construct and cultured for 1 week to stably express SPOP F133V protein.

value: prostate cancer cell line

tag: passage

tag: genotype/variation

value: SPOP WT


title: COVID-19 Positive samples rep 22


title: MCD1


title: s_22rv1_133_nc1

value: SPOP F133V


title: Kasumi_H3K27ac_3

description: ChIP-Seq for H3K27ac in Kasumi cell line

source_name: Kasumi cell line

tag: input

tag: chip antibody

value: Kasumi


title: Kasumi_Input_2

description: Whole cell extract input control from H3K27ac in Kasumi cell line


title: Kasumi_H3K27ac_2


title: Kasumi_Input_1


title: IR2


title: Kasumi_Input_3


title: s_22rv1_133_nc2


title: Kasumi_H3K27ac_1


title: MV411_Input

description: Whole cell extract input control from H3K27ac in MV411cell line

source_name: MV411 cell line


title: CVB Stem Cell Cytoplasm Fraction Replicate 1

description:
CVB_iPSC_cyto_rep1
deseq2_normalized_counts.txt

value: Cytoplasm


title: COVID-19 Positive samples rep 25

tag: subject status

value: COVID-19 Positive

tag: sample type


title: BM106029_Input

description: Whole cell extract input control from H3K27ac in primary patient samples

source_name: Human primary ficolled whole bone marrow sample

tag: cell type


title: MV411_H3K27ac

description: ChIP-Seq for H3K27ac in MV411 cell line


title: IR1


title: s_22rv1_ev_nc1_rep1

tag: cell line


title: COVID-19 Positive samples rep 21

value: nasopharyngeal or oropharyngeal swabs

tag: molecule subtype


title: MCF7 sgMGAT4EP R3

first: Yiwen

last: Chen

address: 1400 Pressler Street,  Unit 1410

department: Bioinformatics & Comp Biology

institute: UT MD Anderson Cancer Center

data_processing:
Library strategy: PCR amplicon sequencing
For the RNASeq data: Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome and GENCODEV25 transcriptome using STAR-2.6.1b with parameters "--outSAMunmapped Within --outFilterType BySJout --twopassMode Basic --outSAMtype BAM SortedByCoordinate". Counting reads in features with htseq-count (htseq/0.11.0) with parameters "--stranded reverse --additional-attr gene_name gene_type" (human annotation file: hg38/gencode.v25.primary_assembly.annotation.gff3). The normalization of raw read count and differential expression were done by DESeq2/1.22.2 in R/3.5.1.
For the CRISPRi data: sequencing reads were mapped to the sgRNA library using bowtie/1.2.2 with parameters "bowtie --best --strata -a --norc -m 1  -5 20 -3 30 -S -p 12 sgRNAlibrary prefix.fastq 2>prefix.log|samtools view -Sb -F 4 - |samtools sort -@ 5 -o prefix.bam". The sgRNA read count was obtained using "samtools idxstats". The depleted or enriched genes were called using MAGECK/v 0.5.7 using parameters "mageck test -k PseudoMCF7_readcounts.tsv -t MCF7PSED21R1,MCF7PSED21R2,MCF7PSED21R3 -c MCF7PSED0R1,MCF7PSED0R2,MCF7PS  ED0R3 --norm-method control --gene-lfc-method secondbest -n MCF7D21VD0 --control-sgrna PseudoMCF7_negctrl.lst --norm  counts-to-file --additional-rra-parameters \"--permutation 10000\" 2>MCF7D21VD0.log"
Genome_build: human hg38 genome
Supplementary_files_format_and_content: RNASeq: read count and differential expression result in Excel file; CRISPRi: read count in text files and MAGECK call result in Excel files.

growth_protocol: MCF7-dCas9, MDA-MB-231-dCas9 cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Hyclone #SH30022.01), supplemented with 10% Fetal Bovine Serum, and 1% penicillin/streptomycin. The authenticated MCF7 and MDA-MB-231 cells were cultured in RPMI-1640 (Hyclone #SH30027.1) supplemented with 10% FBS (Gibco #10437-028) and 1% penicillin/streptomycin (Corning # 30-002-CI). All cell lines were cultured in an incubator (Thermo, HEARCELL VIOS 160i) with 5% CO2 at 37 °C.

extract_protocol:
Total genomic DNA was extracted from MCF7 and MDA-MB-231 cells using QIAamp DNA Mini Kit.Total RNA was extracted from MCF7 cells using the RNeasy Mini kit.
Two rounds of PCR were employed to prepare the next-generation-sequencing (NGS)-ready sgRNA libraries with the KAPA HiFi HotStart ReadyMix (Roche # KK2602). The first-round PCR was conduced for 16 cycles, using 40 g of input genomic DNA from each replicate at D0 or D21 as a template. The PCR product of different samples was pooled and 20 l of the mixed product was used as a template for the second-round PCR, which was conducted for 12 cycles to incorporate Illumina barcode sequences. The final PCR product was purified from 2% agarose gel with QIAquick Gel Extraction Kit. Concentration of different libraries was measured using the Qubit dsDNA HS (High Sensitivity) Assay Kit (Thermo # Q32851) on a Qubit Fluorometer (Thermo fisher). Two ug of RNA was used for RNA-seq library construction with TruSeq Stranded mRNA Library Prep kit (Illumina # 20020594).

treatment_protocol: MCF7-dCas9 and MDA-MB-231-dCas9 cell lines were infected with lenti virus containing the sgRNA library

value: MGAT4EP knockdown


title: BM106029_H3K27ac

description: ChIP-seq for H3K27ac in primary patient samples

value: Human primary ficolled whole bone marrow


title: BDL3

source_name: Liver, BDL

value: Cholestatic liver injury


title: COVID-19 Positive samples rep 18

value: ribodepleted RNA


title: COVID-19 Positive samples rep 19


title: COVID-19 Positive samples rep 16