title: 74_B1_BTS_0

description: brain.exon.csv


title: K562 4h Input replicate 2

status: Public on Dec 12 2020

type: SRA

city: Ithaca

first: Charles

middle: G

last: Danko

address: Hungerford Hill Rd

country: USA

institute: Baker Institute

description:
i7 index: CCTTCCAT
i5 index: ATTGCGTG

library_source: genomic

data_processing:
Data from each experiment was aligned to genome assemblies as following:
i.) MNase ChIP-seq reads were aligned to hg19 merged to D.iulia assembly (Lewis et al., 2019). All positions with sequence similarity between the two genomes were masked using bedtools maskfasta;
ii.) ChRO-seq data was aligned to hg19 merged to the D.melanogaster dm3 genome assembly. All positions with sequence similarity between the two genomes were masked using bedtools maskfasta;
iii.) CUT&RUN was aligned to hg19 merged to S.cerevisiae SacCer1;
iv.) ATAC-seq was only aligned to hg19.
Masking hg19 was performed with BedTools maskfasta (Quinlan and Hall, 2010). All sequencing data was aligned using bowtie2 version 2.3.5.1 (Langmead and Salzberg, 2012) with parameters: --no-discordant --no-dovetail --no-unal --no-mixed. Reads mapping multiple times were removed with samtools view (Li et al., 2009), parameter: -F 256. The remaining reads were converted to paired-end BigWig files using BedTools and visualized in the WashU genome browser version 46.2 (Li et al., 2019; Zhou et al., 2011).
Supplementary_files_format_and_content: We only provide BigWig files for untreated samples due to normalization, which was performed from BAM files to preserve the identity of each read pair. In our experiments, both the human and spike-in samples were mixed and treated with MNase together, before the antibody incubation. To correct IP signals for biases in MNase cutting efficiency, handling, and other errors, we used the spike adjusted procedure (SAP) method (Bonhoure et al., 2014). We assume that ChIP-seq data reflects a linear combination of three factors: signal from the mark of interest, background which may be partially correlated with the mark, and random noise. SAP assumes that the background signals should be the same in treated and untreated samples and enforces this assumption by subtracting the expected background read count observed in the input.

molecule: genomic DNA

organism: Homo sapiens

source_name: Human K562 cells

growth_protocol: K562 cells (ATCC, CCL-243) were cultured at 37oC, 5% CO2  at a density between 0.3-1 x 106cells/mL in RPMI medium (VWR 45000-396) topped up with 10% Fetal Bovine Serum (Genesee Scientific, cat: #25-514).  Cells were split at a consistent interval of 3 days, when the cells reach 106 cells/mL.

extract_protocol: Library prep was performed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S). The barcodes used were purchased from NEB:NEBNext Multiplex Oligos for Illumina (E6440S).

treatment_protocol: 24h prior to Triptolide treatment, K562 cells were resuspended in fresh (RPMI) medium at a density of 0.6 x 106 cells/mL. On the day of the experiment, cells were recounted, aliquoted in equal cell numbers to 6 T-100 ThermoFisher Tissue Culture Flasks (each flask corresponding to one time point) and treated with Triptolide (Sigma-Aldrich, T3652-1MG) to a final concentration of 500 nM Triptolide. The Triptolide treatment was performed for 0 min, 15 min, 30 min, 1h, and respectively 4h.

tag: cell line

tag: treatment

value: Triptolide treated

tag: time point

tag: replicate


title: 72_B1_F1_0

city: Los Angeles

first: Robert

middle: D.

last: Cooper

state: CA

address: 612 Charles E. Young Drive East

institute: UCLA

description: brain.exon.csv

library_source: transcriptomic

data_processing:
Raw sequences were trimmed for adapter sequence and low quality bases using Trimmomatic
Quality and repetitive regions were assessed across all samples using FASTQC
Reads were mapped to the recently published Mexican Axolotl (Ambystoma mexicanum) genome using STAR
Mapped reads were counted for differential expression analysis using HTSeq-count with exons as the target feature
Genome_build: Reads were mapped to the recently published Mexican Axolotl (Ambystoma mexicanum) genome (Nowoshilow et al., 2018)

molecule: polyA RNA

organism: Ambystoma californiense

source_name: Whole Brain Tissue

extract_protocol:
Samples were extracted using a modified Purelink RNA Mini Kit- TRIzol spin column protocol
Libraries were prepared using Kapa mRNA Stranded Library Prep kits and standard protocols.
RNA-Seq: Libraries were pooled then split across six lanes of 100bp single-end reads on an Illumina HiSeq4000 at the QB3 Genomics Sequencing Laboratory in Berkeley, CA.

treatment_protocol: Individuals in the treatment group were exposed to acute thermal stress until they failed to right themselves for 30 seconds after being placed on their dorsum. (loss of righting response)

tag: tissue

value: Whole Brain Tissue

tag: Sex

value: Female

value: Control

tag: genotype


title: tms030

city: Moscow

first: Alexey

middle: Igorevich

last: Kalinkin

state: Russia

address: Moskvorechie st., 1

department: Epigenetics

country: Russia

institute: RCMG

data_processing:
Basecalls performed using Ion Torrent Suite 4.0
XmaI-RRBS reads were aligned to the hg19 genome assembly using Bismark v0.12.2 with bowtie2 v2.2.3 with settings --non_directional -L 24 --rdg 0,3 --rfg 0,3.
Data were filtered to remove artificial methylation using custom script
Methylation state called using bismark_methylation_extractor
Genome_build: hg19
Supplementary_files_format_and_content: .cov files were generated using bismark_methylation_extractor. Column headers are: Chromosome, Start position, End Position, Methylation percentage, Count of methylated cytosines and Count of unmethylated cytosines.

source_name: Breast

extract_protocol:
Phenol:chloroform protocol after proteinase K treatment
XmaI-RRBS protocol as in: Tanas AS, Borisova ME, Kuznetsova EB et al. Rapid and affordable genome-wide bisulfite DNA sequencing by XmaI-reduced representation bisulfite sequencing. Epigenomics. 9 (6), 833-847 (2017).

value: LumB Breast Cancer


title: tms029


title: K562 1h Input replicate 2

description:
i7 index: GTCAGTCA
i5 index: TAATGCCG


title: 71_B1_BTS_0

description: brain.exon.csv

value: BTS


title: K562 4h Input replicate 1

description:
i7 index: TCCACGTT
i5 index: GTTCAACC


title: K562 0h Input replicate 2

description:
i7 index: AACCAGAG
i5 index: AACCGAAG

value: untreated


title: K562 4h H3K36me3 replicate2 resequence

description:
i7 index: GGAGGAAT
i5 index: AACCGTTC


title: K562 1h Input replicate 1

description:
i7 index: GACGAACT
i5 index: TCGCATTG


title: tms023


title: K562 0h Input replicate 1

description:
i7 index: CCGCTTAA
i5 index: ACGATGAC


title: K562 0h H3K36me3 replicate2 resequence

description:
i7 index: GTCCTAAG
i5 index: TGGTAGCT


title: tms025


title: K562 1h H3K36me3 replicate1 resequence

description:
i7 index: TCATCTCC
i5 index: CTAGCAAG


title: 69_B1_BTS_0

description: brain.exon.csv

value: Male


title: K562 1h H3K36me3 replicate2 resequence

description:
i7 index: GAATCCGT
i5 index: TGGAGTTG


title: K562 0h H3K36me3 replicate1 resequence

description:
i7 index: AAGACCGT
i5 index: CAATCGAC


title: K562 4h H3K36me3 replicate1 resequence

description:
i7 index: TCGGATTC
i5 index: TAGTTGCG


title: tms031


title: 68_B1_BTS_0

description: brain.exon.csv


title: 67_B1_F1_1

description: brain.exon.csv

value: Treatment


title: tms017


title: 66_B1_CTS_0

description: brain.exon.csv

value: CTS


title: K562 0h H3K36me3 replicate2

description:
i7 index: GTCCTAAG
i5 index: TGGTAGCT


title: K562 4h H3K36me3 replicate2

description:
i7 index: GGAGGAAT
i5 index: AACCGTTC


title: K562 1h H3K36me3 replicate2

description:
i7 index: GAATCCGT
i5 index: TGGAGTTG


title: tms014


title: 63_B1_CTS_0

description: brain.exon.csv


title: tms013


title: 60_B1_BTS_0

description: brain.exon.csv


title: K562 1h H3K36me3 replicate1

description:
i7 index: TCATCTCC
i5 index: CTAGCAAG


title: K562 0h H3K36me3 replicate1

description:
i7 index: AAGACCGT
i5 index: CAATCGAC


title: K562 4h H3K4me3 replicate2 resequence

description:
i7 index: AGGATAGC
i5 index: AACCTTGG


title: tms021


title: tms010


title: K562 1h H3K4me3 replicate2 resequence

description:
i7 index: GTAACCGA
i5 index: GGTGTCTT


title: 57_B1_CTS_0

description: brain.exon.csv


title: K562 4h H3K36me3 replicate1

description:
i7 index: TCGGATTC
i5 index: TAGTTGCG


title: tms018


title: K562 4h H3K4me3 replicate1 resequence

description:
i7 index: GGAAGAGA
i5 index: TTCTCTCG


title: K562 0h H3K4me3 replicate2 resequence

description:
i7 index: CTCAGAAG
i5 index: AACTTGCC


title: 53_B1_BTS_1

description: brain.exon.csv


title: 64_B1_F1_0

description: brain.exon.csv


title: g021


title: g014


title: K562 1h H3K4me3 replicate1 resequence

description:
i7 index: AGCCTATC
i5 index: GTTACGCA


title: K562 0h H3K4me3 replicate2

description:
i7 index: CTCAGAAG
i5 index: AACTTGCC


title: K562 1h H3K4me3 replicate2

description:
i7 index: GTAACCGA
i5 index: GGTGTCTT


title: K562 4h H3K4me3 replicate1

description:
i7 index: GGAAGAGA
i5 index: TTCTCTCG


title: r005


title: 49_B1_F1_0

description: brain.exon.csv


title: K562 1h H3K4me3 replicate1

description:
i7 index: AGCCTATC
i5 index: GTTACGCA


title: K562 0h H3K4me3 replicate1

description:
i7 index: TACGGTCT
i5 index: GCAATGGA


title: K562 4h H3K4me1 replicate2 resequence

description:
i7 index: TCCTCATG
i5 index: AGGTGTAC


title: g015


title: K562 0h H3K4me1 replicate2 resequence

description:
i7 index: GCAATTCC
i5 index: TGTTCGAG


title: K562 1h H3K4me1 replicate2 resequence

description:
i7 index: GTCGTTAC
i5 index: GCTTAGCT


title: 38_B1_BTS_1

description: brain.exon.csv


title: K562 4h H3K4me1 replicate1 resequence

description:
i7 index: CGAATTGC
i5 index: CACCTTAC


title: triple negative breast carcinoma sample tn036

data_processing:
Basecalls performed using Ion Torrent Suite 4.0
XmaI-RRBS reads were aligned to the hg19 genome assembly using Bismark v0.12.2 with bowtie2 v2.2.3 with settings --non_directional -L 24 --rdg 0,3 --rfg 0,3.
Data were filtered to remove artificial methylation using custom script
Methylation state called using bismark_methylation_extractor
Genome_build: hg19
Supplementary_files_format_and_content: .cov files were generated using bismark_methylation_extractor

value: Triple Negative Breast Cancer


title: K562 0h H3K4me1 replicate1 resequence

description:
i7 index: TTCCAGGT
i5 index: AAGCACTG


title: K562 1h H3K4me1 replicate1 resequence

description:
i7 index: AGTGACCT
i5 index: CTCCTAGA


title: 30_B1_F1_1

description: brain.exon.csv

value: BTSbc


title: triple negative breast carcinoma sample tn035


title: K562 4h H3K4me3 replicate2

description:
i7 index: AGGATAGC
i5 index: AACCTTGG


title: 52_B1_F1_0

description: brain.exon.csv


title: 26_B1_BTS_0

description: brain.exon.csv


title: triple negative breast carcinoma sample tn034


title: K562 1h H3K4me1 replicate2

description:
i7 index: GTCGTTAC
i5 index: GCTTAGCT


title: g157


title: K562 0h H3K4me1 replicate2

description:
i7 index: GCAATTCC
i5 index: TGTTCGAG


title: triple negative breast carcinoma sample tn014


title: K562 0h H3K4me1 replicate1

description:
i7 index: TTCCAGGT
i5 index: AAGCACTG


title: 25_B1_F1_0

description: brain.exon.csv


title: 44_B1_F1_1

description: brain.exon.csv


title: K562 4h H3K4me1 replicate1

description:
i7 index: CGAATTGC
i5 index: CACCTTAC


title: K562 1h H3K4me1 replicate1

description:
i7 index: AGTGACCT
i5 index: CTCCTAGA


title: triple negative breast carcinoma sample mrnc006


title: 45_B1_F1_0

description: brain.exon.csv


title: g150


title: K562 4h H3K27me3 replicate2 resequence

description:
i7 index: ATCTGACC
i5 index: AAGTCGAG


title: triple negative breast carcinoma sample mrnc003


title: 20_B1_BTS_1

description: brain.exon.csv


title: K562 0h H3K27me3 replicate2 resequence

description:
i7 index: TCTACGCA
i5 index: GGCTATTG


title: K562 4h H3K4me1 replicate2

description:
i7 index: TCCTCATG
i5 index: AGGTGTAC


title: K562 4h H3K27me3 replicate1 resequence

description:
i7 index: GAACGAAG
i5 index: GGTGATTC


title: K562 1h H3K27me3 replicate1 resequence

description:
i7 index: TACTCCAG
i5 index: CCTATACC


title: triple negative breast carcinoma sample tn033


title: K562 1h H3K27me3 replicate2 resequence

description:
i7 index: AGACCTTG
i5 index: GCACGTAA


title: triple negative breast carcinoma sample tn032


title: 17_B1_F1_1

description: brain.exon.csv


title: 19_B1_F1_0

description: brain.exon.csv


title: K562 1h H3K27me3 replicate2

description:
i7 index: AGACCTTG
i5 index: GCACGTAA


title: K562 0h H3K27me3 replicate2

description:
i7 index: TCTACGCA
i5 index: GGCTATTG


title: 24_B1_F1_0

description: brain.exon.csv


title: triple negative breast carcinoma sample tn031


title: 16_B1_F1_1

description: brain.exon.csv


title: K562 4h H3K27me3 replicate1

description:
i7 index: GAACGAAG
i5 index: GGTGATTC


title: triple negative breast carcinoma sample tn030


title: 14_B1_CTS_1

description: brain.exon.csv


title: K562 4h H3K27ac replicate2 resequence

description:
i7 index: CTTAGGAC
i5 index: CAGTGAAG


title: K562 0h H3K27me3 replicate1

description:
i7 index: TCGTCTGA
i5 index: TCAAGGAC


title: triple negative breast carcinoma sample tn029


title: 22_B1_F1_1

description: brain.exon.csv


title: K562 1h H3K27ac replicate2 resequence

description:
i7 index: CAAGGTAC
i5 index: GAGATACG


title: 13_B1_CTS_1

description: brain.exon.csv


title: K562 0h H3K27ac replicate2 resequence

description:
i7 index: GAGAGTAC
i5 index: TGCTTCCA


title: K562 4h H3K27ac replicate1 resequence

description:
i7 index: TTGCGAGA
i5 index: GTGCCATA


title: triple negative breast carcinoma sample tn028


title: 12_B1_BTS_1

description: brain.exon.csv


title: K562 4h H3K27me3 replicate2

description:
i7 index: ATCTGACC
i5 index: AAGTCGAG


title: K562 1h H3K27ac replicate1 resequence

description:
i7 index: TAGGAGCT
i5 index: GTTAAGGC


title: triple negative breast carcinoma sample tn027


title: K562 4h H3K27ac replicate2

description:
i7 index: CTTAGGAC
i5 index: CAGTGAAG


title: triple negative breast carcinoma sample tn026


title: K562 0h H3K27ac replicate2

description:
i7 index: GAGAGTAC
i5 index: TGCTTCCA


title: K562 1h H3K27ac replicate2

description:
i7 index: CAAGGTAC
i5 index: GAGATACG


title: K562 1h H3K27me3 replicate1

description:
i7 index: TACTCCAG
i5 index: CCTATACC


title: K562 4h H3K27ac replicate1

description:
i7 index: TTGCGAGA
i5 index: GTGCCATA


title: K562 1h H3K27ac replicate1

description:
i7 index: TAGGAGCT
i5 index: GTTAAGGC


title: 08_B1_F1_0

description: brain.exon.csv


title: triple negative breast carcinoma sample tn025


title: 07_B1_CTS_1

description: brain.exon.csv


title: K562 0h H3K27ac replicate1

description:
i7 index: TTACCGAC
i5 index: CGTATTCG


title: triple negative breast carcinoma sample tn023


title: 05_B1_F1_0

description: brain.exon.csv


title: 06_B1_F1_1

description: brain.exon.csv


title: triple negative breast carcinoma sample tn021


title: 11_B1_F1_1

description: brain.exon.csv


title: 4990_liver_ChRO-seq

description: barcode: ACTTGA

data_processing:
Library strategy: ChRO-seq
Sequencing data was mapped to EquCab2.0 genome build
Genome_build: EquCab2.0

molecule: total RNA

organism: Equus caballus

source_name: horse liver tissue

extract_protocol: The samples were not cultured. After harvesting (Burns et al., 2018) they were snap frozen in liquid N2, then processed for ChRO-seq (Chu et al., 2018a).

tag: mare identity

value: Chatty Patty (ECA_UCD_AH2 )

tag: breed

value: Quarter Horse

tag: gender

value: female

value: liver

tag: assay

value: ChRO-seq


title: triple negative breast carcinoma sample tn020


title: 4989_liver_ChRO-seq

description: barcode: CAGATC

value: Wild Guneva Star (ECA_UCD_AH1 )


title: 09_B1_F1_0

description: brain.exon.csv

value: Whole Brain Tissue


title: 03_B1_F1_0

description: brain.exon.csv

value: Female


title: triple negative breast carcinoma sample tn024


title: triple negative breast carcinoma sample tn019


title: 02_B1_F1_1

description: brain.exon.csv


title: triple negative breast carcinoma sample tn017


title: PT

city: Shanghai

first: Boshi

last: Wang

address: No.800 Dongchuan Road

country: China

institute: Shanghai Cancer Institute

description: cultured with TGF-β (5ng/ml) for 24 hours

data_processing:
Base-calling was performed by Illumina Casava1.8.
Clean data was generated by trimming the adaptor and filtering rRNAs using Seqtk (https://github.com/lh3/seqtk)
Clean reads were mapped to human reference genome (hg38) with Hisat2(version:2.0.4) to generate the BAM files for each sample.
The uniquely mapped fragments of genes were counted by Stringtie(version:1.3).
Gene expression was evaluated by normalized Fragments Per Kilobase of exon model per Million mapped reads (FPKM) using TMM(trimmed mean of M values) normalization method (Genome Biol 2010, 11(3):R25).
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include FPKM and count values for each gene in each sample.

source_name: HCC cell line

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, USA)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, USA).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using VAHTS mRNA-seq v2 Library Prep Kit for Illumina (Cat# NR601-02, Vazyme).

value: POH1 overexpressing cells

value: cultured with TGF-beta (5ng/ml) for 24 hours


title: PC

description: cultured without TGF-β (control)

value: cultured without TGF-beta (control)


title: triple negative breast carcinoma sample tn016


title: VT

value: Vector control


title: D7-T3

city: Qingdao

first: liqiang

last: yang

address: No.189 Songling Road, Laoshan District, Qingdao

institute: Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences

data_processing:
Sequencing was accomplished by a commercial service (Allwegene Inc., Beijing, China) using the Illumina HiSeq 4000 (Illumina Inc., San Diego, CA).
Prior to assembly, the quality of raw data was assessed with FastQC .
After trimmed and removed the adaptor and low quality reads, the raw reads were aligned to the P. tricornutum version 2.0 set 10 402 filtered gene models  using TopHat (version 2.0.8), and filtered to retrieve uniquely aligned reads with no more than two mismatches.
Genome_build: http://genome.jgi.doe.gov/Phatr2/Phatr2.info.html

organism: Phaeodactylum tricornutum

source_name: D7-T, P. tricornutum Pt-1 inoculated in atrazine-contaminated culture medium for 7 days.

extract_protocol:
Total RNA was extracted from P. tricornutum Pt-1 cell pellets using the Trizol method according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain


title: D7-T2


title: 04_B1_CTS_1

description: brain.exon.csv


title: muscle_48hr_rep3

type: RNA

city: kyoto

first: Yusuke

last: Morita

state: kyoto

address: kyoto

country: Japan

institute: kyoto university

description: Gene expression after 48hr fasting in muscle

hyb_protocol: Samples were then hybridyzed to the SurePrint G3 Mouse GE 8 x 60k Microarray

scan_protocol: The arrays were scanned using Agilent Microarray Scanner

data_processing: Bioinformatic analyses were carried out with packages from Bioconductor in the statistical software R (Version 3.4.0). We performed preprocessing of microarray data using limma package in a organ-fair manner. Background correction was performed with the “normexp” method. The resulting values were log2 transformed and normalized per array by “cyclic loess” method.

organism: Mus musculus

label_protocol: RNA was amplified into cRNA and labeled with Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technologies)

extract_protocol: Total RNA was extracted from the snap frozen organs with TRIzol reagent followed by using RNeasy Mini kit (QIAGEN). The RNA quality was assessed using Agilent 2100 bioanalyzer with RNA 6000 Nano LabChip kit. All samples displayed RNA integrity numer (RIN) >7.

tag: age

value: 6 week-old

tag: tisssue

value: muscle

tag: fasting time


title: muscle_48hr_rep2


title: muscle_48hr_rep1


title: D7-T1


title: muscle_24hr_rep5

description: Gene expression after 24hr fasting in muscle


title: VC

description: cultured without TGF-β (control)


title: muscle_24hr_rep3


title: muscle_24hr_rep4


title: muscle_48hr_rep4


title: muscle_24hr_rep1


title: muscle_24hr_rep2


title: triple negative breast carcinoma sample tn011


title: D7-C3

source_name: D7-C, P. tricornutum Pt-1 inoculated in uncontaminated culture medium for 7 days


title: D7-C2


title: triple negative breast carcinoma sample tn009


title: D7-C1


title: triple negative breast carcinoma sample tn012


title: triple negative breast carcinoma sample tn008


title: muscle_0hr_rep5

description: Gene expression after 0hr fasting in muscle


title: Dbt/iP3F - 24 hr Dox - ATAC-seq - rep1

city: Colum bus

first: Stephanie

middle: D

last: LaHaye

state: OH

address: 575 Children's Crossroads

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

description: paired-end, 150 bp

data_processing:
Initial ChIP-seq Alignment: bowtie2 was used to align reads separately to hg38 and mm10
ChIP-seq Normalization: For PAX3-FOXO1/FOXO1 ChIP and Input samples, sequencing depth was normalized by first using samtools to determine the number of reads aligning to mm10. A scaling factor (f) was determined for each sample by defining the minimum number of mouse reads across all samples (m), and dividing this by the number of mouse reads in a given sample (s), f=m/s. Scaling factors for each sample were used to normalize hg38 aligned BAM files through subsampling with samtools. Picard SamToFastq converted the resulting SAM files to normalized paired-end fastq files.
All ChIP data were subsequently processed with ENCODE ChIP-seq pipeline with chip.xcor_exclusion_range_max set at 30
ENCODE ChIP-seq alignment: normalized paired-end  fastqs were aligned with bowtie2 aligner (version 2.3.4.3) to human genome UCSC hg38, with parameters bowtie2 -X2000 --mm
ENCODE ChIP-seq read filtering: black listed region, unmapped, mate unmapped, not primary alignment, multi-mapped, low mapping quality (MAPQ<30), duplicate reads and PCR duplicate were removed
ENCODE ChIP-seq peak calling: Peaks were called with MACS2 (version 2.2.4), with parameters -p 1e-2 --nomodel --shift 0 --extsize ${FRAGLEN} --keep-dup all -B –SPMR. IDR analyses were performed on peaks from replicate samples, with threshold 0.05
All ATAC-seq data were processed with ENCODE ATAC-seq pipeline with default parameters
ENCODE ATAC-seq adapter trimming: reads are scanned for adaptor sequences and trimmed with cutadapt (version 2.3)
ENCODE ATAC-seq alignment: Reads are then mapped to human genome hg38 with bowtie2 (version 2.3.4.3)
ENCODE ATAC-seq read filtering: Only properly aligned paired reads and non-mitochondrial reads are retained for peak calling
ENCODE ATC-seq peak calling: Peaks are called with MACS2 (version 2.2.4)
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: peak text files, BED format
Supplementary_files_format_and_content: bigwig files, signals represent fold change over Input

growth_protocol: RH4, RH40, RD, SMS-CTR, and C2C12 were grown in DMEM supplemented with 10% FBS. Parental Dbt and Dbt/iP3F cells were grown in Ham’s/F-10 supplemented with 15% FBS, glutamine, sodium pyruvate, creatine monohydrate, and uridine.

extract_protocol:
For spike-in normalized ChIP-seq, human RMS and Dbt/iP3F cells and mouse C2C12 cells were fixed in 1% formaldehyde for 10 minutes before quenching with 125 mM glycine. Cells were combined in a ratio of 3 human:1 mouse cell equivalents for each experiment prior to sonication. Sonicated chromatin was immunoprecipitated with antibodies against FOXO1 (Cell Signaling #2880), H3K27ac (Active Motif #39133), H3K27me3 (Active Motif #39155), BRD9 (Abcam ab137245), or DPF2 (Abcam ab134942). Input and ChIP-enriched DNA was decrosslinked and purified using Qiagen MinElute PCR Purification columns prior to library preparation. For ATAC-seq, 5x104 cells per experiment were first washed with RSB buffer and gently permeabilized with RSB lysis buffer on ice. Cells were suspended in 50 uL of tagmentation master mix prepared from Illumina Tagment DNA TDE1 Enzyme and Buffer Kit components (#20034197), and transposition was performed for 30 minutes at 37°C. Tagmented DNA fragments were isolated using Qiagen MinElute PCR Purification columns prior to library preparation.
ChIP and Input DNA libraries were prepared by blunt end repair using the Lucigen End-It DNA End-Repair Kit, 3’ A-tailing by Klenow fragment (3’-5’ exo-) (NEB), adaptor ligation by T4 DNA ligase(NEB), and size selection on an E-Gel 2% EX agarose gel. Libraries were amplified with barcoded primers for 14 cycles and isolated from unreacted primers by gel purification. ATAC-seq libraries were amplified with barcoded Nextera primers for 14 cycles and excess primers were removed by size selection with AMPure XP beads. Libraries were sequenced on the HiSeq4000 platform running in PEx150bp mode.

treatment_protocol: Dbt/iP3F cells were treated with 500 ng/mL doxycycline (in water) for 0, 8, or 24 hours prior to collection.

tag: cell type

value: Immortalized myoblast

value: 500 ng/mL doxycycline, 24 hr

tag: antibody


title: Dbt/iP3F - 24 hr Dox - ATAC-seq - rep2

description: paired-end, 150 bp


title: Dbt/iP3F - 8 hr Dox - ATAC-seq - rep1

description: paired-end, 150 bp

value: 500 ng/mL doxycycline, 8 hr


title: Dbt/iP3F - 8 hr Dox - ATAC-seq - rep2

description: paired-end, 150 bp


title: muscle_0hr_rep2


title: triple negative breast carcinoma sample tn007

value: Triple Negative Breast Cancer


title: muscle_0hr_rep3


title: muscle_0hr_rep1


title: Dbt/iP3F - 0 hr Dox - ATAC-seq - rep2

description: paired-end, 150 bp


title: triple negative breast carcinoma sample tn010


title: D2-T2

source_name: D2-T, P. tricornutum Pt-1 inoculated in atrazine-contaminated culture medium for 2 days


title: triple negative breast carcinoma sample tn005


title: muscle_0hr_rep4


title: D2-T1


title: triple negative breast carcinoma sample tn003


title: Dbt/iP3F - 0 hr Dox - ATAC-seq - rep1

description: paired-end, 150 bp


title: D2-T3


title: D2-C3

source_name: D2-C, P. tricornutum Pt-1 inoculated in uncontaminated culture medium for 2 days


title: RH4 - ATAC-seq

description: paired-end, 150 bp

value: FP-RMS


title: triple negative breast carcinoma sample tn002


title: D2-C2


title: liver_48hr_rep5

description: Gene expression after 48hr fasting in liver


title: triple negative breast carcinoma sample tn001


title: liver_48hr_rep4


title: liver_48hr_rep3


title: triple negative breast carcinoma sample g101


title: D2-C1


title: RH4 - H3K27ac ChIP

description: paired-end, 150 bp

value: Active Motif #39133


title: liver_48hr_rep2

value: liver


title: D1-T3

source_name: D1-T, P. tricornutum Pt-1 inoculated in atrazine-contaminated culture medium for 12 hours


title: D1-T2


title: RH4 - BRD9 ChIP

description: paired-end, 150 bp

value: Abcam ab137245


title: RH4 - DPF2 ChIP

description: paired-end, 150 bp

value: Abcam ab134942


title: triple negative breast carcinoma sample g077


title: D1-T1


title: RH4 - H3K27me3 ChIP

description: paired-end, 150 bp

value: Active Motif #39155


title: triple negative breast carcinoma sample r043


title: D1-C3

source_name: D1-C, P. tricornutum Pt-1 inoculated in uncontaminated culture medium for 12 hours


title: triple negative breast carcinoma sample r042


title: triple negative breast carcinoma sample r022


title: D1-C2


title: Dbt/iP3F - 24 hr Dox - Input

description: paired-end, 150 bp


title: Dbt/iP3F - 8 hr Dox - PAX3-FOXO1 ChIP

description: paired-end, 150 bp

value: Cell Signaling #2880


title: liver_24hr_rep3

description: Gene expression after 24hr fasting in liver


title: triple negative breast carcinoma sample r003


title: muscle_48hr_rep5


title: Dbt/iP3F - 24 hr Dox - PAX3-FOXO1 ChIP

description: paired-end, 150 bp


title: D1-C1


title: liver_24hr_rep4


title: Dbt/iP3F - 8 hr Dox - Input

description: paired-end, 150 bp


title: liver_24hr_rep2


title: triple negative breast carcinoma sample ob006R


title: liver_24hr_rep5


title: Dbt/iP3F - 0 hr Dox - PAX3-FOXO1 ChIP

description: paired-end, 150 bp


title: liver_48hr_rep1


title: Sample 1

city: Jinan

first: Yaxiao

last: Liu

state: Shandong

address: Wenhuaxi Road 107

institute: Qilu hospital of Shandong University

description: One sample from murine urothelium.

data_processing:
The Cell Ranger software pipeline (version 3.0.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells. We processed the unique molecular identifier (UMI) count matrix using the Seurat R package (version 2.3.4, https://satijalab.org/seurat/). To remove low quality cells and likely multiplet captures, which is a major concern in microdroplet-based experiments, we apply a criterion to filter out cells with UMI/gene numbers out of the limit of mean value +/- 2 fold of standard deviations assuming a Guassian distribution of each cells' UMI/gene numbers. Following visual inspection of the distribution of cells by the fraction of mitochondrial genes expressed, we further discarded low-quality cells where >10% of the counts belonged to mitochondrial genes. After applying these QC criteria, 18,917 single cells and 31,053 genes in total remained and were included in downstream analyses. Library size normalization was performed in Seurat on the filtered matrix to obtain the normalized count
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell.

source_name: mouse bladder urothelium

extract_protocol:
Five mice were sacrificed by cervical vertebra dislocation and bladder was removed. The bladder was incubated in dispase II solution (04942078001, Sigma) at 37°C for 1.5 hours. The bladder was then enlarged to achieve a maximum stretch (Supplement Figure 1E). After dispase II solution was discarded, 10-15ml PBS-EDTA (10mmol/L, CZ0026, Leagene) was added to Sylgard-coated plate and shaking for 1.5 hours. The PBS-EDTA was collected and centrifuge at 300g for 5 minutes. The supernatant was aspirated and the cells were then digested in 1ml TrypLE™ Express Enzyme (12604-013, Thermo Fisher Scientific) for 1min. 10ml 0.04% BSA D-PBS solution (D1040, Solarbio) was added to stop the digestion and then centrifuge at 300g for 5 minutes. Cells were then resuspended in 10ml 0.04% BSA D-PBS solution and were sequentially filtered through 70 and 40 μm filters.
Single-cell RNA-seq libraries were prepared with Chromium Single cell 3’ Reagent v3) Kits according to the manufacturer’s protocol. Single-cell suspensions were loaded on the Chromium Single Cell Controller Instrument (10×Genomics) to generate single cell gel beads in emulsions (GEMs).

value: 8-10 weeks

value: female

value: mouse bladder urothelium


title: Dbt/iP3F - 0 hr Dox - Input

description: paired-end, 150 bp


title: triple negative breast carcinoma sample ob006L


title: triple negative breast carcinoma sample nii025


title: triple negative breast carcinoma sample g158


title: Pancreatic Cancer Samples. Biological Rep 12

city: Ciudad de México

first: Pedro

middle: Antonio

last: Avila

state: CDMX

address: Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco

department: Molecular Biomedicine

country: Mexico

institute: CINVESTAV

description: miRNAs expression data from PDAC samples

hyb_protocol: The reaction mixture was incubated at 99°C for 5 min and placed into the array. The array was covered with Tough-Spots to minimize evaporation and prevent sample drying out. The array was placed inside hybridization oven (Affymetrix) where it was incubated at 48°C and 60 rpm for 16 to 18 h. After this incubation time the array was removed from the oven. The hybridization cocktail was removed and transferred to a new tube for storage at -80°C. The array was equilibrated at room temperature with Array Holding buffer before washing and staining.

scan_protocol: After washing and staining the array probes, they were read in a microarray scanner model 3000 7G with autoloader and workstation (Affymetrix).

data_processing: The Bioconductor platform was used. Oligo software was used for pre-processing. For background correction and normalization, RMA was used. Differential expression analysis was performed with limma.

label: biotin

source_name: Pancreatic Cancer Patients

label_protocol: The polyadenylated miRNAs were ligated with a biotin-labeled DNA probe. For this, the Flash Tag Biotin HSR Ligation Mix and 2 µl of T4 DNA ligase (Affymetrix) were added to the miRNA sample.

growth_protocol: PDAC and normal pancreatic tissue samples were obtained from patients.

extract_protocol: Total RNA extraction with the PureLink FFPE Total RNA Isolation Kit method (Invitrogen, K1560-02). Subsequently, to purify the miRNAs present in the total RNA previously obtained, the miRvana system was used.

treatment_protocol: Regions with normal tissue and with neoplastic tissue were obtained by macrodissection.

tag: method

value: Macrodissection

value: Pancreatic Cancer


title: triple negative breast carcinoma sample g154


title: Pancreatic Cancer Samples. Biological Rep 11


title: liver_0hr_rep4

description: Gene expression after 0hr fasting in liver

value: 6 week-old


title: triple negative breast carcinoma sample tn022


title: Pancreatic Cancer Samples. Biological Rep 10


title: liver_0hr_rep3


title: triple negative breast carcinoma sample g149


title: Pancreatic Cancer Samples. Biological Rep 9


title: liver_24hr_rep1


title: triple negative breast carcinoma sample g166


title: heart_48hr_rep5

description: Gene expression after 48hr fasting in heart

value: heart


title: liver_0hr_rep1


title: liver_0hr_rep2


title: SMS-CTR - Input

description: paired-end, 150 bp

source_name: SMS-CTR

value: FN-RMS

tag: treatment


title: RD - Input

description: paired-end, 150 bp

source_name: RD


title: SMS-CTR - FOXO1 ChIP

description: paired-end, 150 bp


title: liver_0hr_rep5


title: RD - FOXO1 ChIP

description: paired-end, 150 bp


title: RH30 - Input

description: paired-end, 150 bp


title: Pancreatic Cancer Samples. Biological Rep 8


title: RH30 - PAX3-FOXO1 ChIP

description: paired-end, 150 bp


title: Pancreatic Cancer Samples. Biological Rep 7


title: heart_48hr_rep4


title: Pancreatic Cancer Samples. Biological Rep 6


title: triple negative breast carcinoma sample g142


title: heart_48hr_rep3


title: triple negative breast carcinoma sample g102


title: heart_48hr_rep1


title: RH4 - Input - rep1

description: paired-end, 150 bp


title: RH4 - Input - rep2

description: paired-end, 150 bp


title: triple negative breast carcinoma sample g144


title: heart_48hr_rep2


title: RH4 - PAX3-FOXO1 ChIP - rep1

description: paired-end, 150 bp


title: Pancreatic Cancer Samples. Biological Rep 4


title: HT-29_KO_MIEN1_2

city: Dunedin

first: Oscar

middle: Javier

last: Ortega-Recalde

state: Otago

address: 60 Hanover Street

department: Anatomy

country: New Zealand

institute: University of Otago

data_processing:
Raw reads were filtered to remove adapters and low quality reads (Qscore > 50% bases <= 5 or Ns > 10% bases).
Paired-end reads were aligned to human genome build GRCh38-Ensembl using TopHat2 v2.0.9(Kim et al. 2013).
Gene expression was quantified using HTSeq v0.6.1(Anders, Pyl, and Huber 2015) using the union mode (-m union)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include read counts data for each sample.

source_name: HT-29 cells KO MIEN1 replicate 2

growth_protocol: HT-29 cells (ATCC, Manassas, VA , USA) were seeded at 50.000 cells per well in 24-well culture dishes in Dulbecco´s Modified Eagle´s Medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
HT-29 WT and HT-29-pMIEN1-X cells were cultured in 24-well dishes as mentioned above. Total RNA was extracted from cells (80.000 cells per well) using TRIzol and the Ambion Purelink RNA mini kit (Invitrogen). Equal amounts of RNA from four dishes were pooled (biological replicates, BR). Four independent BR were obtained from WT (WT1-WT4) and mutant conditions (Mut1-Mut4). For eukaryotic transcriptome library constructing the mRNA was selected using poly–T oligo–attached magnetic beads.
Poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads and fragmented using divalent cations under elevated temperature. First strand cDNA was synthetized using reverse transcriptase and random hexamer primer. Then second strand cDNA synthesis was performed using DNA Polymerase I and RNase H. Double-stranded cDNA was purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure was ligated to prepare for hybridization. In order to select cDNA fragments of preferentially ~150-200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Finally, the products were enriched with PCR and purified to create the cDNA library.

treatment_protocol: HT-29 wild type (HT29-WT) cells were cultured and electroporated with a DNA mixture of plasmids expressing C1486_MIEN1_5'gRNA- 1, C1486_MIEN1_3'gRNA-1 and cas9 gene. Two days after transfection the cells were selected by 1.0-1.5 ug/ml of Puromycin for a period of 48 hours. A small portion of the cell culture, presumably containing the mixed population, was subjected to genotype analysis. The mixed culture was diluted to less than 1 cell/200ul culture media and dispersed into each well of a 96-well plate. The cells were allowed to grow for 15 to 20 days. Cells derived from such single cell cloning process were subjected to genotype analysis.  The positive clones for the desired mutation were cultured-expanded and a portion was used to confirm the predicted genotype. Genotyping was performed by using genomic DNA from a single cell clone.  A ~400bp DNA fragment was amplified using specific primers and subjected to direct sequencing

value: HT-29-pMIEN1-X (MIEN1 KO)

tag: cell line


title: del-ntrC_RNASeq

city: Auckland

first: Xue-Xian

last: Zhang

address: 14.02 The Station Cre., Albany

department: School of Natural and Computational Sciences

institute: Massey University

data_processing:
The paired-end reads from Novogene were processed in the Geneious 9.0.5 program following the instructions
Reads were mapped to the reference genome of Pseudomonas fluorescens SBW25 (GenBank: AM181176.4)
Differentially expressed genes were determined based on transcripts comparison normalized using the Median of Gene Expression Ratios method implemented in Geneious 9.0.5.
Genome_build: Pseudomonas fluorescens SBW25 (GenBank: AM181176.4)
Supplementary_files_format_and_content: a csv file exported from Geneious containing raw read counts for both wild type and its derived del-hutC mutants, and ratios of differential expression for all genes in the genome.

organism: Pseudomonas fluorescens

source_name: bacterial cells

growth_protocol: Bacteria were exponentially grown in triplicate in the M9 mininmal salt medium summplemented with succinate (20 mM) and histidine (10 mM)

extract_protocol:
Total RNA was preparated using the SV Total RNA Isolation System purchased from Promega (Madison, WI)
RNA libraries were prepared for sequencing by Novogene Technology Co. Ltd, using the standard Illumina protocols

value: Isogenic ntrC deletion mutant of P. fluorescens SBW25


title: del-cbrB_RNASeq

value: Isogenic cbrB deletion mutant of P. fluorescens SBW25


title: Pancreatic Cancer Samples. Biological Rep 2


title: Pancreatic Cancer Samples. Biological Rep 3


title: HT-29_KO_MIEN1_1

source_name: HT-29 cells KO MIEN1 replicate 1


title: HT-29_KO_MIEN1_3

source_name: HT-29 cells KO MIEN1 replicate 3


title: RH4 - PAX3-FOXO1 ChIP - rep2

description: paired-end, 150 bp

value: FP-RMS


title: HT-29_WT_3

source_name: HT-29 cells wild-type replicate 3

value: HT-29 wild type


title: PXB E077-IFN-α RNA

city: Yoshida-gun

first: Takuto

last: Nosaka

state: Fukui

address: 23-3 Matsuoka, Eiheiji-cho

department: Second Department of Internal Medicine

institute: University of Fukui

hyb_protocol: 0.6 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: A monolayer of primary human hepatocytes derived from chimeric mice with human liver was obtained from PhoenixBio Co., Lid (Hiroshima, Japan) and grown in BioCoatTM Collagen I white plate (Corning Life Science, Tewksburry, MA, USA). Hepatocytes were cultured in dHCGM medium consisting of Dulbecco’s modified Eagle’s medium (Sigma-Aldrich, St Lois, MO, USA) with 10% FBS, 20 mM HEPES (Life Technologies/Gibco), 44 mM NaHCO3 (WAKO, Osaka, Japan), 100 U/ml penicillin G, 100 μg/ml streptomycin, 15 μg/ml L-proline (WAKO), 0.25 μg/ml Insulin (Sigma-Aldrich), 50 nM dexamethasone (Sigma-Aldrich), 5 ng/ml epidermal growth factor (Sigma-Aldrich), 0.1 mM L-ascorbic acid 2-phosphate (WAKO), and 2% dimethyl sulfoxide (Sigma-Aldrich).

extract_protocol: RNAs were extracted with TRIZol reagent (Thermo Fisher Scientific) and cDNA was synthesized with High Capacity RNA-to-cDNA Kit (Applied Biosystems, Foster City CA, USA), following the manufacturer’s instructions.

treatment_protocol: HBV for in vitro viral infection was obtained from the culture medium of HepG2 transfected with HBV plasmids. HBV DNA was isolated using SMITEST EX-R&D (MBL; Medical & Biological laboratories Co., LTD, Nagano, Japan) according to the manufacture’s protocol, and the amount of HBV DNA was determined by real-time PCR. PXB cells were infected with the collected HBV at same equivalents in the presence of 4% polyethylene glycol 8000 (PEG8000, Sigma-Aldrich). PXB cells were harvested after 22 days after the infection. IFN-γ (Recombinant Human IFN-γ; PeproTech, Rocky Hill, NJ, USA), IFN-α (Sumiferon; Dainippon Pharmaceutical Co. Ltd., Osaka, Japan) and ETV were added to PXB cells at 5 × 103 ng/mL, 1 × 105 IU/mL, and 50 μM respectively, at each medium change starting on day 4 post-infection.

value: HBV High t. infection, IFN-α

value: primary human hepatocytes


title: HT-29_KO_MIEN1_4

source_name: HT-29 cells KO MIEN1 replicate 4


title: Pancreatic Cancer Samples. Biological Rep 1


title: heart_24hr_rep5

description: Gene expression after 24hr fasting in heart


title: HT-29_WT_4

source_name: HT-29 cells wild-type replicate 4


title: Normal Pancreatic Samples. Biological Rep 2

description: miRNAs expression data from Control samples

source_name: Normal Pancreas Patients

value: Normal Pancreas


title: Normal Pancreatic Samples. Biological Rep 3


title: poh1-/-ko foxp3+Treg cell

first: yun

last: liu

address: Xie tu road

department: Shanghai Cancer Institute

institute: Shanghai Jiaotong University School

data_processing:
Illumina TruSeq RNA Sample Prep Kit v2 (Cat#RS-122-1001) was used with total RNA for the construction of sequencing libraries according to manufacturer instructions and submitted to the Illumina Hisequation 2500 system.
clean reads were achieved by trimming the adaptor and filtering rRNAs and then mapped tothe mouse genome (mm10) with TopHat.
The mapped fragments of genes were calculated by using HTSeq followed by trimmed mean of M values normalization to evaluate gene expression by normalized Reads Per Kilobase of exon per Megabase of library size (RPKM).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: spleen

extract_protocol:
Splenic CD4+Foxp3+ (YFP+) cells were sorted from 2-week-old poh1fl/fl Foxp3Cre+ or poh1+/+ Foxp3Cre+ mice, using MoFlo XDP. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 (Cat#RS-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spleen


title: heart_0hr_rep3

description: Gene expression after 0hr fasting in heart


title: heart_24hr_rep1


title: heart_0hr_rep5


title: PXB E077-IFN-γ RNA

source_name: primary human hepatocytes derived from chimeric mice with human liver

value: HBV High t. infection, IFN-γ


title: heart_24hr_rep4


title: PXB-E080

value: HBV Medium t. infection, untreated


title: Normal Pancreatic Samples. Biological Rep 1


title: heart_24hr_rep3


title: HT-29_WT_2

source_name: HT-29 cells wild-type replicate 2


title: Six1 cochlea E16.5

status: Public on Dec 11 2020

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The ChIP-seq data was first checked for quality using the various metrics generated by FastQC (v0.11.2). Raw sequencing reads were then aligned to the mouse mm10 genome using default settings of Bowtie (v2.2.0). Only uniquely-mapped reads were retained and duplicates were removed.
Peak-calling was performed using MACS (v2.1.1) with qvalue (minimum FDR) cutoff of 0.05.
Motif enrichment analysis was performed using the Homer package (v4.8.3). The peak annotation and gene ontology analysis was performed using the GREAT program and Panther classification system.
Genome_build: mm10

source_name: cochlea

extract_protocol:
The tissues were fixed with 1%PFA in PBS for 30 min at RT. After washing, the tissues were homogenized to a fine powder using BeadBugTM high-energy benchtop homogenizer in the lysis buffer. Chromatin shearing was performed using the Covaris E220 focused-ultrasonicator system. After preclearing with Protein A beads, the chromatin was immunoprecipitated with antibodies. After IP, the beads were washed in sequential low salt buffer, high salt buffer, LiCl washing buffer and TE buffer.
The libraries were prepared using the ThruPlex DNA-seq Kit (Rubicon Genomics) and according to the manufacturer's instructions.

tag: developmental stage

value: cochlea

value: Anti-Six1 antibody, Rabbit  (Sigma, HPA001893, lot l116428)


title: PXB E077_ETV

value: HBV High t. infection, entecavir


title: PXB-E077

value: HBV High t. infection, untreated


title: wt foxp3＋Treg cell

tag: tissue


title: PXB E077-Nashi RNA


title: E13.5_Cochlea_Six1_ChIP-seq replicate


title: HT-29_WT_1

source_name: HT-29 cells wild-type replicate 1


title: PXB E077_Nashi


title: Pancreatic Cancer Samples. Biological Rep 5

value: Macrodissection

value: Pancreatic Cancer


title: H3K27me3 cochlea E13.5

value: Anti-H3K27me3 antibody, mouse (Abcam, ab6002, lot GR3228496-2)


title: Coptisine vs. PBS

city: Beijing

first: Lan

last: Xie

address: School of Medicine B410, Tsinghua University

institute: Tsinghua University

description: Using PBS-treated cell RNA as a control sample, analyzing differentially expressed genes in the cell sample treated with coptisine

hyb_protocol: Arrays were hybridized was preformed in a CapitalBio BioMixerTM II Hybridization Station overnight at a rotation speed of 8 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Arrays were scanned with a confocal LuxScanTM scanner and the images obtained were then analyzed using LuxScanTM 3.0 software (Both from CapitalBio).

data_processing: A space- and intensity-dependent normalization based on a LOWESS program was employed. Significance Analysis of Microarrays (SAM, version 3.02) were employed to determine the differentially expressed genes.Changes of gene expression at either 2-fold greater or less than 0.5-fold were defined as significant differently expressed genes.

source_name: Coptisine treated

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, GE Healthcare) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. The amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: murine macrophage cell line RAW264.7 was cultured in high glucose DMEM medium containing 10% fetal bovine serum and 1% antibiotic mixture of penicillin (100 U/mL) and streptomycin (100 mg/mL)

extract_protocol: Total RNA was prepared using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.

treatment_protocol: RAW264.7 cells were treated with 1% DMSO, 40 μg/ml RCE, 60 μM berberine, 5 μM coptisine and 80 μM palmitate for 24 h. PBS was set as the control group.

value: RAW264.7 cells

source_name: PBS treated


title: Berberine vs. PBS

description: Using PBS-treated cell RNA as a control sample, analyzing differentially expressed genes in the cell sample treated with berberine

source_name: Berberine treated


title: Palmatine vs. PBS

description: Using PBS-treated cell RNA as a control sample, analyzing differentially expressed genes in the cell sample treated with palmatine

source_name: Palmatine treated


title: Rhizoma Coptidis extract (RCE) vs. PBS

description: Using PBS-treated cell RNA as a control sample, analyzing differentially expressed genes in the cell sample treated with RCE

source_name: Rhizoma Coptidis extract (RCE) treated


title: heart_0hr_rep2

value: 6 week-old

value: heart


title: DMSO vs. PBS

description: Using PBS-treated cell RNA as a control sample, analyzing differentially expressed genes in the cell sample treated with DMSO

source_name: DMSO treated


title: PXB-E082

value: HBV Low t. infection, untreated


title: heart_0hr_rep4


title: heart_24hr_rep2


title: HC [2464C47]

city: Ramat Gan

first: Michael

last: Gurevich

address: Tel Hashomer

department: Multiple Sclerosis Center

country: Israel

institute: Sheba Medical Center

description: PBMC gene expression from HC subject

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
The Supplementary Tables 1-3 included statistically significant genes obtained by comparison of each experimental group Multiple Sclerosis only (MSO), Psoriasis only (PSO), Psoriasis and Multiple Sclerosis comorbid patients (P/MS) with Healthy Controls (HC) The Supplementary Table 4 include upstream regulators for PSO related genes.
Supplementary Table 1 - "MSO Vs HC"
Supplementary Table 2 - "PSO Vs HC"
Supplementary Table 3 - "P/MS Vs HC"
Supplementary Table 4 - "Upstream regulators for PSO genes"

source_name: PBMC from HC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: PBMC were purified from  Ficoll hypaque gradient (Invitrogen, USA)

value: Female

tag: age (years)


title: P/MS [568RMS]

description: PBMC gene expression from P/MS patients

source_name: PBMC from P/MS

value: Male


title: HC [2462C47]

description: PBMC gene expression from HC subject


title: HC [5368C98]

description: PBMC gene expression from HC subject


title: HC [542aRMS]

description: PBMC gene expression from HC subject


title: P/MS [679RMS]

description: PBMC gene expression from P/MS patients


title: PSO [10737PSO182]

description: PBMC gene expression from PSO patients

source_name: PBMC from PSO


title: heart_0hr_rep1


title: HC [1566C46]

description: PBMC gene expression from HC subject


title: MSO [518RMS]

description: PBMC gene expression from MSO patients

source_name: PBMC from MSO


title: PSO [9677PSO182]

description: PBMC gene expression from PSO patients


title: HC [541RMS]

description: PBMC gene expression from HC subject


title: P/MS [836PMS]

description: PBMC gene expression from P/MS patients


title: HC [5369C98]

description: PBMC gene expression from HC subject


title: HC [2120C46]

description: PBMC gene expression from HC subject


title: HC [389PMS]

description: PBMC gene expression from HC subject


title: PXB-Non

value: uninfected, untreated

value: primary human hepatocytes


title: P/MS [452PMS]

description: PBMC gene expression from P/MS patients


title: HC [1439-Control]

description: PBMC gene expression from HC subject


title: MSO [911PMS]

description: PBMC gene expression from MSO patients


title: PSO [10732PSO182]

description: PBMC gene expression from PSO patients


title: triple negative breast carcinoma sample g020

source_name: Breast

value: Triple Negative Breast Cancer


title: PSO [10696PSO182]

description: PBMC gene expression from PSO patients


title: PSO [9668PSO182]

description: PBMC gene expression from PSO patients


title: P/MS [7300RR181]

description: PBMC gene expression from P/MS patients


title: PSO [9632PSO181]

description: PBMC gene expression from PSO patients


title: PSO [9483PSO181]

description: PBMC gene expression from PSO patients


title: MSO [8445RR182]

description: PBMC gene expression from MSO patients


title: P/MS [1642NEWREL46]

description: PBMC gene expression from P/MS patients


title: PSO [9630PSO181]

description: PBMC gene expression from PSO patients


title: P/MS [817COP47]

description: PBMC gene expression from P/MS patients


title: P/MS [8595PR181]

description: PBMC gene expression from P/MS patients


title: MSO [9570RR182]

description: PBMC gene expression from MSO patients


title: P/MS [5730RR145]

description: PBMC gene expression from P/MS patients


title: MSO [7115RR145]

description: PBMC gene expression from MSO patients


title: MSO [6574RR145]

description: PBMC gene expression from MSO patients


title: PSO [9523PSO181]

description: PBMC gene expression from PSO patients


title: P/MS [2111OUT98]

description: PBMC gene expression from P/MS patients


title: MSO [10446RR182]

description: PBMC gene expression from MSO patients


title: P/MS [4446RR182]

description: PBMC gene expression from P/MS patients


title: P/MS [1206-DMS]

description: PBMC gene expression from P/MS patients


title: MSO [7097PRE121]

description: PBMC gene expression from MSO patients


title: P/MS [6921RR181]

description: PBMC gene expression from P/MS patients


title: PSO [9631PSO181]

description: PBMC gene expression from PSO patients


title: P/MS [7236PRE121]

description: PBMC gene expression from P/MS patients


title: MSO [7483WMSBL133]

description: PBMC gene expression from MSO patients


title: MSO [5820TMS121]

description: PBMC gene expression from MSO patients


title: P/MS [7769RELMS133]

description: PBMC gene expression from P/MS patients


title: MSO [10601RR181]

description: PBMC gene expression from MSO patients


title: P/MS [881SP182]

description: PBMC gene expression from P/MS patients


title: PSO [9645PSO181]

description: PBMC gene expression from PSO patients


title: PSO [9774PSO182]

description: PBMC gene expression from PSO patients


title: MSO [621COP47]

description: PBMC gene expression from MSO patients


title: MSO [10422RR181]

description: PBMC gene expression from MSO patients


title: MSO [2145REL46]

description: PBMC gene expression from MSO patients


title: MSO [655-PMS]

description: PBMC gene expression from MSO patients


title: HC_H012_BCR_control

city: Kiel

first: Neha

last: Mishra

address: Rosalind-Franklin-Str. 12

country: Germany

institute: Institute of Clinical Molecular Biology

data_processing:
Base Calling perofmed by RTA1(MiSeq) and RTA3 (Novaseq 6000)
Transcriptome Processing: Fastq files were mapped and aligned using nf-core ((https://github.com/nf-core/rnaseq)) rnaseq pipeline. Adapters and low-quality bases from the RNA-seq reads were removed using Trim Galore (version 0.4.4), which is a wrapper tool for Cutadapt and FastQC. Reads that were shorter than 35 bp after trimming were discarded. . The filtered reads were mapped to the human genome (GRCh38, gencode version 25) using STAR aligner (version 2.5.2b) (Dobin et al., 2013). featureCounts (version 1.5.2) was used to estimate the expression counts of the genes.
BCRseq Processing: Sequencing reads were aligned to BCR gene reference and clonotypes were identified and grouped using the software MiXCR (Bolotin et al., 2015). Relative proportions of IGH classes were calculated. Alpha diversity measures were calculated using the R packages vegan and tcR (versions 1.5-6 and 2.3.2).
Genome_build: (GRCh38, gencode version 25)
Supplementary_files_format_and_content: tab-delimited text files include feature counts and BCR Clonotype count tables

source_name: Peripheral Whole-Blood

extract_protocol:
BCRseq: Library construction protocol was performed as previously described (Bashford-Rogers et al., 2019). In brief, primers for the constant (C) regions of the BCR were used during cDNA synthesis. Product was then amplified via PCR using a multiplex primer set for the variable (V) regions using the Real-Time PCR library amplification kit from KAPA Biosystems. Libraries were sequenced on Illumina MiSeq machine 2×300 bp.
Patient peripheral blood was collected in 2.5mL tubes PAXgene Blood RNA Tubes, RNA was automated isolated in QIAGEN’s QIAcube using the PAXgene Blood miRNA Kit from QIAGEN PreAnalytiX.

tag: remission

value: Healthy

value: f

tag: pseudotime

tag: patient number


title: HC_H014_BCR_control

tag: gender

value: m


title: HC_H013_BCR_control


title: MSO [744REL46]

description: PBMC gene expression from MSO patients


title: PC_6_BCR_TB

value: Remission


title: HC_H011_BCR_control


title: PC_6_BCR_TA2


title: PC_6_BCR_rec


title: PC_6_BCR_TA


title: PC_7_BCR_rec


title: PC_5_BCR_TB2


title: PC_5_BCR_TB


title: MSO [1067-PMS]

description: PBMC gene expression from MSO patients


title: PC_5_BCR_TA


title: PC_5_BCR_TA2


title: PC_4_BCR_TA


title: PC_4_BCR_TB


title: PC_3_BCR_TA

value: No Remission


title: PC_2_BCR_TA2


title: PC_4_BCR_TA2


title: PC_2_BCR_TC


title: PC_1_BCR_TC


title: HC_1_EPIC

type: genomic

hyb_protocol: Standard Illumina Protocol

scan_protocol: The Infinium© MethylationEPIC BeadChip was used to measure the DNA methylation levels. The Infinium© MethylationEPIC BeadChip targets the following regions: CpG islands, CpG sites, open chromatin, transcription factor binding sites, enhancer and miRNA promoter regions. The EPIC arrays were processed according to Illumina recommendations.

data_processing: DNA methylation data was analysed using the Bioconductor package RnBeads (version 1.12.1). Sites that overlapped with SNPs and had unreliable measurements were filtered resulting in the removal of 17,371 sites and 19,745 probes. 2,977 Context-specific probes, 18,976 probes on the sex chromosomes, and 4 probes with missing values were also removed. In total 41,702 out of 866,895 probes were filtered.

label: Cy3, Cy5

source_name: Peripheral Whole Blood

label_protocol: Standard Illumina Protocol

extract_protocol: Blood (2.7 mL) was taken from each patient into an Ethylenediaminetetraacetic acid (EDTA) monovette (Sarstedt) to decelerate blood coagulation. The monovette was centrifuged for 15 min at 3000 rpm and the buffy coat was frozen in micronic tubes at -80°C. DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to manufacturer’s protocol with a QIACube (Qiagen).


title: PC_1_BCR_TA2


title: PC_1_BCR_TA


title: PC_5_EPIC_TA2


title: PC_1_BCR_TB


title: PC_14_BCR_TA2


title: PC_4_EPIC_TA


title: PC_6_EPIC_TA


title: PC_6_EPIC_TA2


title: PC_6_EPIC_TB


title: HC_5_EPIC


title: PC_1_EPIC_TC


title: PC_12_BCR_TD


title: PC_1_BCR_TB2


title: PC_13_BCR_TB


title: PC_12_BCR_TA


title: PC_12_BCR_TC


title: PC_5_EPIC_TB


title: HC_2_EPIC


title: PC_3_EPIC_TA

value: No Remssion


title: PC_11_BCR_TB2


title: PC_1_EPIC_TB2


title: PC_4_EPIC_TB


title: PC_5_EPIC_TA


title: PC_2_EPIC_TA2


title: PC_11_BCR_TB


title: PC_5_EPIC_TB2


title: PC_1_EPIC_TA2


title: PC_11_BCR_TA2


title: PC_1_EPIC_TB


title: HC_6_EPIC


title: PC_10_BCR_TA2


title: PC_10_BCR_TB2


title: PC_10_BCR_TB


title: PC_2_EPIC_TA


title: PC_9_BCR_TB


title: PC_9_BCR_TA


title: PC_9_BCR_TA2


title: PC_10_BCR_TC


title: PC_11_BCR_TA


title: 5C-Nulcei-R2

city: Worcester

first: Houda

last: Belaghzal

state: MA

address: 55 N Lake Ave

department: Program in Systems Biology

institute: University of Massachusetts Medical School

data_processing:
5C was processed as describe in this 5C pipeline https://github.com/dekkerlab/5C-CBFb-SMMHC-Inhib/blob/master/data_processing_steps.md
Genome_build: hg19
Genome_build: 5C*-samples: Custom built based on the 5C primers as described in https://github.com/dekkerlab/5C-CBFb-SMMHC-Inhib/blob/master/data_processing_steps.md
Supplementary_files_format_and_content: hdf5 files contain iced and scaled Hi-C intearction matrices. LOS bedGraphs represent loss of structure for pre-digested genomic bins relative to control for indicated timepoints. half-life bedGraph represents chromatin interaction stability for genomic bins. half-life_residuals bedGraph represents chromatin interaction stability after accounting for digestion efficiency.
Supplementary_files_format_and_content: bedGraphs represent DpnII-seq copy number corrected read coverage for indicated digestion time.
Supplementary_files_format_and_content: Processed data is a matrix file that represents the pair-wise interactions between loci for 1 Mb around the Beta-Globin locus

growth_protocol: RPMI Medium  (Gibco)15% FBS (Gibco) 1% Antibiotic-Antimycotic (Gibco)  1% L-Glutamine (Gibco)

extract_protocol:
5C was performed as described in “From cells to chromatin: Capturing snapshots of genome organization with 5C technology” (Ferraiuolo et al., 2012). And Decsribe in Method
5C

treatment_protocol: Nuclei were purified as described in Methods

value: The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises.

tag: protocol

tag: enzyme

value: EcoRI


title: 5C-Cells-R2

treatment_protocol: No treatment


title: 5C-Nulcei-R1


title: HC_4_EPIC

tag: age


title: 5C-Cells-R1


title: PC_1_EPIC_TA


title: Flag_LARP_TOT_rep1

city: Glasgow

first: Ania

last: Wilczynska

address: Switchback Road

country: United Kingdom

institute: Beatson Insistute for Cancer Research

description: RNA input into Flag-Larp IP

hyb_protocol: 600 ng Cy-3 labelled input sample, 600 ng Cy-3 labelled IP (antibody-treated samples) and the equivalent volume of vehicle control samples taken and all fragmented using fragmentation buffer from the Agilent Gene Expression Hybridisation Kit (Agilent) for 30 min at 60°C. Fragmented samples were mixed 1:1 with Hybridisation Buffer (v/v) and hybridised to a 60K high-density oligonucleotide microarray overnight. Microarrays were loaded as per the manufacturer’s instructions and hybridisation was performed at 65°C, in an Agilent Hybridisation Oven with rotation set to 10 RPM.  Following hybridisation, the microarray slides were washed in Gene Expression wash buffers 1 and 2 (Agilent) and immediately scanned using a DNA Microarray Scanner (Model G2505C, Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_107_Sep09 ) Array analysis performed using limma, using normalised expression background correction, quantile normalisation, filtered for spots with intensity >1.5 of negative control probes, FDR<0.05 applied to linear model fitting

source_name: Total RNA from HeLa cell lysate with overexpressed Flag-Larp1

label_protocol: 100 ng input RNA, and the contents of 10 µl IP RNA was Cy-3 labelled using Agilent Low Input Quick Amp 1-colour Labelling Kit (Agilent).

growth_protocol: 12x 15 cm plates of HeLa cells were seeded at 1.8 million cells per plate in DMEM

extract_protocol: HeLa cells were seeded at 1.6x 106 per plate. 24h later cells were transfected with 5 µg of vector (as indicated in figure legends). After a further 24 hours cells were stimulated with 2% serum, 2mM L-Glutamine for 30min followed by 1h with DMSO (Control) or 200 nM Torin1. Cells were then harvested, lysed and cleared supernatants prepared and normalised for protein concentration as for endogenous IPs (above). Normalised lysates were incubated with end-end rotation with 50 µl Anti-FLAG(R) M2 magnetic beads (Sigma-Aldrich M8823) for 90 min at 4˚C. Beads were then washed 4 times for 5 minutes in IP buffer. At last 1 ml wash beads were split for RNA and protein analysis: 120 µl for protein analysis- spin down, remove supernatant and resuspend in 60 µl 1x sample buffer, 800 µl for RNA analysis- remove wash buffer, and add 1 ml of Trizol.

value: no treatment

tag: replicate

value: HeLa, overexpressed Flag-Larp1

value: RNA input into Flag-Larp IP


title: PC_12_BCR_TE


title: Flag_LARP_IP_rep2

description: RNA Flag-Larp IP

scan_protocol: DNA Microarray Scanner (Model G2505C, Agilent Technologies)

source_name: IP of overexpressed Flag-Larp1 from HeLa cell lysate

value: RNA Flag-Larp IP


title: PC_4_EPIC_TA2


title: PC_10_BCR_TA


title: PC_13_BCR_TA


title: Flag_LARP_TOT_rep2

description: RNA input into Flag-Larp IP

source_name: Total RNA from HeLa cell lysate with overexpressed Flag-Larp2


title: PC_14_BCR_TA


title: Flag_LARP_IP_rep1

description: RNA Flag-Larp IP


title: PABP_IP_Torin_rep3

description: RNA IP with PABP antibody, Torin treated

source_name: HeLa cell lysate PABP IP mRNA Torin treatment

extract_protocol: Meanwhile protein A/G beads were pre-coupled to antibodies as follows; using 100µL bead slurry (Protein A/G plus agarose SC-2003) per IP: bead slurry washed twice with 1 ml lysis buffer and resuspended to initial volume. Beads precoupled with 3ug per IP of either Rabbit IgG (0.4 µg/µl), PABP antibody (1ug/ul) or LARP1 Antibody (0.2 µg/µl). Antibodies preincubated for 2h at 4C with end-end rotation. Pre-incubated beads spiked with 1:100 v/v yeast tRNA for 30min at 4C. Beads then washed 3x 1 ml and 100ul beads used per IP. Following treatments cells washed twice with 8 ml volume of PBS. Cells lysed in 2 mL of IP Lysis buffer per plate (20 mM Tris-HCl pH7.5, 150 mM NaCl, 15 mM MgCl2, 0.5% NP40, 1 mM EDTA, 1 mM EDTA, 0.1% 2-mercaptoethanol, Protease inhibitors cocktail, RNAse inhibitor (40U /ml)). Where RNAse A was used (Supplementary Figure 8), 10 µg/ml was added to the lysis buffer prior to lysis. Lysates incubated for 10min on ice and then lysates scraped and passed through a 21G needle three times. Equilibrated with end/end rotation for 5min. Lysates spun down for 15 min at 4˚C at 13000 rpm, supernatants collected, pooled. Protein concentration determined by Bradford and lysates normalised for protein concentration. (100 µl of lysate reserved for western and 100 µl for input RNA (into 1 ml Trizol reagent). Beads spun down and resuspended in 100 µl lysis buffer per treatment. 90 µl aliquots made for IPs and 12 µl tRNA spiked into each tube. Incubate beads with 1.5 ml normalised protein extract at 4 °C with end over end rotation for 90 min. Beads washed four times for 5 min with end-end rotation with 1.5ml lysis buffer. At last 1 ml wash: beads pooled for each treatment and split for RNA and protein analysis: 120 µl for protein analysis- spun down, supernatant removed and resuspend in 60 µl 1x sample buffer, 800 µl for RNA analysis- remove wash buffer, and add 1 ml of Trizol.

treatment_protocol: 24h later cells medium was supplemented with 2% serum, 2mM L-Glut for 30 min followed by 1h with DMSO or 200 nM Torin1.

value: Torin

value: HeLa

value: RNA IP with PABP antibody


title: PABP_IP_Torin_rep2


title: PABP_IP_Torin_rep1


title: PABP_TOT_Torin_rep3

description: RNA input into PABP IP, Torin treated

source_name: HeLa cell lysate Total mRNA Torin treatment

value: RNA input into PABP IP


title: HC_3_EPIC


title: PABP_IP_DMSO_rep2

description: RNA IP with PABP antibody, DMSO treated

source_name: HeLa cell lysate PABP IP mRNA control DMSO

value: DMSO


title: PABP_TOT_DMSO_rep2

description: RNA input into PABP IP, DMSO treated

source_name: HeLa cell lysate Total mRNA control DMSO


title: PABP_TOT_DMSO_rep3

description: RNA input into PABP IP, DMSO treated


title: PABP_IP_DMSO_rep1

description: RNA IP with PABP antibody, DMSO treated


title: PABP_TOT_Torin_rep2

description: RNA input into PABP IP, Torin treated


title: PABP_TOT_Torin_rep1

description: RNA input into PABP IP, Torin treated


title: PABP_IP_DMSO_rep3

description: RNA IP with PABP antibody, DMSO treated


title: PABP_TOT_DMSO_rep1

description: RNA input into PABP IP, DMSO treated


title: LARP_IP_Torin_rep3

description: RNA IP with Larp antibody, Torin treated

source_name: HeLa cell lysate Larp IP mRNA Torin treatment

value: RNA IP with Larp antibody


title: LARP_IP_Torin_rep4


title: LARP_IP_Torin_rep1


title: LARP_TOT_Torin_rep4

description: RNA input into Larp IP, Torin treated

value: RNA input into Larp IP


title: LARP_TOT_Torin_rep1

description: RNA input into Larp IP, Torin treated


title: LARP_TOT_Torin_rep2

description: RNA input into Larp IP, Torin treated


title: LARP_TOT_DMSO_rep2

description: RNA input into Larp IP, DMSO treated


title: LARP_IP_DMSO_rep1

description: RNA IP with Larp antibody, DMSO treated

source_name: HeLa cell lysate Larp IP mRNA control DMSO


title: LARP_TOT_Torin_rep3

description: RNA input into Larp IP, Torin treated


title: LARP_TOT_DMSO_rep3

description: RNA input into Larp IP, DMSO treated


title: LARP_IP_DMSO_rep2

description: RNA IP with Larp antibody, DMSO treated


title: LARP_IP_DMSO_rep4

description: RNA IP with Larp antibody, DMSO treated


title: R14_Endosperm_rep3

city: Beaucouze

first: Julia

last: Buitink

address: 42 rue Georges Morel

department: BAP

country: France

institute: INRAE

description:
R14_End_4
AllSamples_GeneExpression_Count.txt

data_processing:
Clean reads were mapped to the reference genome tomato SL4.0 using SALMON to calculate gene expression level.
Genome_build: SL4.0
Supplementary_files_format_and_content: AllSamples_GeneExpression_Count.txt: Tab-delimited text file with count values for every gene and every sample.

organism: Solanum lycopersicum

source_name: red plus 14 days endosperm

growth_protocol: Plants were grown under controlled greenhouse conditions in 10 L pots containing substrate (Irish peat, perlite, coconut fiber; 50/40/10; v/v/v), watered with a nutrient solution and supplemented with 16 h of 250 µmol m2 s-1 light. The day and night temperatures were maintained at > 23°C/20°C.

extract_protocol:
Total RNAs were extracted from the frozen grinded seed tissues using the NucleoSpin® RNA Plant and Fungi kit (Macherey-Nagel, Düren, Germany), according to the manufacturer instructions (protocol 5.1) without the incubation step at 56°C using the following recommended sample type: alfalfa for embryo, potato tuber for the endosperm and grape vine leaf for seed coat.
Samples were sent to BGI, Hong Kong, for library preparation. Libraries were constructed following a custom protocol from samples that passed quality controls (mass > 2µg, concentration>80ng/microl, OD260/280 ~= 2.00, OD260/230 ~= 2.20, RIN>6.5, 28S/18S<1.0, baseline smooth). After mRNA enrichment, RNA was fragmented and reverse transcribed to double-strand cDNA (dscDNA) by N6 random primer. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments. The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer, splint oligo and DNA ligase, followed by sequencing on BGISEQ-500 platform, generating an average 20M reads of 50bp per sample.

treatment_protocol: Seeds were manually extracted from the equatorial section of the fruit. The embryo, endosperm and seed coat were hand-dissected, immediately frozen in liquid nitrogen and stored at -80°C prior to RNA isolation.

tag: cultivar

value: Moneymaker

value: Endosperm

tag: age (daf)

value: red plus 14 days


title: LARP_TOT_DMSO_rep4

description: RNA input into Larp IP, DMSO treated

tag: antibody


title: R14_Endosperm_rep2

description:
R14_End_3
AllSamples_GeneExpression_Count.txt


title: LARP_TOT_DMSO_rep1

description: RNA input into Larp IP, DMSO treated


title: LARP_IP_DMSO_rep3

description: RNA IP with Larp antibody, DMSO treated


title: R7_Endosperm_rep3

description:
R7_End_3
AllSamples_GeneExpression_Count.txt

source_name: red plus 7 days endosperm

value: red plus 7 days


title: PC_12_BCR_TB

value: Remission

value: f


title: R7_Endosperm_rep2

description:
R7_End_2
AllSamples_GeneExpression_Count.txt


title: LARP_IP_Torin_rep2


title: R_Endosperm_rep3

description:
R_End_3
AllSamples_GeneExpression_Count.txt

source_name: red endosperm

value: red


title: R_Endosperm_rep1

description:
R_End_1
AllSamples_GeneExpression_Count.txt


title: DO_Endosperm_rep1

description:
DO_End_1
AllSamples_GeneExpression_Count.txt

source_name: dark orange endosperm

value: dark orange


title: DO_Endosperm_rep2

description:
DO_End_2
AllSamples_GeneExpression_Count.txt


title: DO_Endosperm_rep3

description:
DO_End_4
AllSamples_GeneExpression_Count.txt


title: O_Endosperm_rep3

description:
O_End_3
AllSamples_GeneExpression_Count.txt

source_name: orange endosperm

value: orange


title: O_Endosperm_rep1

description:
O_End_1
AllSamples_GeneExpression_Count.txt


title: O_Endosperm_rep2

description:
O_End_2
AllSamples_GeneExpression_Count.txt


title: R7_Endosperm_rep1

description:
R7_End_1
AllSamples_GeneExpression_Count.txt


title: PO_Endosperm_rep2

description:
PO_End_2
AllSamples_GeneExpression_Count.txt

source_name: pale orange endosperm

value: pale orange


title: B_Endosperm_rep3

description:
B_End_4
AllSamples_GeneExpression_Count.txt

source_name: breaker endosperm

value: breaker


title: PO_Endosperm_rep3

description:
PO_End_3
AllSamples_GeneExpression_Count.txt


title: R_Endosperm_rep2

description:
R_End_2
AllSamples_GeneExpression_Count.txt


title: B_Endosperm_rep2

description:
B_End_3
AllSamples_GeneExpression_Count.txt


title: R14_Endosperm_rep1

description:
R14_End_1
AllSamples_GeneExpression_Count.txt


title: R14_Embryo_rep3

description:
R14_Em_4
AllSamples_GeneExpression_Count.txt

source_name: red plus 14 days embryo

value: Embryo


title: B_Endosperm_rep1

description:
B_End_1
AllSamples_GeneExpression_Count.txt


title: MG_Endosperm_rep2

description:
MG_End_3
AllSamples_GeneExpression_Count.txt

source_name: mature green endosperm

value: mature green


title: MG_Endosperm_rep1

description:
MG_End_2
AllSamples_GeneExpression_Count.txt


title: R14_Embryo_rep2

description:
R14_Em_3
AllSamples_GeneExpression_Count.txt


title: R7_Embryo_rep1

description:
R7_Em_1
AllSamples_GeneExpression_Count.txt

source_name: red plus 7 days embryo


title: R7_Embryo_rep2

description:
R7_Em_2
AllSamples_GeneExpression_Count.txt


title: R14_Embryo_rep1

description:
R14_Em_1
AllSamples_GeneExpression_Count.txt


title: R7_Embryo_rep3

description:
R7_Em_3
AllSamples_GeneExpression_Count.txt


title: R_Embryo_rep3

description:
R_Em_3
AllSamples_GeneExpression_Count.txt

source_name: red embryo


title: R_Embryo_rep2

description:
R_Em_2
AllSamples_GeneExpression_Count.txt


title: R_Embryo_rep1

description:
R_Em_1
AllSamples_GeneExpression_Count.txt


title: DO_Embryo_rep3

description:
DO_Em_4
AllSamples_GeneExpression_Count.txt

source_name: dark orange embryo


title: DO_Embryo_rep1

description:
DO_Em_1
AllSamples_GeneExpression_Count.txt


title: DO_Embryo_rep2

description:
DO_Em_2
AllSamples_GeneExpression_Count.txt


title: O_Embryo_rep3

description:
O_Em_3
AllSamples_GeneExpression_Count.txt

source_name: orange embryo


title: PO_Embryo_rep3

description:
PO_Em_4
AllSamples_GeneExpression_Count.txt

source_name: pale orange embryo


title: O_Embryo_rep2

description:
O_Em_2
AllSamples_GeneExpression_Count.txt


title: O_Embryo_rep1

description:
O_Em_1
AllSamples_GeneExpression_Count.txt


title: PO_Endosperm_rep1

description:
PO_End_1
AllSamples_GeneExpression_Count.txt


title: PO_Embryo_rep2

description:
PO_Em_3
AllSamples_GeneExpression_Count.txt


title: MG_Endosperm_rep3

description:
MG_End_4
AllSamples_GeneExpression_Count.txt


title: B_Embryo_rep1

description:
B_Em_1
AllSamples_GeneExpression_Count.txt

source_name: breaker embryo


title: B_Embryo_rep2

description:
B_Em_3
AllSamples_GeneExpression_Count.txt


title: MG_Embryo_rep1

description:
MG_Em_2
AllSamples_GeneExpression_Count.txt

source_name: mature green embryo


title: MG_Embryo_rep3

description:
MG_Em_4
AllSamples_GeneExpression_Count.txt


title: MG_Embryo_rep2

description:
MG_Em_3
AllSamples_GeneExpression_Count.txt


title: hf1_atm_frac_neg

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

data_processing:
RNA-seq reads demultiplexed with Illumina’s bcl2fastq2 and
were then aligned to the Mus musculus Ensembl release 76 top-level assembly with STAR version 2.0.4b (Dobin et al., 2013).
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5 (Liao et al., 2014).
Genome_build: Mus musculus Ensembl release 76 top-level assembly
Supplementary_files_format_and_content: Xls file that includes raw count data for each sample.

source_name: ATMs-HFD

extract_protocol:
RNA was isolated using microRNA isolation kit (Qiagen) according to manufacturer’s instructions.
The library preparation and sequencing were performed at the Genome Technology Access Center (GTAC) at Washington University School of Medicine.
Briefly, the total cellular RNA was also prepared for RNA sequencing with the Clonetech SMARTer kit according to manufacturer’s protocols, ligated with adapters
and unique molecular indexes for each sample for every read, and then sequenced on one single-end 50bp lane on an Illumina HiSeq 3000.

value: high fat, high sucrose diet-Research Diets (cat# D12492)

tag: genotype

value: Cx3Cr1-GFP/WT mouse line

tag: strain

value: adipose

tag: cell type

value: macrophage, frac_neg


title: hfd2_liv_frac_pos

source_name: Cx3cr1pos macs-HFD

tag: treatment

value: liver

value: macrophage, frac_pos


title: hf1_liv_frac_pos

tag: tissue


title: hfd1_atm_frac_neg


title: hfd2_atm_frac_neg


title: hf3_atm_frac_neg


title: hf2_atm_frac_neg


title: hf2_liv_frac_pos


title: hf3_liv_CD68

source_name: HFD KC

value: macrophage, CD68


title: hfd2_liv_frac_neg


title: hf2_liv_CD68


title: hf1_liv_CD68


title: hfd1_liv_frac_neg


title: PO_Embryo_rep1

description:
PO_Em_2
AllSamples_GeneExpression_Count.txt

value: Moneymaker

tag: developmental stage


title: B_Embryo_rep3

description:
B_Em_4
AllSamples_GeneExpression_Count.txt


title: std2_liv_frac_neg

source_name: STD KC

value: standard mouse chow diet


title: std3_liv_frac_neg


title: std1_liv_frac_neg


title: hf3_liv_frac_pos


title: 13234 - 17 weekATAC-seq

city: San Francisco

first: Ryan

last: Ziffra

institute: UCSF

description: 13234 - 17 week

data_processing:
BCL files were generated from Illumina Novaseq 6000 sequencing runs
for scATACseq data, fastq files were generated from BCL files using cellranger-atac (v1.0.0.) mkfastq. Fastq files were then aligned and processed using the cellranger-atac (v1.0.0) count pipeline
for scRNAseq data, fastq files were generated from BCL files using cellranger (v3.0.2) mkfastq. Fastq files were then aligned and processed using the cellranger (v3.0.2) count pipeline.
snap files were generated using SnapTools v1.4.8 from fragment file outputs of cellranger-atac (v1.0.0)
Genome_build: hg38
Supplementary_files_format_and_content: csv file outputs from cellranger-atac containing metadata for scATAC-seq samples
Supplementary_files_format_and_content: Snap files generated from cellranger-atac fragment file outputs using SnapTools v1.4.8
Supplementary_files_format_and_content: cellranger filtered_feature_bc_matrix outputs for scRNAseq samples
Supplementary_files_format_and_content: Rdata containers for Seurat and SnapATAC objects

source_name: induced pluripotent stem cells

growth_protocol: Cortical organoids were cultured using a forebrain directed differentiation protocol. Briefly, 2 genetically normal human induced PSC lines, H28126 and 13234, and the embryonic stem cell line H1, were expanded and dissociated to single cells using accutase. After dissociation, cells were reconstituted in neural induction media at a density of 10,000 cells per well in 96 well v-bottom low adhesion plates. GMEM-based neural induction media includes 20% Knockout Serum Replacer (KSR), 1X non-essential amino acids, 0.11mg/mL Sodium Pyruvate, 1X Penicillin-Streptomycin, 0.1mM Beta Mercaptoethanol, 5uM SB431542 and 3uM IWR1-endo. Media was supplemented with 20uM Rock inhibitor Y-27632 for the first 6 days. After 18 days organoids were transferred from 96 to six well low adhesion plates and moved to an orbital shaker rotating at 90rpm and changed to DMEM/F12-based media containing 1X Glutamax, 1X N2, 1X B27 without Vitamin A and 1X anti-anti. At 35 days, organoids were moved into DMEM/F12-based media containing 1X N2, 1X B27 with Vitamin A and 1x anti-anti. Throughout culture duration organoids were fed every other day.

extract_protocol:
Cerebral organoids were dissociated in Papain containing Deoxyribonuclease I (DNase) for 30 minutes at 37C and samples were triturated to form a single cell suspension. For scATAC-seq, cells were pelleted and lysed for 3 minutes in 100uL chilled Lysis Buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20, 0.1% Igepal CA-630, 0.01% Digitonin, 1% BSA). Lysed cells were then washed with 1mL chilled Wash Buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20, 1% BSA) and nuclei were pelleted at 500rcf for 5 minutes at 4C.
Nuclei were prepared as outlined in the 10X Genomics Chromium single cell ATAC-seq solution protocol (v1.0 kit was used). Nuclei were loaded with a capture target of 10,000 nuclei per sample. scATAC-seq libraries were prepared for sequencing following the 10X Genomics single cell ATAC-seq solution protocol. scATAC-seq libraries were sequenced using PE150 sequencing on an Illumina NovaSeq with a target depth of 25,000 reads per nucleus.

tag: culture type

value: cortical organoid

value: 17 weeks


title: H28126 - 24 weekATAC-seq

description: H28126 - 24 week

value: 24 weeks


title: H28126 - 9 weekRNA-Seq

description: H28126 - 9 week

extract_protocol:
Cerebral organoids were dissociated in Papain containing Deoxyribonuclease I (DNase) for 30 minutes at 37C and samples were triturated to form a single cell suspension. For scRNAseq cells were counted and loaded onto 10x chip.
Single cell RNA-seq libraries were generated using the 10x Genomics Chromium 3’ Gene Expression Kit. Briefly, single cells were loaded onto chromium chips with a capture target of 10,000 cells per sample. Libraries were prepped following the provided protocol and sequenced on an Illumina NovaSeq with a targeted sequencing depth of 50,000 reads per cell. BCL files from sequencing were then used as inputs to the 10X Genomics Cell Ranger pipeline.

value: 9 weeks


title: 13234 - VitA treatedRNA-Seq

description: 13234 - VitA treated

treatment_protocol: At day 35, organoids from each line were split into 3 different conditions: 1) normal media conditions for day 35 and beyond as described above (with Vitamin A), 2) normal media conditions for day 35 and beyond (with Vitamin A) plus 100uM 4-Diethylaminobenzaldehyde (DEAB), an inhibitor of retinoic acid synthesis, 3) normal media conditions for day 35 and beyond as described above except using B27 without Vitamin A. DEAB treatment was ended after one week, and culture conditions remain otherwise the same until day 70, at which time organoids were processed for scRNA-seq and fixed for immunohistochemistry.

value: 10 weeks

value: Vitamin A


title: H1 - 9 weekRNA-Seq

description: H1 - 9 week

source_name: embryonic stem cells


title: 13234 - DEABRNA-Seq

description: 13234 - DEAB

value: 4-Diethylaminobenzaldehyde (DEAB)


title: H1 - 9 weekATAC-seq

description: H1 - 9 week


title: H28126 - 9 weekATAC-seq

description: H28126 - 9 week


title: 13234 - 9 weekATAC-seq

description: 13234 - 9 week


title: day2_pool4_well2

first: George

middle: Christopher

last: Hartoularos

address: 513 Parnassus Ave S965F

department: Graduate Division

institute: University of California, San Francisco

description:
MS_TCZ-2-pool4-2_S5
genetic multiplexing, 10x Genomics

data_processing:
Base-calling and read demultiplexing was done using the NovaSeq S2's on-system BCL to FASTQ conversion tool.
FASTQs were aligned and unique-molecular identifiers were counted using 10x Genomics' cellranger v3.0.1 using the standard hg38 reference. This produces 1 binary sequence alignment map (BAM) file per droplet sequencing lane.
BAMs were inputted into freemuxlet in a batched fashion (3 batches) and was used to annotate filtered barcodes as either singlets or doublets and assign cell-containing droplets to nameless cell donors. This generates a VCF with nameless donors.
The freemuxlet-generated VCF with nameless donors was matched to an orthogonal VCF with patient data to assign singlet droplet barcodes to each named patient, and therefore further attach clinical covariates.
Genome_build: hg38
Supplementary_files_format_and_content: File format is a tar archive containing a gzipped Matrix Market-formatted matrix (.mtx.gz), filtered barcodes (.tsv), and gzipped hg38-annotated genes (.tsv.gz). Content is count matrices with filtered cell barcodes for each lane of droplet sequencing.

source_name: PBMC

growth_protocol: PBMCs were isolated from blood samples by Ficoll-PaqueTM PLUS density gradient centrifugation and frozen in fetal bovine serum containing 10% (vol/vol) dimethyl sulfoxide. Cells were frozen and not thawed until the day of the experiment when they were used directly for in vitro stimulation.

extract_protocol:
Cells were multiplexed into pools of cells from different patients with the intent of using in silico genetic demultiplexing tools to recover more single cells and reduce batch effect. No samples from the same person were multiplexed into the same pool. Pools were loaded onto the 10x Genomics controller using several lanes per pool, and processed using standard protocols, including cell lysis, reverse transcription, amplification and library generation.
Libraries were constructed using standard protocols from 10x Genomics.

treatment_protocol: Cells were stimulated with soluble anti-CD3 and anti-CD28 antibodies at 37 Celsius, 5% CO2 for 24 hours. Unstimulated PBMCs were incubated under identical conditions to reduce any confounding from incubation conditions other than stimulation.

tag: subject status

value: kidney transplant recipient

value: PBMC


title: day2_pool4_well3

description:
MS_TCZ-2-pool4-3_S6
genetic multiplexing, 10x Genomics


title: day2_pool4_well1

description:
MS_TCZ-2-pool4-1_S4
genetic multiplexing, 10x Genomics


title: day2_pool3_well1

description:
MS_TCZ-2-pool3-1_S1
genetic multiplexing, 10x Genomics


title: day2_pool2_well3

description:
MS_TCZ-2-pool2-3_S6
genetic multiplexing, 10x Genomics


title: day2_pool2_well2

description:
MS_TCZ-2-pool2-2_S5
genetic multiplexing, 10x Genomics


title: day2_pool3_well3

description:
MS_TCZ-2-pool3-3_S3
genetic multiplexing, 10x Genomics


title: day1_pool3_well3

description:
MS-TCZ-1_pool_3-3_S4
genetic multiplexing, 10x Genomics


title: day1_pool4_well1

description:
MS-TCZ-1_pool_4-1_S5
genetic multiplexing, 10x Genomics


title: 13234 - non-VitA controlRNA-Seq

description: 13234 - non-VitA control

value: Control


title: day1_pool3_well1

description:
MS-TCZ-1_pool_3-1_S7
genetic multiplexing, 10x Genomics


title: day2_pool3_well2

description:
MS_TCZ-2-pool3-2_S2
genetic multiplexing, 10x Genomics


title: day2_pool1_well1

description:
MS_TCZ-2-pool1-1_S1
genetic multiplexing, 10x Genomics


title: day2_pool1_well2

description:
MS_TCZ-2-pool1-2_S2
genetic multiplexing, 10x Genomics


title: day1_pool4_well3

description:
MS-TCZ-1_pool_4-3_S7
genetic multiplexing, 10x Genomics


title: day1_pool4_well2

description:
MS-TCZ-1_pool_4-2_S6
genetic multiplexing, 10x Genomics


title: day1_pool2_well3

description:
MS-TCZ-1_pool_2-3_S6
genetic multiplexing, 10x Genomics


title: day1_pool2_well2

description:
MS-TCZ-1_pool_2-2_S5
genetic multiplexing, 10x Genomics


title: day2_pool2_well1

description:
MS_TCZ-2-pool2-1_S4
genetic multiplexing, 10x Genomics


title: day1_pool3_well2

description:
MS-TCZ-1_pool_3-2_S8
genetic multiplexing, 10x Genomics


title: Nonmemory NK cells_Rep2

city: Tyler

first: Sachin

last: Mulik

state: Texas

department: Pulmonary Immunology

institute: The University of Texas Health Science Center at Tyler

data_processing:
Reads were trimmed using Trim galore
Reads were aligned to mouse genome (mm10) using HISAT2
Counting of aligned reads in the BAM files that overlap features in a GFF file using HTseq-counts
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited txt file; Htseq counts data; deseq2 normalized data;

growth_protocol: NK cells were harvested from mice spleen on day 37 post-infection

extract_protocol:
Total RNA was isolated using nucleospin RNA XS kit (Machery-Nagel, Duren, Germany)
Low-Input RNA-Sequencing Library Prep for Illumina

treatment_protocol: CD27+ and CD27- cells were FACS sorted and frozen at -80oC till RNA isolation.

tag: strain background

value: Spleen

value: Nonmemory NK cells


title: Nonmemory NK cells_Rep3


title: Nonmemory NK cells_Rep1


title: day1_pool1_well3

description:
MS-TCZ-1_pool_1-3_S3
genetic multiplexing, 10x Genomics


title: day1_pool1_well1

description:
MS-TCZ-1_pool_1-1_S1
genetic multiplexing, 10x Genomics


title: day1_pool2_well1

description:
MS-TCZ-1_pool_2-1_S4
genetic multiplexing, 10x Genomics


title: SCMNK cells_Rep3

value: SCMNK cells


title: day1_pool1_well2

description:
MS-TCZ-1_pool_1-2_S2
genetic multiplexing, 10x Genomics


title: COV1933: patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1933

city: Muenster

first: I-Na

last: Lu

state: NRW

address: Domagkstraße 20

department: Department of Pediatric Hematology and Oncology

institute: University Children's Hospital Münster

description: single-cell RNA seq data of a patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1933

data_processing:
Raw bcl files were de-multiplexed using the cellranger mkfastq pipeline (cellranger v3.1.0)
Subsequent reads alignments and transcript counting was done individually for each sample using the cellranger count pipeline with standard parameters
 The cellranger aggr pipeline was employed to aggregate samples with mapping normalization to leave each sample with similar sequencing depth per cell.
Genome_build: GRCh38
Supplementary_files_format_and_content: Standard cellranger output format

source_name: CSF

extract_protocol:
CSF samples were collected into round bottom polypropylene tubes and then centrifuged for 10 min at 300 x g. The CSF supernatant was removed and CSF cells were resuspended in 5 ml of X-Vivo15 media (Lonza) and stored at 4°C. The samples were then transported to the laboratory of the Department of Neurology with Institute of Translational Neurology at the University Clinic Münster, Germany for scRNA-seq. Transport time of samples collected in Münster was 10-30 minutes. Transport time of samples collected in Essen was < 60 minutes. Cell suspensions were then centrifuged again for 5 min at 400 x g and then resuspended in 40 μl of media. Out of this volume, 6 μl were used for cell counting and the remaining volume was entirely used for scRNA-seq.
Four Neuro-COVID samples were processed with the Chromium Single Cell 5’ Library & Gel Bead Kit and barcoded, full-length VDJ segments from T cells were enriched from first-strand cDNA via PCR amplification with the Chromium Single Cell VDJ Enrichment Kit, Human T Cell (from 10X Genomics) following the manufacturer’s instructions. Further library preparation was performed using the Chromium Single Cell 5' Library Construction Kit (10X Genomics). Three Neuro-COVID samples were processed with the Chromium Single Cell 3’ Library & Gel Bead Kit and we developed a novel method to sequence antigen receptor information  from 3’ scRNA-seq libraries. The method allows removing the constant region of antigen receptors during enrichment, while maintaining their cell barcode and unique molecular identifier (UMI) information attached to the 3' of the cDNA molecules. In summary, the method involves self-circulating the cDNA library, enriching the VDJ region and re-linearizing. Each step maintains the VDJ region together with the cell barcode and UMI in the same molecule. Sample processing and library preparation was performed according to manufacturer instructions using AMPure XP beads (Beckman Coulter). Sequencing was either carried out on a local Illumina Nextseq 500 using the High-Out 75 cycle kit with a 26-8-0-57 read setup or commercially (Microanaly, China) on a NovaSeq 6000 using the 300 cycle kit with paired end 150 read setup. All the samples were sequenced with a sequencing depth >50,000 reads per cell.

value: CSF-derived leukocytes

tag: diagnosis

value: Neuro-COVID

tag: type of library

value: RNA expression

tag: subject id


title: day2_pool1_well3

description:
MS_TCZ-2-pool1-3_S3
genetic multiplexing, 10x Genomics


title: IIH53423: patient with idiopathic intracranial hypertension (IIH), patient#IIH53423

description: single-cell RNA seq data of a patient with idiopathic intracranial hypertension (IIH), patient#IIH53423

value: IIH


title: HC_H006_RNA_control

source_name: Peripheral Whole-Blood

extract_protocol:
RNA sequencing libraries were prepared according to the Illumina TruSeq® messenger (mRNA) sequencing protocol (TruSeq® RNA Seq Library Prep Kit v2). The resulting libraries were sequenced on the NovaSeq 6000 (2× 50 bp, S2 chemistry).
Patient peripheral blood was collected in 2.5mL tubes PAXgene Blood RNA Tubes, RNA was automated isolated in QIAGEN’s QIAcube using the PAXgene Blood miRNA Kit from QIAGEN PreAnalytiX.

tag: remission

value: Healthy

tag: gender

value: m

tag: age

tag: pseudotime

tag: patient number


title: IIH68490: patient with idiopathic intracranial hypertension (IIH), patient#IIH68490

description: single-cell RNA seq data of a patient with idiopathic intracranial hypertension (IIH), patient#IIH68490


title: IIH91012: patient with idiopathic intracranial hypertension (IIH), patient#IIH91012

description: single-cell RNA seq data of a patient with idiopathic intracranial hypertension (IIH), patient#IIH91012


title: SCMNK cells_Rep2


title: IIH47578: patient with idiopathic intracranial hypertension (IIH), patient#IIH47578

description: single-cell RNA seq data of a patient with idiopathic intracranial hypertension (IIH), patient#IIH47578


title: HC_H008_RNA_control