title: WT-rep2

city: Beijing

first: Ruixue

last: Zhao

state: Beijing

address: Qinghua yuan street

department: School of life sciences

institute: Tsinghua University

data_processing:
Basic processing for all data: FastQC assessed the quality score, adaptor content, and duplication rates of sequencing read. And Trim_galore (version0.6.0) was used to remove the low-quality bases and adaptor sequences with default parameters.
ChIP-seq reads were aligned to a mixed reference worm genome using BWA(version 0.7.17). The reference genome was mixed in advance with Caenorhabditis elegans DNA toplevel assembly (WBcel235 from ensemble) and Drosophila melanogaster DNA toplevel assembly (BDGP6.32 from ensemble). The aligned reads were separated into two sequence-alignment map(SAM) files. The SAM file of Caenorhabditis elegans was then converted into binary alignment map(BAM) files with samtools software(version 1.9) for further analysis while the SAM file of Drosophila melanogaster was used for calculating spike-in factors.
The sorted and indexed BAM file of Caenorhabditis elegans underwent filtration using sambamba software(version 0.6.6) with ` view -h -f bam  -F "not unmapped and not duplicate" `.
The filtered BAM file was then converted to bigwig(bw) file using deeptools software(version 3.3.1) with `bamCoverage --binSize 10 --scaleFactor α --effectiveGenomeSize 100286401 --extendReads --ignoreDuplicates --bam ` where α stood for the Spike-in factors calculated from SAM file of Drosophila melanogaster. The Spike-in factors are calculated as David A. described.
Big wig files were visualized with Integrative Genomics Viewer(IGV, version 2.7.2) and deeptools software (version 3.3.1)
Genome_build: WBcel235 and BDGP6.32
Supplementary_files_format_and_content: wig files were generated using deeptools software(version 3.3.1)

organism: Caenorhabditis elegans

source_name: young adults

growth_protocol: Caenorhabditis elegans were cultivated at 20 °C on nematode growth medium (NGM) agar plates seeded with the Escherichia coli OP50

extract_protocol:
Synchronized young adults were harvested and washed 3 times with M9 to remove excess bacteria. Using 200 μl pipette tip, drip worm mix into a 100 ml beaker that contains liquid nitrogen to make frozen worm “popcorn”. Grind worms into a frozen powder with mortar and crosslinked with 1.1% formaldehyde for 15 min at room temperature, then formaldehyde was quenched by addition of glycine and the fixed powder was washed by cold PBS 3 times. The fixed powder was resuspended and homogenized 2-3 strokes using a glass Dounce homogenizer that is assumed to gently disaggregate cells. Nuclei preparation and chromatin digestion were conducted with SimpleChIP® Enzymatic Chromatin IP Kit (CST,#9003). Briefly, resuspend cells using buffer A and incubate on ice for 10 min; Pellet nuclei was collected and resuspended with buffer B, add Micrococcal nuclease and incubate for 4-12 min at 37°C to digest DNA to the length of approximately 150-900 bp, stop digestion by adding EDTA. Then samples were resuspended in ice-cold FA buffer with 0.1% SDS, and sonicated using a Bioruptor sonication system at 70% power for 20 cycles of 30 s on and 30 s off. The sonicated samples were then centrifuged at 4°C for 15 min at 16,000g and transfer supernatant to a new tube. Then, the cross-linked chromatin concentration was measured by BCA Protein Assay Kit (TIANGEN,#PA115) and and 2% of the extract was saved as the input sample. 5 μg chromatin were precleaned with protein A/G agarose beads. Add 10 ng Drosophila line 2 (S2) cells spike-in chromatin (Active Motif, Catalog No. 53083) to each sample, and immunoprecipitated overnight using 2 ug H3 antibody (Abcam, AB195277) and 0.5 ug spike-in antibody (Active Motif, Catalog No. 61686). Add 30 µl protein A/G agarose beads to each ChIP sample and rotate at 4°C for 2 h. 150 µl ChIP Elution Buffer was added and vortex gently at 1200 rpm for 30 min at 65°C. Reverse crosslink the samples with proteinase K. DNA were purified using QIAquick PCR Purification Kit (Catalog No. 28106),
According to the manufacturer, we used 20 ng purified DNA samples to construct the ChIP–seq library, DNA library construction was conducted with VAHTSTM Universal DNA Library Prep Kit for Illumina® V3 (Vazyme, ND607).

treatment_protocol: Wild type and H2B TKO;unc-85(cas1100) worms were cultivated at 20 °C on nematode growth medium (NGM) agar plates seeded with the Escherichia coli OP50.

value: Wild type

tag: chip antibody

value: H3 antibody(Abcam,ab195277);Spike-in antibody(Active motif, 61686)


title: 20065FL-02-01-06

status: Public on Apr 03 2022

type: SRA

city: Balice

first: Kacper

last: Zukowski

address: Krakowska 1 Street

country: Poland

institute: National Research Institute of Animal Production

library_source: genomic

data_processing:
trimming/raw data cleaning - flexbar and data quality check - fastqc
additional adaptors removal - NGmerge
bwa - alignment
atacseq filtration for aligned reads/marking duplicates - samtools, samjdk, picard, own scripts
peak calling with background tissues - genrich
annotation and resutls data manipulation - R (own scripts)
Assembly: Sscrofa11.1
Supplementary files format and content: compressed gzip file containing raw peaks

molecule: genomic DNA

organism: Sus scrofa

source_name: liver

growth_protocol: All pigs were female and they were maintained at Pig Test Station under the same feeding and housing conditions and were slaughtered when they reached 100±2 kg.

extract_protocol:
Up to twenty minutes letter, liver tissue was sampled  in media tissue-specific for liver tissue (William’s E medium with 1x hepatocyte plating/thawing medium A; Thermofisher). Then samples were transported in +4C to the laboratory. Then they were centrifuged and undergone 10-minutes digestion in 37°C using 1xAcutase (Stempro). After that, they will be filtered by using a 70um cell strainer (Sigma), washed with 10% FCS DMEM/F12 (Gibco) and then slowly frozen in cryotubes with cryoprotectant Cryostor 10 (Stemcell) and Mr Frosty™ Freezing Container to the temperature -80°C.
ATAC libraries were prepared using TruePrepTM DNA Library Prep Kit V2 for Illumina® (Vazyme) according to attached protocol.

tag: breed

value: Zlotnicka White

tag: day

tag: Sex

value: female

tag: tissue

value: liver

tag: shear force

value: high fat content_200

tag: replicant


title: Day 0-4

city: Boston

first: Yae-Huei

last: Liou

state: MA

address: 665 Huntington Ave.

department: MET

country: USA

institute: Harvard School of Public health

description:
Lee_processed-1
20-WT_B6_Day_0_S12

library_source: transcriptomic

data_processing:
Trimming of Illumina adapters (CLC Genomics Workbench v.10 )
Quality control for individual samples (CLC Genomics Workbench v.10 )
Mapping against the reference genome (CLC Genomics Workbench v.10 )
Calculation of expression values using unique matches (CLC Genomics Workbench v.10)
Normalisation by scaling 10.000.000 reads per sample per transcript (TPM),
Genome_build: Genome_build: mouse mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM, Total counts, TPM, and CPM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: imortalized mouse preadipocyte

growth_protocol: Sample are day 0 or day 6 differentiated preadipocyte.

extract_protocol:
RNA was harvest by spin column.
RNA libraries were prepared for sequencing using Illumina’s TruSeq Stranded mRNA Library Preparation Kit based on the Kit’s manual. 2 ug total RNA was used as input.

treatment_protocol: with or without Il13 pre-treatment for 16hr

tag: strain

tag: genotype

value: wild type

tag: agent

tag: time point

value: Day 0


title: HAEC_0dy_0h_3

city: Changchun

first: luya

last: pu

address: No. 126 Xinmin St, Changchun, Jilin

country: China

institute: Jilin University

data_processing:
The libraries were sequenced on an Illumina HiSeq X Ten platform, and 150-bp paired-end reads were generated. Approximately 98.19 M raw reads for each sample were generated. Raw data (raw reads) in fastq format were first processed using Trimmomatic software. In this step, clean data (clean reads) were obtained by removing reads containing adapter and ploy-N or low-quality reads from raw data.
Approximately 13.47 M clean reads for each sample were retained for subsequent analyses. Sequencing reads were mapped to the human genome (GRCh38) using HISAT2. For mRNAs, the FPKM of each gene was calculated using Cufflinks, and the read counts of each gene were obtained using HTSeq-Count. For lncRNAs, the transcriptome from each dataset was assembled independently using the Cufflinks 2.0 program. All transcriptomes were pooled and merged to generate a final transcriptome using Cuffmerge.
RNA expression profile data were analyzed with the DESeq2 package of R. By setting the | log2FoldChange | ≥ 1 and P value ≤ 0.05 as criteria, DE lncRNAs and DE mRNAs were screened for subsequent analysis.
Assembly: hg18
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: human aortic endothelial cells

extract_protocol:
Total RNA of the three groups of HAECs was extracted using TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold (Illumina, Cat. No. RS-122-2301) according to the manufacturer’s instructions. RNA (1 μg) from each sample was used for library construction. First, ribosomal RNA (rRNA) was removed using Ribo-Zero Gold rRNA Removal Kit (Illumina), and RNA was fragmented using a fragment reagent. Subsequently, sequencing libraries were constructed using rRNA-depleted RNA. Finally, products were puriﬁed (Agencourt AMPure XP, BECKMAN COULTER), and library quality was assessed using the Agilent Bioanalyzer 2100 system.

tag: cell type

value: Human aortic-derived endothelial cells

tag: treatment

value: Untreated


title: HAEC_after_24h_3

value: 24h recovery after Lss treatment


title: Day 0-3

description:
Lee_processed-1
19-WT_B6_Day_0_S11


title: Day 6-2

description:
Lee_processed-2
42-WT_B6_Day_6_S26

value: Day 6


title: H2B-TKO;unc-85(cas1100)-rep2

value: H2B TKO;unc-85(cas1100)


title: 20065FL-02-01-03

value: low fat content_200


title: WT-rep1


title: 20065FL-02-01-02


title: HAEC_0dy_0h_2


title: Day 0-2

description:
Lee_processed-1
18-WT_B6_Day_0_S10


title: 20065FL-02-01-01


title: Day 0-1

description:
Lee_processed-1
17-WT_B6_Day_0_S9


title: Wildtype_3_6

status: Public on Apr 02 2022

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/DanieleBarreca/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCm38 (UCSC Genome Browser mm10) and Ensembl reference transcriptome e100 (April 2020) with STAR 2.7.1a and options recommended by the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Bioconductor 3.9 package DESeq2 1.24.0, running under R 3.6.0.
Genome_build: UCSC mm10 based on GRCm38
Supplementary_files_format_and_content: Per gene and sample raw (integer) counts and DESeq2-calculated FPKMs in tab-separated value (TSV) format

extract_protocol:
LSKs were sorted into lysis buffer from the bone marrow of wiltype and mutCALR homozygous mice
For the generation of full-length cDNA, the Smart-seq2 protocol (Picelli, S. et al, Nat Protoc. 2014 Jan;9(1):171-81. doi:10.1038/nprot.2014.006) was used.
The subsequent library preparation from the amplified cDNA was performed using the Nextera XT DNA library prep kit (Illumina).
For sequencing, libraries were pooled, diluted and sequenced on Illumina HiSeq 3000/4000 using 50 bp single-read chemistry.

value: Hematopoietic stem cells (LSKs) sorted from Mouse Bone marrow

tag: gender

value: Male

value: vavCre


title: H2B-TKO;unc-85(cas1100)-rep1


title: HAEC_0dy_0h_1


title: HCT116 ShSrx cells

type: RNA

city: Lexington

first: Qiou

last: Wei

state: KY

address: 324 HSRB, 1095 VA Drive

institute: University of Kentucky College of Medicine

description: total RNA extracted using Qiagen kit

hyb_protocol: standard

scan_protocol: Affymetrix chip standard

data_processing: TAC or Partek Flow recommended

label: biotin

source_name: HCT116 cells

label_protocol: Superscript III indirect cDNA labelling system (invitrogen)

growth_protocol: normal cell culture medium and conditions.

extract_protocol: Qiagen RNA mini kit

treatment_protocol: none.

tag: srx depetion

value: cancer cells ShSrx

tag: assays

value: microRNA 4.0 array


title: Wildtype_3_5


title: Wildtype_3_1


title: mutCALR_Homozygous_3_6

description: mutCALR Homozygous_HSCs

value: CALRdel52 fl/fl; vavCre


title: mutCALR_Homozygous_3_4

description: mutCALR Homozygous_HSCs


title: mutCALR_Homozygous_3_5

description: mutCALR Homozygous_HSCs


title: HCT116 control ShNT cells

description: total RNA extracted using Qiagen kit

value: cancer cells control


title: mutCALR_Homozygous_3_2

description: mutCALR Homozygous_HSCs


title: mutCALR_Homozygous_3_1

description: mutCALR Homozygous_HSCs


title: mutCALR_Homozygous_2_5

description: mutCALR Homozygous_HSCs


title: mutCALR_Homozygous_2_4

description: mutCALR Homozygous_HSCs


title: mutCALR_Homozygous_2_2

description: mutCALR Homozygous_HSCs


title: mutCALR_Homozygous_2_3

description: mutCALR Homozygous_HSCs


title: mutCALR_Homozygous_2_1

description: mutCALR Homozygous_HSCs


title: mutCALR_Homozygous_1_5

description: mutCALR Homozygous_HSCs

value: Female


title: mutCALR_Homozygous_1_6

description: mutCALR Homozygous_HSCs


title: mutCALR_Homozygous_1_3

description: mutCALR Homozygous_HSCs


title: mutCALR_Homozygous_1_2

description: mutCALR Homozygous_HSCs


title: Wildtype_2_6


title: Wildtype_3_4


title: Wildtype_3_3


title: mutCALR_Homozygous_3_3

description: mutCALR Homozygous_HSCs


title: Wildtype_2_3


title: Wildtype_2_2


title: Wildtype_2_4


title: Wildtype_3_2


title: Wildtype_2_1


title: mutCALR_Homozygous_2_6

description: mutCALR Homozygous_HSCs


title: Wildtype_1_5


title: Wildtype_1_4


title: Wildtype_1_3


title: Wildtype_1_2


title: Wildtype_1_1


title: mutCALR_Homozygous_1_4

description: mutCALR Homozygous_HSCs


title: mutCALR_Homozygous_1_1

description: mutCALR Homozygous_HSCs


title: Wildtype_2_5


title: Control-Ig, 3

city: NEW YORK

first: Phillip

last: Galbo

state: NY

institute: Albert Einstein college of medicine

data_processing:
Alignment was done using STAR (version 2.6.1b).
The number of RNA-seq fragments mapped to each gene in the reference gene annotation (downloaded from the UCSC genome browser in 11/2019) was then counted using Htseq (version 0.6.1)
Differntial expression analysis prformed using DESeq2 (version 3.11)
Assembly: mm10/GRCm38
Supplementary files format and content: Tab-delimited text files include raw count values for each sample one for the in vitro and another for the in vivo RNA-seq data

source_name: cells in vitro

growth_protocol: In vivo: flow-sorted GFP+ tumor-infiltrating Tregs from MC38-B7x and MC38-Control tumors engrafted in Foxp3-GFP/DTR mice. In vitro: flow-sorted GFP+ iTregs following treatment protocol (see below)

extract_protocol:
RNA was subsequently extracted with the RNeasy Mini Kit (Qiagen) and stored at –80°C.
Library preparation and sequencing was performed by Admera Health. SMARTer Stranded Total RNA Pico (Takara) was used for library preparation, and sequencing was performed to obtain 40 million paired-end (PE) reads per sample.

treatment_protocol: In vitro: differentiated splenic CD4+ T cells from Foxp3-GFP/DTR mice into iTregs in vitro in the presence of either B7x-Ig or Control-Ig, and subsequently flow-sorted GFP+ iTregs for RNA extraction.

tag: group

value: Control-Ig


title: Tregs from MC38-Control tumors engrafted in Foxp3-GFP/DTR mice, 1

source_name: cells in vivo


title: B7x-Ig, 1


title: Tregs from MC38-Control tumors engrafted in Foxp3-GFP/DTR mice, 2


title: Control-Ig, 2


title: Tregs from MC38-B7x tumors engrated in Foxp3-GFP/DTR mice, 2


title: B7x-Ig, 3


title: Tregs from MC38-B7x tumors engrated in Foxp3-GFP/DTR mice, 3


title: B7x-Ig, 2


title: Wildtype_1_6


title: Control-Ig, 1


title: siRfx1-FemalePN8h-2

city: Shanghai

first: Shaorong

last: Gao

state: Shanghai

address: 1239 Siping Road, Yangpu District

department: School of life science and technology

institute: Tongji University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using bwa mem command, reads that have map quality score less than 10 were removed from downstream analysis.
Pair-end reads were centered to generated the fragmenrts, then extended to 147bp, then center 73bp of the fragment were piled up using bedtools, each sample were normalized to 50M reads.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files are generated using bedtools by pile up the fragments in MNase-seq bam files, each sample were normalized to 50M reads.

source_name: siRfx1 treated female pronucleus 8h post fertilization

growth_protocol: For ESC samples, R1 embryonic stem cell lines were cultured in DMEM medium with 15% ES-qualified FBS, 0.055 mM β-mercaptoethanol, 2 mM glutamine, 0.1 mM nonessential amino acid and 1000 U/ml LIF. For pronucleus sample, embryos were maintained in Q2 medium before harvested.

extract_protocol:
Harvested cells or pronuclei were transferred into lysis buffer and MNase master mix were added to digest the chromatin. The reaction was stopped by EDTA and protease was added to digest proteins. Then fragmented and naked genomic DNA were released.
The released genomic DNA were directly subjected to library construction using KAPA Hyper Prep Kit for the Illumina platform, following the manufacturer’s instructions.

treatment_protocol: For ESC samples, cells were harvested by trypsin digestion and the requested amounts of cells were collected with a capillary sucking device under a phase-contrast microscope. For pronucleus samples, embryos were stained with hoechst 33342 dye and the visible pronuclei were isolated by the piezo-drill micromanipulator.

tag: development stage

value: Zygote stage (8 hr post fertilization)

value: female pronucleus 8h post fertilization


title: siCtrl-MalePN8h-2

source_name: siCtrl treated male pronucleus 8h post fertilization

value: male pronucleus 8h post fertilization

value: siCtrl


title: siMlx-FemalePN8h-2

source_name: siMlx treated female pronucleus 8h post fertilization

value: siMlx


title: siMlx-MalePN8h-1

source_name: siMlx treated male pronucleus 8h post fertilization


title: siMlx-MalePN8h-2


title: Tregs from MC38-Control tumors engrafted in Foxp3-GFP/DTR mice, 3


title: siRfx1-FemalePN8h-1


title: siCtrl-FemalePN8h-2

source_name: siCtrl treated female pronucleus 8h post fertilization


title: Tregs from MC38-B7x tumors engrated in Foxp3-GFP/DTR mice, 1


title: siRfx1-MalePN8h-2

source_name: siRfx1 treated male pronucleus 8h post fertilization


title: siCtrl-FemalePN8h-1


title: siMlx-FemalePN8h-1


title: siRfx1-MalePN8h-1


title: JQ1-MalePN6h-3

source_name: JQ1 treated male pronucleus 6h post fertilization

value: Zygote stage (6 hr post fertilization)

value: male pronucleus 6h post fertilization


title: JQ1-MalePN6h-2


title: JQ1-MalePN6h-1


title: JQ1-FemalePN6h-2

source_name: JQ1 treated female pronucleus 6h post fertilization

value: female pronucleus 6h post fertilization


title: JQ1-FemalePN6h-1


title: Hdac-MalePN6h-2

source_name: Hdac1 and Hdac2 treated male pronucleus 6h post fertilization

value: Hdac1 and Hdac2


title: siCtrl-MalePN8h-1


title: Hdac-MalePN6h-1


title: Hdac-FemalePN6h-1

source_name: Hdac1 and Hdac2 treated female pronucleus 6h post fertilization


title: aphidicolin-MalePN6h-1

source_name: aphidicolin treated male pronucleus 6h post fertilization

value: aphidicolin


title: aphidicolin-FemalePN6h-3

source_name: aphidicolin treated female pronucleus 6h post fertilization


title: a-amanitin-MalePN6h-3

source_name: a-amanitin treated male pronucleus 6h post fertilization

value: a-amanitin


title: aphidicolin-FemalePN6h-1


title: aphidicolin-FemalePN6h-2


title: aphidicolin-MalePN6h-2


title: aphidicolin-MalePN6h-3


title: a-amanitin-MalePN6h-2


title: a-amanitin-MalePN6h-1


title: a-amanitin-FemalePN6h-1

source_name: a-amanitin treated female pronucleus 6h post fertilization


title: a-amanitin-FemalePN6h-3


title: DMSO-MalePN6h-3

source_name: DMSO treated male pronucleus 6h post fertilization

value: DMSO


title: Ctrl-MalePN6h-1

source_name: Water treated male pronucleus 6h post fertilization

value: Water


title: Ctrl-FemalePN6h-2

source_name: Water treated female pronucleus 6h post fertilization


title: Ctrl-MalePN6h-2


title: DMSO-MalePN6h-2


title: DMSO-MalePN6h-1


title: DMSO-FemalePN6h-1

source_name: DMSO treated female pronucleus 6h post fertilization


title: a-amanitin-FemalePN6h-2


title: DMSO-FemalePN6h-3


title: DMSO-FemalePN6h-2


title: 2-cell-siRfx1-2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using STAR (v2.5.2b)  with default parameters.
Gene expression for each sample was quantified to TPM using stringtie v1.3.4.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each transcript.

source_name: Mouse embryo

growth_protocol: After siRNA injection, GV-stage oocytes were incubated in αMEM medium with 5% FBS and 1.5 IU/ml hCG for in vitro maturation. Then the matured MII oocytes were incubated with sperm for in vitro fertilization. The fertilized embryos were cultured in Q2 medium until harvested.

extract_protocol:
Harvested blastomeres were placed into lysis buffer, and Superscript II-triggered reverse transcription followed by cDNA amplification were performed. The amplified cDNA was then fragmented using a Covaris sonicator.
The fragmented DNA were subjected to library construction using KAPA Hyper Prep Kit for the Illumina platform, following the manufacturer’s instructions.

treatment_protocol: Embryos were treated with 0.5% protease E to remove zona pellucida and the released blastomeres were washed thoroughly in PBS with 0.5% BSA.

value: Mouse embryo

value: Late 2-cell stage (36 hr post fertilization)

tag: overexpression


title: 2-cell-siRfx1-3


title: Hdac-FemalePN6h-2


title: 2-cell-siRfx1-1


title: 2-cell-siMlx-3


title: 2-cell-siEtv5-1


title: 2-cell-siMlx-1


title: 2-cell-siMlx-2


title: 2-cell-siCtrl-3


title: 2-cell-siCtrl-1


title: 2-cell-siCtrl-2


title: Ctrl-FemalePN6h-1


title: zygote-siRfx1-3

value: Late zygote stage (14 hr post fertilization)


title: zygote-siMlx-2


title: zygote-siRfx1-2


title: zygote-siRfx1-1


title: Mut_Lac3

city: La Jolla

first: Aleksandr

last: Arzamasov

state: CA

address: 10901 N Torrey Pines Rd

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Raw reads were demultiplexed and quality checked via FastQC (v0.11.9)
Illumina sequencing adapters and short reads (< 20 bp) were trimmed by Cutadapt (v3.4) with parameters: -m 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC
Reads were aligned to rRNA gene sequences extracted from the Bifidobacterium longum subsp. infantis ATCC 15697 genome using Bowtie2 (v2.4.4) to filter rRNA reads
Unmapped (filtered) reads were pseudoaligned to the Bifidobacterium longum subsp. infantis ATCC 15697 transcriptome via Kallisto (v0.46.2) with parameters: --single -l 200 -s 20
Kallisto transcript quantification data were imported into R using the TxImport package and normalized by the TMM method in the edgeR package
Genes with < 1 count per million (CPM) in ≤ 3 samples were filtered out
Normalized, filtered data were variance-stabilized using the VOOM function in the Limma package in R
Differentially expressed genes (>2-fold and <1% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Genome_build: Bifidobacterium longum subsp. infantis ATCC 15697 (GenBank accession no. CP001095.1; locus tags Blon_xxxx)
Supplementary_files_format_and_content: tab-delimited txt file that includes a matrix with raw gene counts for every gene and every sample

organism: Bifidobacterium longum subsp. infantis

source_name: Cell culture

growth_protocol: Bifidobacterium longum subsp. infantis ATCC 15697 WT and nagR knockout mutant (nagR-KO or Mut) were grown in MRS-CS supplemented with either 1% lactose or 1% LNnT. Samples (2 ml in triplicates) were collected at the early-mid exponential phase (OD600=0.35) and immediately pelleted in a prechilled centrifuge at 4,800 × g for 5 min. Cell pellets were snap-frozen in liquid nitrogen and stored at −80 °C until further use

extract_protocol:
Frozen cell pellets were kept on dry ice and resuspended in a solution containing 250 µL of acid-washed glass beads (212-300 μm), 710 µL of extraction mixture (200 mM NaCl, 20 mM EDTA, 20% SDS), and 500 µL of a mixture of phenol:chloroform:isoamyl alcohol (125:24:1, pH 4.5). Cells were disrupted using Bead Ruptor 12 (Omni International) by alternating 2 min of homogenizing at 6 m/s and 2 min of cooling on ice. Cellular debris was removed by centrifugation (16,000 × g for 10 min), and the aqueous phase was collected. RNA was precipitated with isopropanol and sodium acetate (pH 5.5) at −20 °C overnight, then washed in ice-cold 70% ethanol and resuspended in 100 µL of nuclease-free water. Total RNA was subjected to two consecutive DNase treatments (30 min each) with Baseline-ZERO DNase (Lucigen) and Turbo DNase (Ambion), respectively. Each treatment was followed by cleanup using MEGAclear Transcription Clean-Up Kit (Ambion). RNA was quantified via Qubit Broad Range RNA Assay Kit (Invitrogen), and RNA integrity was confirmed by gel electrophoresis in 1 % agarose and 4200 TapeStation System (Agilent). All samples had RIN > 7.5
Ribosomal RNA was depleted with NEBNext rRNA Depletion Kit for Bacteria (New England Biolabs). Barcoded libraries were made with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Libraries were pooled and sequenced (single-end 75 bp reads) on Illumina NextSeq 500 using High Output V2 Kit (Illumina)

tag: background strain

tag: nagr genotype

value: Mut

tag: carbon source

value: Lac


title: Mut_LNnT3

value: LNnT


title: zygote-siMlx-3

tag: tissue


title: WT_LNnT3

value: WT


title: Mut_Lac1


title: WT_LNnT1


title: Mut_Lac2


title: Mut_LNnT1


title: WT_Lac2


title: WT_LNnT2


title: zygote-siEtv5-1


title: WT_Lac3


title: zygote-siMlx-1


title: zygote-siEtv5-2


title: zygote-siEtv5-3


title: WT_Lac1


title: Mut_LNnT2


title: zygote-siCtrl-3

value: siCtrl


title: zygote-siCtrl-2


title: 2-cell-siEtv5-2


title: Exosomes silica-48h rep2

city: Changsha

first: Zhiyuan

last: Niu

state: Hunan

address: 172 Tongzipo Road

department: School of Basic Medical Science

institute: Central south university

description: microRNA

data_processing:
Sequenced reads were trimmed for adaptor sequence using trim_galore with the default parameters,then mapped to mm10  whole genome using AASRA.
Bowtie  is used to map clean reads to the reference genome and to other sRNA databases
miRDeep2 (for animals) is used  to predict novel miRNA by exploring the characteristic hairpin structureof miRNA precursor
The small RNA expression level is calculated by using Transcripts Per Kilobase Million  (TPM)
After align to the mm10 genome, counts file was created by htseq-count with parameters -m union -s no.
Assembly: Assembly: mm10
Supplementary files format and content: Supplementary files format and content: counts

source_name: Exosome

growth_protocol: RAW264.7 cells were seeded in a 100mm culture dish with 1×106 / ml and maintained in Dulbecco’s modified Eagle’s medium (DMEM； Gibco) containing 10% Fetal bovine serum (FBS; BI, Kibbutz Beit-Haemek)

extract_protocol:
Extraction of exosomes by ultracentrifugation, total RNA was harvested using Trizol reagent
Small RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols

treatment_protocol: Exo_24h means cells treated with silica for 24h,Exo_48h means cells treated with silica for 48h,each has three replicate

tag: cell line

value: treated with silica for 48 hours


title: Sperm-5min-2U

source_name: sperm

value: Sperm

value: sperm


title: zygote-siCtrl-1

tag: strain


title: Exosomes silica-48h rep1

description: microRNA


title: Exosomes silica-48h rep3

description: microRNA


title: Exosomes silica-24h rep3

description: microRNA

value: treated with silica for 24 hours


title: Sperm-5min-0.2U


title: Exosomes silica-24h rep1

description: microRNA


title: Sperm-5min-0.02U


title: Exosomes NC rep1

description: microRNA

value: untreated


title: Sperm-7.5min-0.2U


title: Sperm-5min-0.0002U


title: Sperm-7.5min-2U


title: E3

city: LuoYang

first: Fan

last: Zhang

state: HeNan

address: No. 263 Kaiyuan Road, Luolong District

institute: HeNan university of science and technolgy

data_processing:
Raw reads were preprocessed with Seqtk to filter out adapter sequences in reads, bases near 3'-end with quality value lower than 20, and reads of length smaller than 25, and reads of ribosome RNA.
Clean reads were aligned to reference genome (ensemble Bos taurus.UMD3.1) by Hisat2 (Ver2.0.4) with default parameters.
Gene expression was quantified and then normalized as FPKM(Fragments Per Kilobase of exon model per Million mapped reads). In this step, fragments of each gene were counted with Stringtie(version 1.3.0) and normalized into trimmed mean of M values (TMM), after which FPKM values of every gene were calculated by Perl scripts.
Genome_build: ensemble Bos taurus.UMD3.1

organism: Bos taurus

source_name: ovary

growth_protocol: Oocytes were placed in the droplet of IVM medium (TCM-199 supplemented with 10% [v/v] FBS, 5 μg/mL LH, 0.5 μg/mL FSH, 100 μM cysteine, and 3% [v/v] follicular fluid) covered with mineral oil and incubated at 38.5°C in an atmosphere containing 5% CO2 at maximum humidity for 22–24 h.

extract_protocol:
Extractions from single cells were amplified for cDNA with SMARTer Ultra Low Input RNA for Illumina Kit, after which QC was performed with Qubit and Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US).
Library was constructed in steps: amplification if needed, fragmentation, end repairment, poly-A appending at 3'-end, adapter ligation, and enrichment. These steps were completed with SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech), Ovation Single Cell RNA-Seq System (Nugen), Ovation Ultralow Library System V2 (Nugen), Agencourt AMPure XP Beads (Beckman), Qubit dsDNA HS Assay Kit (Invitrogen), and Agilent High Sensitivity DNA Kit (Agilent).

treatment_protocol: After IVM, the oocytes were treated with hyaluronidase (100 IU/mL) for 1–2 min to eliminate the cumulus cells and then washed several times with DPBS solution.

value: Bovine IVM oocytes

value: oocytes vitrified in liquid nitrogen with 6.6 M cryoprotective agent concentrations.

value: ovary


title: Sperm-7.5min-0.005U


title: Sperm-7.5min-0.0002U


title: Exosomes silica-24h rep2

description: microRNA


title: Sperm-7.5min-0.001U


title: Sperm-7.5min-0.02U


title: D1

value: oocytes vitrified in liquid nitrogen with 5.6 M cryoprotective agent concentrations.


title: D2


title: D3


title: Sperm-10min-2U


title: E2


title: E1


title: Sperm-10min-0.2U


title: C3

value: fresh oocytes


title: Sperm-10min-0.02U


title: C2


title: Sperm-5min-0.001U


title: Exosomes NC rep2

description: microRNA


title: C1


title: Sperm-5min-0.005U


title: B3

value: oocytes vitrified in liquid helium with 6.6 M cryoprotective agent concentrations.


title: Sperm-10min-0.001U


title: B1


title: A5

value: oocytes vitrified in liquid helium with 5.6 M cryoprotective agent concentrations.


title: RSFemalePN3h-2

source_name: female pronucleus 3h post fertilization using round spermatid

value: Zygote stage (3 hr post fertilization)


title: Sperm-10min-0.0002U


title: RSFemalePN3h-1

value: female pronucleus 3h post fertilization using round spermatid


title: RSFemalePN2h-2

source_name: female pronucleus 2h post fertilization using round spermatid

value: Zygote stage (2 hr post fertilization)


title: RSFemalePN2h-1

value: female pronucleus 2h post fertilization using round spermatid


title: RSFemalePN1h-2

source_name: female pronucleus 1h post fertilization using round spermatid

value: Zygote stage (1 hr post fertilization)


title: A4


title: A3


title: RSFemalePN1h-1

value: female pronucleus 1h post fertilization using round spermatid


title: P7

city: Hangzhou

first: zuorui

last: xie

address: Zhejiang Gongshang University

institute: ZFM

data_processing:
Library strategy: 16S rDNA DNA-seq
Total DNA extracted from the sample
Using FLASH v1.2.7 software, the reads of each sample were spliced by overlapping, and the obtained splicing sequence was the original Tag data (Raw Tags)
Using Trimmomatic v0.33 software to filter the spliced Raw Tags to obtain high-quality Tag data (Clean Tags)
Using UCHIME v4.2 software to identify and remove chimera sequences to obtain final effective data (Effective Tags)
Use Usearch software to cluster effective data at the 97% similarity level to obtain OTU. By comparing the representative sequences of OTUs with the Silva (bacteria) taxonomy database, the species classification information corresponding to each OTU can be obtained, and then the community composition of each sample can be counted at each level (phylum, class, order, family, genus, species). The QIIME software was used to generate species abundance tables at different taxonomic levels, and then the R language tool was used to draw the community structure map of the samples at each taxonomic level.
Assembly: V3-V4 region of the 16S rDNA gene
Supplementary files format and content: tab-delimited text file includes OTU relative abundance of each sample

organism: human feces metagenome

source_name: fecal

growth_protocol: Anaerobic fermentation (10% H2, 10% CO2 and 80% N2) at 37 °C was performed in an anaerobic workstation (DG250, Don Whitley Scientific, Bingley, UK). After 24 h, fecal fermentation suspension (1 mL) was collected.

extract_protocol:
Genomic DNA was extracted from the fecal fermentation suspension with a QIAamp PowerFecal DNA extraction kit, according to the manufacturer’s instructions.
16S rDNA gene high-throughput sequencing of the V3-V4 region was performed by Biomarker Bio-Tech Co., Ltd. (Beijing, China), with an Illumina MiSeq platform.

treatment_protocol: The fresh fecal samples were immediately collected, weighed and diluted in anaerobic, sterile phosphate-buffered saline (PBS, pH 7, 0.10 M) to prepare 10% fecal homogenate suspensions (w/v). Each culture consisted of sterilized VIS medium (5 mL) fecal suspension (500 μL), and CPFE sample (0.10 g/mL, 500 μL).

value: fecal

value: Original fecal in-vitro fermentation for 24 h


title: RSFemalePN0.5h-2

source_name: female pronucleus 0.5h post fertilization using round spermatid

value: Zygote stage (0.5 hr post fertilization)


title: B2


title: P2


title: P4


title: P5


title: P3


title: RSFemalePN0.5h-1

value: female pronucleus 0.5h post fertilization using round spermatid


title: RSMalePN3h-2

source_name: male pronucleus 3h post fertilization using round spermatid


title: RSMalePN2h-1

source_name: male pronucleus 2h post fertilization using round spermatid


title: RSMalePN3h-1

value: male pronucleus 3h post fertilization using round spermatid


title: RSMalePN2h-2

value: male pronucleus 2h post fertilization using round spermatid


title: P1


title: RSMalePN1h-2

source_name: male pronucleus 1h post fertilization using round spermatid


title: Ori6

value: Original fecal without treatment (blank control)


title: P6


title: Ori4


title: RSMalePN1h-1

value: male pronucleus 1h post fertilization using round spermatid


title: Ori3


title: Exosomes NC rep3

description: microRNA

value: untreated


title: Ori2


title: Ori7


title: Ori1


title: N7

value: In-vitro co-fermentation of feces and bergamot flavonoids for 24 h


title: RoundSpermatids-2

source_name: round spermatid

value: Round spermatid

value: round spermatid


title: RoundSpermatids-3


title: N6


title: RoundSpermatids-1


title: N5


title: N4


title: FemalePN12h-1

source_name: female pronucleus 12h post fertilization

value: Zygote stage (12 hr post fertilization)


title: FemalePN12h-3

value: female pronucleus 12h post fertilization


title: FemalePN12h-2


title: FemalePN8h-4

source_name: female pronucleus 8h post fertilization

value: Zygote stage (8 hr post fertilization)

value: female pronucleus 8h post fertilization


title: N2


title: Ori5


title: N3


title: N1


title: FemalePN8h-3


title: M7

value: In-vitro co-fermentation of feces and lemon flavonoids for 24 h


title: FemalePN8h-1


title: RSMalePN0.5h-2

source_name: male pronucleus 0.5h post fertilization using round spermatid


title: FemalePN8h-2


title: M6

value: fecal


title: M4


title: FemalePN6h-4

source_name: female pronucleus 6h post fertilization

value: Zygote stage (6 hr post fertilization)

value: female pronucleus 6h post fertilization


title: M3


title: FemalePN6h-3


title: M1


title: L6

value: In-vitro co-fermentation of feces and Wogan flavonoids for 24 h


title: L3


title: L4


title: FemalePN4h-2

source_name: female pronucleus 4h post fertilization

value: Zygote stage (4 hr post fertilization)

value: female pronucleus 4h post fertilization


title: L5


title: FemalePN4h-3


title: FemalePN4h-4


title: FemalePN6h-1


title: L7


title: FemalePN3h-4

source_name: female pronucleus 3h post fertilization

value: Zygote stage (3 hr post fertilization)

value: female pronucleus 3h post fertilization


title: FemalePN3h-2


title: RSMalePN0.5h-1

value: Zygote stage (0.5 hr post fertilization)

value: male pronucleus 0.5h post fertilization using round spermatid


title: L1


title: M2


title: FemalePN3h-3


title: FemalePN6h-5


title: FemalePN3h-1


title: K6

value: In-vitro co-fermentation of feces and grapefruit flavonoids for 24 h


title: M5


title: FemalePN4h-1


title: L2


title: FemalePN2h-3

source_name: female pronucleus 2h post fertilization

value: Zygote stage (2 hr post fertilization)

value: female pronucleus 2h post fertilization


title: K7


title: K5


title: FemalePN6h-2


title: K4


title: FemalePN2h-1


title: FemalePN1.5h-3

source_name: female pronucleus 1.5h post fertilization

value: Zygote stage (1.5 hr post fertilization)


title: K3


title: K1


title: FemalePN1h-2

source_name: female pronucleus 1h post fertilization

value: Zygote stage (1 hr post fertilization)

value: female pronucleus 1h post fertilization


title: K2


title: J7

value: In-vitro co-fermentation of feces and dekopon flavonoids for 24 h


title: FemalePN1.5h-2

value: female pronucleus 1.5h post fertilization


title: FemalePN0.5h-2

source_name: female pronucleus 0.5h post fertilization


title: FemalePN2h-2


title: FemalePN1.5h-1


title: FemalePN0.5h-1

value: female pronucleus 0.5h post fertilization


title: J2

value: fecal


title: J6


title: FemalePN0.5h-3


title: FemaleMIIOocyte-5

source_name: MII stage oocyte

value: MII stage oocyte


title: J4

source_name: fecal


title: J5


title: J3


title: J1


title: I6

value: In-vitro co-fermentation of feces and longyan kumquat flavonoids for 24 h


title: FemaleMIIOocyte-4


title: FemalePN1h-1


title: I7


title: FemaleMIIOocyte-3


title: FemaleMIIOocyte-2


title: I5


title: FemalePN1h-3


title: I4


title: MalePN12h-3

source_name: male pronucleus 12h post fertilization

value: Zygote stage (12 hr post fertilization)

value: male pronucleus 12h post fertilization


title: I3


title: MalePN12h-2


title: FemaleMIIOocyte-1


title: I2


title: H7

value: In-vitro co-fermentation of feces and sichuan kumquat flavonoids for 24 h


title: MalePN8h-3

source_name: male pronucleus 8h post fertilization

value: Zygote stage (8 hr post fertilization)

value: male pronucleus 8h post fertilization


title: MalePN8h-4


title: H6


title: MalePN12h-1


title: MalePN8h-1


title: H3


title: MalePN6h-4

source_name: male pronucleus 6h post fertilization

value: Zygote stage (6 hr post fertilization)

value: male pronucleus 6h post fertilization


title: H5


title: MalePN6h-5


title: H2


title: H4


title: MalePN8h-2


title: H1


title: MalePN6h-2


title: G7

value: In-vitro co-fermentation of feces and majia pomelo flavonoids for 24 h


title: MalePN6h-3


title: G6


title: MalePN6h-1


title: MalePN4h-3

source_name: male pronucleus 4h post fertilization

value: Zygote stage (4 hr post fertilization)

value: male pronucleus 4h post fertilization


title: G5


title: MalePN4h-2


title: I1


title: G4


title: G3


title: MalePN3h-2

source_name: male pronucleus 3h post fertilization

value: Zygote stage (3 hr post fertilization)

value: male pronucleus 3h post fertilization


title: MalePN4h-1


title: G2


title: G1


title: MalePN3h-1


title: Sperm-10min-0.005U

source_name: sperm

value: Sperm

value: sperm


title: MalePN2h-1

source_name: male pronucleus 2h post fertilization

value: Zygote stage (2 hr post fertilization)

value: male pronucleus 2h post fertilization


title: F6

value: fecal

value: In-vitro co-fermentation of feces and apple pomelo flavonoids for 24 h


title: MalePN2h-2


title: MalePN2h-3


title: F7


title: F3


title: F2


title: MalePN1.5h-3

source_name: male pronucleus 1.5h post fertilization

value: Zygote stage (1.5 hr post fertilization)

value: male pronucleus 1.5h post fertilization


title: MalePN1.5h-1


title: MalePN1h-3

source_name: male pronucleus 1h post fertilization

value: Zygote stage (1 hr post fertilization)

value: male pronucleus 1h post fertilization


title: E6

value: In-vitro co-fermentation of feces and blood orange flavonoids for 24 h


title: MalePN0.5h-1

source_name: male pronucleus 0.5h post fertilization

value: Zygote stage (0.5 hr post fertilization)

value: male pronucleus 0.5h post fertilization


title: MalePN0.5h-2


title: MalePN1.5h-2


title: F4


title: MalePN1h-2


title: MalePN1h-1


title: E7


title: E5


title: F5


title: E4


title: MaleSperm-3


title: F1


title: E2


title: MaleSperm-1


title: MaleSperm-2


title: D7

value: In-vitro co-fermentation of feces and lane late navel orange flavonoids for 24 h


title: D6


title: D5


title: ESCP5-4

source_name: embryonic stem cells

value: R1 embryonic stem cell

value: embryonic stem cells


title: D2


title: ESCP5-1


title: ESCP5-3


title: ESC1-3


title: D1


title: C7

value: In-vitro co-fermentation of feces and ponkan flavonoids for 24 h


title: E3


title: C6


title: ESC1-1


title: E1


title: C4


title: ESCP100-2


title: C3


title: ESCP100-1


title: D3


title: D4


title: ESCP5-2


title: C1


title: C2


title: B7

value: In-vitro co-fermentation of feces and chachiensis flavonoids for 24 h


title: ESC1-2


title: C5


title: BA-48h RNA-seq

city: hangzhou

first: zhaolun

last: wang

address: cangqian street

institute: inheregene

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the Zv9 genome assembly using Tophat version 2.0.6 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using DEGseq function package in R program version 2.10.0
Assembly: UCSC Zv9
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

molecule: polyA RNA

organism: Danio rerio

source_name: liver progenitor

growth_protocol: Fish were maintained in aerated water at 23±1°C, 7.8±1 pH, 0.25 g·L-1 hardness, on a 12 h/12 h light/dark photoperiod cycle, the density was 1 fish per liter water.

extract_protocol:
Total RNA was extracted with AMBION AM1560 kit.
Following "TruSeq RNA Sample Preparation Guide".

treatment_protocol: Zebrafish were divided into Control, Binaprofen 0.8 mM, Zebrafish were exposed drugs for 12h/24h/48h

value: FVB N/J

value: liver

value: liver progenitor


title: BA-24h RNA-seq


title: B3

value: fecal


title: BA-12h RNA-seq


title: B2


title: B1


title: B5


title: B4


title: A6

value: In-vitro co-fermentation of feces and satsuma orange flavonoids for 24 h


title: A5


title: A4


title: negative RNA-seq

value: negative control


title: Unstimulated splenocytes day 7 post infection mouse 6

city: Siena

first: Francesco

last: Santoro

state: SI

address: Viale Bracci, 16, V lotto, I piano

department: Department of Medical Biotechnologies

country: Italy

institute: University of Siena

data_processing:
Base-calling, filtering, alignment and counting were performed by the Ion Proton Server
Assembly: GRCm38
Supplementary files format and content: Mouse_counts_20191024.csv contains read counts for all the samples

source_name: Splenocytes

extract_protocol:
NucleoSpin® RNA kit (Macherey-Nagel)
Ion AmpliSeq™ Transcriptome Mouse Gene Expression Kit

tag: infection

tag: day after infection

tag: in vitro stimulation


title: Unstimulated splenocytes day 7 post infection mouse 5


title: Stimulated splenocytes day 7 post infection mouse 6


title: Stimulated splenocytes day 7 post infection mouse 4


title: Unstimulated splenocytes day 7 post infection mouse 4


title: B6


title: Stimulated splenocytes day 7 post infection mouse 3


title: A2


title: A3


title: Study participant 100-913

city: St Louis

first: Jose

middle: P

last: Zevallos

state: MO

address: 660 South Euclid Avenue, Campus Box 8115

department: Otolaryngology - Head and Neck Surgery

institute: Washington University School of Medicine

hyb_protocol: Transcripts were hybridized to a panel of 770 probes (Nanostring IO360)

scan_protocol: Counts of hybridized transcripts were read using the nCounter platform

data_processing: Raw counts were normalized with the nSolver software (4.0) package using the geometric mean of both positive control probes and housekeeping probes. A background threshold count was set to 20.

source_name: Primary p16(+) oropharyngeal squamous cell carcinoma

label_protocol: Hybridized transcripts were purified and immobilized on a sample cartridge

extract_protocol: RNA was extracted from samples using QIAGEN RNeasy kits

tag: age(years)

tag: sex (1=male,2=female)

tag: race (1=white,2=asian)

tag: tobacco (1=current,2=former,3=never)

tag: subsite(1=tonsils and pillars,2=base of tongue,3=pharyngeal overlapping)

tag: clin_stage(1=stage i,2=stage ii,3=stage iii,4=stage iv)

tag: disease state

value: human papillomavirus (HPV)-associated oropharyngeal squamous cell carcinoma (OPSCC)

value: HPV(+) OPSCC tumor


title: A1

tag: treatment


title: Study participant 100-905


title: Unstimulated splenocytes day 1 post infection mouse 1


title: Stimulated splenocytes day 2 post infection mouse 6


title: Stimulated, uninfected splenocytes mouse 3


title: Study participant 100-988


title: Study participant 100-931


title: Stimulated splenocytes day 7 post infection mouse 2


title: Stimulated splenocytes day 7 post infection mouse 5


title: Unstimulated splenocytes day 2 post infection mouse 4


title: Unstimulated splenocytes day 7 post infection mouse 2


title: Stimulated splenocytes day 2 post infection mouse 5


title: Unstimulated splenocytes day 4 post infection mouse 2


title: Study participant 100-740


title: Stimulated splenocytes day 4 post infection mouse 2


title: Study participant 100-797


title: Unstimulated, uninfected splenocytes mouse 3


title: Unstimulated splenocytes day 1 post infection mouse 6


title: Unstimulated splenocytes day 7 post infection mouse 1


title: Study participant 100-796


title: Study participant 100-883


title: Unstimulated splenocytes day 2 post infection mouse 5


title: Unstimulated splenocytes day 2 post infection mouse 6


title: Stimulated splenocytes day 1 post infection mouse 5


title: Study participant 100-347


title: Study participant 100-406


title: Study participant 100-352


title: Study participant 100-378


title: Study participant 100-346


title: Study participant 100-136


title: Study participant 100-162


title: Unstimulated splenocytes day 1 post infection mouse 5


title: Study participant 100-126


title: Stimulated splenocytes day 2 post infection mouse 4


title: Study participant 100-1211


title: Unstimulated splenocytes day 7 post infection mouse 3


title: Study participant 100-1189


title: A7


title: Stimulated splenocytes day 1 post infection mouse 1


title: Study participant 100-1171


title: Study participant 100-1177


title: Study participant 100-1158


title: Unstimulated splenocytes day 2 post infection mouse 2


title: Unstimulated splenocytes day 2 post infection mouse 1


title: Study participant 100-1164


title: Stimulated splenocytes day 2 post infection mouse 2


title: Stimulated splenocytes day 1 post infection mouse 6


title: Stimulated splenocytes day 7 post infection mouse 1


title: Stimulated splenocytes day 2 post infection mouse 3


title: Study participant 100-1149


title: Study participant 100-1114


title: Study participant 100-1145


title: Stimulated splenocytes day 4 post infection mouse 1


title: Study participant 100-1107


title: Study participant 100-1146


title: Unstimulated splenocytes day 2 post infection mouse 3


title: Stimulated splenocytes day 2 post infection mouse 1


title: Unstimulated splenocytes day 4 post infection mouse 1


title: Stimulated splenocytes day 1 post infection mouse 4


title: Unstimulated splenocytes day 1 post infection mouse 4


title: Stimulated splenocytes day 1 post infection mouse 3


title: Unstimulated splenocytes day 1 post infection mouse 3


title: Study participant 100-1104


title: Stimulated splenocytes day 1 post infection mouse 2


title: Study participant 100-1106


title: Study participant 100-1076


title: Study participant 100-1040


title: Stimulated, uninfected splenocytes mouse 2


title: Study participant 100-1038


title: Study participant 100-1033


title: Unstimulated splenocytes day 1 post infection mouse 2


title: Study participant 100-1026


title: Unstimulated, uninfected splenocytes mouse 2


title: Study participant 100-1050


title: Stimulated splenocytes day 4 post infection mouse 6


title: Stimulated splenocytes day 4 post infection mouse 5


title: Study participant 100-072


title: Q848_LP_CD49f+_EpCAM+

type: genomic

city: Woolloongabba

first: Jodi

middle: M

last: Saunus

state: Qld

address: 37 Kent St

department: Mater Research Institute

country: Australia

institute: The University of Queensland

description: normal breast tissue sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio (methylation module)

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from snap-frozen cell samples using the Qiagen DNA/RNA Allprep mini kit according to standard instructions

treatment_protocol: Surgical tissue was collected, enzymatically processed to a single-cell suspension, and cell subpopulations sorted by FACS within 24 hours

tag: gender

value: female

value: cosmetic reduction mammoplasty

tag: histopathology

value: normal, no neoplastic change


title: Study participant 100-070


title: Q848_indistinct_CD49f-_EpCAM-

description: normal breast tissue sample


title: Stimulated, uninfected splenocytes mouse 6


title: Study participant 100-1006


title: ATAC-seq_2D hepatocyte differentiation

city: Cambridge

first: Haiting

last: Ma

address: 455 Main Street

institute: Whitehead Institute

description: ATAC-seq 2D hPSC-hepatocytes

data_processing:
Images analysis and base calling was done using the Illumina standard pipeline.
After removing adaptors with cutadapt (cutadapt -a CTGTCTCTTATA), ATAC-seq results were aligned to Hg38 with bowtie2 (using “--very-sensitive --no-discordant -X 2000”). The generated SAM filers were converted to BAM files, sorted, and indexed using samtools. Bigwig files were generated from BAM files with bamCoverage (-of bigwig), and peak visualizations were performed in a customized session of genome browser(Kent et al., 2002). The total number of reads were obtained with “samtools view -c”, and reads mapped to mitochondrial genomes were removed with “samtools view | grep -v chrM”. PRC duplicates were removed with picard tools (“MarkDuplicates REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT”), and properly paired reads were obtained with samtools (“samtools view -h -b -F 1804 -f”). Then reads were shifted (+4 for the forward strand, -5 for the reverse strand) by deeptools (“alignmentSieve --numberOfProcessors 8 –ATACshift”), and blacklist (hg38.blacklist.bed.gz) were used to filter unspecific reads. Post alignment quality controls were performed with ATACseqQC. TSS enrichment scores were calculated with Encode ATAC-seq pipeline (caper run atac.wdl). Fragment length were visualized with Picard CollectInsertSizeMetrics or deeptools bamPEFragmentSize, and reads enrichments were visualized with ngs.plots.
ATAC-seq peaks were called with macs2(Zhang et al., 2008) (macs2 callpeaks -f BAMPE -q 0.001 --nomodel -g hs --keep-dup all --cutoff-analysis), and fraction of reads in peaks (FRiP) were performed with BEDTools(Quinlan and Hall, 2010) and SAMtools(Li et al., 2009) (bedtools sort -i peaks.narrowPeak| bedtools merge -i stdin | bedtools intersect -u -nonamecheck -a /final.shifted.bam -b stdin -ubam | samtools view -c). Motif analyses were performed using homer(Heinz et al., 2010) (findMotifsGenome.pl hg38 -size 200 -mask). The analyses of overlapping between THRB-FLAG ChIP-seq (peaks were called from GSM2534017 using the ChIP-seq analysis methods described below) and ATAC-seq peaks were performed using BEDTools.
Genome_build: hg38
Supplementary_files_format_and_content: Bed files of called peaks

source_name: 2D hPSC-hepatocytes

growth_protocol: H1 ES cell were routinely cultured in mTeSR medium in matrigel-coated 6-well plates, and passaged every 3-4 days with versene passaging. Differentiation to hepatocytes-like cells were describe in the manuscript.

extract_protocol:
The ATAC-seq tagmentation and library preparation methods were described in the manuscript.
Library were prepared based on previous method(Buenrostro et al., 2013). After amplifying ATAC-seq library of the specific cycles based on q-PCR measurements, the libraries were double-side selected (0.5-1.3x) with SPRI beads (Beckman), followed by 1x selection to remove primer dimers and sequenced on a Hi-seq 2500 equipment with 60 bp pair-end sequencing.

treatment_protocol: The 2D, 3D hepatocytes differentiation were described in the manuscript.

tag: cell type

value: 2D hPSC-differentiated hepatocytes-like cells


title: ATAC-seq_3D hepatocyte differentiation

description: ATAC-seq 3D hPSC-hepatocytes-S4

source_name: 3D hPSC-hepatocytes-S4

value: 3D hPSC-differentiated hepatocytes-like cells-S4


title: 3D hepatocyte differentiation-S5-1

data_processing:
Images analysis and base calling was done using the Illumina standard pipeline.
RNA-seq reads were aligned to the hg38 genome assembly using STAR version 2.7.1a with the following configurations: Ensemble 93 transcripte models, and '--sjdbOverhang 100'.
Gene counts were generated with featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: Raw counts table.

source_name: 3D hPSC-hepatocytes-S5

extract_protocol:
Total RNA extraction were performed with Rneasy-micro plus kit based on Qiagen's instruction.
About 10-20 ng total RNA samples were used for constructing stranded RNA libraries with Swift RNA-seq library preparation kit according to the instructions. Final libraries went through QC with the Fragment Analyzer and qPCR on a Roche Light Cycler 480 II. All libraries were then pooled and sequenced at single-end 40-50 base-pair using the Illumina HiSeq 2500.

treatment_protocol: The 2D, 3D hepatocytes differentiation, S4 and S5 medium components were described in the manuscript.

value: 3D hPSC-differentiated hepatocytes-like cells-S5

tag: culture method

value: 3D hepatocytes differentiation-S5


title: 3D hepatocyte differentiation-S5-2


title: 3D hepatocyte differentiation-S4-2

value: 3D hepatocytes differentiation-S4


title: Study participant 100-062

tag: tissue


title: Study participant 100-068


title: 3D hepatocyte differentiation-S4-1


title: ATAC-seq_Primary_hepatocytes

description: ATAC-seq Primary human hepatocytes

source_name: Primary human hepatocytes

value: Primary human hepatocytes


title: Study participant 100-1086


title: 2D hepatocyte differentiation-4

description: 2D hPSC-hepatocytes

value: 2D hepatocytes differentiation


title: Stimulated splenocytes day 4 post infection mouse 4

tag: strain


title: Stimulated, uninfected splenocytes mouse 4

tag: infection


title: Q848_luminal_CD49f-_EpCAM+

description: normal breast tissue sample


title: Study participant 100-057


title: 2D hepatocyte differentiation-5

description: 2D hPSC-hepatocytes


title: Study participant 100-047


title: Stimulated, uninfected splenocytes mouse 1

tag: day after infection


title: Undifferentiated ES control

description: Undifferentiated human ES cells H1

source_name: H1 ES cells

value: H1-ES cells

value: non-differentiated


title: Unstimulated splenocytes day 4 post infection mouse 6

tag: in vitro stimulation


title: Primary_hepatocytes_AQL

description: 2D hPSC-hepatocytes

value: non-cultured


title: Study participant 100-026

tag: age(years)


title: Stimulated splenocytes day 4 post infection mouse 3


title: Q695_LP_CD49f+_EpCAM+

description: normal breast tissue sample


title: Unstimulated splenocytes day 4 post infection mouse 5


title: SM14.d.25

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

data_processing:
FASTQ files were created with the Illumina supplied scripts in the BCL2FASTQ software (v2.20)
Illumina adapters trimmed with Trim Galore! v0.4.3
FASTQs aligned to the hg19 reference genome with STAR v2.5.2a using default parameters
--quantMode GeneCounts option in STAR used to count genes against the GENCODE v19 GTF annotation file
Genome_build: hg19
Supplementary_files_format_and_content: Processed files is a tab delimited matrix file with the first column representing the Ensembl gene name and subsequent columns raw gene counts generarted by --quantMode GeneCounts option in STAR. A read is counted if it overlaps (1bp or more) with an exon of only one gene on the appropriate strand.

source_name: dopaminergic neurons

growth_protocol: iPSCs were differentiated in a first stage into floor plate cells (mesencephalic neural precursors, days 0-11) via dual SMAD inhibition combined with ventral midbrain patterning. In a second stage, these floor plate cells were further differentiated (days 11-25) into early postmitotic mesencephalic dopamine neurons.

extract_protocol:
Total RNA was extracted from day 11 floor plate cells and day 25 early post-mitotic dopaminergic neurons differentiated from all eight iPSC lines using the Qiagen RNeasy Mini Kit according to the manufacturer’s protocol. Cell lysates were homogenized using QIAshredder spin columns (Qiagen) and genomic DNA was removed by an on-column DNase treatment (Qiagen). The concentration and quality of RNA samples was assessed using a Bioanalyzer RNA kit (Agilent Technologies) and RNA integrity numbers for all RNA samples ranged between 8.3 to 10.
cDNA libraries were generated with the Illumina TruSeq Stranded kit with a poly-A selection.

value: iPSC-derived postmitotic dopaminergic neurons

tag: individual derived from

value: SM

tag: age

value: day 25 of differentiation


title: Q695_basal_CD49f+_EpCAM-

description: normal breast tissue sample


title: Q848_basal_CD49f+_EpCAM-

description: normal breast tissue sample


title: Q695_luminal_CD49f-_EpCAM+

description: normal breast tissue sample


title: Q695_indistinct_CD49f-_EpCAM-

description: normal breast tissue sample


title: SM15.d.25


title: PM17.d.25

value: PM


title: Unstimulated splenocytes day 4 post infection mouse 4


title: SM5.d.25


title: Unstimulated splenocytes day 4 post infection mouse 3


title: Unstimulated, uninfected splenocytes mouse 1


title: Unstimulated, uninfected splenocytes mouse 6


title: SM3.d.25


title: PM18.d.25


title: Unstimulated, uninfected splenocytes mouse 4


title: Primary_hepatocytes_SMC

description: Undifferentiated human ES cells H1


title: Pink1-4

data_processing:
Trimming of Illumina adapters (CLC Genomics Workbench v.10 )
Quality control for individual samples (CLC Genomics Workbench v.10 )
Mapping against the reference genome (CLC Genomics Workbench v.10 )
Calculation of expression values using unique matches (CLC Genomics Workbench v.10)
Normalisation by scaling 10.000.000 reads per sample per transcript (TPM),
Genome_build: Genome_build: mouse mm10
Supplementary_files_format_and_content: abundance measurements

source_name: Primary hepatocyte_Ad-Pink1

growth_protocol: All sample are 48hr post-infected primary hepatocyte.

extract_protocol:
RNA was harvest by spin column.
RNA libraries were prepared for sequencing using Illumina’s TruSeq Stranded mRNA Library Preparation Kit based on the Kit’s manual. 2 ug total RNA was used as input.

treatment_protocol: Ad-LacZ, Ad-Pink1 infected

tag: genotype

value: wild type

value: Primary hepatocyte

value: Ad-Pink1 infected


title: PM12.d.25


title: Pink1-3


title: SM15.d.11

source_name: neural progenitor cells

value: iPSC-derived mesencephalic neural precursor cells

value: day 11 of differentiation


title: PM1.d.25


title: PAEC treated with siRNA targeting KLF2/4_RepB [HiChIP_KLF-RNAi_LK2]

city: Stanford

first: Jan-Renier

last: Moonen

address: 269 Campus Drive, CCSR 1220

department: Pediatrics

institute: Stanford University

data_processing:
library strategy: HiChIP
Basecalls were performed using Bcl2fastq.
Data were filtered for duplicate reads, aligned to the hg19 genome, and filtered for valid interactions using the HiC-Pro pipeline v.2.11.1 (https://github.com/nservant/HiC-Pro) using the default settings.
FitHiChIP (https://github.com/ay-lab/FitHiChIP) was used to determine statistically significant interactions using default settings, with the exception of allowing interactions with a minimum size of 1 Kb.
Assembly: Hg19
Supplementary files format and content: bed

growth_protocol: PAEC were grown in commercial EC media containing 5% FBS (Sciencell) in a 5% CO2 air atmosphere and used at passages 3–7.

extract_protocol:
Cells were trypsinized, washed with ice-cold PBS, and lysed to isolate the nuclei.  Libraries were constructed as previously described (Mumbach et al. Nat Methods. 2016) using 1,000,000 cells.
HiChIP (Mumbach et al 2016)

treatment_protocol: PAEC were transfected with siRNA targeting KLF2 and KLF4 (siKLF), or non targeting controls (siC), followed by 24 h of exposure to 15 dyne/cm2 of LSS.

value: Pulmonary Artery Endothelial Cells

value: KLF2/4 siRNA

value: 24 h exposure to 15 dyne/cm2 of LSS


title: PAEC treated with siRNA targeting KLF2/4_RepA [HiChIP_KLF-RNAi_LK1]


title: PAEC treated with control siRNA_RepB [HiChIP_KLF-RNAi_LC2]

source_name: PAEC treated with control siRNA

value: control siRNA


title: SM14.d.11


title: SM5.d.11


title: PAEC treated with control siRNA_RepA [HiChIP_KLF-RNAi_LC1]


title: LacZ-4

city: Boston

first: Yae-Huei

last: Liou

institute: Harvard School of Public health

source_name: Primary hepatocyte_Ad-LacZ

value: Ad-Lacz infected


title: Pink1-1


title: LacZ-3


title: LacZ-2


title: SM3.d.11


title: PM18.d.11


title: Lymphatic endothelial cells_PBS_24 hour_rep3

city: shanghai

first: Junli

last: Chang

address: Wanping South Road 725

institute: Long hua Hospital

description:
Control_3
Gene expression after 24hours in PBS treated lymphatic endothelial cells.
Cell line

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse Gene Expression 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) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with GeneSpring 13.0 (Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: Lymphatic endothelial cells, PBS, 24 hour

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Lymphatic endothelial cells were incubated with growth medium comprising FBS (10%), streptomycin (100 μg/ml) and penicillin (100 U/ml) in a 5% CO2-humidified incubator. The cells was cultured at 37 °C with DMEM culture media.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556) following the manufacturer's instructions.

treatment_protocol: Lymphatic endothelial cells were seeded in 6-well (15*10^4 cells/well) for 24 h at 37°C. Then the cells were treated with PBS and 300μg/ml MSU for 24h, respectively.

value: Lymphatic endothelial cells

value: PBS for 24h


title: Lymphatic endothelial cells_PBS_24 hour_rep1

description:
Control_1
Gene expression after 24hours in PBS treated lymphatic endothelial cells.
Cell line


title: Lymphatic endothelial cells_MSU_24 hour_rep1

description:
MSU1
Gene expression after 24hours in MSU (300μg/ml) treated lymphatic endothelial cells.
Cell line

source_name: Lymphatic endothelial cells, MSU, 24 hour

value: MSU for 24h


title: Lymphatic endothelial cells_PBS_24 hour_rep2

description:
Control_2
Gene expression after 24hours in PBS treated lymphatic endothelial cells.
Cell line


title: scRNA data for RCC Chromophobe patient presented in Fig. 1

city: New York

first: Christina

last: Leslie

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Cell Ranger v3.0.2 (10x genomics) was used for pre-processing of scRNA-seq data
Additional gene/cell filters were applied as described in the methods of the manuscript
Seurat v2.3.4 was used for analysis of all scRNA-seq data.   DESeq was used for analysis of bulk RNA-sequencing data.
Assembly: hg19
Supplementary files format and content: Seurat object RDS files containing raw and normalized count matrices, UMAP coordinates
Supplementary files format and content: RDS object with raw and normalized counts for all scRNA-seq data
Supplementary files format and content: RDS object with metadata for each cell in the Seurat object
Supplementary files format and content: Ensembl IDs and gene symbols for all genes in the scRNA-seq analysis
Supplementary files format and content: Text file with miscellaneous scRNA-seq analysis details

source_name: kidney

extract_protocol:
Tumor samples were directly obtained from the operating room during nephrectomy.  Tissue samples were placed in separate labeled containers containing Roswell Park Memorial Institute (RPMI) medium and transported in regular ice to the laboratory. The CPTs were transported at room temperature. Overall transit time in all cases was less than 1 hour (from specimen extraction to cell dissociation) and the tissue samples were always kept in this medium. The chRCC patient was an 84-year-old female with stage III disease and was treatment-naïve at the time of sample collection.
RNA libraries were prepared for sequencing using standard Illumina protocols.  A suspension of 10,000 FACS sorted live cells in 1X PBS (calcium and magnesium free) containing 0.04% BSA (Sigma) were used as input to the 10X chromium controller system (10x Genomics Inc., product code 120223). Cells were barcoded using the 10x™ GemCode™ Technology to separately index each cell’s transcriptome by partitioning them into Gel Bead-in-EMulsions (GEMs). GEMs were generated by combining barcoded Single Cell 5’ Gel Beads, RT Master Mix with cells, and Partitioning Oil on a microfluidic chip. The GEM RT reaction was performed in thermocycler (53°C for 45 minutes, 85°C for 5 minutes, 4°C hold overnight). After RT incubation, the GEMs were broken, and the first strand of cDNA was recovered using DynaBeadsR MyOne™ Silane beads. 2 – 50 ng of amplified cDNA and the target enriched product respectively were used as input for library construction. Fragmentation, end repair and A tailing were performed to obtain final libraries containing the P5 and P7 priming sites used in IlluminaR sequencing. High sensitivity DNA chips and the Agilent 2100 bioanalyzer (Agilent Technologies) were used for 5’ gene expression quality control and quantification. Quality control was performed twice before sequencing. The 5’ gene expression library was sequenced on NovaSeq 6000 S1 with sequencing depth of approximately 300-500 million reads per sample. For the mouse dataset, live, CD45+CD3-NK1.1+ innate lymphocytes from the pooled tumors of one PyMT mouse were sorted into 1X PBS containing 0.04% BSA. Library preparation, quality control and single-cell RNA sequencing were performed by the Integrated Genomics Operations Core of Sloan Kettering Institute at MSKCC.

tag: type

value: scRNA

tag: model

value: RCC Chromophobe

tag: celltype

value: CD45+ cells


title: Lymphatic endothelial cells_MSU_24 hour_rep3

description:
MSU3
Gene expression after 24hours in MSU (300μg/ml) treated lymphatic endothelial cells.
Cell line

tag: treatment


title: LacZ-1

address: 665 Huntington Ave.


title: Neuroblastoma cells sgGPR91-2

first: Kai

last: Chen

address: NO.1665, Kongjiang Road

institute: Xinhua hospital

data_processing: Briefly, after filtering the sequencing data using SOAPnuke, clean reads were obtained in FAtSTQ format. Then, HISAT2 was used to map clean reads to the reference genome, while Bowtie2 was used to align clean reads to the reference coding gene set. Gene expression levels were analyzed using RSEM.

source_name: Neuroblastoma cells

growth_protocol: Cells were seeded onto 6-well plates as two groups as sgGPR91 and sgControl, and were interfered by DOX (1.5 μg/ml) for 48 hours before the next step.

extract_protocol:
RNA was harvested using Trizol reagent.RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer ® spectrophotometer (IMPLEN, CA, USA) . RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA) A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: treated with doxorubicin(Dox) 100 nmol/L for 48 hours

value: Neuroblastoma

value: Control


title: Neuroblastoma cells sgGPR91-3


title: Lymphatic endothelial cells_MSU_24 hour_rep2

description:
MSU2
Gene expression after 24hours in MSU (300μg/ml) treated lymphatic endothelial cells.
Cell line


title: PM17.d.11

value: PM


title: Pink1-2

value: wild type

value: Primary hepatocyte

value: Ad-Pink1 infected


title: PM12.d.11

value: iPSC-derived mesencephalic neural precursor cells

value: day 11 of differentiation


title: PM1.d.11


title: Neuroblastoma cells sgGPR91-1


title: Neuroblastoma cells sgcon-3

value: GPR91 knockout


title: Neuroblastoma cells sgcon-2


title: Col-0 WT primary root tips control condition Rep3 [WT_CTRL_3_resequencing]

city: Cerdanyola

first: Fidel

last: Lozano-Elena

state: Barcelona

address: Edifici CRAG - Campus UAB

department: Molecular Genetics

country: Spain

institute: Center for Research in Agricultural Genomics (CRAG)

description: RESEQUENCING

data_processing:
Quality filter and read trimming: 75bp paired-reads were quality checked with FastQC software (v0.11.2) and trimmed with Trimmomatic (v0.38) 9bp at 3’ end and trimmed until minimum average quality of 25. Minimum read length to keep of 45bp.
Alignment to TAIR10 genome using HISAT2 (v2.1) aligner
Features quantification: Gene expression calculated as raw fragment counts, at gene level, using FeatureCounts (v1.6.2) on Araport11.gff3 annotation file.
Downstream processing included low-counts genes filtering out, TMM normalization and differential expression analysis using edgeR (v3.34.1) package in R
Raw counts for each sample were sum for the sequencing and resequencing
Assembly: TAIR10
Supplementary files format and content: Tab-separated text file containing raw fragment counts of each Arabidopsis thaliana gene and for each sample

organism: Arabidopsis thaliana

source_name: 6DAG Primary root tips

growth_protocol: Arabidopsis thaliana seeds were surfaced sterilized with 35% sodium hypochlorite and grown vertically in plates containing half-strength Murashige and Skoog (MS) medium supplemented with vitamins. Plates were grown at 22ºC in long-day conditions (16h light + 8h dark), at 60% relative humidity and under white light at 80umol/m2/s for 6 days.

extract_protocol:
RNA was extracted from root tip tissue with the Maxwell RSC Plant RNA Kit (Promega) using the Maxwell RSC instrument (Promega) accroding to the manufacturer recommendations.  Quality of RNA was checked with Bioanalyzer. All samples had a RNA Integrity Number (RIN) > 7.
TruSeq Stranded mRNA Sample Prep kit. Further purification steps with 0.81X Agencourt AMPure XP beads.

treatment_protocol: 6-day-old seedlings were transferred to liquid media supplemented with DMSO (mock) or 2uM Zeocin and incubated for 2h prior to RNA extraction.

value: Col-0 WT

tag: replicate


title: Col-0 WT primary root tips 2h Zeocin Rep3 [WT_Zeo_3_resequencing]

description: RESEQUENCING

value: 2h 10µM Zeocin treatment


title: Neuroblastoma cells sgcon-1

tag: cell type


title: brl3-2 primary root tips control condition2 Rep3 [brl3_CTRL_3_resequencing]

description: RESEQUENCING


title: Pacliataxel treated MDA-MB-231 cells, replicate 4

first: Won-Min

last: Song

state: New York

address: One Gustave L. Levy Place, Box 1123

institute: Icahn school of medicine at Mount Sinai

data_processing:
The 150bp paired-end RNA-sequencing data were generated from Illumina NovaSeq platform
The reads were mapped to hg38 by STAR aligner (v2.7.5b)(Dobin and Gingeras, 2016), and the gene counts for fragments mapped into exonic regions were called for hg38 ensembl genes by featureCounts in subread package (v2.0.1, parameters: -t exon -g gene_id -p)(Liao et al., 2014).
The gene counts were subsequently normalized by Counts Per Million (CPM), followed by Trimmed Mean of M (TMM) scaling normalization(Robinson and Oshlack, 2010).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts
Supplementary files format and content: tab-delimited text files include TMM-normalized, log2(x+1) transformed data adjusted for RNA concentration as confounding variable.

source_name: human TNBC epithelial cell line

growth_protocol: MDA-MB-231 cells were obtained from American Type Culture Collection (ATCC; Manassas, VA, USA) and cultured in DMEM (Corning, Cat #10-013-CM) supplemented with 10% fetal bovine serum (Corning, Cat #35-016-CV) and 1% penicillin/streptomycin (Gibco Cat #15140-122). Cells were cultured in a humidified incubator at 37°C with 5% CO2 and passaged every 3 – 4 days with 0.05% trypsin-EDTA (Gibco, Cat #15400-054).

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Paclitaxel and Doxorubicin were obtained from Mount Sinai Hospital and Afatinib (BIBW2992) from Selleckchem (Cat #S1011).

value: Pacliataxel

tag: rna concentration (ng/ul)


title: brl3-2 primary root tips 2h Zeocin Rep3 [brl3_Zeo_3_resequencing]

description: RESEQUENCING


title: brl3-2 primary root tips 2h Zeocin Rep2 [brl3_Zeo_2_resequencing]

description: RESEQUENCING


title: Pacliataxel treated MDA-MB-231 cells, replicate 3


title: Pacliataxel treated MDA-MB-231 cells, replicate 2


title: brl3-2 primary root tips control condition2 Rep2 [brl3_CTRL_2_resequencing]

description: RESEQUENCING


title: Col-0 WT primary root tips 2h Zeocin Rep2 [WT_Zeo_2_resequencing]

description: RESEQUENCING


title: Col-0 WT primary root tips control condition Rep2 [WT_CTRL_2_resequencing]

description: RESEQUENCING


title: Pacliataxel treated MDA-MB-231 cells, replicate 1


title: DMSO treated MDA-MB-231 cells, replicate 3

value: DMSO


title: DMSO treated MDA-MB-231 cells, replicate 2


title: brl3-2 primary root tips control condition2 Rep1 [brl3_CTRL_1_resequencing]

description: RESEQUENCING


title: LCMV, d14, cd69p, 2

first: Julia

last: Belk

state: California

address: 450 Serra Mall

data_processing:
scATAC-seq fastq files were processed using cellranger atac pipeline
Assembly: mm10
Supplementary files format and content: fragments file containing trimmed, deduplicated, high quality atac-seq fragments and cell barcodes

source_name: liver

extract_protocol:
Nuclei were isolated from frozen, flow cytometry sorted CD8+ T cell subsets
scATAC-seq libraries were constructed using 10X genomics reagents and protocols
10X genomics single cell ATAC-seq

tag: tissue

value: liver

tag: sorted

value: yes

value: LCMV

tag: days p.i.

tag: phenotype

value: T cell


title: brl3-2 primary root tips 2h Zeocin Rep1 [brl3_Zeo_1_resequencing]

description: RESEQUENCING


title: LCMV, d7, 2

tag: infection


title: LCMV, d14, cd69n, 2


title: Col-0 WT primary root tips 2h Zeocin Rep1 [WT_Zeo_1_resequencing]

description: RESEQUENCING


title: LCMV, d30, cd69p, 1


title: pBRL3_BL_Rep2

description: Source material is transgenic Arabidopsis plants expressing proBRL3:nls-YFP

hyb_protocol: Standard Affymetrix cDNA synthesis, labeling and hybridization protocols

data_processing: Raw intensities from CEL files were quality-checked and converted to an expression dataset by correcting the background with Robust Multi-Array average expression measure (RMA, affy version >1.1) and normalized using quantile normalization. These steps were performed in R (v4.1.1) using “affy” package (v1.70.0) and its wrapper function rma. Microarray annotation was retrieved from Bioconductor (ath1121501.db) and genes names and descriptions were retrieved from Araport11 annotation file. Differential expression was calculated by fitting to lineal models and running empirical Bayes test implemented in “limma” package (v3.48.3)

source_name: FACS-selected cells BL treatment

extract_protocol: Protoplasting, FACS and RNA extracction were performed as described in Vilarrassa-Blase et al., 2014 and Birnbaum et al., 2005

treatment_protocol: 6-day-old seedlings were transferred to liquid media supplemented with EtOH (mock) or 10nM of Brassinolide (BL) and incubated for 2h prior to protoplasting.

value: expressing the reporter pBRL3:nlsYFP

tag: tssue

value: Primary root tips

value: 10 nM of BL for 2h


title: LCMV, d14, cd69p, 1


title: LCMV, d14, cd69n, 1


title: Col-0 WT primary root tips control condition Rep1 [WT_CTRL_1_resequencing]

description: RESEQUENCING

value: Control


title: brl3-2 primary root tips 2h Zeocin Rep3 [brl3_Zeo_3]

description: T-DNA insertion mutant (SALK_006024C)


title: Afatinib and pacliataxel treated MDA-MB-231 cells, replicate 4

value: Afatinib + Paclitaxel


title: Afatinib and pacliataxel treated MDA-MB-231 cells, replicate 3


title: DMSO treated MDA-MB-231 cells, replicate 1


title: pBRL3_BL_Rep1

scan_protocol: Standard Affymetrix cDNA synthesis, labeling and hybridization protocols


title: LCMV, d7, 1


title: brl3-2 primary root tips control condition2 Rep3 [brl3_CTRL_3]

description: T-DNA insertion mutant (SALK_006024C)


title: DMSO treated MDA-MB-231 cells, replicate 4


title: Afatinib and pacliataxel treated MDA-MB-231 cells, replicate 2


title: pBRL3_CTRL_Rep3

source_name: FACS-selected cells control conditions

label_protocol: Standard Affymetrix cDNA synthesis, labeling and hybridization protocols


title: pBRL3_CTRL_Rep1


title: Afatinib and pacliataxel treated MDA-MB-231 cells, replicate 1


title: pBRL3_CTRL_Rep2


title: HSV, d30, ln, 2

source_name: skin dLN

value: skin dLN

value: HSV

value: gBT-I


title: HSV, D30, skin, cd69p, 2

source_name: skin

value: skin


title: Liver endothelial cells at postnatal developmental timepoint P30

first: Franco

last: Izzo

address: 1470 Madison Avenue

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
FastQC (v0.11.3) to check FASTQ quality.
CellRanger (v4.0.0) for alignment and count matrix generation.
Seurat (v3.2.2) for downstream single cell analysis.
RData file generated through the Seurat (v 3.2.3) pipeline, using the cellRanger (v4.0.0.) count matrices as input.
Genome_build: mm10
Supplementary_files_format_and_content: Gene count matrices per sample and complete metadata (.csv)

source_name: Liver endothelium

extract_protocol:
Cells were isolated by fluorescence-activated cell sorting and subjected to single cell RNA-sequencing in 10X Chromium.
RNA-seq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

tag: organ

value: Liver

tag: developmental stage


title: Col-0 WT primary root tips 2h Zeocin Rep3 [WT_Zeo_3]

description: Wild-type plant (Columbia-0 ecotype)

tag: genotype

value: Col-0 WT

value: 2h 10µM Zeocin treatment


title: Col-0 WT primary root tips control condition Rep3 [WT_CTRL_3]

description: Wild-type plant (Columbia-0 ecotype)


title: Afatinib treated MDA-MB-231 cells, replicate 4

value: Afatinib


title: Afatinib treated MDA-MB-231 cells, replicate 3


title: Liver endothelial cells at postnatal developmental timepoint P15


title: HSV, d14, skin, cd69p, 2


title: brl3-2 primary root tips 2h Zeocin Rep2 [brl3_Zeo_2]

description: T-DNA insertion mutant (SALK_006024C)


title: HSV, d14, ln, 2


title: Afatinib treated MDA-MB-231 cells, replicate 2


title: Liver endothelial cells at postnatal developmental timepoint P8


title: brl3-2 primary root tips control condition2 Rep2 [brl3_CTRL_2]

description: T-DNA insertion mutant (SALK_006024C)


title: Liver endothelial cells at postnatal developmental timepoint P2


title: Liver endothelial cells at fetal developmental timepoint E18


title: HSV, d30, ln, 1


title: HSV, D30, skin, cd69p, 1


title: Liver endothelial cells at fetal developmental timepoint E16


title: H1_H3K27Ac_Input

description: H3K27Ac ChIP-input from H1 ES cells

data_processing:
Images analysis and base calling was done using the Illumina standard pipeline.
ChIP-seq datasets were aligned using bowtie (Langmead et al., 2009) to the hg38 reference genome using only the standard chromosomes (i.e. chr1 through chr19, chrX, chrY and chrM) with parameter –k 1 –m1 –best and –l set to read length.
Peaks were called using MACS (Zhang et al., 2008) with parameters -p 1e-9 –keep-dup=auto and input control. These files were subsequently normalized to the millions of mapped reads and displayed in the UCSC Genome Browser (Kent et al., 2002). Peaks from H3K27Ac ChIP-Seq were used for super-enhancer analyses were performed suing ROSE (Whyte et al., 2013) (https://bitbucket.org/young_computation/rose) with parameters –s 12500 –t 2000. Stitched enhancers were assigned to the single expressed RefSeq gene whose transcription start site was nearest the center of the stitched enhancer.
Genome_build: hg38
Supplementary_files_format_and_content: Bed files of called peaks

source_name: H1 ES cells

extract_protocol:
The H3K27Ac ChIP-seq and library preparation methods were described in the manuscript.
Crosslinked material was resuspended in 0.1% SDS (50mM Tris-HCl (pH 8), 10mM EDTA) and sonicated for 5min with a Covaris E220 instrument (5% duty cycle, 140 Peak Incident Power, 200 cycles per burst, 1ml AFA Fiber milliTUBEs). Soluble chromatin (5 µg) is immunoprecipitated with Protein A/G Dynabeads (Thermo Fisher Scientific, 10002D, 10004D) and 10μg of H3K27ac (Diagenode, C15410196).
ChIP-seq libraries were constructed using Accel-NGS 2S DNA library kit from Swift Biosciences. Fragments of the desired size were enriched using AMPure XP beads (Beckman Coulter). Libraries were sequenced on an Illumina NovaSeq 6000 instrument with 50 bp paired-end sequencing.

value: H1-ES cells

tag: chip antibody

value: none (input)


title: HSV, d14, skin, cd69p, 1

value: yes


title: Liver endothelial cells at fetal developmental timepoint E14


title: Col-0 WT primary root tips 2h Zeocin Rep2 [WT_Zeo_2]

description: Wild-type plant (Columbia-0 ecotype)


title: Col-0 WT primary root tips control condition Rep2 [WT_CTRL_2]

description: Wild-type plant (Columbia-0 ecotype)


title: brl3-2 primary root tips 2h Zeocin Rep1 [brl3_Zeo_1]

description: T-DNA insertion mutant (SALK_006024C)


title: Liver endothelial cells at fetal developmental timepoint E12


title: H1_H3K27Ac

description: H3K27Ac ChIP-seq from H1 ES cells

value: H3K27Ac  (Diagenode, C15410196)


title: Liver, Tem, 2

value: liver

value: LCMV

value: T cell


title: Endothelial cells and hematopoietic cells  from c-Maf KO endothelial cell mice from one male and one female at P15

data_processing:
FastQC (v0.11.3) to check FASTQ quality.
CellRanger (v4.0.0) for alignment and count matrix generation.
RData file generated through the Seurat (v 3.2.3) pipeline, using the cellRanger (v4.0.0.) count matrices as input.
Genome_build: mm10
Supplementary_files_format_and_content: Gene count matrices per sample and complete metadata (.csv)

value: KO


title: 20200304_HM_3D_2020_H3K27AC_KL7876_S27

description: H3K27Ac ChIP-seq from 3D PSC-differentiated hepatocytes (S5)

source_name: 3D hPSC-hepatocytes-S5

value: 3D hPSC-differentiated hepatocytes-like cells-S5


title: brl3-2 primary root tips control condition2 Rep1 [brl3_CTRL_1]

description: T-DNA insertion mutant (SALK_006024C)

value: Control


title: Liver, Tcm, 2


title: 20191030_Hepatocytes_3D-H3K27AC_KL7532_S5

description: H3K27Ac ChIP-seq from 3D PSC-differentiated hepatocytes (S4)

source_name: 3D hPSC-hepatocytes-S4

value: 3D hPSC-differentiated hepatocytes-like cells-S4


title: Col-0 WT primary root tips 2h Zeocin Rep1 [WT_Zeo_1]

description: Wild-type plant (Columbia-0 ecotype)


title: Spleen, Tcm, 2

source_name: spleen

value: spleen


title: 20200304_HM_2D_2020_H3K27AC_KL7876_S26

description: H3K27Ac ChIP-seq from 2D PSC-differentiated hepatocytes

source_name: 2D hPSC-hepatocytes

value: 2D hPSC-differentiated hepatocytes-like cells


title: Afatinib treated MDA-MB-231 cells, replicate 1


title: 20200304_HM_2D_20180906_H3K27AC_KL7876_S25


title: Spleen, Tem, 2


title: Endothelial cells and hematopoietic cells  from Control endothelial cell mice from one male and one female at P15

value: Liver

value: WT


title: T rep3

city: Harbin

first: Sihong

last: Li

address: 600 Changjiang Road

institute: Northeast Agricultural University

description:
treat with AFB1 and curcumin
T3

data_processing:
Illumina Casava software used for basecalling.
The sequencing data obtained from Illumina Hiseq™ was filtered to get clean reads using Trimmomatic.
Index of the reference genome was built using bowtie2 v2.3.2 and paired-end clean reads were aligned to the reference sequence (Gallus_gallus-5.0, NCBI) using HISAT2 v2.1.0.
FPKM was calculated with StringTie v1.3.3b.
Genome_build: Gallus_gallus-5.0
Supplementary_files_format_and_content: csv files include RPKM values for each Sample.

organism: Gallus gallus

source_name: treat with AFB1 and curcumin

growth_protocol: 32 (1 day old) commercial Arbor Acres broilers were bought from Yi Nong Commercial hatchery (Harbin, Heilongjiang, China) and were assigned randomly to three groups namely control group, AFB1 group, AFB1+curcumin group.Broilers were provided fresh, clean water, free diet and 12 hours dark/light cycle。On day 28, broilers were euthanized by heart puncture and liver samples were collected.

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Total RNA Extractor (Trizol).
RNA libraries were prepared for sequencing using standard Illumina protocols and was validated on the Illumina HiSeq™ 2000.

treatment_protocol: Control group (C): No treatment control, fed with the same environment, keeping up with the end of the experiment. AFB1 group (A): diet with 1mg/kg AFB1. AFB1+curcumin group (T): diet with 1mg/kg AFB1 and 300mg/kg curcumin. Chickens were continuously fed 28 days.

tag: strain

value: Arbor Acres broilers

tag: age

value: 28 day old


title: Liver, Trm, 2


title: Met-Metl replicate 3

first: Qiong

state: Zhejiang

address: Yuhangtang Road 866

department: animal science

institute: Zhejiang University

data_processing:
Clustering and sequencing:The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina, San Diego, California, USA) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina Hiseq 4000 platform and 150 bp paired-end reads were generated.
Quality control :Raw sequencing data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter or ploy-N and low quality reads. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Mapping to the reference genome:Reference genome and gene model annotation files were downloaded from genome  website directly (FA Download Link: ftp://ftp.ensembl.org/pub/release-90/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz; GTF Download Link: ftp://ftp.ensembl.org/pub/release-90/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz). Index of the reference genome was built using bowtie 2 v 2.2.8, and paired-end clean reads were aligned to the reference genome using HISAT2 (Langmead et al., 2012) v2.0.4. HISAT2 was run with ‘--rna-strandness RF’, other parameters were set as default.
Transcriptome assembly:The mapped reads of each sample were assembled by StringTie (v1.3.1) (Pertea et al., 2016) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full length transcripts representing multiple splice variants for each gene locus.
Conservative analysis:Phast (v1.3) is a software package contains statistical programs, most used in  phylogenetic analysis (Hubisz et al., 2011), and phastCons (Siepel et al., 2005) is a conservation scoring and identification program of conserved elements. We used phyloFit to compute phylogenetic models for conserved and non-conserved regions among species and then gave the model and HMM transition parameters to phyloP to compute a set of conservation scores of coding genes.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM

source_name: The 4th inguinal mammary gland

extract_protocol:
RNA was isolated with TRIzol (Invitrogen, CA, USA). RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and gel electotrophoresis. The concentration was measured using Qubit ® RNA Assay Kit in Qubit ® 2.0 Flurometer (Life Technologies, CA, USA). Then, RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In the Met group, pregnant mice at pregnant day (P) 0 were fed a methionine-deficient diet with i.p. injection of 35% methionine contained in the control diet. The Met-Met group was treated as the Met group, except that 25% of injected methionine was replaced with methionyl-methionine dipeptide. At P 17, mammary gland was collected, n=4.

value: ICR

value: The 4th inguinal mammary gland

tag: condition

value: Pregnant day 17


title: Met-Met replicate 2


title: 20200304_Donor2_H3K27AC_KL7876_S32

description: H3K27Ac ChIP-seq from primary human hepatocytes

source_name: Primary human hepatocytes

value: Primary human hepatocytes

value: H3K27Ac  (Diagenode, C15410196)


title: Naive, 2

value: yes

value: n


title: Met-Met replicate 1


title: 20200304_AQL_H3K27AC_KL7876_S31


title: Met replicate 4


title: T rep1

description:
treat with AFB1 and curcumin
T1

value: liver


title: T rep2

description:
treat with AFB1 and curcumin
T2


title: Liver, Tcm, 1

value: LCMV

value: T cell


title: Spleen, Tcm, 1


title: Col-0 WT primary root tips control condition Rep1 [WT_CTRL_1]

description: Wild-type plant (Columbia-0 ecotype)

value: Col-0 WT

tag: treatment

value: Control


title: Spleen, Tem, 1

value: spleen


title: C rep1

description:
Control
C1

source_name: Control


title: Liver, Trm, 1


title: M145Dgbn_45h 2

city: Ledien

first: Gilles

middle: P.

last: van Wezel

address: Sylviusweg 72

department: Institute of Biology Leiden

country: Netherlands

institute: Leiden University

description: 45 hours sample on MM plate with cellophane

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastqc version 0.11.9. In this step, clean data (clean reads) were obtained by triming reads containing adapter and removing poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2 version 2.4.4. (Langmead, B. and S.L. Salzberg, 2012)
featureCounts (version 2.0.1) from subreads used to generate count table

organism: Streptomyces coelicolor

source_name: bacteria culture

growth_protocol: 10e8 spores were plated on MM medium covered with cellophane at 30°C for 24 or 45 h before extraction.

extract_protocol:
At time of harvest, mycelium scraped off from cellophane, snap freeze in liquid N2, bioruptor 30 s at 30 Hz for two times, extract using Kirby mix and then phenol/chloroform extraction. Treated with DNaseI and phenol/chloroform extracted again.
Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA)
First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were 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). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: time

value: 45 hours


title: M145Dgbn_24h 3

description: 24 hours sample on MM plate with cellophane

value: 24 hours


title: M145Dgbn_45h 3


title: A rep3

description:
treat with AFB1
A3

source_name: treat with AFB1

value: Arbor Acres broilers


title: Met replicate 3