title: BI5CST

city: New York

first: Johannes

middle: C

last: Melms

state: New York

address: 650 W 168th Street

department: Medicine

institute: Columbia University

description:
Single-nuclei RNA sequencing
BI5_slyper_processed_data.csv
BI5_slyper_meta_data.csv

library_source: transcriptomic single cell

data_processing:
Raw sc/snRNA-seq data were analyzed using Cell Ranger (v5.1 for uveal melanoma liver metastasis and cutameous melanoma metastasis datasets, v6.1 for all other datasets). Transcripts were aligned to the human GRCh38 reference genome.
Ambient RNA was removed using CellBender (v0.1.0). Gene expression matrices were processed individually in R (v4.0.2) using Seurat (v4.0.1).
For cutaneous melanoma metastasis samples, we applied filters to keep only cells with 300-10000 genes, 400-30000 UMIs, and <10% of mitochondrial reads. For uveal melanoma liver metastasis samples, we kept cells with at least 200 genes, 100 UMIs, and <10% of mitochondrial reads. Additionally, we removed cells with gene or UMI counts that were above a sample-specific maximum limit, based on the observed saturation curve between gene and UMI counts for each sample. Please refer to Extended Data Table 4 of the paper for the exact limits. Finally, for all other datasets, we kept cells with at least 300 genes and <20% of mitochondrial reads.
Scrublet was applied to identify and remove doublets with an expected doublet rate of 9.6%.
Assembly: GRCh38
Supplementary files format and content: Gene expression matrix

source_name: Melanoma metastasis (brain)

extract_protocol:
Single-cell samples: Samples from surgical resections were dissociated using the human tumor dissociation kit from Miltenyi and viable populations were sorted as indicated. Of each sorting population 12,000-15,000 cells were loaded for droplet-based RNA capture and reverse transcription using 10x Genomics 5' reagents and a Chromium controller. Single-nuclei samples: Single-nuclei suspension from frozen samples were generated using methods published in Slyper et al. (Nature Medicine, 2020) with modifications to improve quality and yield while sparing tissue. Salt-tris buffer with Tween-20 (TST) was used for dissociation followed by a high-volume wash in salt-tris buffer (ST). Nuclei were counted and 9,000-15,000 nuclei were separated for droplet-based RNA capture and reverse transcription using 10x Genomics reagents and a Chromium controller as indicated. Control samples were processed as described as in Slyper et al. (Samples BI5TST/CST and NR1TST/CST).
Single-cell RNA sequencing (scRNA-seq) libraries were generated using Chromium 5' reagents and T cell enrichment kit according to the manufacturer protocol. SingleSingle-nuclei RNAseq (snRNA-seq) libraries were generated using Chromium 3' or 5' reagents (and T cell enrichment kit) as indicated according to the manufacturer protocol with one additional cycle during library amplification to account for lower material input from nuclei compared to whole cells.
Other: single-cell/nuclei RNAseq

value: Melanoma metastasis (brain)

tag: fresh vs frozen

value: frozen

tag: sequencing chemistry

tag: library type

value: Gene Expression

tag: protocol

value: CST

tag: cellranger version

value: Cellranger v6.1.0

tag: cellbender version

value: Cellbender v0.1.0

tag: timepoint


title: BI5TST

status: Public on Oct 19 2022

type: SRA

country: USA

molecule: total RNA

organism: Homo sapiens

tag: tissue

value: TST

tag: treatment


title: NR1TST

description:
Single-nuclei RNA sequencing
NR1_processed_data.csv
NR1_meta_data.csv

source_name: Non-small cell lung cancer metastasis (brain)


title: SET-2; ASH1(Y888F) RNAseq

city: Eugene

first: Elizabeth

middle: Toomey

last: Wiles

state: OR

address: 1229 University of Oregon; 1318 Franklin Blvd.

department: Biology, Institute of Molecular Biology

institute: University of Oregon

library_source: transcriptomic

data_processing:
Reads were mapped and gene counts generated using RNA STAR (2.6.0)
DESeq2 version 1.18.1 was used to generate differential count files.
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: Tabular files contain counts for every gene as outlined in process above. Excel workbook files (.xlsx) include the differential gene expression values for each mutant background as determined by DESeq2.

organism: Neurospora crassa

source_name: germinated conidia

growth_protocol: Strains were grown, crossed, and maintained according to standard procedures (Davis RH, 2000). Briefly, polyA RNA was isolated from strains grown at 32°C with shaking for 18 hours in Vogel’s liquid medium.

extract_protocol:
RNA was isolated ( D), Dnase treated (ThermoFisher Scientific) and cleaned (Agencourt RNAClean XP beads; Beckman Coulter)
Poly-A+RNA-seq libraries were prepared using KAPA Stranded mRNA-seq kit (KAPA Biosystems)

tag: genotype/variation

value: mycelia


title: H3G34R_H3K9me3_ChIP-seq

library_source: genomic

data_processing:
All sequencing reads were mapped to the corrected N. crassa OR74A (NC12 genome) (Galazka et al., 2016) using Bowtie2 (Langmead and Salzberg, 2012).
ChIP-seq read coverage was averaged, normalized, and analyzed using tools available from deepTools2 on the open-source platform Galaxy (Afgan et al., 2016). Sequencing tracks are displayed as 25-nt-window TDF or bigWig files with the Integrative Genomics Viewer (IGV) (Robinson et al., 2011).
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: For ChIP-seq files: The tdf files were generated using the "count" function in igvtools (Integrative Genomics Viewer; Broad Institute, Robinson et al, 2011) and bigwig files were generated using DeepTools (Ramirez et al., 2016) using a window size of 20 -200bp (tdf and bigwig files are binary files that shows enrichment peaks for each ChIP sample and have been processed for faster display of the data in IGV).

molecule: genomic DNA

growth_protocol: Strains were grown, crossed, and maintained according to standard procedures (Davis RH, 2000). Briefly, tissue was harvested from strains grown at 32°C with shaking for 18 hours in Vogel’s liquid medium.

extract_protocol:
Tissue was cross-linked for 10 min in 0.5% formaldehyde. Tissue was disrupted by sonication and chromatin sheared using a biorupter (Diagenode).
Libraries were prepared using the NEBNext ChIP-seq Library Prep Master Mix for Illumina.

tag: antibody use

value: H3K9me3 (ActiveMotif, Cat#39161)


title: ribas_on_later_slide

description: Single-nuclei RNA sequencing, SlideSeqV2

data_processing:
We used the Slide-seq tools pipeline (Stickels et al., 2021) to process our Slide-seq data, and loaded the data into Seurat. For MBM05_rep3_slide and MBM11_rep3_slide, due to their lower quality compared to other samples, we filtered out cells with fewer than 20 unique genes. For all other samples, we imposed no further quality control thresholds.
Assembly: GRCh38
Supplementary files format and content: raw counts and spatial coordinates
raw_counts.csv (csv file of individual gene expression count matrix for each sample)
spatial_coordinates.csv (csv file of SlideSeqV2 bead coordinates and barcodes for each sample)

source_name: Melanoma subcutaneous metastasis

extract_protocol:
RNA from 10 uM frozen tumor sections was extracted and spatially indexed as described in Stickels et al. (Nature Biotechnology, 2021). Briefly, sections were cut and then mounted on a "puck". RNA was hybridized for 15 min in 6x SCC and then reveres transcribed using Maxima RT.  Tissue was then digested and cleared using clearing buffer and proteinase K and unbound capture oligos were removed using EXO-I treatment. 2nd strand synthesis was then performed using sn-SMRT oligos and Klenow Enzyme and the libraries were amplified using PCR with Truseq and SMART PCR primers.
Libraries after PCR amplification were tagmented and indexed using Nextera XT kit and Nextera N70x oligos. After SPRI cleanup libraries were quantified using D5000 tapestation and perpared for sequencing.
Other: single-nuclei RNAseq; SlideSeqV2

value: Melanoma subcutaneous metastasis

tag: metastatic site

value: Extra-cranial metastasis

tag: patient id

value: ribas

tag: mutation status

value: BRAF V600E

tag: sequencing technique

value: snRNA-seq

tag: tcr-seq

value: no


title: ribas_pre_slide


title: SW008

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

description: mRNA

data_processing:
During sequencing, Read 1 was assigned 26 base pairs and was used to identify the Illumina library barcode, cell barcode, and UMI. Read 2 was assigned 60 base pairs and used to map to the zebrafish GRCz11 with BWA-MEM4. Data was demultiplexed as described in Grün et al. Mapping and generation of count tables were automated using the MapAndGo script. Unsupervised clustering and differential gene expression analysis was performed with the Seurat R toolkit.
Grün D, Kester L, van Oudenaarden A. Validation of noise models for single-cell transcriptomics. Nat Methods. 2014 Jun;11(6):637-40. doi: 10.1038/nmeth.2930.
MapAndGo: https://github.com/anna-alemany/transcriptomics/tree/master/mapandgo
Genome_build: GRCz11
Supplementary_files_format_and_content: *.tsv

organism: Danio rerio

source_name: 3 dpf HSPCs

extract_protocol:
Embryos were dissociated using liberase, buffered to 0.1% FBS, and filtered for flow cytometry. Single live mCherry+ cells were sorted into individual wells of 384 well plates, with both sample types represented on each plate to account for potential batch effects. Each well contained 50 nl droplets of barcoded RT primers in 10uL of mineral oil.
RNA libraries were prepared for sequencing using the SORT-seq protocol - see Muraro et al. 2016 (Cell Syst).

tag: transgenic line

tag: developmental stage

value: 3 dpf embryo

tag: cell type

value: HSPCs

tag: morpholino

value: std MO cells 1-188, irf8 MO cells 189-384


title: SW007

description: mRNA


title: ribas_on_slide


title: Elys_1_KD_ATAC

city: Nashville

first: Logan

last: Richards

state: Tennessee

address: 465 21st Ave S

department: Biological Sciences

institute: Vanderbilt University

description: ATAC-Seq performed on Drosophila S2 cells RNAi treated for Elys for 5 days

data_processing:
Sequencing reads were aligned to genome assembly dm6 using Bowtie2 (version 2.4.2) with defuallt setting and "--very sensitive local"
Aligned reads were flagged using Picard: MarkDuplicates (version 2.18.2.2)
Coverage files were generated using deeptools: bamcoverage (version 3.3.2.0.0) with deafult settings. For ATAC-seq, coverage was normalized to counts per million. For ChIP-Seq, coverage was normalized to background. For CUT&RUN, coverage was normalized to 1X.
Peak calling was performed with MACS2 (version 2.1.1.20160309.6) with default settings using the option "-- no model"
Assembly: dm6
Supplementary files format and content: Processed data files are in bigwig format for coverage visualization using the UCSC genome browser.

organism: Drosophila melanogaster

source_name: embryonic cells

extract_protocol:
RNAi treated cells were lysed and treated with Tn5 transposase.
Libraries constructed following Active Motif kit instructions

tag: cell line

value: Embryonic cells

value: 5 day RNAi against Elys

tag: method/antibody

value: ATAC-seq (Active Motif 53150)


title: SW002 Plate 2

description: mRNA

source_name: embryonic macrophages

extract_protocol:
Tails were amputated at the tip of yolk extension in ice cold PBS, dissociated using liberase, buffered to 0.1% FBS, and filtered for flow cytometry. Single live EGFP+mCherry+ or EGFP+mCherry- cells were sorted into individual wells of 384 well plates, with both sample types represented on each plate to account for potential batch effects. Each well contained 50 nl droplets of barcoded RT primers in 10uL of mineral oil.
RNA libraries were prepared for sequencing using the SORT-seq protocol - see Muraro et al. 2016 (Cell Syst).

value: mpeg1:EGFP; runx1+23:mCherry

value: macrophages

tag: facs profile

value: EGFP+Cherry+ cells 1-192, EGFP+mCherry- cells 193-384


title: SW006

description: mRNA


title: ORC2_1_KD_ATAC

description: ATAC-Seq performed on Drosophila S2 cells RNAi treated for ORC2 for 5 days

value: 5 day RNAi against ORC2


title: SW001 Plate 1

description: mRNA


title: 143B transmitochondrial cybrid H7 13708G>A replicate 5 clone 5, replicate 1

city: Philadelphia

first: Patrick

middle: M.

last: Schaefer

state: PA

address: 3501 Civic Center Blvd

department: CMEM

institute: Children's Hospital of Philadelphia

description:
23
370-5 5

data_processing:
Base calling was done using [Genewiz NGS Laboratory]
Sequenced reads mapped to hg38 whole genome and Gencode v23 annotation using STAR v2.5.2b with parameters --readFilesCommand zcat --outSAMtype None --outSAMunmapped Within --quantMode TranscriptomeSAM --outSAMattributes NH HI AS NM MD --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --limitBAMsortRAM 50000000000
Expected counts and Fragments Per Kilobase of transcript per Million mapped reads (FPKM) for all genes in Gencode v23 annotation were obtained from aligned bams using RSEM v1.2.28 with parameters --paired-end --no-bam-output --no-qualities -p 4 --forward-prob 0.5 --seed-length 25 --fragment-length-mean -1.0
Assembly: hg38
Supplementary files format and content: tab-delimited matrix table with Expected counts for every gene and every sample
Supplementary files format and content: tab-delimited matrix table with FPKM values for every gene and every sample

molecule: polyA RNA

source_name: Osteosarcoma cells

growth_protocol: 2.5 mio cells were seeded in a T75 cell culture flask in 10ml DMEM medium (11966, Gibco) supplemented with 10% heat-inactivated fetal calf serum, 1 mM glucose and 2 mM uridine. After 48h cells were harvested by trypisization and 1.5mio cells were flash frozen in liquid nitrogen and  sent to Genewiz (Azenta Life Science, South Plainfield, NJ) for RNA sequencing using Poly-A-primers.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
Extracted RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).
The sequencing libraries were clustered on 3 flowcell lanes. After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions.  The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

treatment_protocol: no treatment

value: Osteosarcoma cells


title: 143B transmitochondrial cybrid H7 13708G>A replicate 6 clone 5, replicate 1

description:
24
370-5 6


title: 143B transmitochondrial cybrid H7 13708G>A clone 5, replicate 4

description:
22
370-5 4


title: 143B transmitochondrial cybrid H7 13708G>A clone 5, replicate 3

description:
21
370-5 3


title: 143B transmitochondrial cybrid H7 13708G>A clone 5, replicate 2

description:
20
370-5 2


title: Nup98_1_KD_ATAC

description: ATAC-Seq performed on Drosophila S2 cells RNAi treated for Nup98 for 5 days

value: 5 day RNAi against Nup98


title: NR1CST

value: Non-small cell lung cancer metastasis (brain)

tag: fresh vs frozen

value: frozen

tag: sequencing chemistry

tag: library type

value: Gene Expression

tag: protocol

value: CST

tag: cellranger version

value: Cellranger v6.1.0

tag: cellbender version

value: Cellbender v0.1.0

tag: timepoint


title: 143B transmitochondrial cybrid H7 13708G>A clone 1, replicate 5

description:
15
370-1 5


title: 143B transmitochondrial cybrid H7 13708G>A clone 5, replicate 1

description:
19
370-5 1


title: 143B transmitochondrial cybrid H7 13708G>A clone 1, replicate 6

description:
16
370-1 6


title: NA13, ctrl, IgG, 3

city: Los Angeles

first: Minhyung

last: Kim

state: CA

address: 8700 Beverly Blvd

department: Urology

institute: Cedars-Sinai Medical Center

description: xenograft tumor generated by NA13 bladder cancer cell line treated with scrambled shRNA.

data_processing:
Transcript quantification was performed using RSEM (v1.2.31) with default parameters and Bowtie 2 (v2.1.0) as the read aligner. Reads were mapped directly to mouse transcripts and summarized at the gene level using annotations from Ensembl r91, genome build GRCm38.p5. Quantification of genes as expected counts was compiled. Differential expression was performed using voom function in the limma R package. Geneswith an average expected count less than five were removed, normalization factors were calculated, and comparisons between groups were made using the voom function using default parameters.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with TMM normalized gene expression for every gene and every sample.

organism: Mus musculus

source_name: xenograft bladder cancer

extract_protocol:
Tumors were mechanically disassociated with a homogenizer (Omni International) and then passed through a QIAshredder (Qiagen), gDNA eliminator columns (Qiagen), and RNeasy Plus Mini Kit, as per the manufacturer’s instructions, for RNA extraction.
Library preparation and sequencing were performed by Novogene. Quality and quantity of RNA were analyzed using NanoDrop, agarose gel electrophoresis, and Agilent 2100. mRNA was purified fromtotal RNA using poly-T oligo-attached magnetic beads. mRNA was first fragmented randomly by fragmentation buffer, followed by NEB library preparation (New England Biolabs). First-strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H−), with second-strand cDNA synthesized using DNA polymerase I and RNase H. Double-stranded cDNA was purified using AMPure XP beads (Beckman Coulter). Exonuclease was used to eliminate overhangs on the double-stranded cDNA. 3′ ends were adenylated, and NEBNext adaptors were ligated in preparation for hybridization. Library fragments were purified with AMPure XP system (Beckman Coulter). Sequencingwas performed byNovogene on an Illumina platform paired-end 150 bp with 20 million reads per sample.

tag: strain

value: NA13 murine tumor cell line

value: bladder cancer cell

tag: treatment 1

value: scrambled shRNA

tag: treatment 2

value: IgG


title: NA13, shDDR2, IgG, 1

description: xenograft tumor generated by NA13 bladder cancer cell line treated with shDdr2.


title: 143B transmitochondrial cybrid H7 13708G>A clone 1, replicate 4

description:
14
370-1 4


title: NA13, ctrl, IgG, 2


title: SW005

description: mRNA

tag: transgenic line

value: 3 dpf embryo

value: HSPCs

value: std MO cells 1-188, irf8 MO cells 189-384


title: NA13, shDDR2, IgG, 3


title: miR-29a KO-1

city: Wenzhou

first: Dewei

last: Peng

address: No.270, Xueyuanxi Road

country: China

institute: Wenzhou Medical University

data_processing:
The clean reads were obtained after removal of reads containing adapter, poly-N and at low quality from raw data.
Mapping reads were obtained by mapping clean reads to the mouse reference genome mm10 by HISAT2.
The RNA expression were calculated by FPKM (fragments per kilobase of exon per million fragments mapped) values.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include both count and FPKM values.

source_name: Retina

extract_protocol:
After the mice were euthanized, total RNA Kit II (Omega Bio-tek, Norcross, GA, USA) was used to extract the total RNA from retinas isolated from wild-type (WT) and miR-29a KO mice. Retinas from three mice were pooled as one sample. T10 basic S25 ULTRA-TURRAX Disperser (IKA, Guangzhou, China) was used to homogenize retinas. The quantity and integrity of RNA yield was assessed by using the NanoPhotometer spectrophotometer (Implen, Westlake Village, CA, USA) and Agilent 2100 bioanalyzer (Agilent Technologies, USA) separately.
cDNA libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, Ipswich, MA) after removed the ribosomal RNA by Ribo-Zero kit (Epicentre, Madison, WI) according to the manufacturer’s recommendations. The purified library products were evaluated using the Agilent 2200 TapeStation and The Qubit 2.0 Fluorometer (Thermo Fisher Scientific). The libraries were sequenced at Novogene Co., Ltd. (Beijing, China) using Illumina HiSeq 3000 platform.

tag: genotype

value: miR-29a KO

tag: tissue

value: Retina

tag: age

value: 8 weeks


title: NA13, ctrl, IgG, 1

tag: cell line

tag: cell type


title: NA13, shDDR2, IgG, 2


title: 143B transmitochondrial cybrid H7 13708G>A clone 1, replicate 3

description:
13
370-1 3

value: Osteosarcoma cells


title: SW012

description: mRNA

tag: developmental stage

tag: morpholino


title: 143B transmitochondrial cybrid H7 13708G>A clone 1, replicate 2

description:
12
370-1 2


title: CHIP_sev 3

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: KAIST

description:
nCoV_CHIP_3
New upload

data_processing:
Raw sequencing outputs were automatically converted to fastq file by the sequencer built-in software
raw fastq files were de-multiplexed into relative fastq files for each samples with truncated index sequence through splitBarcode version 0.1.6 provided by MGI Tech.
The demultiplexed files were aligned using cellranger count (v3.0.2; --r1-length 28 --r2-length 91) to cellranger reference GRCh38 (v 3.0.0).
Genome_build: hg38
Supplementary_files_format_and_content: gene expression count matrix, cell barcode information, and gene name list in gzfile format

source_name: PBMC

extract_protocol:
polyA RNA was extracted using the Chromium Single Cell 3' Library & Gel Bead Kit v3.
The library was constructed using the Chromium Single Cell 3' Library & Gel Bead Kit v3.
droplet based single cell RNA seq

value: blood

tag: patient type

value: CHIP


title: CHIP_sev 2

description:
nCoV_CHIP_2
New upload


title: 78-dko-D73_S1

city: Padova

first: Bert

last: Blaauw

address: Via Ugo Bassi 58/b

department: Department of Biomedical Sciences

country: Italy

institute: University of Padova

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp v0.20.0 (parameters: qualiﬁed_quality_phred=20, unqualiﬁed_percent_limit=30, average_qual=25, low_complexity_ﬁlter=True, complexity_threshold=30)
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR v2.7.0 (with standard parameters, except for sjdbOver-hang option set to 74 due to read length)
Read count extraction and TPM quantification were performed using RSEM v1.3.3.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts and TPM values for each Sample

source_name: Gastrocnemius muscles

extract_protocol:
RNA was extracted from gastrocnemius muscles using Trizol/Chloroform extraction protocol. 450 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using QuantSeq 3'mRNA FWD (LEXOGEN) Kit following manufacturer's protocols.

treatment_protocol: Muscle-specific wildtype, Raptor floxed and Raptor mTOR double floxed adult mice (3mo-old) were treated with tamoxifen to induce gene deletion. Mice were sacrificed 7 months from the beginning of the treatment.

value: Gastrocnemius muscles

value: tissue

value: Raptor mTOR double knock-out

tag: treatment

value: tamoxifen-induced deletion


title: 77-wt-D68_S82

value: wildtype


title: 81-dko-D74_S2


title: 143B transmitochondrial cybrid H7 replicate 6

description:
8
399-2 6


title: 74-dko-D71_S85


title: Day 6 differentiating adipocytes scRNA-seq DKO2

city: Bethesda

first: Michael

last: Bustin

state: MD

address: Building 37, Room 3122

department: NCI

institute: NIH

data_processing:
The standard 10x Genomics cellranger (version 6.0.0) pipeline was used to extract Fastqs
10X Genomics cellranger (version 6.0.0) pipeline was used to perform data processing
Sequenced reads were aligned to the 10x Genomics provided mouse reference sequence (refdata-gex-mm10-2020-A)
Genome_build: mm10
Supplementary_files_format_and_content: TXT file containing cluster information for detected genes
Supplementary_files_format_and_content: H5, mtx matrix

source_name: Inguinal white adipose tissue

growth_protocol: Preadipocytes were isolated from inguinal white adipose tissue of WT and DKO mice and cultured on collagen coated plates.

extract_protocol:
For sc-RNA seq live cells were trypsinized and then collected.
Cell partitioning, reverse transcription, cDNA amplification and all steps of library preparation were performed according to the manufacturer specifications on the Chromium Connect instrument.

treatment_protocol: Proliferating preadipocytes were replated and grown until confluency. Two days after reaching confulency,  Preadipocytes were treated to differentiate into adipocytes using differentiation media (Insulin (0.5 μg/ml), dexamethasone (5 μM), IBMX (0.5 mM), T3 (1 nM), Rosiglitazone (1 μM)) for 4 days and maintained in maintenance medium (Insulin (0.5 μg/ml), T3 (1 nM)) for 4 days.

value: Hmgn1-/- and Hmgn2-/-


title: CHIP_sev 1_1

description:
nCoV_CHIP_1_1
New upload


title: 73-wt-D67_S81


title: Day 6 differentiating adipocytes scRNA-seq DKO1


title: WT-1

value: WT


title: 143B transmitochondrial cybrid H7 replicate 5

description:
7
399-2 5


title: Day 6 differentiating adipocytes scRNA-seq WT2

value: Wild type


title: 76-dko-D72_S86


title: CHIP_sev 1_2

description:
nCoV_CHIP_1_2
New upload


title: Day 6 differentiating adipocytes scRNA-seq WT1


title: 54-ko-D77_S91

value: Raptor knock-out


title: 41-wt-D70_S84


title: 47-ko-D76_S90


title: Preadipocytes scRNA-seq DKO2


title: Preadipocytes scRNA-seq WT1


title: 143B transmitochondrial cybrid H7 13708G>A clone 1, replicate 1

description:
11
370-1 1


title: 143B transmitochondrial cybrid H7 replicate 4

description:
6
399-2 4


title: Preadipocytes scRNA-seq DKO1


title: 143B transmitochondrial cybrid H7 replicate 3

description:
5
399-2 3


title: 143B transmitochondrial cybrid H7 replicate 2

description:
4
399-2 2


title: Preadipocytes scRNA-seq WT2


title: 38-wt-D69_S83


title: adult kidney 4C-Seq Lef1

city: Milan

first: Pierluigi Giuseppe

last: Manti

address: Via Festa del Perdono 7

institute: University of Milan

data_processing:
library strategy: 4C-seq
De-multiplexing, mapping and 4C-seq were done through HTSstation (David et al, 2014 PLoS ONE and http://htsstation.epfl.ch/).
Reads were mapped to the mm10 genome assembly with bowtie2 version 2.2.1with parameters −k 20 −−end−to−end −−sensitive −p 5
Mapped reads were translated to restriction fragments using the HTSstation (David et al, 2014 PLoS ONE and http://htsstation.epfl.ch/).
Reads were normalized to the total number of reads. Smoothed data were obtained by applying a running mean algorithm with 11 fragments per window.
Profile corrected data have been generated by applying an approach similar to the one described in (Tolhuis et al., 2011) using a fit with a slope -1 in a log-log scale (Lieberman-Aiden et al., 2009).
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files respectively contain the normalised & smoothed, and the profile corrected & smoothed fragment counts, for every fragment and every sample.
Supplementary_files_format_and_content: track_normMedianTADreg.tgz is an archive containing 4C-seq tracks
Supplementary_files_format_and_content: table_raw_and_rawSmoothed.txt is a matrix table with raw counts and smoothed raw counts (11 fragments per window), for every fragment and every sample.

source_name: whole adult kidney digested to single cells

extract_protocol:
Whisker pads or adult kidney were removed, digested to single cells and processed with the 4C-Seq protocol. For each sample, we harvested at least 1×107 cells and obtained 7-10 μg of output double-digested, double-ligated DNA. NlaIII and DpnII were used as primary and secondary cutter respectively; ligation was performed by using the Concentrated T4 DNA ligase from Promega.
The DNA libraries were prepared for sequencing using standard Illumina protocols

value: murine primary cells freshly isolated

tag: sample group

value: Lef1 viewpoint

value: adult


title: 36-ko-D75_S89


title: 143B transmitochondrial cybrid H7 replicate 1

description:
3
399-2 1


title: whisker pad e12.5 4C-Seq Leaf

source_name: whole whisker pad digested to single cells

value: Leaf viewpoint

value: e12.5 embryo


title: CDK8iIEC-KO/Cdk19wt/D173A -3

city: Clayton

first: Ron

last: Firestein

state: VIC

address: 21 Wright street

department: CCR

country: Australia

institute: Hudson Institute of Medical Research

description: 14 days

data_processing:
Basecalling using BGI
Alignment using STAR 2.5.2
Using Featurecounts function (Subread 1.6.3) to generate counts file based on Gencode annotation
Assembly: mm10
Supplementary files format and content: Gene level counts

source_name: small intestinal epithelial cells

growth_protocol: Organoids were cultured in Matrigel (Corning® Matrigel® Matrix, phenol red-free, BDAA356231) in DMEM/F-12 (Thermo Fisher, 21041025) supplemented 2mM L-glutamine (Life technologies #25030081), 100 units/mL penicillin and 0.1% (w/v) streptomycin (Life technologies #15140122), 10mM HEPES (Thermo Fisher, 15630-080), 10% Noggin conditioned media (produced in house), 5% R-Spondin conditioned media), 1.25mM n-Acetylcysteine (Merck, A7250-5G), 1x N2 supplement (Thermo Fisher, 17502048), 1x B27 supplement (Thermo Fisher, 17504044) and 50ng/ml EGF (Lonza, AF-100-15-1000).

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen,#74106) following manufacturer’s instructions.
100bp Paired end

treatment_protocol: Mice received one daily ip injections of tamoxifen (80mg/kg) for 5 consecutive days. Intestinal epithelial cells were collected 14 days after the last injection. Organois were treated with 100nM 4-OHT or 0.001% EtOH as vehicle for 24h before the media was replaced. Organoids were collected at the indicated time point.

value: VillinCreERT2; Cdk8 fl/fl; Cdk19 wt/D173A

tag: cre recombinase activation

value: tamoxifen


title: CDK8iIEC-KO/Cdk19KO/D173A -3

description: 14 days

value: VillinCreERT2; Cdk8 fl/fl; Cdk19 ko/D173A


title: whisker pad e12.5 4C-Seq Lef1


title: CDK8iIEC-KO/Cdk19wt/D173A -2

description: 14 days


title: Retina Pde6brd1 P17

city: Kunming

first: kangwei

last: Jiao

state: Yunnan

address: 176 Qingnian

department: Ophthalmology

institute: Yunnan University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Rd1 and C3H mice at different time points of P11(n = 3; Retina n = 6), P13 (n = 3; Retina n = 6) and P17 (n = 3; Retina n=6) were sacrificed regardless of gender. The eyeballs were quickly placed into DPBS (phosphatide-buffered Saline without calcium and magnesium CAT:21-040-CVC, CORNING) which was pre-cooled at 4℃ in order to remove blood and impurities, incubated in 0.12% Proteinase K at 37℃ for 1 min and Basal medium with 50% Fetal Bovine Serum  for 2 min, and then transferred to fresh DPBS for final wash. After the cornea, sclera, iris, lens and vitreous were removed on ice under the microscope, the retinal tissues containing retina-RPE-choroid were completely immersed in MACS Tissue Storage Solution which was pre-cooled at 4℃ and de-tected immediately to ensure that the activity and numbers of retinal cells are suffi-cient for further experimental analysis.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Retina

value: Postnatal day 17


title: CD40L+IL4_3

city: New Haven

first: Hiromitsu

last: Asashima

state: CT

address: 300George St

institute: Yele School of Medicine

data_processing:
low quality ends (less than phred score=30) and short read length (minimum length=30) was trimmed using PRINSEQ++(version1.2).
Trimmed reads were aligned to the hg38 genome reference using STAR(v2.7.1), and subsequently RSEM (RNA-Seq by Expectation-Maximization) was used to count reads mapping to the genes from Ensembl release 93.
For remove unwanted variation, the top 5000 genes as ranked by edgeR p-values were set as a “in-silico empirical” negative controls and RUVSeq was performed
Read count normalization were performed using DESeq2CLC genomic benchwork
Supplementary files format and content: hg38
Supplementary files format and content: Three Matrix tables with raw gene counts for every gene and every sample

source_name: blood

growth_protocol: CD20+CD27+ B cells were stimulated under RPMI 1640 medium with 10% FBS

extract_protocol:
RNAs were isolated using RNeasy Plus Micro Kit (QIAGEN)
cDNAs were generated using the SMART-Seq v4 Ultra Low Input RNA Kit for sequencing (Takara/Clontech) and barcoded libraries were generated by the Nextera XT DNA Library Preparation kit (Illumina)

treatment_protocol: B cells were treated with CD40L (0.1 ug/ml) ± each cytokine for 2 days

tag: disease state

value: Healthy

value: blood

tag: time

value: memory B cells

tag: subject

value: Healthy Donor_15


title: CD40L_3


title: adult kidney 4C-Seq Leaf

tag: strain


title: CD40L+IL4_2

value: Healthy Donor_14


title: CDK8iIEC-KO/Cdk19KO/D173A -2

description: 14 days


title: MEF2/KRAS G12D/siBCL6 cells RNA-seq.rep3

city: China

first: Yanan

last: Liu

address: 500 Dongchuan Road, Minhang District, Shanghai, China

department: School of Life Sciences

institute: East China Normal University

description:
G3
Gene-FPKM-expression of G I J

data_processing:
Quality control; Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC  content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome; We selected Hisat2 as the mapping tool; Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level; featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for  the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: GRCh38(HPNE, HK and HK siBCL6 cells) and mm9 (MEF1, MEF1/KRAS G12D, MEF2/KRAS G12D and MEF2/KRAS G12D/siBCL6 cells)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Mouse embryonic fibroblasts

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mouse embryonic fibroblasts

value: MEF2 cells induced by cre adenovirus for 96h and treated with siBCL6


title: Retina Pde6brd1 P11

description: 10x Genomics

value: tissue

value: Postnatal day 11


title: MEF2/KRAS G12D/siBCL6 cells RNA-seq.rep2

description:
G2
Gene-FPKM-expression of G I J


title: CD40L_2


title: MEF2/KRAS G12D/siBCL6 cells RNA-seq.rep1

description:
G1
Gene-FPKM-expression of G I J


title: Retina WT P17

description: 10x Genomics

value: Wide type


title: Retina WT P13

description: 10x Genomics

value: Postnatal day 13


title: CDK8iIEC-KO/Cdk19wt/D173A -1

description: 14 days


title: MEF2/KRAS G12D cells RNA-seq.rep3

description:
F3
Gene-FPKM-expression of F

value: MEF2 cells induced by cre adenovirus for 96h


title: CD40L+IL4_1

value: Healthy Donor_13


title: MEF2/KRAS G12D cells RNA-seq.rep2

description:
F2
Gene-FPKM-expression of F


title: CD40L_1


title: SI Org Cdk19 D173A - 4-OHT -3

description: 7 days

source_name: small intestinal organoid


title: SI Org Cdk19 D173A - 4-OHT -2

description: 7 days


title: Retina WT P11

description: 10x Genomics


title: MEF2/KRAS G12D cells RNA-seq.rep1

description:
F1
Gene-FPKM-expression of F


title: SI Org Cdk19 D173A - 4-OHT -1

description: 7 days


title: MEF1/KRAS G12D cells RNA-seq.rep3

description:
I3
Gene-FPKM-expression of G I J

value: MEF1 cells induced by cre adenovirus for 96h


title: SI Org Cdk19 D173A - EtOH1 -3

description: 7 days

value: VillinCreERT2; Cdk8 fl/fl; Cdk19 ko/D173A

value: EtOH


title: TIGIT_3

value: CD40L+IL-21 (sorted TIGIT+IL10- cells)

value: Healthy Donor_12


title: MEF1/KRAS G12D cells RNA-seq.rep2

description:
I2
Gene-FPKM-expression of G I J


title: DN_3

value: Healthy

value: blood

value: CD40L+IL-21 (sorted TIGIT-IL10- cells)


title: ESC RING1B

city: Yokohama-shi

first: Junichiro

last: Takano

state: Kanagawa-kwn

department: IMS

country: Japan

institute: RIKEN

description: Wild type

data_processing:
For ChIP-seq without spike-in genome, reads were aligned to mm9 using bowtie2(Langmead et al., 2012). ChIP-seq experiments which contained a spike-in genome were aligned against concatenated genome of mm9 and dm3 using bowtie2 and resulting SAM files were then split such that reads aligning to mouse and drosophilia were placed in separate files. The SAM files were converted to the BAM format using Samtools, version 1.6.0 (Li et al., 2009). The PCR duplicates were removed by Picardtools (http://broadinstitute.Github.io/picard).
The BAM files were converted to bigwig files by deepTools2 (Ramirez et al. 2016) for visualization. For comparison across ChIP-seq samples without spike-in genome, the bigwig files were normalized to reads per million mapped sequence reads (RPKM). For ChIP-seq with spike-in genome, RPKM were further normalized according to normalization factors calculated as 1 over the number of reads (per million) mapping to drosophilia as previously reported(Orland et al., 2016).
Assembly: mm9 or concateenated genomes of Mm9 and dm3
Supplementary files format and content: bigwig files described in the data processing step columns

source_name: ESC

growth_protocol: Culture with TSt4 stroma cells by IMDM supplemented with IL7, SCF,Fl3L

extract_protocol: ChIP for TY1, RING1B, SUZ12, H3K27me3 and H3K27ac were performed as described previously (Isono et al., 2013). Cultured IdHP cells were cross-linked with 1% formaldehyde/PBS for 10 min at room temperature. Chromatin was sheared and used for each immunoprecipitation with indicated antibodies. ChIP for H2AK119ub was performed as described before (Mochizuki-Kashio et al., 2015). Cultured IdHP cells were cross-linked with 0.5% formaldehyde/PBS for 2 min at 37℃. Chromatin was sheared and used for each immunoprecipitation. MNase-seq:One million cells were cross-linked by adding formaldehyde to 1% and incubated for 10 min at RT, quenched using 1 M glycine, and washed three times in PBS. Collected cells were lysed in 1 ml PBS + 0.5% Triton X-100 for 3 min on ice. Nuclei were pelleted and washed by MNase digestion buffer (10 mM Tris-HCl, pH 7.4, 15 mM NaCl, 60 mM KCl, 0.5 mM spermidine), spun down and resuspended in the same buffer. Ca2+ concentration was adjusted to 1mM with 1M CaCl2 and MNase was added to 10 U/ml. The reaction mixture was incubated at 37°C for 10 min and the reaction was stopped by adding 150 μL of stop buffer (20 mM EDTA, 20 mM EGTA, 0.4% SDS, 0.5 mg/ml proteinase K) and then incubated for overnight at 65°C. DNA was purified using a MinElute PCR purification Kit (28006; QIAGEN) and loaded to 1.5% Agarose Gel. Mononucleosomal bands were excised and purified by a gel extraction kit (28705; QIAGEN).

value: ESC

tag: passage

value: normal karyotype

tag: antibody

value: anti RING1B (in house)


title: ESCSUZ12

description: Wild type

tag: genotype

value: anti SUZ12 (D39F6) (Cell Signaling, #3737)


title: Retina Pde6brd1 P13

description: 10x Genomics

value: tissue

tag: tissue

value: Retina


title: SI Org Cdk19 D173A - EtOH1 -2

description: 7 days


title: Pcgf2/4 -/- PHC2 2

description: Pcgf2/4 -/- PHC2 2

source_name: Bone marrow

value: Hemtopoietic progenitor cells

value: anti PHC2 (in house)


title: Pcgf2/4 -/- PHC2 1

description: Pcgf2/4 -/- PHC2 1


title: MEF1/KRAS G12D cells RNA-seq.rep1

description:
I1
Gene-FPKM-expression of G I J

value: Mouse embryonic fibroblasts


title: IL10_2

value: memory B cells

value: CD40L+IL-21 (sorted TIGIT-IL10+ cells)

value: Healthy Donor_11


title: MEF1 cells RNA-seq.rep3

description:
J3
Gene-FPKM-expression of G I J

value: untreated


title: TIGIT_2

value: CD40L+IL-21 (sorted TIGIT+IL10- cells)


title: CDK8iIEC-KO/Cdk19KO/D173A -1

description: 14 days

value: VillinCreERT2; Cdk8 fl/fl; Cdk19 ko/D173A

value: tamoxifen


title: IL10_3

value: Healthy

value: blood

value: Healthy Donor_12


title: Pcgf2/4 f/f PHC2 2

description: Pcgf2/4 f/f PHC2 2

value: Pcgf2/4 f/f


title: Wnt3-CM 4-OHT -2

description: 10 days

value: VillinCreERT2; Cdk8 fl/fl; Cdk19 ko/ko

value: 4-OHT + Wnt3-conditioned media


title: MEF1 cells RNA-seq.rep1

description:
J1
Gene-FPKM-expression of G I J


title: DN_2

value: CD40L+IL-21 (sorted TIGIT-IL10- cells)


title: IL10_1

value: Healthy Donor_10


title: MEF1 cells RNA-seq.rep2

description:
J2
Gene-FPKM-expression of G I J


title: SI Org Cdk19 D173A - EtOH1 -1

description: 7 days

value: EtOH


title: Pcgf2/4 f/f PHC2 1

description: Pcgf2/4 f/f PHC2 1

value: Hemtopoietic progenitor cells

value: anti PHC2 (in house)


title: MNase-Seq KO + ACBl1 2

description: MNase-Seq KO + ACBl1 2

value: Pcgf1 -/-


title: DN_1

value: memory B cells


title: 3759 K15BKO BAT RT+fasting

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

data_processing:
Illumina reads were mapped to mouse genome release mm10 using STAR Aligner program.
The expression levels of genes were determined using Cufflinks and presented as FPKM
Differential expression analysis was done using Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: TSV text file containing FPKM for all samples and genes

source_name: K15BKO BAT RT+fasting

extract_protocol:
Cell lysates were isolated using the Roche HighPure RNA isolation kit. 1ug of RNA was used for library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: 2 months

value: brown adipose tissue (BAT)

value: Room temperature (Fasting)


title: 3760 K15BKO BAT RT+fasting


title: MNase-Seq WT + ACBl1 2

description: MNase-Seq WT + ACBl1 2

value: Pcgf1 fl/fl


title: Wnt3-CM EtOH1 -2

description: 10 days

value: EtOH + Wnt3-conditioned media


title: 3763 K15BKO BAT RT+fasting


title: MS_5

value: Multiple Sclerosis

value: blood

value: Multiple Sclerosis Patients_5


title: Wnt3-CM EtOH1 -1

description: 10 days

value: VillinCreERT2; Cdk8 fl/fl; Cdk19 ko/ko


title: 102 K15FF BAT RT+fasting

source_name: K15FF BAT RT+fasting

value: KLF15 flox/flox


title: MNase-Seq WT + ACBl1 1

description: MNase-Seq WT + ACBl1 1


title: MNase-Seq KO2

description: MNase-Seq KO2


title: MS_4

value: Multiple Sclerosis Patients_4


title: 101 K15FF BAT RT+fasting


title: MS_3

value: Multiple Sclerosis Patients_3


title: Wnt3-CM 4-OHT -1

description: 10 days

value: 4-OHT + Wnt3-conditioned media


title: MNase-Seq KO + ACBl1 1

description: MNase-Seq KO + ACBl1 1

value: Hemtopoietic progenitor cells


title: MNase-Seq KO1

description: MNase-Seq KO1


title: Wnt3-CM EtOH1 -3

description: 10 days


title: 100 K15FF BAT RT+fasting


title: MNase-Seq WT2

description: MNase-Seq WT2


title: MS_2

value: Multiple Sclerosis Patients_2


title: MS_1

value: Multiple Sclerosis Patients_1


title: HD_4

value: Healthy

value: memory B cells

value: Healthy Donor_4


title: DKO+T-D10 Org rep1

description:
Counts data_DKO (D3,5,7,10).csv
1002D10T1

data_processing:
Basecalling using BGI
Alignment using STAR 2.5.2
Using Featurecounts function (Subread 1.6.3) to generate counts file based on Gencode annotation
Genome_build: mm10
Supplementary_files_format_and_content: Gene level counts

value: small intestinal organoid

tag: overexpression

value: 10 days


title: MNase-Seq WT1

description: MNase-Seq WT1

tag: cell type

value: Pcgf1 fl/fl


title: MINCE-Seq KO + ACBl1 2

description: MINCE-Seq KO + ACBl1 2

value: Pcgf1 -/-


title: DKO+T-D10 Org rep3

description:
Counts data_DKO (D3,5,7,10).csv
1002D10T3


title: TIGIT_1

value: blood

value: CD40L+IL-21 (sorted TIGIT+IL10- cells)

value: Healthy Donor_10


title: DKO+E-D10 Org rep2

description:
Counts data_DKO (D3,5,7,10).csv
1002D10E2

value: VillinCreERT2; Cdk8 fl/fl; Cdk19 ko/ko

value: EtOH


title: DKO+E-D10 Org rep1

description:
Counts data_DKO (D3,5,7,10).csv
1002D10E1


title: Wnt3-CM 4-OHT -3

description: 10 days


title: 3774 K15BKO BAT RT

source_name: K15BKO BAT RT

value: 2 months

value: brown adipose tissue (BAT)

value: Room temperature (Fed)


title: DKO+T-D10 Org rep2

description:
Counts data_DKO (D3,5,7,10).csv
1002D10T2


title: HD_2

value: Healthy Donor_2


title: DKO+T-D7 Org rep3

description:
Counts data_DKO (D3,5,7,10).csv
1002t-d7-3

value: 7 days


title: 3778 K15BKO BAT RT


title: 3768 K15BKO BAT RT


title: 3775 K15FF BAT RT

source_name: K15FF BAT RT

value: KLF15 flox/flox


title: 202 K15FF BAT RT


title: HD_1

value: Healthy

value: memory B cells

value: Healthy Donor_1


title: DKO+E-D10 Org rep3

description:
Counts data_DKO (D3,5,7,10).csv
1002D10E3

value: small intestinal organoid

value: 10 days


title: MINCE-Seq WT + ACBl1 1

description: MINCE-Seq WT + ACBl1 1

value: Hemtopoietic progenitor cells

value: Pcgf1 fl/fl


title: 200 K15FF BAT RT


title: DKO+T-D7 Org rep2

description:
Counts data_DKO (D3,5,7,10).csv
1002t-d7-2


title: DKO+T-D7 Org rep1

description:
Counts data_DKO (D3,5,7,10).csv
1002t-d7-1


title: day 29 2D monolayer PSC Skeletal myogenic differentiated cells-rep 2

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.17.1.14
Sequences were aligned to the genome reference hg38 sequence using the STAR aligner 2.5.2a using default parameters
Read counting was performed using featureCounts version 1.4.5
Genome_build: hg38 gene version 89
Supplementary_files_format_and_content: Tab-delimited text file with reads count per gene for each sample

extract_protocol:
RNA was purified using Trizol (Thermo Fisher Scientific) according to the manufacturer’s instructions. RNA quality was ensured with the Fragment Analyzer from Advanced Analytical by using the standard sensitivity RNA Analysis Kit (DNF-471).
RNA-seq libraries were prepared using a modified strand-specific, massively parallel cDNA sequencing (RNA-Seq) protocol from Illumina, the TruSeqStranded Total RNA. Libraries were sequenced on a HiSeq4000 platform (Illumina) generating 50 bp single end reads (30-40 Mio reads/sample).

value: PSC-derived skeletal myogenic cells

value: untreated

tag: karyotype

value: Normal

tag: time point

value: day 29


title: 3521 K15-BKO BAT cold+fasting

source_name: K15-BKO BAT cold+fasting

value: 2 months

value: Cold + Fasting


title: DKO+E-D7 Org rep3

description:
Counts data_DKO (D3,5,7,10).csv
1002e-d7-3

value: VillinCreERT2; Cdk8 fl/fl; Cdk19 ko/ko

value: EtOH


title: MINCE-Seq KO1

description: MINCE-Seq KO1

value: Pcgf1 -/-


title: MINCE-Seq KO + ACBl1 1

description: MINCE-Seq KO + ACBl1 1


title: MINCE-Seq WT2

description: MINCE-Seq WT2


title: DKO+E-D7 Org rep2

description:
Counts data_DKO (D3,5,7,10).csv
1002e-d7-2

value: 7 days


title: HD_3

value: Healthy

value: blood

value: Healthy Donor_3


title: day 29 2D monolayer PSC Skeletal myogenic differentiated cells-rep 1


title: 3525 K15-BKO BAT cold+fasting

value: brown adipose tissue (BAT)


title: day 60 2D monolayer PSC Skeletal myogenic differentiated cells-rep 3

value: day 60


title: day 60 2D monolayer PSC Skeletal myogenic differentiated cells-rep 4


title: MINCE-Seq WT + ACBl1 2

description: MINCE-Seq WT + ACBl1 2

value: Hemtopoietic progenitor cells


title: DKO+E-D7 Org rep1

description:
Counts data_DKO (D3,5,7,10).csv
1002e-d7-1

value: small intestinal organoid


title: 3524 K15-BKO BAT cold+fasting


title: 3516 K15FF BAT cold+fasting

source_name: K15FF BAT cold+fasting

value: KLF15 flox/flox


title: day 29 2D monolayer PSC Skeletal myogenic differentiated cells-rep 4

value: PSC-derived skeletal myogenic cells

value: untreated


title: MINCE-Seq WT1

description: MINCE-Seq WT1

value: Pcgf1 fl/fl


title: Pcgf2/4 -/- RING1B 2

description: Pcgf2/4 -/- RING1B 2

value: anti RING1B (in house)


title: MINCE-Seq KO2

description: MINCE-Seq KO2


title: 3523 K15FF BAT cold+fasting

value: 2 months

value: Cold + Fasting


title: DKO+T-D5 Org rep3

description:
Counts data_DKO (D3,5,7,10).csv
1002-t-d5-4

value: VillinCreERT2; Cdk8 fl/fl; Cdk19 ko/ko

value: 5 days


title: DKO+T-D5 Org rep2

description:
Counts data_DKO (D3,5,7,10).csv
1002-t-d5-3


title: day 29 2D monolayer PSC Skeletal myogenic differentiated cells-rep 3

value: Normal

value: day 29


title: 3522 K15FF BAT cold+fasting


title: Pcgf2/4 -/- RING1B 1

description: Pcgf2/4 -/- RING1B 1


title: DKO+T-D5 Org rep1

description:
Counts data_DKO (D3,5,7,10).csv
1002-t-d5-2


title: day 22 2D monolayer PSC Skeletal myogenic differentiated cells-rep 3

value: day 22


title: Pcgf2/4 f/f RING1B 2

description: Pcgf2/4 f/f RING1B 2

value: Pcgf2/4 f/f


title: day 13 2D monolayer PSC Skeletal myogenic differentiated cells-rep 2

value: day 13


title: Pcgf2/4 f/f RING1B 1

description: Pcgf2/4 f/f RING1B 1


title: DKO+E-D5 Org rep3

description:
Counts data_DKO (D3,5,7,10).csv
1002-e-d5-3

value: EtOH


title: 3453 K15-BKO BAT cold

source_name: K15-BKO BAT cold

value: brown adipose tissue (BAT)

value: Cold challenge


title: day 13 2D monolayer PSC Skeletal myogenic differentiated cells-rep 1


title: BCOR delta E9-10 RING1B 2

description: BCOR delta E9-10 RING1B 2

value: Hemtopoietic progenitor cells

value: BCOR delta E9-10


title: 3455 K15-BKO BAT cold


title: DKO+E-D5 Org rep2

description:
Counts data_DKO (D3,5,7,10).csv
1002-e-d5-2

value: small intestinal organoid


title: 3458 K15-BKO BAT cold


title: BCOR delta E9-10 RING1B 1

description: BCOR delta E9-10 RING1B 1


title: DKO+E-D5 Org rep1

description:
Counts data_DKO (D3,5,7,10).csv
1002-e-d5-1


title: day 60 2D monolayer PSC Skeletal myogenic differentiated cells-rep 1

value: PSC-derived skeletal myogenic cells

value: untreated

value: day 60


title: day 60 2D monolayer PSC Skeletal myogenic differentiated cells-rep 2


title: BCOR WT  RING1B 2

description: BCOR WT  RING1B 2

value: BCOR WT

value: anti RING1B (in house)


title: 3452 K15-BKO BAT cold

value: 2 months


title: DKO+T-D3 Org rep3

description:
Counts data_DKO (D3,5,7,10).csv
1002-t-d3-3

value: VillinCreERT2; Cdk8 fl/fl; Cdk19 ko/ko

value: 3 days


title: day 22 2D monolayer PSC Skeletal myogenic differentiated cells-rep 2

value: Normal

value: day 22


title: DKO+T-D3 Org rep2

description:
Counts data_DKO (D3,5,7,10).csv
1002-t-d3-2


title: 1609 K15FF BAT cold

source_name: K15FF BAT cold

value: KLF15 flox/flox


title: BCOR WT  RING1B 1

description: BCOR WT  RING1B 1


title: DKO+T-D3 Org rep1

description:
Counts data_DKO (D3,5,7,10).csv
1002-t-d3-1


title: 1608 K15FF BAT cold


title: day 22 2D monolayer PSC Skeletal myogenic differentiated cells-rep 1


title: 1607 K15FF BAT cold


title: Pcgf2/4 -/- H3K27me3 2

description: Pcgf2/4 -/- H3K27me3 2

value: anti H3K27me3 (CST #9733)


title: Pcgf2/4 -/- H3K27me3 1

description: Pcgf2/4 -/- H3K27me3 1


title: day 8 2D monolayer PSC Skeletal myogenic differentiated cells-rep 3

value: day 8


title: day 4 2D monolayer PSC Skeletal myogenic differentiated cells-rep 4

value: day 4


title: day 8 2D monolayer PSC Skeletal myogenic differentiated cells-rep 4


title: DKO+E-D3 Org rep2

description:
Counts data_DKO (D3,5,7,10).csv
1002-e-d3-2

value: EtOH


title: 3454 K15FF BAT cold

value: brown adipose tissue (BAT)

value: Cold challenge


title: DKO+E-D3 Org rep3

description:
Counts data_DKO (D3,5,7,10).csv
1002-e-d3-4

value: small intestinal organoid


title: 36bf hypoxia stp2d 48h

city: Jena

first: Bettina

last: Böttcher

address: Albert Einstein Str. 10

department: Septomics Research Center

institute: Friedrich Schiller University

data_processing:
Fastq files were assessed for sequence quality using FastQC (version 0.11.9) and a genome index from file C_albicans_SC5314_A22_current_chromosomes.fasta fom http://www.candidagenome.org/ was created with bowtie2 (version 2.4.2). Mapping of reads to the index was performed with bowtie2. Reads were counted and assigned to the corresponding genome using function featureCounts of R package Rsubread (version 2.2.6). Contrasts were calculated using R package DESeq2 (version 1.28.1). R version 4.0.4 was used.
Genome_build: C_albicans_SC5314_A22_current_chromosomes.fasta
Supplementary_files_format_and_content: Raw.Counts.Stp2.Biofilms.csv, Comma seperated text file containing counts of all samples

organism: Candida albicans

source_name: biofilm cells

growth_protocol: C. albicans cells were pre-grown in YPD overnight and PBS washed cells were set to OD600 nm of 0.5 in 4 ml RPMI medium in 6 well plates (Costar®, Corning®). Following cell adherence, 4 ml of pre-warmed RPMI medium was added and biofilms were formed for 8h , 24 h or 48 h at 37 °C and 180 rpm. Next, supernatants were discarded, and biofilm cell were harvested.

extract_protocol:
The pellets were processed for total RNA extraction using acid phenol-chloroform and DNase treatment to remove genomic DNA. RNA degradation and contamination were monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 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. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). 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 of3’ 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.
Paired end RNA sequencing of cDNA fragments of preferentially 150~200 bp in length.

treatment_protocol: Cells were separated from biofilm medium by centrifugation 2 min at 4000g and 4ºC, the supernatant was removed and the falcons with the pellet were flash frozen in liquid nitrogen and stored at -80ºC

value: strain

tag: genotype/variation


title: DKO+E-D3 Org rep1

description:
Counts data_DKO (D3,5,7,10).csv
1002-e-d3-1


title: day 4 2D monolayer PSC Skeletal myogenic differentiated cells-rep 3

value: PSC-derived skeletal myogenic cells

tag: treatment

value: untreated


title: 35bf hypoxia stp2d 48h


title: DKO+T Org rep3

description:
Counts data_Batch1-1w.csv
1003-1w-T4

value: 7 days


title: 34bf hypoxia stp2d 48h


title: BCOR WT H3K27me3 1

description: BCOR WT H3K27me3 1

value: Hemtopoietic progenitor cells

value: BCOR WT


title: BCOR WT H3K27me3 ２

description: BCOR WT H3K27me3 ２


title: DKO+T Org rep2

description:
Counts data_Batch1-1w.csv
1003-1w-T2

value: VillinCreERT2; Cdk8 fl/fl; Cdk19 ko/ko


title: day 1 2D monolayer PSC Skeletal myogenic differentiated cells-rep 4

value: Normal

value: day 1


title: day 1 2D monolayer PSC Skeletal myogenic differentiated cells-rep 3


title: 33bf hypoxia stp2d 24h


title: Pcgf2/4 f/f H3K27me3 2

description: Pcgf2/4 f/f H3K27me3 2

value: Pcgf2/4 f/f


title: BCOR delta E9-10 H3K27me3 ２

description: BCOR delta E9-10 H3K27me3 ２

value: BCOR delta E9-10

value: anti H3K27me3 (CST #9733)


title: DKO+T Org rep1

description:
Counts data_Batch1-1w.csv
1003-1w-T1


title: 32bf hypoxia stp2d 24h


title: BCOR delta E9-10 H3K27me3 1

description: BCOR delta E9-10 H3K27me3 1


title: WT+T Org rep3

description:
Counts data_Batch1-1w.csv
3983-1w-T5


title: day 0 2D monolayer PSC Skeletal myogenic differentiated cells-rep 3

value: day 0


title: day 0 2D monolayer PSC Skeletal myogenic differentiated cells-rep 4


title: Ty1 Pcgf1 (Nascent DNA)_2

description: Ty1 Pcgf1 (Nascent DNA)

value: Ty1 Pcgf1 (Nascent DNA)

value: H3K27me3 (Merk Millipore, 07-449)


title: Pcgf2/4 f/f H3K27me3 1

description: Pcgf2/4 f/f H3K27me3 1


title: 31bf hypoxia stp2d 24h


title: day 8 2D monolayer PSC Skeletal myogenic differentiated cells-rep 2

value: day 8


title: 30bf hypoxia stp2d 8h


title: Cdk19KO+T Org rep3

description:
Counts data_Batch1-1w.csv
407-1w-T6

value: small intestinal organoid

value: Cdk8 fl/fl; Cdk19 ko/ko


title: 29bf hypoxia stp2d 8h

value: strain


title: day 8 2D monolayer PSC Skeletal myogenic differentiated cells-rep 1

value: PSC-derived skeletal myogenic cells

value: untreated


title: Ty1 Pcgf1 (Nascent DNA)_1

description: Ty1 Pcgf1 (Nascent DNA)

value: Hemtopoietic progenitor cells


title: Ty1 Pcgf1 (Bulk)_2

description: Ty1 Pcgf1 (Bulk)

value: Ty1 Pcgf1


title: Ty1 Pcgf1 (Bulk)_1

description: Ty1 Pcgf1 (Bulk)


title: Cdk19KO+T Org rep2

description:
Counts data_Batch1-1w.csv
407-1w-T5

value: 7 days


title: day 4 2D monolayer PSC Skeletal myogenic differentiated cells-rep 2

value: Normal

value: day 4


title: day 1 2D monolayer PSC skeletal muscle differentiation-rep 2

source_name: PSC Skeletal myogenic differentiated cells

value: day 1


title: 28bf hypoxia stp2d 8h


title: 27bf hypoxia WT 48h

value: wild type


title: Negetive control for Ty1-Pcgf1_2

description: Negetive control for Ty1-Pcgf1

value: Pcgf1 fl/fl

value: Anti-acetyl-Histone H3(Lys27) (Merk Millipore, 07-360)


title: 26bf hypoxia WT 48h


title: WT+T Org rep2

description:
Counts data_Batch1-1w.csv
3983-1w-T3


title: Negetive control for Ty1-Pcgf1_1

description: Negetive control for Ty1-Pcgf1


title: WT+T Org rep1

description:
Counts data_Batch1-1w.csv
3983-1w-T2


title: 25bf hypoxia WT 48h


title: day 1 2D monolayer PSC skeletal muscle differentiation-rep 1


title: Pcgf1_-/-_H2AK119ub_2

value: ESC

value: Pcgf1 -/-

value: anti Ubiquityl-Histone H2A (Lys119) (Cell Signaling, #8240)


title: 24bf hypoxia WT 24h


title: Cdk8KO+T Org rep2

description:
Counts data_Batch1-1w.csv
1134T_2

value: small intestinal organoid

value: VillinCreERT2; Cdk8 fl/fl


title: day 4 2D monolayer PSC Skeletal myogenic differentiated cells-rep 1


title: day 0 2D monolayer PSC skeletal muscle differentiation-rep 2

value: day 0


title: Pcgf1_-/-_H2AK119ub_1


title: day 0 2D monolayer PSC skeletal muscle differentiation-rep 1

value: PSC-derived skeletal myogenic cells


title: Cdk8KO+T Org rep1

description:
Counts data_Batch1-1w.csv
1134T_1


title: 23bf hypoxia WT 24h

value: strain


title: Cdk19KO+T Org rep1

description:
Counts data_Batch1-1w.csv
407-1w-T4

value: Cdk8 fl/fl; Cdk19 ko/ko


title: VilCre+T Org rep3

description:
Counts data_Batch1-1w.csv
1255T_4


title: VilCre+T Org rep2

description:
Counts data_Batch1-1w.csv
1255T_3


title: Pcgf1_f/f_H2AK119ub_2


title: 22bf hypoxia WT 24h


title: 21bf hypoxia WT 8h


title: DexPPT2

city: LONDON

first: Lisa

last: Cameron

state: ON

address: 1151 Richmond street, Dental Sciences Building Room 4035

department: Pathology and Laboratory Medicine

country: Canada

institute: WESTERN UNIVERSITY

data_processing:
FastQC Read Quality reports were generated to assess Per base sequence quality as well as using the 'qualityScores' function from Rsubread (Version 2.8.2) in Rstudio
RNA-seq reads were aligned to the human genome (hg38) using the 'align' function from Rsubread (Version 2.8.2) in RStudio in using both sequence files for each respective condition (paired-end). Default arguments were used for the function.
Gene expression in RNA-Seq experiments was measured using the 'featureCounts' function from Rsubread (Version 2.8.2),  isPairedEnd = TRUE,  annot.inbuilt = "hg38". Remaining arguments were unused/kept at default value
Counts were corrected for batch-effects using 'ComBat_seq' from sva (Version 3.42.0). Default arguments were used for the function.
The 'calcNormFactors' function from EdgeR (Version 3.36.0) was used to apply TMM normalization. Differential expression of count data was determined using EdgeR (Version 3.36.0); Dispersion was estimated for common dispersion, GLM trended dispersion, and tagwise dispersion. Counts were fitted to a negative binomial generalized log-linear model (glmFit) and likelihood ratio test was conducted (glmLRT).
genome build - hg38
processed data files format and content - .xlsx file. Measured gene expression in RNA-Seq experiments (featureCounts), one gene per line. Gene names from org.Hs.eg.db (Version 3.14.0)

source_name: Th2 cells

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from healthy donors by density centrifugation over Ficoll Histopaque PLUS (GE Healthcare, Sweden) and CD4+ T cells were isolated by negative selection (CD4+ T cell Isolation Kit II, Miltenyi Biotech, CA, USA). CD4+ T cell purity was 96.57%. Cells were primed on plate bound antibody (anti-) to CD3 (Clone UCHT1, 1 μg/mL) and anti-CD28 (Clone 37407, 1 μg/mL) in Th2 differentiating conditions; recombinant human (rh) IL-2 (5 ng/mL), rhIL-4 (10 ng/mL) and blocking antibodies against IFNγ (1μg/mL) and IL-12 (1μg/mL) for 3 days in X-VIVO 15 medium (Lonza, USA) supplemented with 10% fetal bovine serum (Hyclone) and 1% penicillin/streptomycin/glutamine (Gibco, Canada). On day 4, cells were re-plated and rested with cytokines and blocking antibodies but without activating CD3 and CD28. After 7 days of differentiation, CRTh2+CD4+ T cells were isolated by positive selection (CRTh2+ cell selection kit, Miltenyi Biotech, CA, USA). CRTh2+CD4+ T cells were maintained on cycles of activation (3 days αCD3/CD28 + IL-2) and rest (4 days IL-2) at a density of 2 million/mL.

extract_protocol:
1 million cells were pelleted and washed once with sterile PBS, then resuspended in 350 ul RNALater (Qiagen). RNA was isolated using a Qiagen RNeasy Plus mini kit and eluted in 30 microliters RNA-free water.
NEBNext_dual rRNA-depleted stranded (HMR) libraries were prepared for sequencing with standard Illumina protocols using the services of Genome Quebec

treatment_protocol: After four days resting in IL-2 only, cells were washed, counted and re-seeded at 1.3 million per mL. The glucocorticoid dexamethasone (Dex) and the Estrogen Receptor alpha agonist 4,4',4''-(4-Propyl-[1H]-pyrazole-1,3,5-triyl)trisphenol (PPT) were dissolved in ethanol and applied to cells; 0.1µM Dex, 10µM PPT. Ethanol was used as a vehicle only control. Cells were incubated for 24 hours prior to RNA isolation

value: Dexamethasone + PPT

tag: cell line


title: DexPPT3


title: Pcgf1_-/-_PCL2_2

value: Hemtopoietic progenitor cells

value: anti PCL2 (Proteintech, 16208-1-AP)


title: Pcgf1_f/f_H2AK119ub_1


title: VilCre+T Org rep1

description:
Counts data_Batch1-1w.csv
1255T_1

value: 7 days


title: PPT3

value: PPT (10 micromolar)


title: Pcgf1_-/-_PCL2_1


title: Pcgf1_f/f_PCL2_2


title: DexPPT1


title: 19bf hypoxia WT 8h

value: wild type


title: DKO IECs rep1

description:
Counts data_IECs-2w.csv
1398D

source_name: small intestinal epithelial cells

value: small intestinal epithelial cells

value: VillinCreERT2; Cdk8 fl/fl; Cdk19 ko/ko

value: tamoxifen

value: 14 days


title: Pcgf1_f/f_PCL2_1

value: Pcgf1 fl/fl


title: DKO IECs rep2

description:
Counts data_IECs-2w.csv
1402D


title: PPT1


title: 18bf stp2d 48h


title: Cdk8KO+T Org rep3

description:
Counts data_Batch1-1w.csv
1134T_4

value: small intestinal organoid


title: Pcgf1_-/-_UTX_2

value: Pcgf1 -/-

value: anti UTX (Merck Millipore ABE1865)


title: 17bf stp2d 48h


title: WT IECs rep2

description:
Counts data_IECs-2w.csv
1542C


title: WT IECs rep3

description:
Counts data_IECs-2w.csv
1543C


title: Dex2

value: Dexamethasone (0.1 micromolar)


title: 20bf hypoxia WT 8h

value: strain


title: Dex3


title: 16bf stp2d 48h


title: 15bf stp2d 24h


title: Pcgf1_f/f_UTX_1


title: Pcgf1_-/-_UTX_1


title: Pcgf1_f/f_UTX_2


title: DKO IECs rep3

description:
Counts data_IECs-2w.csv
1411D


title: Dex1


title: 14bf stp2d 24h


title: 13bf stp2d 24h


title: PPT2


title: Pcgf1_-/-_BCOR 2

description: Pcgf1_-/-_BCOR 2

value: anti BCOR (Proteintech 12107-1-AP)


title: Veh3

value: ethanol


title: WT IECs rep1

description:
Counts data_IECs-2w.csv
1535C


title: Veh2


title: 12bf stp2d 8h


title: Veh1


title: Pcgf1_f/f_BCOR_2

value: Hemtopoietic progenitor cells


title: S6_PA14_TnSeq_planktonic_r2

city: Burnaby

first: Travis

last: Blimkie

state: British Columbia

address: 8888 University Drive

department: MBB

institute: Simon Fraser University

data_processing:
Read quality was assessed using FastQC v0.11.6 and MultiQC v1.6
BioTradis: Default parameters were used to run the Bio-TraDIS pipeline, which aligns reads against the reference genome using SMALT and then determines the insertion counts per gene.
Transit: TPP was first used to map raw reads against the reference genome using BWA v0.7.17 with default parameters and to tabulate the counts of reads per TA site. These counts were passed through TRANSIT’s Gumbel method for calculating the probability of the essentiality of each gene using a Bayesian model.
Any genes predicted to be essential by Bio-TraDIS or Gumbel in at least two of three replicates were considered essential genes.
Assembly: UCBPP‑PA14 reference genome obtained from the Pseudomonas Genome Database v17.1 (NCBI accession number NC_008463; PseudoCAP version 138)
Supplementary files format and content: BioTradis (CSV): Comma-delimited files containing a list of all PA14 genes, along with stats for each gene regarding number of reads mapped by BioTradis e.g. “read count,” “insertion count,” etc.
Supplementary files format and content: Transit (WIG): Number of reads aligned against each TA position in the PA14 genome, as calculated by Transit

organism: Pseudomonas aeruginosa PA14

growth_protocol: Two aliquots of the TnSeq pool were thawed and inoculated into 25 ml SCFM. After reaching mid-log phase, the TnSeq mutants were centrifuged at 4,000×g for 20 mins and resuspended in SCFM. Biofilms were inoculated at an OD600 of 0.1 and formed on HA discs. Planktonic growth wells were inoculated at an OD600 of 0.01 and grown to early stationary phase and pelleted. The TnSeq experiment was performed in three biological replicates each including four technical replicates.

extract_protocol:
Transposon genome junctions were amplified from genomic DNA with a nested PCR protocol of three steps. Genomic DNA was isolated with the DNeasy Blood & Tissue Kit (Qiagen). The protocol was slightly modified for the isolation of genomic DNA from biofilms: HA discs were broken into pieces using forceps, resuspended in buffer ALT, which was provided within the kit, and heated to 99°C for 10 mins. After addition of ethanol, the samples were centrifuged at high speed for 1 min to remove HA particles. DNA quantity and quality were determined by NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies) prior to amplification. Unless stated otherwise, Taq DNA Polymerase (Thermo Scientific) was used according to the manufacturer's instructions. In the first PCR step, transposon genome junctions were randomly amplified. After PCR purification with Agencourt AMPure XP magnetic beads (Beckman Coulter), transposon genome junction-specific products were enriched in a second nested PCR step using primers targeting the inverted repeat (0.4 µM R2-TnM20) as well as the common sequence introduced on the semi-arbitrary primers in PCR1 (0.4 µM ARB2).
After qualitative and quantitative analysis with Bioanalyzer 2100 (Agilent Genomics) and Quant-iTTM dsDNA Assay Kit (Thermo Fisher), the samples were diluted to 4 nM and submitted for single-end sequencing with 100 bp read length on a HiSeq2500 sequencing platform (Illumina). The transposon junction libraries were spiked into highly diverse RNASeq libraries over multiple lanes at a concentration of 3‑6% and prepared for sequencing in accordance with Illumina guidelines.

tag: condition

value: planktonic growth

value: Wild type


title: S7_PA14_TnSeq_biofilm_r2

value: biofilm growth on HA discs


title: Pcgf1_-/-_BCOR 1

description: Pcgf1_-/-_BCOR 1


title: 10bf stp2d 8h


title: 09bf WT 48h

value: wild type


title: S9_PA14_TnSeq_biofilm_r3


title: 11bf stp2d 8h


title: RNA-Seq. of Rattus norvegicus: striatum in METH self-administered rat 3

city: Daegu

first: Taekwon

last: Son

address: 61, Cheomdan-ro, Dong-gu

department: Korea Brain Bank

institute: Korea Brain Research Institute

data_processing:
Sequence reads of the 8 independent samples were trimmed for both PCR and sequencing adapters with Cutadapt (version 1.18).
Trimmed reads were aligned to the rn6 rat reference genome using STAR (version 2.7.0e).
Gene-level read counts were generated using featureCounts function from the Subread package (version 1.6.4).
Assembly: rn6
Supplementary files format and content: Tab-delimited text file include raw counts per gene per sample.

organism: Rattus norvegicus

source_name: striatum

extract_protocol:
Total RNA was extracted using TRIzol® reagent (Invitrogen).
The isolated total RNA was processed for preparation of an mRNA sequencing library using a TruSeq RNA Sample Preparation Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: striatum

value: WT

value: methamphetamine


title: S8_PA14_TnSeq_planktonic_r3


title: S4_PA14_TnSeq_planktonic_r1


title: Pcgf1_-/-_H3K27me3 1

description: Pcgf1_-/-_H3K27me3 1

value: ESC

value: anti H3K27me3 (Cell Signaling,  #9733)


title: 08bf WT 48h


title: 07bf WT 48h


title: RNA-Seq. of Rattus norvegicus: striatum in SA self-administered rat 4

value: saline


title: Pcgf1_f/f_H3K27me3_1, chIP

value: Pcgf1 fl/fl


title: S3_PA14_TnSeq_T0_r3

value: T0 pool


title: 06bf WT 24h


title: S1_PA14_TnSeq_T0_r1


title: S2_PA14_TnSeq_T0_r2


title: 05bf WT 24h


title: RNA-Seq. of Rattus norvegicus: striatum in METH self-administered rat 4


title: RNA-Seq. of Rattus norvegicus: striatum in SA self-administered rat 3


title: Eya1cKO_2_5_2

city: New York

first: Aarthi

last: Ramakrishnan

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw sequencing reads from mice were mapped to mm10 using HISAT2.
Counts of reads mapping to genes were obtained using htseq-count software against Ensembl v90 annotation.
Differential expression was done using the DESeq2 package.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file containing counts

source_name: Kidney

extract_protocol:
6 kidneys for each genotype were harvested from 4 different pregnant females 48 hrs after initiating tamoxifen administration and dissociated into single cells. Five thousand FACS-sorted tdTomato+ cells were used for each biological replicate.
The total RNAs were prepared from 5000 cells using a NucleoSpin RNA XS kit (Cat.740902, TakaraBio), and then mRNA was purified from total RNA using magnetic beads (S1550S, New England Biolabs). Random priming strand-specific RNA-seq libraries were prepared using the SMARTer stranded RNA-seq kit (Cat.634839, TakaraBio).

value: Kidney


title: S5_PA14_TnSeq_biofilm_r1


title: RNA-Seq. of Rattus norvegicus: striatum in SA self-administered rat 2


title: Pcgf1_-/-_H3K27me3 2

description: Pcgf1_-/-_H3K27me3 2

value: Pcgf1 -/-


title: Enterococci from the colony-print formed inside MOLP at 72h_3

first: Diana

middle: K.

last: Morales

address: 1300 York Ave

department: Obstetrics and Gynecology

institute: Weill Cornell Medicine

data_processing:
bioinformatic analyses were conducted at LC Sciences bioinformatic services.
Reads were  filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). including the Q20, Q30 and GC-content of the clean data.
Reads of all samples were aligned to the E. faecalis OG1RF  reference genome using HISAT2 and then using UMI-tools sequence-deoendent bias and amplification noise were removed.
Assembly: The mapped reads were assembled using StringTie and merged using perl scripts and gff compare. Differential gene expression was determined using StringTie by calculating FPKM.
Supplementary files format and content: The excel file include FPKM values for each sample

organism: Enterococcus faecalis OG1RF

growth_protocol: Bacteria were grown on semisolid MOLP agar plates for 24, 48, and 72h.

extract_protocol:
Samples were procesessed as described in Ramos, et al. 2022
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Agar-penetrating (inside) and non-penetrating (outside) bacteria were collected post-inoculation at the indicated time points

value: Surface penetration assay


title: 04bf WT 24h

value: strain


title: Enterococci from the colony-print formed inside MOLP at 72h_2


title: Eya1cKO_1_5_1


title: RNA-Seq. of Rattus norvegicus: striatum in METH self-administered rat 1


title: Pcgf1_f/f_BCOR_1

value: Hemtopoietic progenitor cells

value: anti BCOR (Proteintech 12107-1-AP)


title: 03bf WT 8h


title: Enterococci from the colony-print formed inside MOLP at 72h_1

value: Wild type


title: RNA-Seq. of Rattus norvegicus: striatum in METH self-administered rat 2


title: CRTL_2_3_2

value: Control


title: RNA-Seq. of Rattus norvegicus: striatum in SA self-administered rat 1


title: CRTL_1_3_1


title: Enterococci from the colony-print formed inside MOLP at 48h_3


title: Pcgf1_f/f_H3K27me3_2, chIP


title: 02bf WT 8h

value: wild type


title: enap1-1enap2, Dehydration 4h, BR2

city: Austin

first: Hong

last: Qiao

state: TX

address: 2506 speedway, NMS5.324

department: Department of Molecular Biosciences

institute: The University of Texas at Austin

data_processing:
RNA-seq reads raw data were evaluated with FastQC for quality control.
Low quality reads were removed with Trim Galore (0.6.7) and mapped to Arabidopsis genome (TAIR10) with botwie2 (2.4.2) with default parameters.
Mapped reads were counted by featureCounts (Subread 2.0.1) for each gene.
Differentially regulated genes were identified using DESeq2 (1.32.0) with a p-value <0.01, q-value <0.05 and | log2(fold change) | >1
Assembly: tair10
Supplementary files format and content: tab-delimited text files include reads count for each Sample

organism: Arabidopsis thaliana

source_name: whole seedling

extract_protocol:
RNA was harvest with PureLink™ Plant RNA Reagent (Invitrogen). 1ug total RNA was used for constructing the library.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit  following manufacturer's protocols.

value: whole seedling

value: Dehydration


title: 01bf WT 8h


title: Eya1 ChIP-seq kidney E13.5 replicate 1

data_processing:
Samples were aligned to the reference genome mm10 using HISAT2.
MACS was utilized to obtain sites of Eya1 binding using IgG and Input samples as control.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file containing peaks

extract_protocol:
For Eya1 ChIP-seq, 80 kidneys from E13.5 Eya1HA-FLAG knockin mice were used for each ChIP assay. The kidneys were cross-linked with 1% formaldehyde at room temperature for 60 mins, and then homogenized and lysed in cold lysis buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1´ protease inhibitors). Samples were pelleted at 2000 g at 4°C and resuspended in cold wash buffer (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1´ protease inhibitors) for 10 minutes in 15 ml conical tubes, followed by spinning at 2000 g at 4°C in a benchtop centrifuge. Samples were resuspended in 1 ml cold sonication buffer (10 mM Tris-Cl, pH 8.0, 2 mM EDTA, 0.1% SDS) and sonicated to 200-500 bp fragments using a Covaris S220 Focused-ultrasonicator. Sonicated chromatin was cleared by pelleting insoluble material at 13,000 RPM at 4°C, followed by preclear with protein A/G beads and incubation with 20 ml blocked anti-FLAG M2 beads at 4°C for another 5 hrs. Immunoprecipitated complexes were subjected to series of wash steps with low salt buffer (20 mM Tris-Cl 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), high salt buffer (20 mM Tris-Cl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), LiCl wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP-40, 1% sodium deoxycholate) and TE plus NaCl, followed by elution with Flag peptide and reverse crosslinking overnight at 65°C. The quality controls of ChIPed DNA was performed with Qubit 2.0 Fluoremeter using dsDNA HS assay Kit (Q32854, ThermoFisher Scientific) and Agilent 2200 TapeStation System using High Sensitivity D1000 Reagents (5067-5585, Agilent).
The libraries for sequencing were prepared with the ThruPLEX DNA-seq Kit (R400429, Rubicon Genomics) and sequenced on Illumina NextSeq500.

tag: type of sample

value: Eya1 IP

tag: transcription factor


title: Enterococci from the colony-print formed inside MOLP at 48h_2


title: Col-0, Dehydration 4h, BR2


title: Col-0, Dehydration 4h, BR1


title: IgG control

value: IgG


title: Enterococci from the colony-print formed inside MOLP at 48h_1


title: Eya1 ChIP-seq kidney E13.5 replicate 2


title: gut tissue from patient IMM70

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

institute: University of Florence

data_processing:
library strategy: paired-end amplicon sequencing
demultiplexing: from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
pair merging: micca mergepairs -i pair1.fastq -r pair2.fastq -o out.joined.fastq -l 30 -d 3
primer check and trimming: micca trim -i out.joined.fastq -o out.trimmed.fastq -w CCTACGGGNBGCWSCAG -r GACTACHVGGGTATCTAATCC -W -R -c
quality check: micca filter -i out.trimmed.fastq -o out.hiqual.fastq -e 0.5 -m 350 -f fastq
read merging: micca merge -i *.hiqual.fastq -o merged.fastq -f fastq
OTU table creation by clustering: micca otu -m denovo_greedy -i merged.fasta -o otudata -d 0.97 -c -t 20
taxonomic assignment (RDP): micca classify -m rdp -i otudata/otus.fasta -o otudata/taxa.txt
further analyses: R phyloseq package (see https://github.com/matteoramazzotti/papers/tree/main/2021celiac)

source_name: 16S rRNA V3-V4 sequencing of an intestinal mucosal sample of a potential celiac patient

growth_protocol: Mucosa biopsies were stored at -80°C

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)

tag: status

tag: Sex

value: M

tag: anti-ttg iga (u/ml)

tag: anti-ema-iga

value: Weakly positive

tag: histology(grade marsh)


title: Input control

value: Input

tag: tissue


title: gut tissue from patient IMM61

tag: age

value: Positive


title: Enterococci from the colony-print formed inside MOLP at 24h_2

tag: genotype


title: Col-0, Mock 4h, BR2

value: Mock


title: Enterococci from the colony-print formed inside MOLP at 24h_1


title: gut tissue from patient IMM60

value: F


title: enap1-1enap2, Mock 4h, BR1


title: gut tissue from patient IMM59


title: Lats1-CKO basal, BM8, RNA-seq

city: Rehovot

first: Yael

last: Aylon

address: 234 Herzl St

department: MCB

country: Israel

institute: Weizmann Institute of Science

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were mapped to the mm10 genome
Deduplication was carried out by flagging all reads that were mapped to the same gene and had the same UMI (read 2 ha the UMI)
Counting proceeded over genes (1000 bases of the 3’ UTR) using htseq-count
Normalization and differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes the normalized counts and DESeq2 output

source_name: PyMT tumor derived cell line, FACS purified basal population

growth_protocol: DMEM, P/S, FCS

extract_protocol:
RNA was isolated using the NucleoSpin kit (Macherey Nagel)
30ng of input RNA from each sample was barcoded during reverse transcription and pooled. Following Agencourt AMPure XP beads cleanup (Beckman Coulter), the pooled samples underwent second strand synthesis and were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with Illumina sequences during ligation, RT and PCR.
MARS-seq

treatment_protocol: samples were sterilely FACS separated into tubes containing complete medium, on a FACSAria III instrument (BD Biosciences) equipped with a 407, 488, 561 and 633 nm lasers, using a 100 um nozzle, controlled by BD FACS Diva software v8.0.1 (BD Biosciences).

value: PyMT tumor derived cell line

tag: strain

value: FBV/N

tag: facs purification

value: EpCAM-low; CD49f-high

tag: population

value: basal


title: Lats1-CKO luminal, BM7, RNA-seq

source_name: PyMT tumor derived cell line, FACS purified luminal population

value: EpCAM-high; CD49f-high

value: luminal


title: Enterococci recovered from colonies grown 72h on MOLP_3

value: Wild type

value: Surface penetration assay


title: WT basal, BM6, RNA-seq

value: WT


title: gut tissue from patient IMM39


title: WT luminal, BM5, RNA-seq


title: Col-0, Mock 4h, BR1

value: whole seedling


title: gut tissue from patient IMM22


title: Enterococci recovered from colonies grown 72h on MOLP_1


title: Enterococci recovered from colonies grown 72h on MOLP_2


title: H3G34R_5mC

city: Eugene

first: Elizabeth

last: Wiles

address: 1229 University of Oregon; 1318 Franklin Blvd.

department: Biology, Institute of Molecular Biology

institute: University of Oregon

data_processing:
The BRAT-BW software package (compbio.cs.ucr.edu/brat/) was used to prepare and map the reads to the N. crassa OR74A (annotation NC12) genome, which was converted to a four stranded reference genome to permit bisulfite mapping.
BRAT-BW acgt-count “-B” option cytosine-only files produced for the forward and reverse strand reads were merged.
To display the bisulfite sequencing data, the average 5mC level was determined for specified step-wise window sizes across the genome using the MethPipe program (smithlabresearch.org/software/methpipe/). The resulting file was renamed with an .igv file extension to allow display on the Integrated Genome Viewer.
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: The igv and bigwig files were generated for display of average 5mC levels on IGV (Integrative Genomics Viewer; Broad Institute, Robinson et al, 2011). "bigwig" files were generated using DeepTools (Ramirez et al., 2016) using a window size of 25bp. "igv" files were generated using MethPipe (smithlabresearch.org/software/methpipe/) using a window size of 25bp.

source_name: germinated conidia

growth_protocol: Strains were grown, crossed, and maintained according to standard procedures (Davis RH, 2000). Briefly, genomic DNA was isolated from strains grown at 32°C with shaking for 48 hours in Vogel’s liquid medium.

extract_protocol:
Genomic DNA isolation was performed as previously described (Honda & Selker, 2008).
50ng of genomic DNA was treated with bisulfite using the EZ DNA Methylation Lightning kit (ZYMO Research). Libraries were prepared for sequencing with the EpiGnome Methyl-Seq Kit and EpiGnome Index PCR Primers (Epicentre), purified with Agencourt AMPure XP beads (Beckman Coulter), Qubit HS Assay quantified (Life Technologies), visualized on the Fragment Analyzer (Advanced Analytical), and sequenced on a Illumina HiSeq 2000  or HiSeq4000 (www.illumina.com) at the UO Genomics Core Facility as single-end 75 or 100nt reads.

tag: genotype/variation

tag: tissue type

value: mycleia

tag: bisulfite treated

value: bisulfite


title: gut tissue from patient IMM9

value: M


title: Lats1-CKO basal, BM4, RNA-seq

tag: cell line


title: ash1(Y888F)_5mC


title: Enterococci recovered from colonies grown 48h on MOLP_3

tag: treatment


title: WT_5mC


title: Enterococci from the colony-print formed inside MOLP at 24h_3


title: enap1-1enap2, Mock 4h, BR2


title: gut tissue from patient IMM10


title: gut tissue from patient IMM108


title: Enterococci recovered from colonies grown 48h on MOLP_1


title: Lats1-CKO luminal, BM3, RNA-seq


title: ips8 [RNA]

city: Nanjing

first: Aiwen

last: Jiang

state: Jiangsu

address: Weigang

institute: Nanjing Agricultural University

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perlscript was used to filter the original data (Raw Data). The reference genomes (Sscrofa 11.1) and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html).
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and Fragments Per Kilobase per Millon Mapped Reads (FPKM) was then calculated to estimate the expression level of genes in each sample.
DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non-biological replicates. Under the assumption that the number of reads derived from a gene (or transcript isoform) follows abinomial distribution, DEGseq is proposed based on MA-plot and widely used for differential gene expression analysis. The P-value could be assigned to each gene and adjusted by the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with q≤0.05 and |log2_ratio|≥1 are identified as differentially expressed genes (DEGs).
The GO (Gene Ontology, http://geneontology.org/) enrichment of DEGs was implemented by the hypergeometric test, in which p-value is calculated and adjusted as q-value, and data background is genes in the whole genome. GO terms with q<0.05 were considered to be significantly enriched. KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.kegg.jp/) is a database resource containing a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.
The KEGG enrichment of DEGs was implemented by the hypergeometric test, in which p-value was adjusted by multiple comparisons as q-value. KEGG terms with q<0.05 were considered to be significantly enriched.
Genome_build: Sus_scrofa.Sscrofa11.1.90.chr
Supplementary_files_format_and_content: FPKM

organism: Sus scrofa

source_name: tip of ear of E90

growth_protocol: Longwhite boar and Meishan sow served as male and female parents respectively; at 90 days after mating, the Meishan sow was slaughtered to obtain porcine embryonic fibroblasts (PEF).

extract_protocol:
PEF cell lines were transfected with OSKM plasmid, and incubated in lysis buffer.
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair, A-tailing and adapter added were implemented. The aimed products were retrieved and PCR was performed, then the library was completed. RNA concentration of library was measured using Qubit® RNA Assay Kit in Qubit® 3.0 to preliminary quantify and then dilute to 1ng/μl. Insert size was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and qualified insert size was accurate quantification using StepOnePlus™ Real-Time PCR System (Library valid concentration＞10 nM). The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina novaseq6000 platform and 150 bp paired-end reads were generated.

treatment_protocol: PEF gain pluripotency after transfection of Oct4, Sox2, Klf4, and cMyc (OSKM)

value: embryo

tag: cell type

value: pluripotent cells derived from PEF


title: ips7 [RNA]


title: gut tissue from patient IMM82

source_name: 16S rRNA V3-V4 sequencing of an intestinal mucosal sample of a celiac patient

tag: status

value: celiac

value: Positive


title: ips5 [RNA]


title: Day 9 Brown-like adipocytes Input Rep2 DKO

city: Bethesda

first: Michael

last: Bustin

address: Building 37, Room 3122

department: NCI

institute: NIH

data_processing:
Basecalling was performed using RTA version 2.4.6
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.17) allowing 1 mismatch.
Trimming of adapters and low-quality bases was performed using CutAdapt (v.1.18).
Reads were mapped to UCSC mm10 reference genome using BWA 07.17
Peak detection of enriched binding regions was performed using MACS2 v. 2.1.1.20160309 with the default settings
Genome_build: mm10
Supplementary_files_format_and_content: Predicted peak files in narrowPeak format

source_name: Inguinal white adipose tissue

extract_protocol:
Cells for fixed in tissue culture plates with methonol free 1% paraformaldehyde and then collected.
ChIP libraries were prepared for sequencing using standard Illumina protocols

value: Hmgn1-/- and Hmgn2-/-


title: Enterococci recovered from colonies grown 24h on MOLP_3

state: New York


title: Enterococci recovered from colonies grown 24h on MOLP_2


title: gut tissue from patient IMM73

tag: Sex

value: F


title: PEF8 [RNA]

value: somatic cells


title: Day 9 Brown-like adipocytes Input Rep1 DKO


title: gut tissue from patient IMM68

tag: anti-ttg iga (u/ml)


title: gut tissue from patient IMM8

tag: anti-ema-iga


title: Day 9 Brown-like adipocytes Input Rep2 WT


title: gut tissue from patient IMM13

tag: histology(grade marsh)


title: Enterococci recovered from colonies grown 24h on MOLP_1

tag: tissue


title: Succinate_3

first: Roi

last: Avraham

address: Herzl St 234

data_processing:
Fastq reads were demultiplex to their respective sample by using fastq-multx (version 1.3.1) and aligned to a composite genome of S.Tm 14028S and mouse (mm10) using STAR (version 2.5.3a).
For S.Tm read counts, R2 reads were calculated by HTSeq.
Data of each organism was normalized to a library size factor. Factors were calculated by dividing the total number of reads from each sample to the median of the total number of reads across all samples.
Data was transformed to log scale after DESeq2 normalization.
Genome_build: composite genome of S.Tm 14028S and mouse (mm10)
Supplementary_files_format_and_content: tab-delimited text files include normalized number of reads (log scale) for each sample

organism: Salmonella enterica subsp. enterica serovar Typhimurium

growth_protocol: Culture of WT S.Tm strain was grown in Luria-Bertani (LB) medium at 37 °C shaken for 16 h (overnight culture).  Cells were washed and diluted to OD 600 of 0.005 in 3ml LPM medium (glycerol) or modified LPM medium (without glycerol supplemented with 10mM succinate) and were grown for 16 hours at 37°C without shaking (oxygen-limited conditions).

extract_protocol:
Bacterial pellets were washed with PBS and resuspended in RLT buffer.  Pellets were freeze and thawed for efficient cell lysis and RNA was extracted using the RNeasy mini kit (QIAGEN) with DNase I-treatment (45 minutes at 23°C) (QIAGEN).
RNAtag-seq cDNA libraries was done as previously described in Avraham et al (2016) (Avraham et al., 2016). Bacterial rRNA was depleted using the RiboZero Gold (Bacteria) kit (Illumina) according to the manufacturer’s guidelines. Strand-specific cDNA libraries were prepared and sequenced as Paired-end (R1: 30, R2: 50) using Miniseq machine and 300 mid output kit with total coverage of ~10.5M and mean of ~380K reads per library, ranges from ~35K to ~1.3M. For each condition, biological triplicates were analyzed.

value: succinate

tag: replicate


title: PEF5 [RNA]


title: enap1-1enap2, Dehydration 4h, BR1

tag: genotype

value: Dehydration


title: gut tissue from patient IMM6

tag: age


title: PEF7 [RNA]


title: Enterococci recovered from colonies grown 48h on MOLP_2


title: gut tissue from patient IMM51


title: WT basal, BM2, RNA-seq

value: PyMT tumor derived cell line

tag: strain

value: FBV/N

tag: facs purification

value: EpCAM-low; CD49f-high

value: basal


title: Day 9 Brown-like adipocytes Input Rep1 WT

value: Wild type


title: WT luminal, BM1, RNA-seq

value: EpCAM-high; CD49f-high

tag: population

value: luminal

value: WT


title: Succinate_2


title: Day 6 differentiating adipocytes Input Rep2 DKO


title: gut tissue from patient IMM5


title: Glycerol_3

value: glycerol