title: Pol2CTD ChIP-seq replicate 4 - WT control input

description: input for Pol2CTD-4 WT control, Pol2ser2-2 WT control, Pol2ser5-2 WT control, H3K27Ac-1 WT control, H3K9Ac-1 WT control

tag: genotype


title: Patient5-I_CD4Teff-TCRseq

status: Public on May 22 2020

type: SRA

city: Paris

first: Wilfrid

last: Richer

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: TCR-enrich polyA RNA

library_source: transcriptomic

data_processing:
Library strategy: TCR-seq
TCRβ data were aligned and quantified using MixCR (version 2.1.5).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.TRB.clones.txt: TCRseq; Tab-delimited text files with counts and VDJ-CDR3 description for all clonotypes for each sample.

molecule: total RNA

organism: Homo sapiens

growth_protocol: Ex-vivo

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

tag: disease status

value: Luminal breast cancer

tag: tissue

value: Invaded Lymph Node

tag: cell type

tag: patient


title: Pol2CTD ChIP-seq replicate 3 - KO fear input

city: Baltimore

first: Weidong

last: Wang

state: Maryland

address: 251 Bayview Blvd

country: USA

institute: National Institute on Aging/NIH

description: input for Pol2CTD-3 KO fear, Pol2ser2-3 KO fear, Pol2ser5-3 KO fear

library_source: genomic

data_processing:
base_calling: generate fastq files from BCL reads by bcl2fastq
alignments, mapping and file format convertion: Reads are aligned to mm10 genome by Bowtie2, sorted by samtools 1.9; and are built index,  and transfer to bed format files by bamtools 2.5.1.
filtering, normalization and peakcalling: The bed files are filtered, normalized, and tested for peakcalling by SICER v1.1.
bedgraph generation/normalization: codes avalible upon request
functionl/phenotype analysis: Using bedtools 2.29.0 intersect function , the peak call change values with position information are mapped to the transcription Start Sites and EXON postions grouped by genes. These results are then used as input for PAGE algorithem  to analyze Gene Ontology gene set  and Broad Institute Pathway gene set to obtain functional change lists.  The same results are also used to analyze disease MESH term Gene Set  by the PAGE method to obtain phenotype change lists.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bedgraph files containing FPKM of normalized ChIP-seq

molecule: genomic DNA

organism: Mus musculus

source_name: Brain

growth_protocol: 2-4 month old mice in standard growth condition

extract_protocol:
Mouse brain tissue was homogenized in 1 ml of 1% formaldehyde for 15 min. The sample was added of 50 ml of 2.5M glycine (final concentration 125 mM), incubated at room temperature for 5min, and centrifuged at 1,000 x g for 5 min at 4°C. The pellet was collected and washed with PBS. The pellet was then resuspended in 400 ml of RIPA buffer with protease inhibitor cocktail and 0.5 mM phenylmethylsulfonyl fluoride and centrifuge at 1,000 x g for 10 min at 4°C. The lysates were sonicated to shear the DNA to lengths between 200 and 400 bp, and were centrifuged at 1,000 x g for 10 min at 4°C. In order to pre-clear the chromatin, 100 ml of Protein A beads were added to the sample and incubated for 60 min at room temperature. During preclearing step, Protein A beads were incubated with blocking solution (0.5% BSA in PBS) for 60 min at room temperature. 5 ml of antibody and 20-30 ml of Protein A beads were added into the precleared lysate and incubated for 4 hrs at 4C and mixed on a rotator during all the incubation step. Each sample was washed one-time with 0.3 M NaCl/RIPA buffer, one-time with RIPA buffer, one-time with 0.25 M LiCl and twice with TE. The beads were incubated for 8 hrs at 65C with 100 ml TE, 3 ml of 10% SDS and 3ml of Protease K in a thermocycler, and the liquid was transferred into a new tube. 100 ml of TE was added to the beads, resuspended, and the supernatant was transferred again to the tube in order to reach a final volume of 200 ml.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were placed into the chamber (120 sec) for habituation, followed by 30 sec tone that co-terminated with a 2 -secondsec, 0.5 mA electric foot shock. This was repeated for a total of three tone-shock pairings with an interval of 30 seconds sec between tone presentations. The mice were culled by CO2 after 10 min.

tag: treatment

value: fear

tag: strain background

value: Top3b KO

value: brain


city: New york

first: Yurii

last: Chinenov

state: New York

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

description:
Germinal center B cells from Rock2 conditional KO mice, RNAseq, replica2
edgeR_DEGs_for ver1.3.2_2019-03-15.xlsx
cKO_GCB_2

data_processing:
1. RNASeq: Quality of all RNA and library preparations were evaluated with BioAnalyzer 2100 (Agilent). Sequencing libraries were sequenced by the Epigenomics Core Facility at Weill Cornell Medicine using a HiSeq2500
2. RNASeq: 50-bp paired-end reads at a depth of ~ 22-30 million reads per sample. Read quality was assessed and adaptors trimmed using FASTP. Reads were then mapped to the mouse genome (mm10) and reads in exons were counted against Gencode v27 with STAR2.6
3. RNAseq: Differential gene expression analysis was performed in R using edgeR3.24.3. Genes with low expression levels (<2 counts per million in at least one group) were filtered from all downstream analyses. Replica-associated batch correction was performed by directly incorporating a batch-specific term into a linear model. Differential expression was estimated using quasi-likelihood framework. Benhamini-Hochberg false discovery rate (FDR) procedure was used to correct for multiple testing. Genes with an unadjusted p-value less than 0.01 were considered differentially expressed
4. ATACseq: The nuclei of sorted WT and CD23-Rock2 GC B cells were prepared by incubation of cells with nuclear preparation buffer (0.30M sucrose, 10mM Tris, pH 7.5, 60mM KCl, 15mM NaCl, 5mM MgCl2, 0.1mM EGTA, 0.1% NP40, 0.15mM spermine, 0.5mM spermidine, and 2mM 6AA)
5. The libraries has been constructed as in PMID:24097267
6. ATACseq: Paired-end 50bp sequences were generated from samples with an Illumina HiSeq2500 and, following adapter trimming with FastP, were aligned against mouse genome (mm10) using bowtie2 with --local -q -p options. Peaks were called with MACS2 with --macs2 callpeak -f BAMPE --nomodel --shift -100 --extsize 200 –B --SPMR -g $GENOMESIZE -q 0.01 options
Genome_build: mm10
Supplementary_files_format_and_content: edgeR_DEGs_for ver1.3.2_2019-03-15.xlsx : unfiltered count matrix, filtered  count matrix, log-transformed normalized matrix, differential expression statistics
Supplementary_files_format_and_content: Sample_GRCF-Pernis-ER-6879_cKO_GCB_1_treat_pileup.bw: bigWIG of aligned cKO_GCB_replica 1 ATACseq
Supplementary_files_format_and_content: Sample_GRCF-Pernis-ER-6879_cKO_GCB_2_treat_pileup.bw: bigWIG of aligned cKO_GCB replica 2 ATACseq
Supplementary_files_format_and_content: Sample_GRCF-Pernis-ER-6879_WT_GCB_1_treat_pileup.bw: bigWIG of aligned WT GCB replica1 ATACseq
Supplementary_files_format_and_content: Sample_GRCF-Pernis-ER-6879_WT_GCB_2_treat_pileup.bw: bigWIG of aligned WT GCB replica 2 ATACseq

molecule: polyA RNA

source_name: Germinal center B cells

extract_protocol:
1. RNA-seq: Total RNA was isolated using QIAGEN RNeasy Plus Mini Kit from FACS sorted FoB or GCB cells; 2. ATAC-seq: the nuclei of sorted GCB cells were prepared by incubation of cells with nuclear preparation buffer (0.3M sucrose, 10mM Tris pH7.5, 60mM KCl, 15mM NaCl, 5mM MgCl2, 0.1mM EGTA, 0.1% NP40, 0.15mM spermine, 0.5mM spermidine, 2mM 6AA)
1. RNA-seq: sequence-compatible libraries were prepared by Nextera library preparation at a the Weill Cornell Epigenomics core. Quality of all RNA and library preparations were evaluated with BioAnalyzer 2100 (Agilent). Sequencing libraries were sequenced by the Epigenomics Core Facility at Weill Cornell Medicine using a HiSeq2500; 2. ATAC-seq: sequencing libraries were constructed as described in PMID: 26083756: Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf WJ. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature. 2015 Jul 23;523(7561):486-90. doi:10.1038/nature14590. Epub 2015 Jun 17.

treatment_protocol: WT and CD23-Cre.Rock2 mice were immunized for 7d with 100ug NP-CGG in alum

tag: strain

value: Rock2flox/flox CD23-Cre

value: spleen

value: Germinal center B cells

tag: age

value: 10 weeks


title: Pol2CTD ChIP-seq replicate 4 - WT control

description: ChIP

value: no fear

value: WT


title: A1004MD

city: Salt Lake City

first: Robert

middle: L

last: Judson-Torres

state: Utah

address: 2000 Circle of Hope

department: Dermatology

institute: Huntsman Cancer Institute at the University of Utah

description:
small RNA-Sequencing
McNeal_GEO_processed.txt

data_processing:
fastq files were aligned to GRCh37 using Bowtie.
BAM files resulting from the alignments were summarized to small RNA reference group (miRBase 21) and counted using the feature counts algorithm of DESEq2 in R.
Expression data was normalized using the DESeq2 package's median of ratios method in R.
Differentially expressed genes (£5% false discovery rate) were identified by DESeq2's General Linear Modeling and Bayesian statistics.
Genome_build: human reference genome GRCh37
Supplementary_files_format_and_content: tab-delimited text file includes normalized gene count values from DESeq2 for each sample.

source_name: adult skin-derived melanocytes

growth_protocol: Melanocytes were plated in 10cm culture-treated dishes and placed in a 5% CO2 37 °C incubator.

extract_protocol:
RNA was isolated using the Trizol Reagent (Ambion/ThermoFisher Scientific) and processed as per manufacturer’s instructions. Resulting RNA was then processed using the RNeasy Power Clean Pro Cleanup kit (Qiagen) and processed as per manufacturer's instructions.
MicroRNA Library Preparation was performed by SeqMatic using the SeqMaticMicroRNA Library Preparation Kit and protocols.

value: BRAF WT


title: Patient5-NI_CD4Treg-TCRseq

description: TCR-enrich polyA RNA

value: Non Invaded Lymph Node


title: Pol2CTD ChIP-seq replicate 3 - KO control

description: ChIP


title: Pol2CTD ChIP-seq replicate 3 - KO control input

description: input for Pol2CTD-3 KO control, Pol2ser2-3 KO control, Pol2ser5-3 KO control


title: Patient5-NI_CD4Teff-TCRseq

description: TCR-enrich polyA RNA


title: Pol2CTD ChIP-seq replicate 5 - WT fear input

description: input for Pol2CTD-5 WT fear, H3K27me3-1 WT fear, H3K9me3-1 WT fear


title: Pol2CTD ChIP-seq replicate 3 - KO fear

description: ChIP


description:
Folicular B cells from Rock2 conditional KO mice, RNAseq, replica2
edgeR_DEGs_for ver1.3.2_2019-03-15.xlsx
cKO_FoB_2

source_name: Folicular B cells

value: Folicular B cells


title: Pol2CTD ChIP-seq replicate 3 - WT fear

description: ChIP


title: Patient4-I_CD4Treg-TCRseq

description: TCR-enrich polyA RNA


title: Patient4-I_CD4Teff-TCRseq

description: TCR-enrich polyA RNA


description:
Folicular B cells from Rock2 conditional KO mice, RNAseq, replica1
edgeR_DEGs_for ver1.3.2_2019-03-15.xlsx
cKO_FoB_1


title: Patient4-NI_CD4Treg-TCRseq

description: TCR-enrich polyA RNA


title: Pol2CTD ChIP-seq replicate 3 - WT control

description: ChIP


title: Pol2CTD ChIP-seq replicate 3 - WT control input

description: input for Pol2CTD-3 WT control, Pol2ser2-3 WT control, Pol2ser5-3 WT control


title: Pol2CTD ChIP-seq replicate 3 - WT fear input

description: input for Pol2CTD-3 WT fear, Pol2ser2-3 WT fear, Pol2ser5-3 WT fear


title: Pol2CTD ChIP-seq replicate 2 - KO fear input

description: input for Pol2CTD-2 KO fear, Pol2ser2-1 KO fear, Pol2ser5-1 KO fear


title: mouse2_repl2_24h_RXRi

city: Basel

first: Ilya

last: Lukonin

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute (FMI)

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
Reads were mapped to the UCSC mouse genome mm10 using STAR (version 2.5.2b) using parameters --outFilterType BySJout --outFilterMultimapNmax 20 --outMultimapperOrder Random --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMmultNmax 1.
Genes expression level were quantified with the QuasR Bioconductor package, using gene annotations from the TxDb.Mmusculus.UCSC.mm10.knownGene Bioconductor package.
RPKM (reads per kilobase and million reads) of uniquely mapped reads were used to describe similarities and differences among the samples, for genes that were detected in 2 or more samples with at least one read per million reads.
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited text file with RPKM values for each Sample (columns)

source_name: Intestinal organoids

growth_protocol: Organoids were kept in IntestiCult Organoid Growth Medium (STEMCELL Technologies) with 100 μg/ml Penicillin-Streptomycin for amplification and maintenance. From day 0 to day 3, organoids were cultured in ENR (advanced DMEM/F-12 with 15 mM HEPES (STEM CELL Technologies) supplemented with 100 μg/ml Penicillin-Streptomycin, 1×Glutamax (Thermo Scientific), 1×B27 (Thermo Scientific), 1xN2 (Thermo Scientific), 1mM N-acetylcysteine (Sigma), 500ng/ml R-Spondin (kind gift from Novartis), 100 ng/ml Noggin (PeproTech) and 100 ng/ml murine EGF (Thermo Scientific))  with 20% Wnt3a-conditioned medium (Wnt3a-CM), 10 μM Y-27632 (ROCK inhibitor, STEMCELL Technologies) and 3 µM of CHIR99021 (GSK3B inhibitor, STEMCELL Technologies). From day 3 to 5, ENR was used for organoid culture. Wnt3a-CM was produced in-house by Wnt3a L-cells (kind gift from Novartis)

extract_protocol:
RNA was isolated using Single Cell RNA Purification Kit (Norgen Biotek Corporation, Cat #51800) pooling 3 wells of 24 well plates (C57BL/6 wild type). Organoids were seeded as single cells at 50000 cells per well and cultured as described above. RNA purification was performed in duplicate for two organoid cultures (C57BL/6 wild type, male littermate mice) for all treatment conditions. A step of DNAse treatment was included (RNase-Free DNase I Kit, Cat #25710) for all samples.
RNA sequencing libraries were prepared using the TruSeq Illumina mRNA Library Prep

treatment_protocol: Organoids were treated either with 10μm all-trans retinoic acid (atRA), 10 μm 9-cis retinoic acid (9cisRA) or 5 μm RXR antagonist (RXRi) at day 3 of organoid culture, concomitant with switching to ENR medium.

value: Intestinal organoids

value: wild type

value: 8 weeks

tag: gender

value: male


title: Pol2CTD ChIP-seq replicate 2 - KO fear

description: ChIP


title: Patient4-NI_CD4Teff-TCRseq

description: TCR-enrich polyA RNA

value: Luminal breast cancer


title: mouse2_repl1_24h_RXRi


title: Pol2CTD ChIP-seq replicate 2 - WT fear input

description: input for Pol2CTD-2 WT fear, Pol2ser2-1 WT fear, Pol2ser5-1 WT fear

value: fear


title: Pol2CTD ChIP-seq replicate 2 - KO control

description: ChIP

value: Top3b KO


title: mouse2_repl2_24h_9cisRA


title: Patient3-T_CD4Teff-TCRseq

description: TCR-enrich polyA RNA

value: Breast tumor


title: Pol2CTD ChIP-seq replicate 2 - KO control input

description: input for Pol2CTD-2 KO control, Pol2ser2-1 KO control, Pol2ser5-1 KO control

value: brain


description:
Germinal center B cells from Rock2 conditional KO mice, RNAseq, replica1
edgeR_DEGs_for ver1.3.2_2019-03-15.xlsx
cKO_GCB_1

value: Rock2flox/flox CD23-Cre

value: spleen


title: Pol2CTD ChIP-seq replicate 2 - WT control input

description: input for Pol2CTD-2 WT control, Pol2ser2-1 WT control, Pol2ser5-1 WT control


title: Patient3-I_CD4Treg-TCRseq

description: TCR-enrich polyA RNA

value: Invaded Lymph Node


title: Pol2CTD ChIP-seq replicate 1 - KO fear input

description: input for Pol2CTD-1 KO fear, TDRD3-1 KO fear


title: mouse2_repl1_24h_9cisRA


title: Patient3-I_CD4Teff-TCRseq

description: TCR-enrich polyA RNA


title: Pol2CTD ChIP-seq replicate 1 - KO fear

description: ChIP


title: mouse2_repl2_24h_atRA


title: Pol2CTD ChIP-seq replicate 1 - KO control input

description: input for Pol2CTD-1 KO control, TDRD3-1 KO control, H3K27me3-1 KO control, H3K9me3 KO control

value: no fear


description:
Folicular B cells from Rock2 conditional KO mice, RNAseq, replica3
edgeR_DEGs_for ver1.3.2_2019-03-15.xlsx
cKO_FoB_3

value: 10 weeks


title: mouse2_repl1_24h_atRA


title: Pol2CTD ChIP-seq replicate 1 - KO control

description: ChIP


title: Patient3-NI_CD4Treg-TCRseq

description: TCR-enrich polyA RNA


title: Patient3-NI_CD4Teff-TCRseq

description: TCR-enrich polyA RNA


title: Pol2CTD ChIP-seq replicate 1 - WT fear

description: ChIP

value: WT


title: Pol2CTD ChIP-seq replicate 1 - WT fear input

description: input for sample Pol2CTD-1 WT fear, TDRD3-1 WT fear


title: mouse2_repl2_24h_DMSO


title: Pol2CTD ChIP-seq replicate 1 - WT control input

description: input for sample Pol2CTD-1 WT control, TDRD3-1 WT control, H3K27me3-1 WT control, H3K9me3 WT control


title: Pol2CTD ChIP-seq replicate 1 - WT control

description: ChIP


title: Pol2CTD ChIP-seq replicate 2 - WT fear

description: ChIP


title: Patient2-T_CD4Treg-TCRseq

description: TCR-enrich polyA RNA


title: mouse2_repl1_24h_DMSO


title: RNA-seq2_KO_fear

data_processing:
RNA SEQ fastq files are first passed fastqc to remove potentially low quality bases
Alignment and assembling: After removal of low quality reads, the fastq files are mapped to mouse mm10 genome by Tophat 2.2.1 to generate bam files. They are then assembled by Cufflinks 2.2.1 to produce transcript GTF files for each sample. The files are merged by Culllinks merge to create a common transcript GTF file for Gene Deferential expression analysis.
file conversion: The bam files are sorted by samtools.v1.9 . They are then indexed ,  and coverted to bed format by bamtools.2.5.1 with the convert function.
data analysis: The bam files are used for further gene differential expression analysis by Tuxedo Suite CuffDiff v2.2.1 pipleline. The same files and method is used for genome structrue mapping, merging and obtaining the siginificant defferential gene expression lists for each comparison.
The bed files are used to obtain data of raw counts, as well as normalized data (FPKM) by htseq-count 0.11.2.
bedgraph generation/normalization: The codes are available upon request
Additional gene expression differential analysis: The raw counts files are used as input for edgeR 3.26.8. The data are normalized by TMM normalization to generate additional gene expression significant lists. The lists are then compared with the the significant gene expression change list produced by Cuffdiff.
functionl/phenotype analysis: The gene expression change values from gene differential expression lists are used in PAGE algorithem to analyze Gene Ontology gene set and Broad Institute Pathway gene set to obtain functional change list. The are also used in PAGE algorithem to analyze disease MESH term Gene Set  to obtain phenotype change lists.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bedgraph files includes FPKM values for each Sample

extract_protocol:
Total RNA was extracted from 200 microliter lysate using 1 ml Trizol (InVitrogen, 15596026). The RNA was precipitated in 1.5-fold volume of 2-propanol together with 10% volume 3 M Sodium Acetate. Genomic DNA was removed using DNase I (Sigma Aldrich, AMPT1-1KT). Ribosomal RNA was removed from 1 ug from total RNA using rRNA depletion kit (New England biolab, E6310S).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were placed into the chamber (120 sec) for habituation, followed by 30 sec tone that co-terminated with a 2 -sec, 0.5 mA electric foot shock. This was repeated for a total of three tone-shock pairings with an interval of 30 seconds sec between tone presentations. The mice were culled by CO2 after 10 min.

value: 2-4 month old


title: mouse1_repl2_24h_RXRi


title: RNA-seq2_KO_control


title: Patient2-T_CD4Teff-TCRseq

description: TCR-enrich polyA RNA


title: RNA-seq2_WT_fear


title: mouse1_repl1_24h_RXRi


title: Patient2-I_CD4Treg-TCRseq

description: TCR-enrich polyA RNA


title: RNA-seq1_KO_fear


title: RNA-seq2_WT_control


title: Pol2CTD ChIP-seq replicate 2 - WT control

description: ChIP


title: Patient2-I_CD4Teff-TCRseq

description: TCR-enrich polyA RNA


title: RNA-seq1_KO_control


title: mouse1_repl2_24h_9cisRA


title: Th17(23)_Control RNA-seq rep3

city: Shenzhen

first: Zhijun

last: Han

state: Guangdong

address: No 1088,xueyuan Rd., Nanshan District

country: China

institute: Southern University of Science and Technology

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were mapped to mm10 with refGene annotation downloaded from UCSC Genome Browser using TopHat2 v2.1.0. Gene expression level were counted by htseq-count 0.11.0. Differential expressed genes were called by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: TAB-delimited text file included the raw reads count for each gene from RNA-seq sample.

source_name: TH17(23) cells

growth_protocol: Naïve CD4+ T cells were isolated from lymph nodes or spleen of mice using a CD4+ CD62L+ T cell isolation kit II (Miltenyi Biotec) according to the manufacturer’s instruction. Naïve CD4+ T cells were stimulated with plate-bound anti-CD3ε mAb (5 µg/ml) in the presence of anti-CD28 mAb (2 µg/ml) in a 48-well plate under neutral conditions (10 µg/ml anti–IL-4 mAb and 10 µg/ml anti–IFN-γ mAb), IL-6 conditions (10 ng/ml IL-6, 10 µg/ml anti–IL-4 mAb, and 10 µg/ml anti–IFN-γ mAb), TH17 (23) conditions (20 ng/ml IL-6, 20 ng/ml IL-1β, 20 ng/ml IL-23, 10 µg/ml anti–IL-4 mAb, and 10 µg/ml anti–IFN-γ mAb).

extract_protocol:
Naive CD4+ T cells from control and miR-22-/- mice were differentiated under pathogenic TH17 (23) differentiation condition. Total RNA was prepared from these cells using Trizol reagent (Invitrogen). RNA-seq libraries were prepared using a TruSeq Stranded Total RNA Library Prep Kit (Illumina). For GFP+ TH17 cells sorted from in vivo suspensions, 50,000 cells were resuspended in 700 ul Trizol reagent, total RNA was prepared by miRNeasy Micro Kit (Qiagen), RNA-seq libraries were prepared using SMART-Seq v4 Ultra Low Input RNA Kit (clontech). Sequencing was performed on an Illumina HiSeq X Ten System in a 150 bp/150 bp Paired end mode.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wildtype


title: mouse1_repl1_24h_9cisRA

value: Intestinal organoids


title: RNA-seq1_WT_control


title: mouse1_repl2_24h_atRA

value: wild type


title: Th17(23)_Control RNA-seq rep2


title: Th17(23)_Control RNA-seq rep1


title: RNA-seq1_WT_fear


title: Patient2-NI_CD4Teff-TCRseq

description: TCR-enrich polyA RNA

value: Non Invaded Lymph Node


title: Patient2-NI_CD4Treg-TCRseq

description: TCR-enrich polyA RNA


title: mouse1_repl1_24h_atRA

value: 8 weeks

value: male


title: Patient1-T_CD4Treg-TCRseq

description: TCR-enrich polyA RNA

value: Luminal breast cancer


title: Th17(23)_miR-22-/- RNA-seq rep3

value: mir-22 KO


title: ASC-rep1

city: Hong Kong

first: Tom

last: Cheung

address: Clear Water Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

description: freshly-isolated activated muscle stem cells from unperfused mice 2.5 days after injury

data_processing:
RNA-seq data were aligned using STAR (version 2.5.3a) with the parameters “–twopassMode Basic”, “–outFilterIntronMotifs RemoveNoncanonical”, “--outSAMstrandField intronMotif”, and “--outSAMmultNmax 1”.
Then, StringTie (version 1.3.3) was used with the -e option to quantify gene expression levels according to the reference’s annotations.
Furthermore, StringTie’s -b option was used so that output suitable for Ballgown (version 2.10.0) under R (version 3.4.1) could be produced.
Genome_build: mm9
Supplementary_files_format_and_content: Table of genes by samples of FPKM values, as output by Ballgown.  File format is tab-separated values (ASCII text file).

extract_protocol:
The fixed muscle stem cell isolation was following the isolation protocol of satellite cells, as described previously in Liu et al., 2015, except that Collagenase II for first digestion was used at double amount which is 2000 U/mL. For unfixed muscle stem cell isolation from C57BL/6 mice, the method was following the protocol described in Liu et al., 2015. Mononuclear cells were stained with Vcam-biotin (BD Bioscience, clone 429), CD31-APC (BD Bioscience, clone MEC 13.3), CD45-APC (BD Bioscience, clone 30-F11) and Sca-1-Pacific-Blue (Biolegend, clone D7) at 1:75. Streptavidin-PE-cy7 was used to amplify the Vcam signal (BD Biosciences, 557598, 1:75). Cell suspension was sorted using a BD Influx cell sorter equipped with 405-nm, 488-nm, 561-nm and 633-nm lasers. The machine was carefully optimized for purity and viability.
Total RNA from cells were isolated using NucleoSpin RNA XS (Macherey-Nagel). To get high quality RNA from fixed cells, the total RNA from fixed muscle stem cells were isolated using a miRNeasy FFPE Kit (Qiagen) following the protocol described in Thomsen et al., 2015. cDNA was generated following the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech) protocol. The RNA-Seq libraries were sheared with a Covaris S220 and generated using Ovation Ultralow DR Multiplex System 9-16 (NuGEN Technologies). The libraries were sequenced using Illumina NextSeq 500 (2 x 150).

tag: genotype/variation

value: 2 months old

value: no perfusion

value: Skeletal muscle

value: Muscle stem cells


title: mouse1_repl2_24h_DMSO


title: Patient1-I_CD4Treg-TCRseq

description: TCR-enrich polyA RNA

value: Invaded Lymph Node


title: uSC-rep2

description: freshly-isolated muscle stem cells from unperfused mice


title: Patient1-I_CD4Teff-TCRseq

description: TCR-enrich polyA RNA


title: mouse2_repl2_6h_RXRi


title: uSC-rep1

source_name: freshly-isolated muscle stem cells from unperfused mice


title: mouse1_repl1_24h_DMSO


title: Th17(23)_miR-22-/- RNA-seq rep1


title: mouse2_repl1_6h_RXRi


title: Patient1-NI_CD4Treg-TCRseq

description: TCR-enrich polyA RNA


title: Patient1-NI_CD4Teff-TCRseq

description: TCR-enrich polyA RNA


title: 17678x4_mCherryLowA

description: Bulk RNA Sequencing

data_processing:
The human GRCh38 FASTA and GTF files were downloaded from Ensembl release 98.
The reference database was created using STAR version 2.7.2c with splice junctions optimized for 50 base pair reads.
Optical duplicates removed from NovaSeq runs via Clumpify v38.34
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3
Non-coding features, histones, and ribosomal RNAs were removed and differentially expressed genes were identified using a 5% false discovery rate with DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: FeatureCounts output files combined into a single tab-delimited matrix

extract_protocol:
Trizol, manufacture's protocol
Illumina TruSeq Stranded mRNA Library Prep (RIN 8-10) with UDI

treatment_protocol: FACS isolated reporter high or low

tag: cell line

value: melanoma cell line

tag: population

value: POU3F2 Low


title: mouse2_repl2_6h_9cisRA


title: 17678x5_mCherryLowB

description: Bulk RNA Sequencing


title: 17678x3_mCherryHighC

description: Bulk RNA Sequencing

value: POU3F2 High


title: ASC-rep2

source_name: freshly-isolated activated muscle stem cells from unperfused mice 2.5 days after injury


title: mouse2_repl1_6h_9cisRA


title: Patient1-T_CD4Teff-TCRseq

description: TCR-enrich polyA RNA

value: Breast tumor


title: VpRH2 2869-t2

city: Freiburg

first: Patrick

last: Metzger

address: Breisacher Str. 153

department: Institute for Medical Bioinformatics and Systems Medicine

country: Germany

institute: University Hospital Freiburg

data_processing:
alignment and gene quantification with STAR
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimeted txt files include raw count values for each sample

source_name: Tumour biopsy

extract_protocol:
RNA was isolated from powdered frozen samples using the NucleoSpin RNA kit (Machery Nagel)
Paired-end RNA-sequencing was performed on an Illumina HISEQ4000 device with the Illumina TruSeq Stranded RNA library preparation kit.

treatment_protocol: Renal tissue or tumour biopsy was snap frozen in liquid nitrogen

value: tumor (ccRCC model)


title: 17678x2_mCherryHighB

description: Bulk RNA Sequencing


title: Th17(23)_miR-22-/- RNA-seq rep2


title: VpRH2 2779-t2


title: mouse2_repl2_6h_DMSO

value: Intestinal organoids


title: mouse2_repl2_6h_atRA

value: wild type


title: mouse2_repl1_6h_atRA


title: VpRH2 2820-t1


title: VpRH2 2869-t1


title: mouse2_repl1_6h_DMSO


title: 17678x6_mCherryLowC

description: Bulk RNA Sequencing


title: mouse1_repl2_6h_RXRi


title: mouse1_repl1_6h_RXRi


title: VpRH2 2833-t1


title: CAG67202 pALS14 uninduced [wt_14_un_0]

city: Stanford

first: Anthony

middle: Lyndon

last: Shiver

state: CA

address: 443 Via Ortega Shriram Bldg 062

department: BioEngineering

institute: Stanford University

description:
wt_14_un_0
E. coli K-12 BW25113
processed data file: cts.csv

data_processing:
The indexed raw sequencing data was demultiplexed according to their R1 barcodes and the degenerate linker sequence was clipped using a custom script.
Mapping of individual reads to the E. coli genome (GenBank ID U00096.3) was performed with STAR (Dobin et al., 2013), followed by read counting for individual genome regions according to gene annotations from assembly ASM584v2.
Raw read counts for all 24 samples were used as input for DESeq2 v. 1.22.2 (Love et al., 2014). Information on the strain (parental or mutant), plasmid (pALS13 or pALS14), and induction (yes or no) was used to group samples for statistical analysis.
Estimates for the differential expression of genes in response to induction of RelA* were obtained using the full factorial linear model y ~ strain + plasmid + induction + strain:plasmid + strain:induction + plasmid:induction + strain:plasmid:induction.
Finally, to estimate the effect of the mutant strain alone, we used the average contrast between mutant and wildtype for strains with pALS14 across induced and uninduced conditions. The linear model used was y ~ strain + plasmid + induction + strain:plasmid + strain:induction. The reference factors were set to (strain: parental), (plasmid: pALS14), and (induction: no). The (strain: mutant) versus (strain: parental) contrast was combined with 50% of the strain:induction interaction term as output.
Genome_build: U00096.3
Supplementary_files_format_and_content: cts.csv: Comma-separated table of mapped read counts for all samples and replicates.
Supplementary_files_format_and_content: mut.13.p.csv: Differential expression; output from DESeq2 including log2-fold change and p-values.
Supplementary_files_format_and_content: mut.13.p.full.csv: Differential expression; output from DESeq2 including log2-fold change and p-values.
Supplementary_files_format_and_content: mut.14.p.csv: Differential expression; output from DESeq2 including log2-fold change and p-values.
Supplementary_files_format_and_content: wt.13.p.csv: Differential expression; output from DESeq2 including log2-fold change and p-values.
Supplementary_files_format_and_content: wt.13.p.full.csv: Differential expression; output from DESeq2 including log2-fold change and p-values.
Supplementary_files_format_and_content: wt.14.p.csv: Differential expression; output from DESeq2 including log2-fold change and p-values.
Supplementary_files_format_and_content: mutdiff.14.csv: Differential expression; output from DESeq2 including log2-fold change and p-values.

organism: Escherichia coli BW25113

source_name: in vitro culture of E. coli

growth_protocol: Cells were grown overnight in Teknova Rich Defined Media (EZ-RDM) with 100 µg/mL ampicillin to maintain plasmid selection. Overnight cultures were inoculated into fresh EZ-RDM with 100 µg/mL ampicillin to maintain plasmid selection.

extract_protocol:
RNA was isolated from frozen cell pellets using Trizol (Invitrogen) extraction according to the manufacturer's protocol.
One microgram of purified RNA was fragmented at 95 C for 7 min in 1X T4 RNA Ligase buffer (NEB) with an equal volume of 2X alkaline fragmentation buffer (0.6 volumes of 100 mM Na2CO3 plus 4.4 volumes of 100 mM NaHCO3). After 3'-end healing with PNK (NEB) in T4 RNA ligase buffer for 1 h, 3' ligation to a pre-adenylated, barcoded TruSeq R1 adapter with 5 random bases at its 5' end was performed overnight. The barcoded samples were then pooled and run onto a 6% TBE-Urea gel for size selection (>15 nucleotide insert size), eluted, and ethanol precipitated before performing ribosomal RNA subtraction (RiboZero). Reverse transcription with SuperScript IV (Invitrogen) was performed using a TruSeq R1 RT primer, followed by ligation of the TruSeq R2 adapter to the 3' end of the cDNA overnight, prior to another gel size selection as described above. A final PCR of the library was performed with indexed TruSeq PCR primers to add the index and P5/P7 flowcell adapters, followed by gel extraction, precipitation, and a BioAnalyzer (Agilent) run for quality control before sequencing on a NextSeq500 platform.

treatment_protocol: After the strains had grown to mid-log phase, samples were taken for the uninduced control, isopropyl _-d-1-thiogalactopyranoside (IPTG) was added at a final concentration of 1 mM to induce expression of the relA alleles, and samples were taken 5 min after induction. All samples were immediately stored on ice with a 1:8 volume of 5% phenol in ethanol as a stop solution. Samples were transferred to a -80ûC freezer for storage before further processing.

tag: mutation

value: RpoB+

tag: plasmid

tag: induction

value: uninduced


title: CAG67202 pALS14 uninduced [wt_14_un_1]

description:
wt_14_un_1
E. coli K-12 BW25113
processed data file: cts.csv


title: VpRH2 2797-t1


title: mouse1_repl2_6h_9cisRA

value: 8 weeks

value: male


title: CAG67202 pALS14 induced [wt_14_ind_2]

description:
wt_14_ind_2
E. coli K-12 BW25113
processed data file: wt.14.p.csv
processed data file: cts.csv

value: induced


title: VpRH2 2875-t2


title: VpRH2 2795-t1


title: VpRH2 2341-t1


title: mouse1_repl1_6h_9cisRA


title: CAG67202 pALS14 induced [wt_14_ind_1]

description:
wt_14_ind_1
E. coli K-12 BW25113
processed data file: wt.14.p.csv
processed data file: cts.csv


title: CAG67202 pALS14 induced [wt_14_ind_0]

description:
wt_14_ind_0
E. coli K-12 BW25113
processed data file: wt.14.p.csv
processed data file: cts.csv


title: VpRH1 2941_t1


title: CAG67202 pALS14 uninduced [wt_14_un_2]

description:
wt_14_un_2
E. coli K-12 BW25113
processed data file: cts.csv


title: CAG67202 pALS13 uninduced [wt_13_un_2]

description:
wt_13_un_2
E. coli K-12 BW25113
processed data file: cts.csv


title: mouse1_repl2_6h_atRA


title: VpRH1 2612_t1


title: 17678x1_mCherryHighA

description: Bulk RNA Sequencing


title: VpRH2 2871-t1


title: CAG67202 pALS13 uninduced [wt_13_un_1]

description:
wt_13_un_1
E. coli K-12 BW25113
processed data file: cts.csv


title: mouse1_repl1_6h_atRA


title: CAG67202 pALS13 induced [wt_13_ind_2]

description:
wt_13_ind_2
E. coli K-12 BW25113
processed data file: wt.13.p.csv
processed data file: wt.13.p.full.csv
processed data file: cts.csv


title: WT Cortex 2549

source_name: Wild type renal cortex biopsy

value: WT

value: renal cortex


title: VpR 2756_t1

value: VpR


title: mouse1_repl1_6h_DMSO


title: CAG67202 pALS13 uninduced [wt_13_un_0]

description:
wt_13_un_0
E. coli K-12 BW25113
processed data file: cts.csv


title: mouse2_repl2_0h_none


title: VpRH1 2909_t1


title: mouse2_repl1_0h_none


title: CAG67202 pALS13 induced [wt_13_ind_1]

description:
wt_13_ind_1
E. coli K-12 BW25113
processed data file: wt.13.p.csv
processed data file: wt.13.p.full.csv
processed data file: cts.csv


title: CAG67202 pALS13 induced [wt_13_ind_0]

description:
wt_13_ind_0
E. coli K-12 BW25113
processed data file: wt.13.p.csv
processed data file: wt.13.p.full.csv
processed data file: cts.csv


title: WT Cortex 2517


title: mouse1_repl2_0h_none


title: CAG68095 pALS14 uninduced [mut_14_un_2]

description:
mut_14_un_2
E. coli K-12 BW25113
processed data file: cts.csv


title: VpR 2753_t1


title: mouse1_repl1_0h_none


title: VpRH1 2908_t1


title: Female ribosomal RNA-depleted nuclear liver RNA pool 3 [G119-M14]

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

data_processing:
Sequence reads were mapped to mm9 using TopHat2 (Kim et al., Genome Biol., 2013)
LncRNA  expression level for each sample was quantified based on mapped sequence reads that overlap any lncRNA exon by at least one bp using featureCounts (Liao et al., Bioinformatics, 2014). FeatureCounts was also used to obtain read counts for RefSeq genes. Mature (spliced) mRNAs were quantified by counting sequence reads that map to a concatenated sequence comprised of the union of the exonic regions for all isoforms of a given gene (GeneBody).
edgeR (Robinson et al. 2010) was used to compute differential expression between male and female samples.
Genome_build: mm9
Supplementary_files_format_and_content: A Microsoft Excel sheet containing expression levels and male/female differential expression analysis for lncRNAs and RefSeq genes.

growth_protocol: Untreated male and female CD-1 mice (Charles River Laboratories), 7-11 weeks old, were euthanized and their livers were extracted.

extract_protocol:
Total RNA was extracted from flash frozen mouse liver using Trizol per the manufacturer's instructions. Nuclei were isolated from mouse liver by homogenization and ultracentrifugation through a sucrose buffer. RNA was extracted from purified nuclei using Trizol LS following standard protocol.
RNA samples were pooled to make 3 biological replicates per condition comprised of 12-17 individuals each. RNA was depleted of ribosomal RNA with the NEBNext rRNA-depletion kit, Partial depletion of rRNA was achieved. Libraries were prepared with the NEBNext Ultra Directional RNA Library Prep kit for Illumina (NEB, Cat# E7420) and multiplexed using NEBNext Multiplex Oligos for Illumina (NEB, Cat# E7335, E7500), according to the manufacturer's instructions.

value: CD-1 (Charles River)

tag: Sex

value: Female

value: 7-11 weeks

value: liver

value: Intact

tag: molecule subtype

value: Ribosomal RNA-depleted nuclear RNA


title: WT Cortex 2518

tag: genotype


title: mouse1_repl2_6h_DMSO

tag: tissue


title: VpRH1 2907_t1

value: tumor (ccRCC model)


title: Female ribosomal RNA-depleted nuclear liver RNA pool 2 [G119-M13]


title: CAG68095 pALS14 uninduced [mut_14_un_0]

description:
mut_14_un_0
E. coli K-12 BW25113
processed data file: cts.csv


title: CAG68095 pALS14 uninduced [mut_14_un_1]

description:
mut_14_un_1
E. coli K-12 BW25113
processed data file: cts.csv


title: Female ribosomal RNA-depleted nuclear liver RNA pool 1 [G119-M12]


title: CAG68095 pALS14 induced [mut_14_ind_1]

description:
mut_14_ind_1
E. coli K-12 BW25113
processed data file: mut.14.p.csv
processed data file: mutdiff.14.csv
processed data file: cts.csv


title: CAG68095 pALS14 induced [mut_14_ind_0]

description:
mut_14_ind_0
E. coli K-12 BW25113
processed data file: mut.14.p.csv
processed data file: mutdiff.14.csv
processed data file: cts.csv


title: CAG68095 pALS14 induced [mut_14_ind_2]

description:
mut_14_ind_2
E. coli K-12 BW25113
processed data file: mut.14.p.csv
processed data file: mutdiff.14.csv
processed data file: cts.csv


title: VpR 3319_t1


title: Male ribosomal RNA-depleted nuclear liver RNA pool 1 [G119-M9]

value: Male


title: CAG68095 pALS13 uninduced [mut_13_un_2]

description:
mut_13_un_2
E. coli K-12 BW25113
processed data file: cts.csv


title: Male ribosomal RNA-depleted nuclear liver RNA pool 3 [G119-M11]


title: WT Cortex 2326


title: CAG68095 pALS13 uninduced [mut_13_un_1]

description:
mut_13_un_1
E. coli K-12 BW25113
processed data file: cts.csv


title: VpRH1 2899_t3


title: Female ribosomal RNA-depleted total liver RNA pool 2 [G119-M1]

value: Ribosomal RNA-depleted total RNA


title: CAG68095 pALS13 induced [mut_13_ind_2]

description:
mut_13_ind_2
E. coli K-12 BW25113
processed data file: mut.13.p.csv
processed data file: mut.13.p.full.csv
processed data file: cts.csv


title: VpR 2530_t1


title: Female ribosomal RNA-depleted total liver RNA pool 1 [G118-M22]


title: VpRH1 2899_t2


title: CAG68095 pALS13 induced [mut_13_ind_1]

description:
mut_13_ind_1
E. coli K-12 BW25113
processed data file: mut.13.p.csv
processed data file: mut.13.p.full.csv
processed data file: cts.csv


title: Male ribosomal RNA-depleted total liver RNA pool 3 [G118-M21]


title: Male ribosomal RNA-depleted nuclear liver RNA pool 2 [G119-M10]


title: Male ribosomal RNA-depleted total liver RNA pool 2 [G118-M20]


title: VpR 2542_t1


title: VpRH1 2899_t1


title: CAG68095 pALS13 induced [mut_13_ind_0]

description:
mut_13_ind_0
E. coli K-12 BW25113
processed data file: mut.13.p.csv
processed data file: mut.13.p.full.csv
processed data file: cts.csv


title: Male ribosomal RNA-depleted total liver RNA pool 1 [G118-M19]


title: VpR 2535_t1


title: MDA-MB-231_3fS_unt_CUTandRUN_Ig

city: Dallas

first: Cheng-Ming

last: Chiang

state: Texas

address: 5323 Harry Hines Blvd. ND2.210H

department: Simmons Comprehensive Cancer Center

institute: UT Southwestern Medical Center

data_processing:
Library strategy: CUTandRUN
Raw reads were trimmed by TrimGalore for ChIP-seq or FASTP for CUTandRUN.
Reads were mapped to hg19 using BWA for BRD4 CUTandRUN and BWA-MEM for ChIP-seq and EN1 datasets.
Alignments with mapping quality less than 15 were filtered out.
Duplicate alignments were removed using Sambamba or SAM/BAM RmDuP.
Peaks were called using MACS2 following the Galaxy default configuration (effective genome size 2.45e+09, band width 300, model fold [5, 50], q-value cutoff 0.05, larger dataset scaled towards smaller dataset, range for calculating regional lambda 1000 bps and 10000 bps) for BRD4 CUTandRUN or (p cutoff 0.01 --nomodel --shift 0 --extsize 90 --keep-dup all -B --SPMR) for ChIP-seq and EN1 data sets.
Supplementary_files_format_and_content: ChIP-seq bigwig files containing relative signal fold change (fc) of sample/control were generated by BICF ChIP-seq Analysis Workflow.  CUTandRUN bigwig files contain spike-in-normalized signals were generated using Galaxy bamcompare.
Genome_build: hg19

source_name: MDA-MB-231 3F:BRD4-S(a)

growth_protocol: MDA-MB-231 and its derived 3F:BRD4-S(a) line were maintained in high-glucose DMEM + 10% heat-inactivated FBS + Penicillin (100 units/ml) & Streptomycin (0.1 mg/ml).

extract_protocol:
Unfixed cells were immobilized on Concanavalin A-coated magnetic beads and permeablized with 0.05% digitonin. After antibody binding and pA-Mnase digestions, antibody-bound DNA fragments were released into solution, purified, and used for library construction.
Sequencing libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) with modification for shorter DNA fragments (< 100 bp).

treatment_protocol: no treatment

value: breast cancer cell line MDA-MB-231 ectopic 3f:BRD4-S(a) expression

tag: er/pr/her2 statue

value: triple negative – ER-; PR-; HER2-

tag: chip antibody

value: IgG

tag: bet inhibitor jq1 treatment

value: untreated (unt)


title: MDA-MB-231_3fS_unt_CUTandRUN_BRD4_L


title: Infected_1hpi_Infected_1.5hpi

city: Taipei

first: Chuan

last: Ku

address: 128 Academia Road, Section 2, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

data_processing:
Read_1 files were mapped onto the reference sequences of the virus and the host using bowtie 2 (v2.2.4) (-p 10)
Demultiplexing and UMI counting (unique molecular identifiers (UMI) and cell barcodes are in read 2; pool barcodes are in read 1) was performed using the pipeline described in Keren-Shaul et al. 2019 (https://doi.org/10.1038/s41596-019-0164-4)
Each pool is marked by a unique pool barcode. Each plate corresponds to either one (RT1 primers gr1, gr2, gr3, and gr4) or two pools. In the latter case, each pool is a half plate (RT1 primers gr3 and gr4) where columns 1-12 are the processed data file A.txt and columns 13-24 B.txt.
Genome_build: EhV201 (virus) genome: JF974311; Emiliania (host) transcriptome reference (both forward and reverse complement (_rev) sequences): Schatz et al. 2017 Nature Microbiol. (https://doi.org/10.1038/s41564-017-0024-3); ERCC RNA Spike-In Mix
Supplementary_files_format_and_content: Tab-delimited table of UMIs (genes/transcripts by wells)

organism:
Emiliania huxleyi
Coccolithovirus

source_name: Cell culture

growth_protocol: 16/8 h light/dark cycle; K/2 medium; 18 °C; light: 100 μmol photons m-2s-1

extract_protocol:
RNA capture: Plates were forzen at -80C and thawed. Lysis solution (ddH2O, 0.1%triton, RNase inhibitors) was evaporated and reverse transcription was performed directly in the wells.
MARSseq library prepartion was performed as described in Keren-Shaul et al. 2019 (https://doi.org/10.1038/s41596-019-0164-4). Briefly, cDNA from different cells (barcoded in the reverse transcripiton step) was pooled and amplified by in vitro transcription. Amplified RNA was then fragmented, reverse transcribed, and Illumina adaptors were added by PCR.

treatment_protocol: Single cells were separated using fluorescence-activated cell sorting (FACS) directly into a lysis solution in 384-well plates.

tag: host strain

tag: virus strain

tag: well prefix

tag: pool barcode


title: VpR 2020t


title: CAG68095 pALS13 uninduced [mut_13_un_0]

description:
mut_13_un_0
E. coli K-12 BW25113
processed data file: cts.csv

value: uninduced


title: Infected_2hpi_Control_2.5hpi


title: MDA-MB-231_unt_CUTandRUN_Ig_3

value: breast cancer cell line MDA-MB-231


title: MDA-MB-231_unt_CUTandRUN_Ig_2


title: VpR 2017-1t


title: VpR 2018-t


title: MDA-MB-231_3fS_unt_CUTandRUN_BRD4_S


title: Female ribosomal RNA-depleted total liver RNA pool 3 [G119-M2]

tag: strain

tag: age

tag: treatment


title: WT Cortex 2528

value: WT

value: renal cortex


title: WT Cortex 2540


title: MDA-MB-231_unt_CUTandRUN_Ig_1

tag: cell line


title: WT Cortex 2014-n


title: WT Cortex 2015-n


title: VpR 2017-2t

value: VpR


title: VpR 2028-t


title: MDA-MB-231_unt_CUTandRUN_EN1_2


title: MDA-MB-231_unt_CUTandRUN_BRD4_S_2


title: MDA-MB-231_unt_CUTandRUN_EN1_1


title: WT Cortex 2011-n


title: VpR 2009-t


title: MDA-MB-231_unt_CUTandRUN_BRD4_S_1


title: MDA-MB-231_unt_CUTandRUN_BRD4_L


title: MDA-MB-231_unt_ChIP_Input

data_processing:
Raw reads were trimmed by TrimGalore for ChIP-seq or FASTP for CUTandRUN.
Reads were mapped to hg19 using BWA for BRD4 CUTandRUN and BWA-MEM for ChIP-seq and EN1 datasets.
Alignments with mapping quality less than 15 were filtered out.
Duplicate alignments were removed using Sambamba or SAM/BAM RmDuP.
Peaks were called using MACS2 following the Galaxy default configuration (effective genome size 2.45e+09, band width 300, model fold [5, 50], q-value cutoff 0.05, larger dataset scaled towards smaller dataset, range for calculating regional lambda 1000 bps and 10000 bps) for BRD4 CUTandRUN or (p cutoff 0.01 --nomodel --shift 0 --extsize 90 --keep-dup all -B --SPMR) for ChIP-seq and EN1 data sets.
Supplementary_files_format_and_content: ChIP-seq bigwig files containing relative signal fold change (fc) of sample/control were generated by BICF ChIP-seq Analysis Workflow.  CUTandRUN bigwig files contain spike-in-normalized signals were generated using Galaxy bamcompare.
Genome_build: hg19

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated by IP with anti-BRD4-L or BRD4-S [i.e., S(a)] antibody or with Abcam EN1 antibody (Cat# ab108598).
Sequencing libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) following manufacturer’s protocol.

treatment_protocol: Cells were either untreated (unt) or treated with 1 µM inactive JQ1(-) (i.e., JQ1-neg) or active JQ1(+) (i.e., JQ1-pos) for 4 hours.

value: input


title: POLR1A low epithelium tumor cells from patient derived xenograft (1441)

type: RNA

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

hyb_protocol: cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA)

scan_protocol: Arrays were scanned with GeneChip scanner GSC3000 (Affymetrix, Santa Clara, CA)

data_processing: RMA normalization method as implemented in affy Bioconductor R package

label: biotin

label_protocol: 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Tumor xenografts were grown from sucutaneous injection of patient derived organoids into immunodeficient mice. Cells were isolated once the tumors reach an average size of 100mm3.

extract_protocol: RNA was isolated using magnetic beads from 2000 cels. Library preparation and amplification were performed as described by Gonzalez et al., 2010. Amplification was performed for 22 cycles.

treatment_protocol: No treatment was used in this study

tag: disease state

value: CRC

tag: biological replicate

tag: cell population

value: POLR1A low


title: POLR1A high epithelium tumor cells from patient derived xenograft (1440)

value: POLR1A high


title: POLR1A low epithelium tumor cells from patient derived xenograft (1439)


title: Female, 8 weeks of age, fed phyto-oestrogen-free diet, oocytes, treated with BPS 4

city: Prague

first: Lukáš

middle: Farhád

last: Mirchi

state: Czech Republic

address: Albertov 4

department: First Faculty of Medicine

country: Czech Republic

institute: Charles University

description: Espression data obtained from mice oocytes after BPS treatment

hyb_protocol: hybridization was perfomermed using GeneAtlas® WT Expression Kit User Manual

scan_protocol: GeneChips were scanned using the GeneAtlas® Imaging station with GeneAtlas®Instrument Control Software 2.0.0.460

data_processing: The data were analyzed with Affymetrix® Transcriptome Analysis Console (TAC) Software (version 4.0.1) using GC-MRA as normalization method.

label_protocol: labelling was perfomermed using GeneAtlas® WT Expression Kit User Manual

growth_protocol: Six- to seven-week-old ICR mice were purchased from Velaz Ltd. (Prague, Czech Republic). Mice were kept under  12 hours light-dark cycle, fed phyto-oestrogen-free diet 1814P (Altromin) and given access to ultra pure water ad libitum. Animals were randomly separated into five groups (N = 3 each, N = 4 for transcriptomic experiment) and allowed to acclimate for at least one week. Each group was treated with one of four different BPS doses (0.001, 0.1, 10, and 100 ng BPS x g bw-1 x day-1, hereafter named BPS1, BPS2, BPS3, and BPS4, respectively). Only BPS2 (0.1 ng x g bw-1 x day-1) was used for transcriptomic profiling. BPS was dissolved in 50 μl 50% glycerol containing 0.1% DMSO and administered daily for 7 days by oral gavage. After the exposure period, mice were euthanised by cervical dislocation, and their ovaries were collected for RNA extraction and further experiments.

extract_protocol: Total mice oocyte RNA was isolated using TRIzol reagent (Invitrogen) and homogenised using a TissueLyser LT (Qiagen) for 5 min. Chloroform was used for phase separation, and the aqueous phase was mixed 1:1 with 70% ethanol. RNA was purified with RNeasy MinElute spin columns (Qiagen) and quantified by qRT-PCR. Integrity was assessed using a 2100 Bioanalyzer and an RNA 6000 Pico Kit (Agilent, Böblingen, Germany) were used to ensure the quality and quantity of the extracted RNA Only samples showing RNA integrity numbers (RIN) above 8 were used for furhter analysis.

treatment_protocol: Animals were randomly separated into five groups (N = 3 each) and allowed to acclimate for at least one week. Each group was treated with one of four different BPS doses (0.001, 0.1, 10, and 100 ng BPS x g bw-1 x day-1, hereafter named BPS1, BPS2, BPS3, and BPS4, respectively), in five independent experiments (75 animals total). BPS was dissolved in 50 μl 50% glycerol containing 0.1% DMSO and administered daily for 7 days by oral gavage. Only BS2 were used for transcriptomic analysis. After the exposure period, mice were euthanised by cervical dislocation, and their ovaries were collected for RNA isolation.

value: 8 weeks

value: mice oocytes

value: 0.1 ng BPS per 1 g of body weight per day

tag: Sex

value: Female


title: MDA-MB-231_unt_ChIP_EN1


title: POLR1A high epithelium tumor cells from patient derived xenograft (1438)


title: purified Ephb2-high epithelium cells from tumor colonic samples (576)

source_name: surgically resected primary CRCs from human patients

growth_protocol: Surgically resected primary CRCs from human patients

extract_protocol: RNA was isolated using magnetic beads from 2000 cels. Library preparation and amplification were performed as described by Gonzalez et al., 2010. Amplification was performed for 23 cycles.

value: epithelium from tumor colonic samples


title: Female, 8 weeks of age, fed phyto-oestrogen-free diet, oocytes, treated with BPS 3


title: purified Ephb2-low epithelium cells from tumor colonic samples (578)


title: MDA-MB-231_3f:S_JQ1_pos_ChIP_Input

value: breast cancer cell line MDA-MB-231 ectopic 3f:BRD4-S(a) expression

value: triple negative – ER-; PR-; HER2-

value: active JQ1, i.e. JQ1_pos or JQ1(+)


title: MDA-MB-231_3f:S_JQ1_neg_ChIP_Input

value: inactive enantiomer JQ1, i.e. JQ1_neg or JQ1(-)


title: Female, 8 weeks of age, fed phyto-oestrogen-free diet, oocytes, treated with BPS 1


title: Female, 8 weeks of age, fed phyto-oestrogen-free diet, oocytes, treated with BPS 2


title: MDA-MB-231_3f:S_JQ1_neg_ChIP_EN1


title: MDA-MB-231_3f:S_JQ1_pos_ChIP_S


title: purified Ephb2-low epithelium cells from normal colonic samples (574)

value: epithelium from normal colonic samples


title: Female, 8 weeks of age, fed phyto-oestrogen-free diet, oocytes, without treatment 4

description: Espression data obtained from mice oocytes without tretament


title: purified Ephb2-low epithelium cells from tumor colonic samples (570)


title: purified Ephb2-high epithelium cells from normal colonic samples (572)


title: Female, 8 weeks of age, fed phyto-oestrogen-free diet, oocytes, without treatment 2


title: Female, 8 weeks of age, fed phyto-oestrogen-free diet, oocytes, without treatment 3


title: MDA-MB-231_3f:S_JQ1_neg_ChIP_S


title: purified Ephb2-low epithelium cells from normal colonic samples (566)


title: MDA_MB_231_JQ1_pos_ChIP_Input

value: breast cancer cell line MDA-MB-231


title: U87-THZ1

city: New York

first: Markus

last: Siegelin

department: Pathology and Cell Biology

institute: Columbia University

data_processing:
Galaxy (from fasq file to bigwig file)
Integrated Genome Brower (compared peak between control and treated samples)
Genome_build: hg38

source_name: Glioblastoma cell line

extract_protocol:
DNA was extracted using the SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads) #9005 from Cell Signalling
Next generation sequencing (NGS) from Genewiz, New Jersey

tag: cell type

value: H3k27ac(Cell Signalling 4535)


title: purified Ephb2-high epithelium cells from tumor colonic samples (568)

tag: tissue


title: purified Ephb2-high epithelium cells from normal colonic samples (564)


title: Female, 8 weeks of age, fed phyto-oestrogen-free diet, oocytes, without treatment 1


title: U87-DMSO (THZ1 control)

value: DMSO


title: MDA_MB_231_JQ1_neg_ChIP_Input

tag: er/pr/her2 statue

value: input


title: Patient 62

city: Rochester

first: Xuewei

address: 200 1st street

institute: Mayo Clinic

data_processing:
Base calling by CASAVA
Alignment by STAR
Gene count by featureCount
Normalization by TPM
Genome_build: hg38
Supplementary_files_format_and_content: TPMs

source_name: Primary Patient Sample

extract_protocol:
AllPrep DNA/RNA Kit (Qiagen #80204)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Multiple Myeloma

tag: patient id

tag: venetoclax auc

value: No


title: purified Ephb2-low epithelium cells from tumor colonic samples (247)

value: CRC


title: MDA_MB_231_JQ1_pos_ChIP_BRD4_S

tag: chip antibody

tag: bet inhibitor jq1 treatment


title: purified Ephb2-high epithelium cells from tumor colonic samples (245)


title: MDA_MB_231_JQ1_neg_ChIP_BRD4_S


title: Patient 36


title: Patient 52

value: Yes


title: Patient 44


title: purified Ephb2-low epithelium cells from tumor colonic samples (243)


title: purified Ephb2-high epithelium cells from tumor colonic samples (241)


title: purified Ephb2-high epithelium cells from tumor colonic samples (189)


title: Patient 10


title: MCF_7_RNA_siBRD4_S_1

description: MCF7_RNA_siBRD4_igenomes_known_GENES_CPM.text

data_processing:
Fastq files with single-end 75 bp read length were checked for quality using FastQC (v0.11.2) and Fastq Screen (v0.4.4).
Reads were quality-trimmed using fastq-mcf (ea-utils, v1.1.2-806).
Trimmed fastq files were mapped to human genome using TopHat (v2.0.12).
Duplicates were marked using Picard-tools (v1.127).
Read counts were generated using featureCounts (subread) for coding genes from igenomes (hg19).
Normalized read counts generated using edgeR
Supplementary_files_format_and_content: tab delimited txt file including normalized read counts for each sample per gene
Genome_build: hg19

growth_protocol: Cells were maintained in high-glucose DMEM + 10% heat-inactivated FBS + Penicillin (100 units/ml) & Streptomycin (0.1 mg/ml).

extract_protocol:
RNA was harvested using miRNeasy Mini Kit (Qiagen #217004) following the manufacturer's instructions. Integrity was verified using the Agilent 2100 Bioanalyzer. All samples had a RIN score of 9 or higher.
One microgram of total DNase-treated RNA was prepared by using the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina (Illumina  #RS-122). Total RNA was depleted of its rRNA and fragmented before strand-specific cDNA synthesis.  cDNA was A-tailed and then ligated with indexed adapters. After adapter ligation, samples were PCR-amplified and purified with AmpureXP beads, then validated again on the Agilent 2100 Bioanalyzer. Samples were quantified by Qubit before being normalized and pooled for sequencing.

treatment_protocol: Cells were transfected by BRD4 pan or isoform-specific siRNA or universal negative control siRNA (Sigma cat# SIC001) twice with 48-hour treatment each time.

value: breast cancer cell line MCF-7

value: ER+; PR+

tag: sirna treatment

value: siRNA for BRD4-S(a) isoform (S)

value: untreated (unt)


title: MCF_7_RNA_siBRD4_S_3


title: OX_HNS_BAL_1238

type: genomic

city: Stockholm

first: Mikael

last: Ringh

state: Choose state (US & Canada)

address: Medical Epigenetics, CMM L8:00, Karolinska University Hospital Solna

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Conventional bisulfite conversion as well as oxidative bisulfite conversion using TrueMethyl conversion kit from Cambridge Epigenetix (CEGX). 250 ng of DNA per reaction followed by llumina MethylationEPIC BeadChip hybridization via Standard Illumina Protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina HiScan

data_processing: SQN normalisation

label: Cy5 and Cy11

source_name: Bronchoalveolar lavage cells

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacturer’s protocol

value: F

tag: diagnosis

value: H

tag: group

value: HNS

value: NS

tag: fvc


title: MCF_7_RNA_siBRD4_S_2


title: OX_MSNS_BAL_1028

label: Cy5 and Cy7

tag: age

value: MS

value: MSNS

tag: treatment

value: IFNb

value: Avonex

value: remisson

value: RRMS


title: OX_HS_BAL_1229

label: Cy5 and Cy10

value: HS

value: S


title: OX_MSNS_BAL_1026

label: Cy5 and Cy6

value: relapse


title: OX_MSS_BAL_1168

label: Cy5 and Cy8

value: MSS

value: Other

value: Mabthera

value: remission


title: OX_MSNS_BAL_1020

label: Cy5 and Cy4

value: F

value: Tysabri


title: purified Ephb2-low epithelium cells from tumor colonic samples (191)

tag: disease state

value: CRC

value: epithelium from tumor colonic samples


title: MCF_7_RNA_siBRD4_L_3

tag: cell line

value: breast cancer cell line MCF-7

value: ER+; PR+

value: siRNA for BRD4-L isoform (L)

value: untreated (unt)


title: Patient 26

value: Multiple Myeloma

value: No


title: Patient 109

description: MMPT 109 sort control


title: purified Ephb2-low epithelium cells from tumor colonic samples (821)

tag: biological replicate

value: hmt

tag: cell population


title: OX_MSS_BAL_1023

label: Cy5 and Cy5

tag: Sex

value: MS

value: S

value: Untreated

value: RRMS


title: purified Ephb2-low epithelium cells from tumor colonic samples (819)

tag: tissue


title: Patient 30


title: purified Ephb2-high epithelium cells from tumor colonic samples (820)


title: OX_HNS_BAL_1005

label: Cy5 and Cy3

value: H

value: HNS

value: NS


title: OX_MSS_BAL_982

value: F

value: MSS

value: Tysabri

value: remission


title: MCF_7_RNA_siBRD4_Pan_3

value: breast cancer cell line MCF-7

tag: er/pr/her2 statue

value: ER+; PR+

value: siRNA for all BRD4 isoforms (pan)


title: OX_MSNS_BAL_951

value: MSNS

value: IFNb

value: Avonex


title: Patient 107

description: MMPT  107 control

value: Multiple Myeloma

tag: patient id

value: No


title: OX_HNS_BAL_980


title: MCF_7_RNA_siBRD4_L_2

value: siRNA for BRD4-L isoform (L)

value: untreated (unt)


title: Patient 106

description: MMPT  106 control

tag: venetoclax auc


title: OX_MSNS_BAL_963

value: MS

value: Untreated

value: PPMS


title: purified Ephb2-high epithelium cells from tumor colonic samples (817)

value: CRC

value: epithelium from tumor colonic samples


title: Patient 108

description: MMPT  108 control


title: MCF_7_RNA_siBRD4_Pan_1


title: purified Ephb2-low epithelium cells from tumor colonic samples (816)


title: Patient 101


title: OX_MSNS_BAL_1204

label: Cy5 and Cy9

value: F

value: NS

value: Other

value: Mabthera

value: RRMS


title: OX_HS_BAL_943

value: H

value: HS

value: S


title: purified Ephb2-medium epithelium cells from tumor colonic samples (815)


title: Patient 95

value: Multiple Myeloma


title: OX_MSNS_BAL_928

value: MSNS

value: IFNb

value: Avonex

value: remission


title: OX_MSS_BAL_1001

value: MS

value: MSS

value: Tysabri


title: OX_HNS_BAL_972

value: HNS


title: Patient 92

value: No


title: purified Ephb2-high epithelium cells from tumor colonic samples (814)

value: CRC

value: epithelium from tumor colonic samples


title: OX_MSS_BAL_940

value: F


title: OX_HNS_BAL_926

value: NS


title: purified Ephb2-medium epithelium cells from tumor colonic samples (818)


title: OX_HS_BAL_920

value: H


title: MCF_7_RNA_siBRD4_Pan_2

value: breast cancer cell line MCF-7

value: ER+; PR+

value: siRNA for all BRD4 isoforms (pan)

value: untreated (unt)


title: OX_HS_BAL_944

value: HS

value: S


title: MCF_7_RNA_siControl_1

value: universal negative control siRNA (Sigma cat# SIC001)


title: Patient 91

value: Multiple Myeloma


title: MCF_7_RNA_siControl_2


title: MDA_MB_231_RNA_siBRD4_S_3

description: X_231_RNA_siBRD4_igenomes_known_GENES_counts_normalized.counts.CPM.txt

value: breast cancer cell line MDA-MB-231

value: triple negative – ER-; PR-; HER2-

value: siRNA for BRD4-S(a) isoform (S)


title: MCF_7_RNA_siBRD4_L_1

value: siRNA for BRD4-L isoform (L)


title: Patient 87

value: Yes


title: Patient 11-2

value: No


title: MDA_MB_231_RNA_siBRD4_S_2


title: purified Ephb2-high epithelium cells from tumor colonic samples (797)

value: CRC

value: epithelium from tumor colonic samples


title: OX_HS_BAL_916

value: F

value: H


title: MDA_MB_231_RNA_siBRD4_S_1


title: purified Ephb2-medium epithelium cells from tumor colonic samples (798)


title: Patient 86


title: MDA_MB_231_RNA_siBRD4_L_3


title: purified Ephb2-low epithelium cells from tumor colonic samples (794)


title: OX_HS_BAL_913


title: MCF_7_RNA_siControl_3

value: breast cancer cell line MCF-7

value: ER+; PR+


title: purified Ephb2-low epithelium cells from tumor colonic samples (799)


title: Patient 84


title: purified Ephb2-high epithelium cells from tumor colonic samples (792)


title: Patient 81


title: 3678DG

city: Gainesville

last: Foster

state: FL

address: 1149 Newell Drive

institute: University of Florida

data_processing:
ERCC analysis was performed with the ERCC analysis plugin in the Torrent. Spiked samples had an R2 above 0.9.
Ion Torrent derived reads were  aligned to the rattus norvegicus genome rn6 using STAR 2.5.3a in the in the Partek Flow servers Partek, Inc., St. Louis, MO.
Gene read counts were generated from Binary Alignment Map BAM files and annotated to the genome using Ensembl version 92; Partek, Inc..
Reads from FASTQ files produced by the Ion Torrent System were trimmed from both ends until all samples’ collective average Phred quality score was > 25. Reads shorter than 25 base pairs bps were also excluded.
Gene lists were filtered to exclude genes with an average count of 5 or less averaged across all samples included in a comparison.
Normalization and pairwise differential expression analysis were conducted using the DESeq2 package version 3.5 for comparisons by age, cognitive performance or hippocampal subregion. The threshold of significance was set at p<0.025 for differences by age.
Genome_build: Ensembl version 92; Partek, Inc..
Supplementary_files_format_and_content: Comma-separated values .csv files that contain the normalized counts for each sample

organism: Rattus norvegicus

source_name: DG region of the hippocampus

extract_protocol:
Rats were briefly anesthetized with isoflurane Patterson Veterinary, Greenly, CO and swiftly decapitated. The brains were then rapidly removed, and the hippocampi were dissected according to previously described methods Lein 2004; Zeier 2011. The hippocampal regions DG, CA1, and CA3 were separated, placed in the tubes, and flash-frozen in liquid nitrogen. All samples were stored in at -80°C until processed. RNA was isolated from subregions of a hippocampus from a single hemisphere of each animal. RNA Isolation was performed according to methods previously described Ianov 2016; Barter 2019. Briefly, RNA was isolated using the RNeasy Lipid Tissue Mini kit Qiagen, catalog number 74804. Total RNA was treated with DNase using the RNase-Free DNase Set Qiagen, catalog number 79254. Concentration of total RNA was assessed using the NanoDrop 2000 spectrophotometer Thermo Fisher catalog number ND-2000 and the RNA integrity number RIN was quantified using the Agilent 2200 Tapestation system with High Sensitivity RNA Screen Tape Agilent Technologies, Santa Clara, CA. Mean RNA integrity across all samples was 9.05 SEM ± 0.02 with values ranging from 8.2 to 9.3. Poly-A-selection for mRNA was performed using 250 ng of isolated total RNA in the Dynabeads mRNA DIRECT Micro kit Thermo Fisher, catalog number 61021. External RNA Controls Consortium ERCC RNA Spike-In Control Mixes were included in all isolated mRNA samples Thermo Fisher, catalog number 4456740.
Library preparation was performed using the Ion Total RNA-seq Kit v2 Thermo Fisher, catalog number 4475936. Ion Xpress barcodes Thermo Fisher, catalog number 4475485 were included with libraries for multiplex sequencing. In summary, isolated mRNA was fragmented with RNase III then ligated to the Ion Adapter Mix v2. RNA samples were then reverse transcribed. cDNA from each biological replicate was uniquely barcoded and amplified with 16 PCR cycles. Library concentration from each sample was quantified using the Qubit dsDNA HS Assay Thermo Fisher, catalog number Q32851. DNA fragment size distribution was subsequently evaluated using High Sensitivity D1000 ScreenTape in the 2200 Tapestation system Agilent Technologies, Santa Clara, CA.   Templates were prepared using the Ion Chef system Thermo Fisher, catalog number 4484177 and sequencing was performed using the Ion Proton system Thermo Fisher, catalog number 4476610 or Ion GeneStudio S5 system Thermo Fisher, catalog number A38194.

tag: strain

value: DG region of the hippocampus

value: 12 months

value: male


title: Patient 14-2


title: 3678CA3

source_name: CA3 region of the hippocampus

value: CA3 region of the hippocampus


title: purified Ephb2-medium epithelium cells from tumor colonic samples (793)


title: OX_HS_BAL_910

value: HS

value: S


title: MDA_MB_231_RNA_siBRD4_L_1

value: breast cancer cell line MDA-MB-231

value: triple negative – ER-; PR-; HER2-

tag: bet inhibitor jq1 treatment

value: untreated (unt)


title: Patient 75

value: Multiple Myeloma


title: MDA_MB_231_RNA_siBRD4_Pan_3

tag: sirna treatment

value: siRNA for all BRD4 isoforms (pan)


title: MDA_MB_231_RNA_siBRD4_Pan_2


title: OX_HS_BAL_921

tag: diagnosis


title: 3678CA1

source_name: CA1 region of the hippocampus

value: CA1 region of the hippocampus


title: MDA_MB_231_RNA_siBRD4_L_2

value: siRNA for BRD4-L isoform (L)


title: Patient 63

value: No


title: OX_MSNS_BAL_878

value: F

value: MS

tag: group

value: MSNS

value: NS

value: IFNb

value: Avonex

value: remission

value: SPMS


title: MDA_MB_231_RNA_siBRD4_Pan_1


title: 3677CA3

value: CA3 region of the hippocampus

value: 12 months

value: male


title: MDA_MB_231_RNA_siControl_3

value: breast cancer cell line MDA-MB-231

value: triple negative – ER-; PR-; HER2-

value: universal negative control siRNA (Sigma cat# SIC001)

value: untreated (unt)


title: 3677CA1

value: CA1 region of the hippocampus


title: Patient 48

value: Multiple Myeloma

value: Yes


title: 3676DG

value: DG region of the hippocampus


title: 3677DG


title: MDA_MB_231_RNA_siControl_2


title: OX_HNS_BAL_903

value: F

value: H

value: HNS

tag: fvc


title: MDA_MB_231_RNA_siControl_1


title: Patient 43

value: No


title: OX_MSS_BAL_873

tag: age

value: MS

value: MSS

value: S

value: Other

value: Gilenya

value: remission

value: RRMS


title: Patient 41


title: Patient 46


title: 3676CA1

value: 12 months

value: male


title: lag3nc_anti_pd1_tx

city: Pittsburgh

middle: Richard

last: Cillo

state: PA

address: The Assembly, Room 4070C Bay 10, 5051 Centre Ave

department: Immunology

institute: University of Pittsburgh

data_processing:
Demultiplexing using CellRanger mkfastq
Alignment and generation of gene/barcode matrices using CellRanger count
Genome_build: mm10
Supplementary_files_format_and_content: gzipped files containing gene/barcode matrices

source_name: tumor tissue

extract_protocol: 10x 3' v2 scRNAseq

treatment_protocol: Generation of single-cell suspensions from MC38 tumors, fluorescence acivated cell sorting for T cells

tag: tumor

tag: genotype/variation

value: mutant M38

tag: treatment


title: 3676CA3

value: CA3 region of the hippocampus


title: OX_MSS_BAL_854

value: IFNb

value: Avonex


title: wild_type_anti_pd1_tx

value: wild type


title: Patient 50

last: Wang

tag: disease state

value: Multiple Myeloma

value: Yes


title: Patient 40

value: No


title: 3675DG

value: DG region of the hippocampus


title: lag3nc_isotype_tx

value: isotype


title: wild_type_isotype_tx


title: OX_MSS_BAL_872

value: F

value: MS

value: MSS

value: S

value: relapse


title: Patient 35


title: OX_HS_BAL_828

value: H

value: HS


title: 3674DG

value: 12 months

value: male


title: 3675CA1

value: CA1 region of the hippocampus


title: Patient 24


title: 3675CA3

value: CA3 region of the hippocampus


title: Patient 25


title: LEC BALB/c_control

first: Menglan

last: Xiang

address: 450 Serra Mall

data_processing:
Read 1: 26 bp; Read 2: 98 bp
Read alignment and quality control were performed using the 10x Genomics Cell Ranger (v3.0.2) and the mm10 reference genome. Loupe Cell Browser (v3.1.1; 10x Genomics) was used to manually gate on LEC (Pdpn+ CD31+) for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file of raw count data

source_name: Peripheral lymph nodes

extract_protocol:
Axillary, inguinal and brachial LNs from 25-30 male and female BALB/cJ or C57BL/6J mice were combined, minced, washed with Hanks’ Balanced Salt solution, and dissociated for 30 min at 37 °C with gentle rocking in HBSS (with calcium and magnesium) medium containing 0.2 mg/ml Collagenase P, 0.8 mg/ml Dispase II and 0.01 mg/ml DNase I (Sigma-Aldrich). Hematopoietic cells were depleted with anti-CD45 mouse MicroBeads according to the manufacture’s protocol (Miltenyi) and stained with anti-CD31 BV605 (clone 390) and anti-Podoplanin PE-Cy7 (clone 8.1.1) antibodies, as well as dump antibodies consisting of anti-CD45 (clone 30-F11), anti-EpCAM (clone G8.8), anti-TER119 (clone TER-119), anti-CD11a (clone H155-78) and anti-CD11b (clone M1/70). Total EC (lin- CD31+) were sorted into 100% fetal bovine serum using FACS Aria III (BD Biosciences; 100 um nozzle; ~2500 cells/second) and washed.
scRNA-seq libraries were generated using the Chromium Single Cell 3’ Library and Gel Bead Kit v2 (10x Genomics) according to manufacturer’s instructions.

value: BALB/c

value: 6-8 weeks

value: Peripheral lymph nodes


title: OX_MSS_BAL_821

value: Untreated

value: remission

value: RRMS


title: 3674CA3


title: Patient 17

value: Multiple Myeloma

value: No


title: LEC C57BL/6

value: 8-12 weeks


title: 3674CA1


title: DEK-rep2

description: freshly-isolated quiescent muscle stem cells from PFA-perfused Pax7CreERT2/+; H11DEK-EGFP/+ mice

data_processing:
RNA-seq data were aligned using STAR (version 2.5.3a) with the parameters “–twopassMode Basic”, “–outFilterIntronMotifs RemoveNoncanonical”, “--outSAMstrandField intronMotif”, and “--outSAMmultNmax 1”.
Then, StringTie (version 1.3.3) was used with the -e option to quantify gene expression levels according to the reference’s annotations.
Furthermore, StringTie’s -b option was used so that output suitable for Ballgown (version 2.10.0) under R (version 3.4.1) could be produced.
Genome_build: mm9
Supplementary_files_format_and_content: Table of genes by samples of FPKM values, as output by Ballgown.  File format is tab-separated values (ASCII text file).

source_name: Skeletal muscle

extract_protocol:
The fixed muscle stem cell isolation was following the isolation protocol of satellite cells, as described previously in Liu et al., 2015, except that Collagenase II for first digestion was used at 2000 U/mL.Cell suspension was sorted using a BD Influx cell sorter equipped with 405-nm, 488-nm, 561-nm and 633-nm lasers. The machine was carefully optimized for purity and viability.
To get high quality RNA from fixed cells, the total RNA from fixed muscle stem cells were isolated using a miRNeasy FFPE Kit (Qiagen) following the protocol described in Thomsen et al., 2015. cDNA was generated following the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech) protocol. The RNA-Seq libraries were sheared with a Covaris S220 and generated using Ovation Ultralow DR Multiplex System 9-16 (NuGEN Technologies). The libraries were sequenced using Illumina NextSeq 500 (2 x 75).

value: Pax7CreERT2/+; H11DEK-EGFP/+

tag: cell type

value: Muscle stem cells

value: PFA-perfused mice


title: Patient 14


title: 3673DG

value: DG region of the hippocampus

tag: Sex


title: Patient 13


title: DEK-rep1


title: Patient 11


title: 3673CA3

tag: tissue

value: 12 months


title: YFP-rep2

description: freshly-isolated quiescent muscle stem cells from PFA-perfused Pax7CreERT2/+; ROSA26YFP/+ mice

value: Pax7CreERT2/+; ROSA26YFP/+


title: 3673CA1

value: CA1 region of the hippocampus

value: male


title: Patient 9

value: Yes


title: LEC BALB/c_Oxa-48h

value: BALB/c

value: 6-8 weeks


title: OX_HNS_BAL_707

value: F

value: H

value: HNS

value: NS


title: YFP-rep1


title: 3598DG

value: 5 months


title: Patient 67

value: Multiple Myeloma

value: No


title: OX_HNS_BAL_719


title: pSC-rep2

description: freshyl-isolated muscle stem cells from PBS-perfused mice

extract_protocol:
The fixed muscle stem cell isolation was following the isolation protocol of satellite cells, as described previously in Liu et al., 2015, except that Collagenase II for first digestion was used at double amount which is 2000 U/mL. For unfixed muscle stem cell isolation from C57BL/6 mice, the method was following the protocol described in Liu et al., 2015. Mononuclear cells were stained with Vcam-biotin (BD Bioscience, clone 429), CD31-APC (BD Bioscience, clone MEC 13.3), CD45-APC (BD Bioscience, clone 30-F11) and Sca-1-Pacific-Blue (Biolegend, clone D7) at 1:75. Streptavidin-PE-cy7 was used to amplify the Vcam signal (BD Biosciences, 557598, 1:75). Cell suspension was sorted using a BD Influx cell sorter equipped with 405-nm, 488-nm, 561-nm and 633-nm lasers. The machine was carefully optimized for purity and viability.
Total RNA from cells were isolated using NucleoSpin RNA XS (Macherey-Nagel). To get high quality RNA from fixed cells, the total RNA from fixed muscle stem cells were isolated using a miRNeasy FFPE Kit (Qiagen) following the protocol described in Thomsen et al., 2015. cDNA was generated following the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech) protocol. The RNA-Seq libraries were sheared with a Covaris S220 and generated using Ovation Ultralow DR Multiplex System 9-16 (NuGEN Technologies). The libraries were sequenced using Illumina NextSeq 500 (2 x 150).

tag: strain background

value: 2 months old

value: PBS-perfused mice

value: Skeletal muscle

value: Muscle stem cells


title: Pp_0-5_rep3 (Postia placenta 0-5 mm_rep3)

city: saint paul

first: Jonathan

last: Schilling

state: minnesota

address: 2004 folwell ave

institute: University of Minnesota

data_processing:
RNA-seq data analysis was performed on the Galaxy platform (https://usegalaxy.org/) using described procedures for differential expression analysis (Trapnell et al., 2012). Raw reads were cleaned with Trimmomatic (v0.3) and mapped against the R. placenta MAD698-R (v1.0) and G. trabeum ATCC11539 (v1.0) genomes together as a concatenated genome using TopHat (v2.0.13). Previously generated RNA-seq data (GSE108189) from single-species cultures of both species grown on equivalent aspen wafers were used for comparison to data generated in this study (Zhang et al., 2016)(Zhang et al., 2019). In specific, these previouly geneated datasets are GSM2892065, GSM2892066 and GSM2892067 for R. placenta, and GSM2892074, GSM2892075 and GSM2892076 for G. trabeum. Expression levels found at the leading hyphal edge of fungal cultures on aspen and 5 mm outside of the IZ toward each species were compared to expression levels found at the IZ. Reference transcript models from the JGI mycocosm database were used to determine differences in expression levels as Reads Per Kilobase Per Million (RPKM) in pairwise comparisons among samples using Cuffdiff (Galaxy Tool Version 2.2.1.3) using geometric normalization. FDR was set at <0.05. Transcripts with 4-fold greater RPKM values in the IZ sample relative to other samples were identified.
Genome_build: Postia placenta MAD-698-R v1.0 and Gloeophyllum trabeum v1.0 from JGI (https://genome.jgi.doe.gov/programs/fungi/index.jsf)
Supplementary_files_format_and_content: Excel file (.xlsx) includes pairwise comparison and RPKM levels.

organism: Rhodonia placenta

source_name: brown rot decayed wood

growth_protocol: Gloeophyllum trabeum ATCC 11539 and Rhodonia (Postia) placenta MAD 698-R were maintained on malt extract agar and 1 cm diameter agar plugs were used to inoculate soil block microcosms as previously described (Presley and Schilling, 2017). Sterile 19 mm aspen blocks were degraded for 4 weeks in soil block jars for each species and then were used as inoculum for interaction microcosms. Interactions were simulated by placing one G. trabeum and one R. placenta block opposing one another in empty soil microcosms and laying a 60 x 23 x 3 mm aspen wafer (largest face in cross section) across the top of the two blocks (Figure 1). Fungal hyphae grew together until they met in the center of the wafer, forming an interaction zone which was then sampled along with surrounding hyphae for protein and RNA, as described below.

extract_protocol:
Total fungal RNA was extracted from fresh wood sections with TRIzol (Life Technologies) and cleaned up with a Qiagen RNeasy Mini Kit (Qiagen, Inc.) prior to RNA sequencing or quantitative RT-PCR (qRT-PCR), a method validated in Zhang et al. (2016).
For RNA sequencing, TruSeq RNA v2 libraries were prepared and sequenced on a HiSeq 2500 System (Illumina Inc., San Diego, CA) by using the standard protocols from Illumina.

treatment_protocol: not applicable

value: Postia placneta colonized wood


title: BS_MSS_BAL_1168

value: MS

value: MSS

value: S

value: Other

value: Mabthera

value: remission

value: RRMS


title: OX_HNS_BAL_694

value: F

value: H

value: HNS


title: BS_MSNS_BAL_1026

value: MSNS

value: NS

value: IFNb

value: Avonex

value: relapse


title: fSC-rep2

description: freshly-isolated quiescent muscle stem cells from PFA-perfused mice

value: 2 months old

value: PFA-perfused mice

value: Skeletal muscle

value: Muscle stem cells


title: BS_MSNS_BAL_1204

value: MS


title: BS_MSNS_BAL_1028

value: remisson


title: Pp_0-5_rep2 (Postia placenta 0-5 mm_rep2)

value: Postia placneta colonized wood


title: OX_HS_BAL_698

value: HS

value: S


title: 3598CA3

value: CA3 region of the hippocampus

value: 5 months

value: male


title: OX_HNS_BAL_703

value: F

value: H

value: HNS


title: OX_HNS_BAL_722

value: NS


title: BS_HNS_BAL_1238


title: 3597DG

value: DG region of the hippocampus


title: BS_HS_BAL_1229


title: BS_MSNS_BAL_1020

value: MSNS

value: Tysabri

value: remission

value: RRMS


title: fSC-rep1

source_name: freshly-isolated quiescent muscle stem cells from PFA-perfused mice

value: 2 months old

value: PFA-perfused mice

value: Skeletal muscle

value: Muscle stem cells


title: 3597CA1

value: CA1 region of the hippocampus


title: IZ-5Pp_rep2

description: Current project: combat between brown rot fungi was sptially acomplished by wafer design

value: Postia placneta colonized wood


title: 3597CA3

value: CA3 region of the hippocampus

value: 5 months


title: 3598CA1

value: male


title: colorectal peritumoral tissue rep4

city: Nanjing

first: Linping

last: Yan

state: Jiangsu

address: Baizi Ting No. 42

institute: Jiangsu Cancer Hospital

description: SE-lncRNAs and mRNA expression in CRC peritumoral tissue

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, SE-LncRNAs and mRNAs that at least 4 out of 8 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed SE-LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

source_name: colorectal, peritumoral tissue

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, California, USA) following the manufacturer’s protocol and diluted with double-distilled water (ddH2O).RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis or Agilent 2100 Bioanalyzer. mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre)

treatment_protocol: All clinical samples were obtained from patients with no exposure to chemotherapy before resection and stored at −80°C until analysis

value: colorectal

tag: gender


title: 24h_PE_JQ1_2

city: Montreal

first: Jason

last: Tanny

state: Quebec

address: 3655 Promenade Sir William Osler

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

data_processing:
Fastq files were trimmed with TrimGalore (v0.6.0)  with the settings --phred33 --length 36 -q 5 --stringency 1 -e 0.1
Fastq files were aligned rn6 genome assembly using STAR (v2.7.1a)
Transcript assembly was completed using StringTie (v1.3.4d)
The tximport (v1.12.3) R package was used to import into R (3.6.1) and summarize transcript abundance (t_data.ctab) to gene-level counts
Differential gene expression was completed with DESeq2 (v1.24.0)
Genome_build: Rattus_norvegicus.Rnor_6.0.94
Supplementary_files_format_and_content: StringTie transcript-level expression measurements for each sample are provided as tab-delimited files

source_name: Cardiomyocytes

growth_protocol: Cardiomyocytes were isolated from 1-3 day old Sprague-Dawley rats and plated on 10 cm dishes coated with 0.1% gelatin and 10 μg/mL fibronectin at a density of 40 000 cells/cm2. Neonatal rat cardiomyocytes were cultured for 24 h in DMEM low glucose + 7% FBS + P/S + 10 μM cytosine β-d-arabinofuranoside (AraC). Media was changed and neonatal rat cardiomyocytes cultured for 24 h with DMEM low glucose + ITS + P/S +  10 μM AraC. Media was changed to DMEM low glucose + ITS + P/S for an additional 24 h before initiation of treatments.

extract_protocol:
RNA isolated with Qiagen RNeasy kit with on-column DNAse I
Libraries were prepared using the NEBNext rRNA-depleted (HMR) stranded library kit

treatment_protocol: Neonatal rat cardiomyocytes were treated for 24 h with the indicated agonist and antagonist

value: Cardiomyocytes

value: Neonatal

tag: agonist

value: 10 μM PE

tag: antagonist

value: 1 μM JQ1


title: 3596DG

tag: strain

value: DG region of the hippocampus


title: Pp_0-5_rep1 (Postia placenta 0-5 mm_rep1)


title: colorectal peritumoral tissue rep3


title: colorectal peritumoral tissue rep2


title: BS_MSS_BAL_1001

value: F

value: MS

value: MSS

value: S

value: Tysabri

value: remission


title: 3596CA3


title: BS_HNS_BAL_972

value: H

value: HNS

value: NS


title: 24h_ET1_JQ1_2


title: BS_MSS_BAL_1023

value: Untreated

value: relapse

value: RRMS


title: pSC-rep1

last: Cheung

source_name: freshyl-isolated muscle stem cells from PBS-perfused mice

value: 2 months old

value: PBS-perfused mice

value: Skeletal muscle

value: Muscle stem cells


title: colorectal peritumoral tissue rep1

value: colorectal

value: male


title: BS_MSS_BAL_982

value: F

value: MS


title: 3596CA1

value: CA1 region of the hippocampus

value: 5 months


title: BS_MSNS_BAL_963

value: MSNS

value: remission

value: PPMS


title: 24h_Acetic_JQ1_2

value: Cardiomyocytes

value: Neonatal

value: Acetic Acid (Vehicle)

value: 1 μM JQ1


title: OX_HNS_BAL_641

value: H

value: HNS

value: NS


title: 24h_PE_DMSO_2

value: 10 μM PE

value: DMSO (Vehicle)


title: BS_HNS_BAL_980


title: colorectal tumoral tissue rep2

description: SE-lncRNAs and mRNA expression in CRC tissue

source_name: colorectal, tumoral tissue

value: colorectal

value: male


title: BS_HNS_BAL_1005

value: F


title: 3595CA3

value: CA3 region of the hippocampus


title: colorectal tumoral tissue rep3


title: 3595CA1

value: CA1 region of the hippocampus

value: 5 months


title: 3595DG

value: DG region of the hippocampus


title: BS_MSS_BAL_940

value: MS

value: MSS

value: S

value: IFNb

value: Avonex

value: remission

value: RRMS


title: 24h_PE_JQ1_1

value: Cardiomyocytes

value: Neonatal

value: 1 μM JQ1


title: BS_HS_BAL_944

value: H

value: HS


title: 24h_ET1_JQ1_1


title: BS_MSNS_BAL_951

value: F

value: MSNS

value: NS


title: iMG [GCGTAGTA]

city: Clayton

first: Jan

last: Schroeder

state: VIC

address: Building 75 Innovation Walk

department: Anatomy & Developmental Biology

country: Australia

institute: Monash University

data_processing:
Sabre for demultiplexing based on 8bp sample barcode
RNAsik for alignment, deduplication and counting (Tsyganov, K., Perry, A., Archer, S. and Powell, D. (2018). RNAsik: A Pipeline for complete and reproducible RNA-seq analysis that runs anywhere with speed and ease. Journal of Open Source Software 3.)
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts of transcripts are provided as .txt files. Gene lists are provided as excel spreadsheets.
Supplementary_files_format_and_content: Text file of RNA-seq gene counts

source_name: iPS-derived microglia like cells

growth_protocol: Differentiation of iPS/ES cells to microglia-like cells  iHPC Differentiation Base Medium: IMDM (50% v/v, 12440053, ThermoFisher Scientific), F12 (50% v/v 11765054, ThermoFisher Scientific), ITS-X (2% v/v, 51500056, ThermoFisher Scientific), L-ascorbic acid 2-Phosphate magnesium (64 μg/ml, A8960, Sigma), monothioglycerol (400 μM, M6145, Sigma), PVA (10 μg/ml, P8136, Sigma), Glutamax (1X, 35050061, ThermoFisher Scientific), chemically-defined lipid concentrate (1X, 11905031, Thermo Fisher Scientific), non-essential amino acids (NEAA, 1X, 11140050, ThermoFisher Scientific), Penicillin/Streptomycin (P/S, 1% v/v, 15140122, ThermoFisher Scientific). Use 0.22 μm filter.     iMGLs Differentiation Medium: phenol-free DMEM/F12 (1:1, 11039021, ThermoFisher Scientific), ITS-G, (2% v/v, 41400045, ThermoFisher Scientific), B27 (2% v/v, 17504044, ThermoFisher Scientific), N2 (0.5% v/v, 17502048, ThermoFisher Scientific), monothioglycerol (200 μM, M6145, Sigma), Glutamax (1X, 35050061, ThermoFisher Scientific), NEAA (1X, 11140050, ThermoFisher Scientific), and additional insulin (5 μg/ml, I2643, Sigma), filtered through a 0.22 μm filter; supplemented with M-CSF (25 ng/ml, 130-096-492, Miltenyi biotec), IL-34 (100 ng/ml, 130-108-977, Miltenyi biotec), and TGF-1 (50 ng/ml, 130-108-969, Milteniy biotec) and cholesterol (1.5 μg/ml, 700000P, Avanti Polar Lipids).    The protocol for iMGL derivation was adapted from Abud et al. with modifications from the StemDiff Hematopoietic Kit (05310, Stem Cell Technologies). H9 CX3CR1-tdTomato cells were cultured on vitronectin (A14700, Thermo Fisher Scientific)-coated T25 flasks in E8 medium (A1517001, Thermo Fisher Scientific). 2 days prior to differentiation, cells were detached in 0.5mM EDTA and 40-80 colonies /well were seeded into a 12 well plate in E8 medium. On day 0, E8 medium was exchanged for 1 mL of supplemented iHPC Differentiation Base Medium per well. iHPC Differentiation Base Medium supplemented with FGF2 (50 ng/ml, 130-093-564, Miltenyi biotec), BMP4 (50 ng/ml, 130-111-165, Miltenyi biotec), Activin-A (12.5 ng/ml, 130-115-010, Miltenyi biotec), ROCKi (1 μM, 130-103-922, Milteniy biotec) and LiCl (2 mM, L7026, Sigma), and incubated in a hypoxic incubator. On day 2, medium was changed to 1 mL of iHPC Differentiation Base Medium supplemented with FGF2 (50 ng/ml) and VEGF (50 ng/ml, 130-109-385) and incubated in a hypoxic incubator. On day 4, medium was changed to 1 mL iHPC Differentiation Base medium containing humam FGF2 (50 ng/ml), VEGF (50 ng/ml), TPO (50 ng/ml, 130-095-752, Miltenyi biotec), SCF (10 ng/ml, 130-096-695, Miltenyi biotec), IL-6 (50 ng/ml, PHC0061, ThermoFisher Scientific), and IL-3 (10 ng/ml, PHC0031, ThermoFisher Scientific) and incubated under normoxia. Half the medium was replaced on days 5 and 7 with the same medium as day 4. On day 10, the supernatant containing the HPCs was collected, centrifuged (300 x g for 5 min at room temperature; RT), then 0.5ml cell-containing medium was replaced and supplemented with 0.5ml fresh medium. On day 12, the supernatant containing HPCs was collected and plated onto matrigel (1:40, 354277, hESC-qualified Matrix, LDEV-Free, Falcon)-coated 12 well plates at 1x105 cells/well in iMGL complete differentiation medium. Every two days, each well was supplemented with 0.5 ml per well of complete differentiation medium, and at day 22 a 50% media change was performed. From day 35, iMGLs were cultured in complete iMGL differentiation medium supplemented with human CD200 (100 ng/ml, C311, Novoprotein) and CX3CL1 (100 ng/ml, 300-31, Peprotech) for an additional three days.

extract_protocol:
RNA extraction from 1-10 x104 FACS-sorted CX3CR1+ iMGLs or from 2 wells of iMGLs harvested directly from 12 well plates, was performed on the QIAcube (Qiagen) using the RNeasy Micro Kit (Qiagen, Hilden, Germany) and RNA quality was assessed using the Bioanalyser (Agilent RNA 6000 Pico kit).
The libraries were prepared using 0.5-2 ng RNA with RIN value ≥ 8. An 8 bp sample index (Supplementary table 2) and a 10 bp unique molecular identifier (UMI) were added during initial poly(A) priming and pooled samples were amplified using a template switching oligonucleotide. The Illumina P5 (5' AAT GAT ACG GCG ACC ACC GA 3') and P7 (5' CAA GCA GAA GAC GGC ATA CGA GAT 3') sequences were added by PCR and Nextera transposase, respectively. The library was designed so that the forward read (R1) utilizes a custom primer (5' GCC TGT CCG CGG AAG CAG TGG TAT CAA CGC AGA GTA C 3') to sequence directly into the index and then the 10 bp UMI. The reverse read (R2) uses the standard R2 primer to sequence the cDNA in the sense direction for transcript identification.

treatment_protocol: ReN cells (Millipore) were maintained and differentiated as previously described (Choi et al. 2014). Briefly, cells were maintained on Matrigel-coated flasks (BD Biosciences, San Jose, CA, USA) in DMEM/F12 (11320033, ThermoFisher Scientific) supplemented with 2 µg/ml heparin (07980, StemCell Technologies, 07980), 2% (v/v) B27, 20 µg/ml EGF (130-097-749, Miltenyi biotec), 20 µg/ml bFGF and 1% (v/v) P/S. Neuronal and glial differentiation was achieved by growth factor withdrawal, with twice-weekly half media changes. For co-culture assays, iMGLs were added to 21 d differentiated ReN cells for a further 21 d.

value: iMG


title: BS_HS_BAL_943


title: 3594CA3

value: CA3 region of the hippocampus

value: 5 months

value: male


title: 3594CA1

value: CA1 region of the hippocampus


title: colorectal tumoral tissue rep4

value: colorectal


title: BS_HNS_BAL_926

value: HNS


title: iPS [CGGAGCCT]

source_name: iPS

value: iPS


title: BS_MSNS_BAL_928

value: MS

value: IFNb

value: Avonex

value: remission

value: RRMS


title: iMG_Chol [GGAGCTAC]

value: iMG+cholesterol


title: 3593DG

value: DG region of the hippocampus


title: 24h_ET1_DMSO_1

value: Cardiomyocytes

value: Neonatal

value: DMSO (Vehicle)


title: 24h_PE_DMSO_1

value: 10 μM PE


title: 24h_Acetic_DMSO_2

value: Acetic Acid (Vehicle)


title: 24h_Acetic_DMSO_1


title: 3593CA3

value: CA3 region of the hippocampus

value: 5 months

value: male


title: IZ-5Pp_rep1

value: Postia placneta colonized wood


title: iMG [TAGGCATG]

description:
FACS sorted tdTomato+
sikRun/bamFiles/245_TAGGCATG_sorted_umi_mdups.bam

value: iMG


title: 3594DG


title: colorectal tumoral tissue rep1

value: colorectal


title: 3593CA1

value: CA1 region of the hippocampus


title: 3349CA1

value: 12 months


title: BS_HS_BAL_921

value: F

value: H

value: HS

value: S


title: iMG [TCCTGAGC]