title: Input DNA BAMS rep2

city: Marseille

first: Frederique

last: Magdinier

address: 27 Bvd Jean Moulin, Aix-Marseille Université. Faculté de Médecine. Campus La Timone

country: France

institute: Aix-Marseille Université - Marseille Medical Genetics

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg38 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Peak calling was performed using MACS2(v2.2.6) with –broad parameter for (H3K4me3 and H3K27me3), --nomodel –extsize 200 for replicates with lower quality, -q 0.05
Genome_build: hg38
Supplementary_files_format_and_content: Wig files were generated using with an in-house script from IGBMC (Variable step, span=25, reads were elongated to 200b).

source_name: muscle cells

growth_protocol: The hIPSc were differentiated into functional muscles according to the protocol described in Mazaleyrat et al. (DOI: 10.3390/cells9061531)

extract_protocol:
Between 10-20 millions cells  were cross-linked with 1% formaldehyde in fixation solution directly in culture dishes and incubated for 5 minutes at RT and then 40 minutes at 4°C. Cross linking reaction was stopped by addition of 0.125M Glycine. For ChIP-seq, we used the iDeal ChIP-seq kit for Transcription Factors and iDeal ChIP-seq kit for Histones (Diagenode). Chromatin extraction, immunoprecipitations and DNA purifications is performed as recommended by the manufacturer
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7  cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

tag: disease

value: BAMS (bosma arhinia microphthalmia syndrome)


title: Input DNA BAMS rep1

status: Public on Dec 31 2023

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens


title: tumor treated with PBS replicate 1

city: Richmond

first: Guizhi

last: Zhu

state: VA

address: 410 N 12th St

country: USA

institute: Virginia Commonwealth University

library_source: transcriptomic

data_processing:
Raw reads QC with fastqc [fastqc ${FASTA} -t ${NTHRDS} --outdir=${OUTDIR} --extract --quiet]
Trimming adapters with BBMap tools [BBMap/bbmap/bbduk.sh in1=${FASTA_R1} in2=${FASTA_R2} out1=${OUT1} out2=${OUT2} ref=${ref} stats=${fbname}_stats.txt threads=${NTHRDS} ktrim=r k=23 mink=11 hdist=1 tbo]
Alignment with STAR-2.7.9a [${SPLICE_AWARE_ALIGNER_} --runThreadN ${NTHRDS} --genomeDir ${INDEX_DIR} --readFilesIn ${FASTA_R1} ${FASTA_R2} --readFilesCommand gunzip -c --outFileNamePrefix ${OUT_FileNamePrefix} --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts]
Library strandness inferred with RSeQC tool [RSeQC/bin/infer_experiment.py --input-file=$INPUT_FILE --refgene=$REFGENE_BED]
Counting with featureCounts from subread-2.0.3-Linux-x86_64 [featureCounts -p --countReadPairs -B -T 16 -s 2 -t exon -g gene_name -a ${GTF_} -o ${FILE_OUT} ${FILES_}]
Assembly: mm39vM30
Supplementary files format and content: TXT file: full featureCounts results
Supplementary files format and content: CSV file: filtered read counts table [keeping genes with row sum >= 10]

molecule: total RNA

organism: Mus musculus

source_name: tumor tissue

extract_protocol:
Total RNA was isolated following the instructions for the AllPrep DNA/RNA Mini Kit (QIAGEN) with in-column DNase 1 digestion to ensure DNA-free RNA. The integrity of extracted RNA was analyzed using the Agilent RNA 6000 Pico Kit (Agilent).
An aliquot of 1 μg of total RNA (RIN > 8) was used to prepare mRNA-seq libraries following the instruction of Illumina stranded mRNA-seq preparation Guide (Illumina). In short, mRNA was captured by oligo (dT) magnetic beads from total RNA, cation fragmented, and reverse transcribed into complementary DNA (cDNA). cDNA was end repaired, ligated with RNA index anchor and PCR amplified to produce indexed libraries with IDT for illumined UD indexes. Following quality control, the resulting barcoded libraries were pooled in equal molarities and were paired-end (2 x 150 bp) sequenced on NextSeq 2000 instrument (Illumina).

tag: tissue

value: tumor tissue

tag: cell type

value: tumor cells

tag: genotype

value: WT

tag: treatment

value: PBS


title: Sub-Chronic Levodopa Treated 1

city: Birmingham

first: David

last: Figge

state: AL

address: 1719 6th Ave. S, CIRC 520

department: Neurology

institute: University of Alabama-Birmingham

library_source: transcriptomic single cell

data_processing:
Sequencing files were processed, mapped to mm10, and count matrices were extracted using the Cell Ranger 308 Single Cell Software (v 3.1.0)
Assembly: mm10
Supplementary files format and content: barcodes, features, and matrix files are tsv, mtx, and gunzipped

source_name: pooled dorsal striata

extract_protocol:
Sorted cells were loaded onto the 10X Chromium 303 platform (10X genomics), and libraries were constructed using the Single Cell 3′ 304 Reagent Kit V2 according to the manufacturer’s instructions.
10x Genomics Single Cell 3' Reagent Kit V2. Samples were sequenced to an average  depth of 20,000 reads per cell on an Illumina NovaSeq

value: Pooled Dorsal Striatum from 6-OHDA Lesioned Animals Treated with L-DOPA For 4D

tag: strain


title: Acute Levodopa Treated 1

value: Pooled Dorsal Striatum from 6-OHDA Lesioned Animals Treated with L-DOPA for 1 D


title: Acute Levodopa Treated 2


title: Sub-Chronic Levodopa Treated 2


title: CTCF BAMS rep2

tag: chip antibody


title: Vehicle Unlesioned 2

value: Pooled Dorsal Striatum from the unlesioned side of 6-OHDA Lesioned Animals Treated with Saline For 7D


title: BMDCs treated with mRNA-OVA for 24 h replicate 3

data_processing:
Raw reads QC with fastqc [fastqc ${FASTA} -t ${NTHRDS} --outdir=${OUTDIR} --extract --quiet]
Alignment with STAR-2.7.9a [${SPLICE_AWARE_ALIGNER_} --runThreadN ${NTHRDS} --genomeDir ${INDEX_DIR} --readFilesIn ${FASTA_R1} ${FASTA_R2} --readFilesCommand gunzip -c --outFileNamePrefix ${OUT_FileNamePrefix} --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts]
Library strandness inferred with RSeQC tool [RSeQC/bin/infer_experiment.py --input-file=$INPUT_FILE --refgene=$REFGENE_BED]
Counting with featureCounts from subread-2.0.3-Linux-x86_64 [featureCounts -p --countReadPairs -B -T 16 -s 2 -t exon -g gene_name -a ${GTF_} -o ${FILE_OUT} ${FILES_}]
Assembly: mm39vM30
Supplementary files format and content: TXT file: full featureCounts results
Supplementary files format and content: CSV file: filtered read counts table [keeping genes with row sum >= 10]

source_name: bone marrow cells

value: bone marrow cells

value: mRNA-OVA


title: Vehicle Unlesioned 1


title: Vehicle Lesioned 1

value: Pooled Dorsal Striatum from 6-OHDA Lesioned Animals Treated with Saline For 7D


title: CTCF BAMS rep1


title: Vehicle Lesioned 2


title: Chronic Levodopa Treated 2

value: Pooled Dorsal Striatum from 6-OHDA Lesioned Animals Treated with L-DOPA For 7D


title: BMDCs treated with mRNA-OVA for 24 h replicate 2


title: H3K27me3 BAMS rep2

value: Diagenode C15410195


title: BMDCs treated with mRNA-OVA for 24 h replicate 1


title: Chronic Levodopa Treated 1


title: BMDCs treated with circRNA-SIINFEKL for 24 h replicate 3

value: circRNA-SIINFEKL


title: BMDCs treated with circRNA-SIINFEKL for 24 h replicate 2


title: H3K4me3 BAMS rep2


title: BMDCs treated with circRNA-SIINFEKL for 24 h replicate 1


title: AML12-siDUSP6-3

city: Beijing

first: Xiangyang

last: Wang

address: No.5 Yiheyuan Road, Haidian District

department: College of Life Sciences

country: China

institute: Peking University

data_processing:
Alignment: mapping reads to genome
Transcript assembly: sequence assembly
Gene expression quantity: estimating gene expression level
Differential expression: DESeq2 for 2 groups of biological replicates
GO and KEGG enrichment: testing the enrichment of GO term and KEGG pathway with specific gene set
Assembly: mm10
Supplementary files format and content: Text files containing raw counts for each sample

growth_protocol: AML12 cells were cultured in DMEM/F12 supplemented with 10% FBS, 40 ng/ml Dexamethasone, 1% ITS in 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted by Trizol.
RNA library was prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®.

treatment_protocol: AML12 cells were transfected with GFP or GFP-DUSP6 plasmid, and 24 hours later harvested. AML12 cells were transfected with NC or DUSP6-specific siRNA, and 48 hours later harvested.

tag: cell line

value: liver cells

value: DUSP6 knockdown


title: AML12-NC-3


title: AML12-NC-2


title: AML12-siDUSP6-1


title: AML12-NC-1


title: AML12-siDUSP6-2


title: AML12-GFP-DUSP6-3

value: GFP-DUSP6 overexpression


title: Input DNA FSHD2 rep2


title: AML12-GFP-DUSP6-2


title: BMDCs treated with PBS for 24 h replicate 3


title: AML12-GFP-3

value: GFP overexpression


title: Input DNA FSHD2 rep1


title: BMDCs treated with PBS for 24 h replicate 2


title: CTCF FSHD2 rep2


title: BMDCs treated with PBS for 24 h replicate 1


title: AML12-GFP-2


title: CTCF FSHD2 rep1


title: H3K27me3 BAMS rep1

value: BAMS (bosma arhinia microphthalmia syndrome)


title: E16 Tbx4rtta; tetocre; Sin3a F/F, CKO; Biol rep 2

city: San Diego

middle: James

last: McCulley

state: CA

address: 9500 Gilman Drive, MC 0735, Leichtag Building, Room 132

department: Pediatrics

institute: University of California, San Diego

description: 10x genomics

data_processing:
Duplexing, barcoded processing, gene quantification, aggregation were performed using the Cell Ranger Toolkit v6.1.1
R v4.0.2 and Seurat v4.0.5 were used for the integration and analysis of scRNA-seq samples
Assembly: mm10
Supplementary files format and content: excel file with differential gene expression for each sample

source_name: bulk lung

extract_protocol:
RNA was harvested from sorted mesenchymal cells using the TRIzol (Fisher) RNA extraction protocol and analyzed using Aligent Bioanalyzer RNA kit.
cDNA libraries were made using the 10x Genomics Single Cell 3' v3.1 Reagent's Kit (10x Genomics) following manufacturer's protocols. Briefly, Gel Bead-In-Emulsions (GEMs) were created using the Chromium Controller instrument (10x Genomics) and GEM-RT was performed using an Eppendork Mastercycler Pro thermal cycler. GEMs collected and cDNA amplified using Aglient Bioanalyser High Sensitivity chip. Duel indexed sequencing libraries were created using Chromium Single-Cell 3' Library Construction Kit, and barcoded libraries were quantified using Qubit High Sensitivity DNA reagents (Invitrogen Qubit). Barcoded libraries were analyzed on a Aglient Bioanalyzer DNA 1000 chip.

treatment_protocol: Induction of Sin3a conditional deletion occured at E12 by feeding pregnant mice with doxycycline

value: bulk lung

tag: developmental stage

value: Embryonic day 16

value: mesenchymal cells

value: conditional knockout


title: SOD1-G93A Lepob/+ 3

city: Madrid

first: Silvia

last: Corrochano

address: Calle del Prof Martín Lagos

department: Neurología

country: Spain

institute: Instituto de Investigación Sanitaria del Hospital Clínico San Carlos

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2 Version 2.1.0
featureCounts version 2.0.2 was used for counting reads to genes
Differential expression analysis between genotypes was performed using the DESeq2 R package (2_1.6.3)
Assembly: mm10
Supplementary files format and content: tab-delimited file includes raw counts for each samples and the results of the differential expression analysis

source_name: iWAT

extract_protocol:
RNA was extracted from iWAT of wild type, SOD1-G93A, Lep ob/+  and SOD1-G93A Lep ob/+  female mice at 90 days of age  using Qiazol followed by the mini Lipid tissue RNAeasy kit (Qiagen).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated. Total number of reads was 30 million per sample.

value: iWAT

tag: Sex

value: female

tag: age

value: 90 days

value: SOD1-G93A Lepob/+


title: SOD1-G93A Lepob/+ 1


title: SOD1-G93A Lepob/+ 2


title: H3K27me3 FSHD2 rep2


title: H3K4me3 BAMS rep1


title: E16 Tbx4rtta; tetocre; Sin3a F/F, CKO; Biol rep 1

description: 10x genomics


title: SOD1-G93A 4


title: H3K27me3 FSHD2 rep1


title: H3K4me3 FSHD2 rep2


title: SOD1-G93A 2


title: AML12-GFP-DUSP6-1


title: Embryonic day 16 (E16) Tbx4rtta; tetocre; Sin3a F/+, Control; Biol rep 1

description: 10x genomics

value: control


title: SOD1-G93A 3


title: E16 Tbx4rtta; tetocre; Sin3a F/+, Control; Biol rep 2

description: 10x genomics


title: Lepob/+ 4

value: Lepob/+


title: AML12-GFP-1


title: H3K4me3 FSHD2 rep1


title: SOD1-G93A Lepob/+ 4


title: Lepob/+ 2


title: Input DNA CT rep2

value: Control


title: Lepob/+ 3


title: WT 3

value: Wild type


title: kidney, PND7, input for HNF1b ChIP

city: Research Triangle Park

first: Hong Soon

last: Kang

state: NC

address: 111 T.W. Alexander Dr.

department: IIDL

institute: NIH/NIEHS

data_processing:
Reads were filtered to remove any  with mean base quality score < 20.
Adapters were removed by Cutadapt v1.12 and filtered to retain only those with length at least 30nt.
Filtered and trimmed reads were mapped via Bowtie v1.2 with parameter "-m 1".
Alignment files were combined via MergeSamFiles.jar (Picard tools v1.110) for samples with multiple sequencing runs.
Duplicate mapped reads were removed via MarkDuplicates.jar (Picard tools v1.110) with flag "REMOVE_DUPLICATES=TRUE".
Peak calls were made by HOMER (v4.10.3) with parameters “-style factor” then re-sized to 300bp centered on the called peak midpoints.
For visualization purposes, uniquely-mapped non-duplicate reads were extended to the 200bp estimated fragment size via BEDTools v2.29.2 "slop -s -r 125 -l 0", converted to bedGraph via BEDTools v2.29.2 "genomecov -bg", scaled to 10 million fragments per sample, then converted to bigWig format via UCSC utility bedGraphToBigWig.
Assembly: mm10
Supplementary files format and content: peak calls (BED)
Supplementary files format and content: normalized depth tracks (bigWig)

source_name: kidney

extract_protocol:
Immunoprecipitated chromatin was washed and ChIPed-DNA was eluted, reverse cross-linked, and DNA fragments purified using PCR purification kit form Qiagen.
NEXTflex DNA-Seq kit from PerkinElmer was used.

value: kidney


title: Lepob/+ 1


title: kidney, PND7, HNF1b ChIP

value: HNF1b (Invitrogen #720259)


title: WT 4


title: WT 2


title: CTCF CT rep2


title: Me-DNA ApcDhep

city: Paris

first: Angelique

last: Gougelet

address: 15 rue de l'école de médecine

institute: INSERM U1138

data_processing:
mapped to the genome using the BWA algorithm with default settings
Illumina’s purity filter, align with no more than 2 mismatches
MACS and Sicer for peak finding
Assembly: mouse genome (mm10)
Supplementary files format and content: BigWig

source_name: mouse hepatocytes

extract_protocol:
phenol/chloroform
MeDIP-seq service (Active motif)

value: mouse hepatocytes

value: ApcDhep

value: tamoxifen


title: input DNA

value: pool DNA


title: WT 1


title: CTCF CT rep1


title: SOD1-G93A 1


title: Mouse heart, normal

city: Hangzhou

first: Yongcheng

state: Zhejiang

address: 1369 Wenyixi Rd.

institute: Liangzhu Laboratory

data_processing:
the first 28bps were extracted  from R1 and used as spot barcode (16bps) and
UMI (12bps). The polyA sequences in R2 were identified by searching for 10 consecutive A's.
The sequence after polyA sequence was also trimmed with the polyA sequence.
The genome alignement was done by starsolo software and the expression matrix
was generated with the built-in function in starsolo.
Assembly: mm39
Supplementary files format and content: matrix.mtx.gz: gene expression counts data in Matrix Market Exchange format
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: tissue HE imgae in tif format

source_name: FFPE heart

extract_protocol:
Tissues were paraffin embedded, and 5 μm FFPE sections were cut
Library preparations were performed with the spRandom-seq protocol
spatial transcriptomics

value: FFPE heart

value: reverse transcription using RT primer without cell barcode 2


title: Me-DNA wt

value: wt


title: MC903+Dexamethasone_4

city: Aarhus

first: Hakim

last: Ben Abdallah

state: Denmark

address: Palle Juul-Jensens Boulevard 45

department: Dermatology and Venerology

country: Denmark

institute: Aarhus University Hospital

description:
2x150 Sequence mode to obtain at approx. 20 million read pairs
Raw counts.xlsx

data_processing:
R package Subread (version 2.10.3)
Raw reads were aligned to the mouse reference genome (GRCm39 primary assembly)
Gene counts were obtained by uniquely aligned unambiguous reads
Assembly: GRCm39 primary assembly
Supplementary files format and content: xlsx

source_name: Ear

extract_protocol:
Total RNA was isolated using the SV 96 Total RNA Isolation System (Promega) according to the manufacturer’s instructions
RNA sequencing library was prepared with 100 ng of total RNA using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

value: Ear

value: WT


title: MC903+Dexamethasone_1


title: MC903+Dexamethasone_3


title: MC903+RGRN-305_8


title: H3K27me3 CT rep1

value: Diagenode C15410195


title: MC903+RGRN-305_7


title: Input DNA CT rep1


title: CCL206 fibroblasts, exposed to 30k nylon fibers, mouse 4 [N30k4_fib]

city: Groningen

first: Barbro

middle: N

last: Melgert

address: Antonius Deusinglaan 1

department: Molecular Pharmacology

country: Netherlands

institute: University of Groningen

data_processing:
The generated data were subsequently demultiplexed using sample-specific barcodes and changed into fastq files using bcl2fastq (Illumina; version 1.8.4). The quality of the data was assessed using FastQC. The STL barcodes of the first mate were separated from the sequenced fragments using an in-house Perl script. Low quality bases and parts of adapter sequences were removed with Cutadapt (version 1.12; settings: q=15, O=5, e=0.1, m=36). Sequenced poly A tails were removed as well, by using a poly T sequence as adapter sequence (T (100); reverse complement after sequencing). Reads shorter than 36 bases were discarded. The trimmed fragment sequences were subsequently aligned to all known murine cDNA sequences using HISAT2 (version 2.1.0; settings: k=1000, --norc). The number of reported alignments, k, was given a high number in order to not miss any alignment results (some genes have up to 62 transcripts). Reads were only mapped to the forward strand (directional sequencing). Fragment sequences that mapped to multiple genes were removed (unknown origin). When fragments mapped to multiple transcripts from the same gene all but one were given a non-primary alignment flag by HISAT2 (flag 256). These flags were removed (subtraction of 256) by the same Perl script in order to be able to use the Bash-based shell script (dqRNASeq; see below) that is provided by Bioo Scientific (Perkin Elmer, MA, USA). Fragments that mapped to multiple transcripts from the same gene were considered unique and were counted for each of the transcripts. The number of unique fragments (or read pairs) was determined for each transcript using the script provided by Bioo Scientific (dqRNASeq; settings: s=8, q=0, m=1). Counts that were used for further analysis were based on a unique combination of start and stop positions and barcodes (USS + STL).
Assembly: mm10
Supplementary files format and content: CVS file includes raw counts for each sample

source_name: Organoid culture

growth_protocol: 200,000 murine EpCAM+ primary cells and 200,000 CCL206 fibroblasts (n=4 independent isolations from 4 mice) were seeded in 1 ml Matrigel diluted 1:1 in DMEM containing 10% FBS in 6-well plates

extract_protocol:
After 7 days, organoid cultures were digested with 50 caseinolytic units/ml dispase for 30 minutes at 37°C, transferred to 15 ml tubes, washed with MACS BSA stock solution and autoMACS rinsing solution (both Miltenyi), and digested further with trypsin (VWR) diluted 1:5 in PBS for 5 minutes at 37°C. The cell suspension was then incubated for 20 minutes at 4°C with anti-EpCAM microbeads in MACS buffer, after which the suspension was passed through LS columns. Both the EpCAM+ (epithelial cells) and EpCAM− (fibroblasts) cell fractions were used for RNA isolation and subsequent sequencing. Total RNA was isolated from EpCAM+ and EPCAM- cell fractions using a Maxwell® LEV simply RNA Cells/Tissue kit (Promega, WI, USA) according to manufacturer’s instructions. RNA concentrations were determined using a NanoDrop One spectrophotometer (Thermo Fisher Scientific).
Total RNA (300 ng) was used for library preparation.
Paired-end sequencing was performed using a NextSeq 500 (Illumina; mate 1 up to 74 cycles and mate 2 up to 9 cycles). Mate 1 contained the first STL (stochastic labeling) barcode, followed by the first bases of the sequenced fragments, and mate 2 only contained the second STL barcode.

treatment_protocol: 12.000 or 30.000 nylon microfibers (equivalent to 2k and 5k fibers in smaller wells) were mixed with Matrigel and cells prior to seeding, control wells were left untreated.

value: Lung

value: Fibroblasts

value: Male

value: ddY

value: exposed to 30k nylon fibers


title: CCL206 fibroblasts, exposed to 30k nylon fibers, mouse 3 [N30k3_fib]


title: H3K4me3 CT rep1

value: Control


title: H3K4me3 CT rep2


title: MC903+RGRN-305_5


title: CCL206 fibroblasts, exposed to 30k nylon fibers, mouse 1 [N30k1_fib]


title: MC903+RGRN-305_4


title: MC903+RGRN-305_6


title: 0027_8B_Control

city: Atlanta

first: Carlos

middle: Sanchez

last: Moreno

state: GA

address: 101 Woodruff Circle NE, Room 2309

department: Pathology and Laboratory Medicine

institute: Emory University

data_processing:
raw reads were checked for quality using FASTQC and trimmed with Trimmomatic version 0.39
RNAseq reads were mapped using STAR mapper version 2.5.2b (Dobin et al., 2013) to the hg38 version of the human genome
fragment per kilobase per million reads (FPKM) values were computed using cufflinks version 2.2.1 (Trapnell et al., 2010).
Genome_build: hg38

source_name: FFPE Breast Tissue

extract_protocol:
Formalin-fixed paraffin-embedded (FFPE) breast cancer biopsy samples were macrodissected for areas of tumor. Ribonucleic acid (RNA) was extracted using the OmegaTek FFPE RNA kit at the Emory Integrated Genomics Core Facility (EIGC) for further processing.
RNA libraries were prepared for sequencing using Illumina TruSeq RNA Library Preparation kit protocols

tag: class

value: Hyperplasia

tag: diagnosis

value: Lobular hyperplasia

tag: patient number


title: CCL206 fibroblasts, exposed to 12k nylon fibers, mouse 4 [N12k4_fib]

value: exposed to 12k nylon fibers


title: Mouse brain, normal

source_name: FFPE brain

value: FFPE brain


title: MC903+RGRN-305_2


title: MC903+RGRN-305_1


title: CCL206 fibroblasts, exposed to 12k nylon fibers, mouse 3 [N12k3_fib]


title: MC903_8


title: 0024_2_BrCa

value: Tumor

value: IDC


title: MC903+Dexamethasone_2


title: H3K27me3 CT rep2


title: CCL206 fibroblasts, exposed to 12k nylon fibers, mouse 2 [N12k2_fib]


title: 0023_6_Normal

value: Normal

value: Normal breast reduction


title: CCL206 fibroblasts, exposed to 30k nylon fibers, mouse 2 [N30k2_fib]


title: MC903_6

value: Ear


title: CCL206 fibroblasts, exposed to 12k nylon fibers, mouse 1 [N12k1_fib]

value: WT


title: CCL206 fibroblasts, control, mouse 4 [ctl4_fib]

value: control


title: MC903_3


title: MC903_4


title: MC903+RGRN-305_3


title: 0022_5_Normal


title: MC903_2


title: 0021_4_Normal


title: MC903_1


title: Vehicle_6

value: vehicle


title: 0025_2_Control

value: Benign


title: Vehicle_4


title: CCL206 fibroblasts, control, mouse 3 [ctl3_fib]

value: Lung

value: Fibroblasts

value: Male


title: 0019_2_Normal


title: Vehicle_3


title: CCL206 fibroblasts, control, mouse 1 [ctl1_fib]

value: ddY


title: Vehicle_2


title: MC903_7


title: Vehicle_1

description:
2x150 Sequence mode to obtain at approx. 20 million read pairs
Rawcounts.xlsx


title: 0018_1_Normal


title: Lung epithelial cells, exposed to 30k nylon fibers, mouse 4 [N30k4_epi]

value: Epithelial cells

value: Female

value: exposed to 30k nylon fibers


title: Postnatal day 3 Tbx4rtta; tetocre; Sin3a F/F; CKO, biol rePostnatal day  4

data_processing:
STAR v2.5.3a software for alignment to mouse reference genome
RSEM v1.3.0 for expression estimation
edgeR for differential gene expression analysis
Assembly: mm10
Supplementary files format and content: excel file with differential gene expression for each sample

extract_protocol:
RNA was harvested from whole lungs using RNeasy Plus Mini Kit (Qiagen) and analyzed using Aligent Bioanalyzer RNA kit.
cDNA libraries at each stage were made using the Illumina TrueSeq RNA Library Prep Kit (Illunima) following manufacturer's protocols

value: bulk lung

value: conditional knockout


title: MC903_5


title: Lung epithelial cells, exposed to 30k nylon fibers, mouse 3 [N30k3_epi]


title: Postnatal day 3 Tbx4rtta; tetocre; Sin3a F/F; CKO, biol rePostnatal day  3


title: Postnatal day 3 Tbx4rtta; tetocre; Sin3a F/F; CKO, biol rePostnatal day  2


title: Lung epithelial cells, exposed to 30k nylon fibers, mouse 2 [N30k2_epi]


title: 0015_10_Control


title: 0020_3_Normal


title: Postnatal day 3 Tbx4rtta; tetocre; Sin3a F/F; Control; biol rePostnatal day  4

value: Control


title: Postnatal day 3 Tbx4rtta; tetocre; Sin3a F/F; Control; biol rePostnatal day  3


title: Postnatal day 3 Tbx4rtta; tetocre; Sin3a F/F; Control; biol rePostnatal day  2


title: Vehicle_5


title: 0014_7_Control

value: Normal


title: Lung epithelial cells, exposed to 30k nylon fibers, mouse 1 [N30k1_epi]


title: Postnatal day 3 Tbx4rtta; tetocre; Sin3a F/F; CKO, biol rePostnatal day  1


title: 0016_13_Control


title: Postnatal day 3 Tbx4rtta; tetocre; Sin3a F/F; Control; biol rePostnatal day  1


title: CCL206 fibroblasts, control, mouse 2 [ctl2_fib]


title: Lung epithelial cells, exposed to 12k nylon fibers, mouse 4 [N12k4_epi]

value: exposed to 12k nylon fibers


title: 0013_3_Control


title: Postnatal day 0 Tbx4rtta; tetocre; Sin3a F/F; CKO; biol rePostnatal day  3


title: Postnatal day 0 Tbx4rtta; tetocre; Sin3a F/F; CKO; biol rePostnatal day  1


title: Lung epithelial cells, exposed to 12k nylon fibers, mouse 2 [N12k2_epi]


title: Postnatal day 0 Tbx4rtta; tetocre; Sin3a F/+; Control; biol rePostnatal day  4


title: 0011_13_BrCa

value: Tumor

value: IDC


title: 0017_14_Control


title: Postnatal day 0 Tbx4rtta; tetocre; Sin3a F/F; CKO; biol rePostnatal day  2


title: Lung epithelial cells, exposed to 12k nylon fibers, mouse 3 [N12k3_epi]

value: WT


title: 0012_14_BrCa

value: ILC


title: Postnatal day 0 Tbx4rtta; tetocre; Sin3a F/+; Control; biol rePostnatal day  3


title: Postnatal day 0 Tbx4rtta; tetocre; Sin3a F/+; Control; biol rePostnatal day  2


title: Lung epithelial cells, exposed to 12k nylon fibers, mouse 1 [N12k1_epi]


title: Lung epithelial cells, control, mouse 4 [ctl4_epi]

value: control


title: Postnatal day 0 Tbx4rtta; tetocre; Sin3a F/+; Control; biol rep 1


title: Embryonic day 16 Tbx4rtta; tetocre; Sin3a F/F, CKO; Biol rep 4


title: 0010_12_BrCa


title: Embryonic day 16 Tbx4rtta; tetocre; Sin3a F/F, CKO; Biol rep 2


title: 0008_10_BrCa


title: 0009_11_BrCa


title: Lung epithelial cells, control, mouse 2 [ctl2_epi]

value: Lung


title: Lung epithelial cells, control, mouse 3 [ctl3_epi]


title: Postnatal day 0 Tbx4rtta; tetocre; Sin3a F/F; CKO; biol rePostnatal day  4


title: Embryonic day 16 Tbx4rtta; tetocre; Sin3a F/F, CKO; Biol rep 3


title: Lung epithelial cells, control, mouse 1 [ctl1_epi]


title: 0007_9_BrCa


title: Embryonic day 16 Tbx4rtta; tetocre; Sin3a F/+, Control; Biol rep 4


title: Embryonic day 16 Tbx4rtta; tetocre; Sin3a F/+, Control; Biol rep 3


title: Embryonic day 16 Tbx4rtta; tetocre; Sin3a F/+, Control; Biol rep 2


title: Embryonic day 16 Tbx4rtta; tetocre; Sin3a F/+, Control; Biol rep 1


title: 0005_6_BrCa

value: IMC


title: SE-KO_EB_POL2_1

city: Oxford

first: Mira

last: Kassouf

state: Oxfordshire

address: John Radcliffe Hospital

country: United Kingdom

institute: Weatherall Institute of Molecular Medicine

description: genome-wide SE-KO_EB_POL2_1 ChIPmentation in EB derived Erythroid cells derived from 129/Ola mice.

data_processing:
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Alignment to the genome (Bowtie2)
Removal of PCR duplicates;
Combining data from multiple replicates
Removal of ploidy regions
Assembly: mm9
Supplementary files format and content: BAM

source_name: EB derived Erythroid cells

growth_protocol: To produce CD71+ erythroid cells in vitro from differentiated mESCs (WT or mutant): 24h prior to differentiation, mESCs were induced by passaging into IMDM base media, trypsinised and plated in differentiation media (IMDM suplemented serum and other reagents and growth factors) in either triple vent petri dishes (Thermo Fisher) or flat-bottom 96-well plates (Thermo Fisher) at 3x104 cells in 10 cm dishes or 250 cells per well of a 96-well plate for up to seven days without disruption. EBs were harvested and disaggregated in 0.25% trypsin for 3 minutes at 37°C. CD71-positive cells were isolated by magnetic column separation (LS Column, Miltenyi), according to the manufacturer’s instructions. Briefly, cells (from disaggregated EBs) were labelled with anti-mouse CD71-FITC (eBioscience 11-0711-85; 1:200) in staining buffer (PBS with 10% FCS; 500 ul per 10^7 cells) for 20 minutes at 4°C, washed, then incubated with MACS anti-FITC separation microbeads (Miltenyi; 10 ul  per 10^7 cells, following the manufacturer’s instructions) and bead-labelled cells were retained by LS columns. Cells were then processed for ChIP-Seq as in Hay D et al, Nature Genetics, 2016.

extract_protocol:
To isolate foetal liver erythroid cells, HetXHet crosses were established. Pregnant mothers were sacrificed at embryonic day 12.5. Foetuses (WT and mutant) were isolated and the foetal liver extracted. Erythroid cells were disaggregated and collected for further processing.
Cells were fixed with 2mM DSG and 1% Formaldehyde, lysed, sonicated and immunoprecipitated with the antibody of interest. IP'd chromatin was tagmented using Tn5 loaded with illumina sequencing adaptors. Samples were sequenced using 40 bp paired end reads on the NextSeq platform.
The strategy was to characterise the chromatin state of primary mouse-derived or the CD71+ erythroid cells (WT and mutant) derived from mESC-EB in vitro differentitation system by isolating and analysing DNA regions bound by the antibodies of interest, genome-wide.

value: EB derived Erythroid cells

value: Santa Cruz sc-899

value: Genome-wide ChIPmentation


title: SE-KO_EB_POL2_2

description: genome-wide SE-KO_EB_POL2_2 ChIPmentation in EB derived Erythroid cells derived from 129/Ola mice.


title: 0003_4_BrCa


title: WJL3885_RLF_N032_JoinT

city: Stanford

first: Jinglong

state: California

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford Medicine

data_processing:
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203) and Liang et al., 2021 PNAS (PMC8166026).
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (https://expressionanalysis.github.io/ea-utils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2.
The cross library contamination in the co-tagged PCR was filtered by the inner barcodes from I7-nested primers.
Assembly: mm9
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)

source_name: vAbl-ProB

growth_protocol: vAbl ProB cells were cultured at 37 °C and 5% CO2 in RPMI supplemented with 10% (vol/vol) FBS, 50 U/mL penicillin/streptomycin, 2 mM L-glutamine , 1× MEM-NEAA, 1 mM sodium pyruvate , 50 μM 2-mercap- toethanol and 20 mM Hepes (pH 7.4).

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step being omitted, using primers associated with the target locus and Illumina NovoSeq  sequencing
LAM-HTGTS

treatment_protocol: G1-arrested cells were treated with STI-571 (3µM) for 96h. Indicated inhibitors were added to some of the samples the same day as STI-571.

value: vAbl-ProB

value: pro-B cells

value: CTR

tag: total reads


title: WJL3888_RLF_N032_JoinT


title: WJL3889_RLF_N032_JoinT


title: 0002_3_BrCa


title: WT_EB_POL2_2

description: genome-wide WT_EB_POL2_2 ChIPmentation in EB derived Erythroid cells derived from 129/Ola mice.


title: WJL3881_RLF_N032_JoinT


title: WJL3879_RLF_N032_JoinT


title: Embryonic day 16 Tbx4rtta; tetocre; Sin3a F/F, CKO; Biol rep 1

value: bulk lung

value: conditional knockout


title: WJL3878_RLF_N032_JoinT


title: WJL3877_RLF_N032_JoinT


title: WJL3876_RLF_N032_JoinT


title: WJL3875_RLF_N032_JoinT


title: SE-KO_EB_GATA1_2

description: genome-wide SE-KO_EB_GATA1_2 ChIPmentation in EB derived Erythroid cells derived from 129/Ola mice.

value: Abcam ab11852


title: SE-KO_EB_GATA1_1

description: genome-wide SE-KO_EB_GATA1_1 ChIPmentation in EB derived Erythroid cells derived from 129/Ola mice.


title: 0006_7_BrCa


title: si-RPL13 biological replicate 2

city: Kunming

first: Yong-Gang

last: Yao

state: Yunnan

address: 32 Jiaochang Donglu

department: Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province

institute: Kunming Institute of Zoology

description:
siRPL13-2
U251-APP cells with RPL13 siRNA interference

data_processing:
The processed final library was sequenced on an IlluminaHiseq 4000 platform, and 150 bp paired-ends reads were generated.
Raw RNA-seq reads were trimmed to remove sequencing adapters and low quality reads by Trimmomatic 0.33.
The clean reads were then aligned to the reference genome (GRCh38.p7) sequence using Tophat.
HTSeq-count (0.6.1p1) was used to count aligned reads that mapped to the annotated human genes (GRCh38.p7).
Gene-level differential expression analyses were performed using DESeq2.
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: .txt file which contains rlog transformed gene expression levels by DESeq2.

source_name: si-RPL13, U251 cell with stable expression of mutant APP (K670N/M671L)

growth_protocol: U251 cells with stable expression of mutant APP (K670N/M671L) were cultured in Roswell RPMI-1640 medium (HyClone, C11875500BT) supplemented with 10% fetal bovine serum at 37 °C in a humidified atmosphere incubator with 5% CO2.

extract_protocol:
Cells were harvested at 72 h after transfection. Total RNA was extracted by using the RNAeasy kit (TianGen, co.td.) according to the manufacturer’s instructions.
1.5 μg total RNA per sample was used to prepare library for RNA-seq. Sequencing libraries were generated using the NEBNextUltraTM RNA Library Prep kit for Illumina (NEB, USA) following the manufacturer’s recommendation and index codes were added to attribute sequence to each sample.

treatment_protocol: Transfection with siRNA was performed using an electroporator (CUY21EDIT, Nepa gene, Japan) and electroporation cuvettes (EC-002S, Nepa gene, Japan) following manufactures’ instructions. U251 cells were harvested by trypsinization and washed three times with Opti-MEM medium. After cell counting, 1×10E6 cells were resuspended in 100 μL Opti-MEM medium with 2.5 μL siRNA (20 μM). After dispensing 100 μL mixture into a cuvette, electroporation was carried out. After electroporation, cells were seeded in pre-warmed growth medium in 6-well plates. Supernatant in each well was replaced with equal volume of new growth medium after 24 h, and 1 μg/mL doxycycline (Sigma; D9891) was added to induce APP expression.

tag: genotype/variation

value: RPL13 knockdown


title: WJL3873_RLF_N032_JoinT


title: si-RPL13 biological replicate 3

description:
siRPL13-3
U251-APP cells with RPL13 siRNA interference

value: U251 cell with stable expression of mutant APP (K670N/M671L)


title: WJL3871_RLF_N032_JoinT


title: WT_EB_GATA1_2

description: genome-wide WT_EB_GATA1_2 ChIPmentation in EB derived Erythroid cells derived from 129/Ola mice.


title: si-RPL13 biological replicate 1

description:
siRPL13-1
U251-APP cells with RPL13 siRNA interference


title: WJL3870_RLF_N032_JoinT


title: siNC biological replicate 3

description:
siNC-3
scramble U251-APP cells with control siRNA

source_name: siNC, U251 cell with stable expression of mutant APP (K670N/M671L)


title: WJL3883_RLF_N032_JoinT


title: WT_EB_GATA1_1

description: genome-wide WT_EB_GATA1_1 ChIPmentation in EB derived Erythroid cells derived from 129/Ola mice.


title: WT_EB_POL2_1

description: genome-wide WT_EB_POL2_1 ChIPmentation in EB derived Erythroid cells derived from 129/Ola mice.


title: WJL3869_RLF_N032_JoinT


title: 0001_1_Control

value: Hyperplasia

value: Ductal hyperplasia


title: SE-KO_EB_H3K4Me3_1

description: genome-wide SE-KO_EB_H3K4Me3_1 ChIPmentation in EB derived Erythroid cells derived from 129/Ola mice.

value: Abcam 8580


title: SE-KO_EB_H3K4Me3_2

description: genome-wide SE-KO_EB_H3K4Me3_2 ChIPmentation in EB derived Erythroid cells derived from 129/Ola mice.


title: WJL3864_RLF_N032_JoinT


title: WJL3867_RLF_N032_JoinT


title: WT_EB_H3K4Me3_2

description: genome-wide WT_EB_H3K4Me3_2 ChIPmentation in EB derived Erythroid cells derived from 129/Ola mice.


title: siNC biological replicate 2

description:
siNC-2
scramble U251-APP cells with control siRNA

value: control


title: WJL3866_RLF_N032_JoinT


title: WJL3840_RLF_N032_JoinT


title: WT_EB_H3K4Me3_1

description: genome-wide WT_EB_H3K4Me3_1 ChIPmentation in EB derived Erythroid cells derived from 129/Ola mice.


title: WJL3865_RLF_N032_JoinT


title: WJL3837_RLF_N032_JoinT


title: siNC biological replicate 1

description:
siNC-1
scramble U251-APP cells with control siRNA


title: WJL3874_RLF_N032_JoinT


title: WJL3841_RLF_N032_JoinT


title: Healthy adult C09_mRNA

first: xiong

last: liu

state: Beijing

address: No.20，Dongdajie Street，Fengtai District

institute: State Key Laboratory of Pathogen and Biosecurity

data_processing:
Basecalls performed using CASAVA version 1.8
Raw data were firstly processed through in-house perl scripts to obtain clean data by removing reads containing adapter, poly-N and with low quality. Indexes of the reference genome were built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
Cufflinks v2.1.1 was used to count the fragment numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and fragments count mapped to this gene.
Genome_build: human NCBI genome build 37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Human peripheral blood

extract_protocol:
Whole blood was preserved in Trizol reagent (Ambion). RNA isolation was performed using the miRNeasy mini Kit (Qiagen Cat.No 217004)
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The library preparations were sequenced on an Illumina Hiseq 4000 platform and 150 bp paired-end reads were generated.

value: peripheral blood

tag: disease status

value: Healthy


title: Healthy adult C08_mRNA


title: Healthy adult C10_mRNA


title: WJL3872_RLF_N032_JoinT


title: WJL3833_RLF_N032_JoinT


title: Healthy adult C07_mRNA


title: SE-KO_EB_H3K27Ac_1

description: genome-wide SE-KO_EB_H3K27Ac_1 ChIPmentation in EB derived Erythroid cells derived from 129/Ola mice.

value: EB derived Erythroid cells

value: Abcam ab4729


title: SE-KO_EB_H3K27Ac_2

description: genome-wide SE-KO_EB_H3K27Ac_2 ChIPmentation in EB derived Erythroid cells derived from 129/Ola mice.

value: Genome-wide ChIPmentation


title: WJL3863_RLF_N032_JoinT

value: vAbl-ProB


title: WJL3830_RLF_N032_JoinT

value: pro-B cells


title: WJL3828_RLF_N032_JoinT

value: CTR


title: WJL3827_RLF_N032_JoinT


title: WT_EB_H3K27Ac_1

description: genome-wide WT_EB_H3K27Ac_1 ChIPmentation in EB derived Erythroid cells derived from 129/Ola mice.


title: WJL3826_RLF_N032_JoinT


title: R2-only_FL_POL2_2

description: genome-wide R2-only_FL_POL2_2 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.

source_name: primary foetal liver erythroid cells

value: Primary erythroid cells derived from FL

value: Santa Cruz sc-899


title: Healthy adult C05_mRNA


title: WJL3825_RLF_N032_JoinT


title: WJL3831_RLF_N032_JoinT


title: Healthy adult C04_mRNA


title: WJL3824_RLF_N032_JoinT


title: R2-only_FL_POL2_1

description: genome-wide R2-only_FL_POL2_1 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.


title: WJL3835_RLF_N032_JoinT


title: WT_EB_H3K27Ac_2

description: genome-wide WT_EB_H3K27Ac_2 ChIPmentation in EB derived Erythroid cells derived from 129/Ola mice.


title: Healthy adult C03_mRNA


title: WJL3822_RLF_N032_JoinT


title: WJL3823_RLF_N032_JoinT


title: WT_FL_POL2_2

description: genome-wide WT_FL_POL2_2 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.


title: WJL3829_RLF_N032_JoinT


title: WT_FL_POL2_1

description: genome-wide WT_FL_POL2_1 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.


title: WJL3818_RLF_N032_JoinT


title: WJL3819_RLF_N032_JoinT


title: WJL3817_RLF_N032_JoinT


title: Healthy adult C01_mRNA


title: WJL3816_RLF_N032_JoinT


title: Healthy adult C06_mRNA


title: WJL3821_RLF_N032_JoinT


title: R2-only_FL_BRD4_2

description: genome-wide R2-only_FL_BRD4_2 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.

value: Bethyl IHC-00396


title: Healthy adult C02_mRNA


title: WJL3815_RLF_N032_JoinT


title: R2-only_FL_BRD4_1

description: genome-wide R2-only_FL_BRD4_1 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.


title: E16 Tbx4rtta; tetocre; Sin3a F/F, CKO; Biol rep 4

extract_protocol:
RNA was harvested from sorted mesenchymal cells using the TRIzol (Fisher) RNA extraction protocol and analyzed using Aligent Bioanalyzer RNA kit.
cDNA libraries were made using theTakara SMARTer RNA v4 with NexteraXT Library Prep Kit (TakaraBio) following manufacturer's protocols

value: bulk lung

value: Embryonic day 16

value: sorted mesenchymal cells

value: conditional knockout


title: E16 Tbx4rtta; tetocre; Sin3a F/F, CKO; Biol rep 3


title: WT_FL_BRD4_2

description: genome-wide WT_FL_BRD4_2 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.


title: E16 Tbx4rtta; tetocre; Sin3a F/F, CKO; Biol rep 2


title: EVD patient L21_mRNA

value: Ebola virus disease


title: EVD patient L20_mRNA


title: E16 Tbx4rtta; tetocre; Sin3a F/F, CKO; Biol rep 1


title: WT_FL_BRD4_1

description: genome-wide WT_FL_BRD4_1 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.


title: E16 Tbx4rtta; tetocre; Sin3a F/+, Control; Biol rep 4

value: control


title: R2-only_FL_MED1_2

description: genome-wide R2-only_FL_MED1_2 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.

value: Bethyl IHC-00149


title: E16 Tbx4rtta; tetocre; Sin3a F/+, Control; Biol rep 3


title: EVD patient L19_mRNA

value: peripheral blood


title: E16 Tbx4rtta; tetocre; Sin3a F/+, Control; Biol rep 2


title: EVD patient L18_mRNA


title: Embryonic day 16 (E16) Tbx4rtta; tetocre; Sin3a F/+, Control; Biol rep 1


title: multiciliated ependymal cell, Edf1 ko,6day induction, rep3

city: Wuhan

first: Haochen

last: Jiang

address: No.9. BoXue Road, economic development District

institute: Jianghan university

data_processing:
The quality of raw data was evaluated using FastQC (v0.11.2)
Sequencing reads were trimmed for adaptor/low-quality sequence using cutadapt (version 1.11)
Clean data were aligned to reference genome via software Hisat2 (v2.1.0)
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes counts for Edf1 WT and KO samples

source_name: multiciliated ependymal cell

growth_protocol: The radial glial cells were isolated from The brains of P0-P3 wild type or Edf1 knockout mice and maintained in DMEM containing 10% FBS and antibiotics in humidified atmosphere with 5%CO2 at 37℃.

extract_protocol:
Total RNA was extracted from the samples using the TRIzol reagent (Invitrogen).
RNA libraries for sequencing were prepared using the MGIEasy mRNA Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: The multiciliated ependymal cells differentiation was induced by FBS free DMEM supplemented with antibiotics for 6 days.

value: multiciliated ependymal cell

tag: strain background

value: Edf1 KO

value: multiciliated ependymal cell differentiation


title: R2-only_FL_MED1_1

description: genome-wide R2-only_FL_MED1_1 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.

value: Genome-wide ChIPmentation


title: multiciliated ependymal cell, Edf1 ko,6day induction, rep1


title: EVD patient L16_mRNA

tag: tissue


title: WT_FL_MED1_2

description: genome-wide WT_FL_MED1_2 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.

tag: cell type


title: multiciliated ependymal cell, WT,6day induction, rep2

tag: genotype

value: WT


title: multiciliated ependymal cell, Edf1 ko,6day induction, rep2

tag: treatment


title: EVD patient L22_mRNA


title: EVD patient L15_mRNA


title: EVD patient L17_mRNA


title: multiciliated ependymal cell, WT,6day induction, rep3


title: WT_FL_MED1_1

description: genome-wide WT_FL_MED1_1 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.

tag: strain


title: multiciliated ependymal cell, WT,6day induction, rep1


title: EVD patient L14_mRNA


title: R2-only_FL_NF-E2_1

description: genome-wide R2-only_FL_NF-E2_1 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.

tag: chip antibody

value: Santa Cruz sc-22827


title: WT_FL_NF-E2_1

description: genome-wide WT_FL_NF-E2_1 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.

value: Primary erythroid cells derived from FL


title: Day 7 post-stroke, X-ray-irradiated cortex, rep 5

city: Hong Kong

first: MA

last: Chi Him Eddie

address: Tat Chee Avenue, Kowloon, Hong Kong

department: Department of Neuroscience

country: Hong Kong

institute: City University of Hong Kong

data_processing:
RNA-seq raw reads were mapped to the UCSC human reference genome (GRCh38) and calculation of gene counts using STAR (version 2.7.8a) with default parameters.
The multi-mapped reads were filtered out and only the uniquely mapped reads were retained.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each sample
Supplementary files format and content: tab-delimited text files include TPM values for each sample

molecule: polyA RNA

source_name: Cerebral Cortex

growth_protocol: Cerebral cortices from adult male C57BL/6 mice

extract_protocol:
Cerebral cortices were dissected out from both groups at days 1, 3 and 7 post-stroke, and total RNA was extracted using Trizol reagent. A total of 1ug of total RNA was used as input RNA for each sample.
RNA libraries for RNA-seq were prepared using KAPA mRNA HyperPrep Kit (KR1352-v5.17) following the manufacturer's protocols.

treatment_protocol: Photothrombotic strokes were induced in the right hemisphere, and the mice were received whole-body X-ray irradiation, or sham-irradiation as controls.

value: Cerebral Cortex

value: Stroke, X-ray-irradiation


title: EVD patient L13_mRNA


title: Day 7 post-stroke, X-ray-irradiated cortex, rep 4


title: Day 7 post-stroke, X-ray-irradiated cortex, rep 1


title: EVD patient L12_mRNA


title: R2-only_FL_GATA1_1

description: genome-wide R2-only_FL_GATA1_1 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.

value: Abcam ab11852


title: Day 7 post-stroke, sham-irradiated cortex, rep 4

value: Stroke, Sham-irradiation


title: Day 7 post-stroke, sham-irradiated cortex, rep 3


title: R2-only_FL_GATA1_2

description: genome-wide R2-only_FL_GATA1_2 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.


title: Day 3 post-stroke, X-ray-irradiated cortex, rep 5


title: Day 7 post-stroke, sham-irradiated cortex, rep 5


title: Day 3 post-stroke, X-ray-irradiated cortex, rep 4


title: EVD patient L11_mRNA


title: WT_FL_GATA1_2

description: genome-wide WT_FL_GATA1_2 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.


title: EVD patient L10_mRNA


title: Day 3 post-stroke, sham-irradiated cortex, rep 2


title: EVD patient L09_mRNA


title: WT_FL_GATA1_1

description: genome-wide WT_FL_GATA1_1 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.


title: Day 3 post-stroke, sham-irradiated cortex, rep 3


title: Day 3 post-stroke, X-ray-irradiated cortex, rep 2


title: Day 3 post-stroke, sham-irradiated cortex, rep 1


title: EVD patient L08_mRNA


title: Day 1 post-stroke, X-ray-irradiated cortex, rep 4


title: R2-only_FL_H3K27Ac_2

description: genome-wide R2-only_FL_H3K27Ac_2 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.

value: Abcam ab4729


title: Day 1 post-stroke, X-ray-irradiated cortex, rep 1


title: R2-only_FL_H3K27Ac_1

description: genome-wide R2-only_FL_H3K27Ac_1 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.


title: Day 1 post-stroke, X-ray-irradiated cortex, rep 3


title: Day 1 post-stroke, sham-irradiated cortex, rep 2


title: Day 1 post-stroke, sham-irradiated cortex, rep 5


title: WT_FL_H3K27Ac_2

description: genome-wide WT_FL_H3K27Ac_2 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.


title: EVD patient L06_mRNA


title: EVD patient L07_mRNA


title: Uninjured X-ray-irradiated cortex, rep 3

value: No stroke, X-ray-irradiation


title: Day 1 post-stroke, sham-irradiated cortex, rep 3


title: WT_FL_H3K27Ac_1

description: genome-wide WT_FL_H3K27Ac_1 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.


title: Uninjured X-ray-irradiated cortex, rep 2


title: R2-only_FL_H3K4Me1_2

description: genome-wide R2-only_FL_H3K4Me1_2 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.

value: Abcam ab8895


title: EVD patient L04_mRNA

value: Ebola virus disease


title: EVD patient L05_mRNA


title: Uninjured sham-irradiated cortex, rep 3

value: No stroke, Sham-irradiation


title: R2-only_FL_H3K4Me1_1

description: genome-wide R2-only_FL_H3K4Me1_1 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.


title: Uninjured X-ray-irradiated cortex, rep 1


title: Uninjured sham-irradiated cortex, rep 2


title: EVD patient L03_mRNA

value: peripheral blood


title: WT_FL_H3K4Me1_2

description: genome-wide WT_FL_H3K4Me1_2 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.


title: EVD patient L02_mRNA


title: Injured DRG from Fmn2-/- mice, rep 1

data_processing:
RNA-seq raw reads were mapped to the UCSC human reference genome (GRCh38) and calculation of gene counts using STAR (version 2.7.2b) with default parameters.
The multi-mapped reads were filtered out and only the uniquely mapped reads were retained.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: L4/5 DRGs

growth_protocol: L4/5 DRGs from adult male WT or Fmn2-/- mice

extract_protocol:
L4/5 DRGs were dissected out from both genotype 5 days after injury, and total RNA was extracted using Trizol reagent. A total of 100ng of total RNA was used as input RNA for each sample.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra II Directional RNA Library Prep Kit following the manufacturer's protocols.

treatment_protocol: Sciatic nerve transection was performed on both WT and Fmn2-/- mice

value: L4/5 DRGs

value: Injured DRG


title: Uninjured sham-irradiated cortex, rep 1


title: EVD patient L01_mRNA


title: WT_FL_H3K4Me1_1

description: genome-wide WT_FL_H3K4Me1_1 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.


title: Uninjured DRG from Fmn2-/- mice, rep 3

value: Uninjured DRG


title: Injured DRG from Fmn2-/- mice, rep 2


title: R2-only_FL_H3K4Me3_2

description: genome-wide R2-only_FL_H3K4Me3_2 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.

value: Abcam 8580

value: Genome-wide ChIPmentation


title: Retinal ECs, BMP9-10 Abs + CDK4/6i treated, replicate 3

city: Charlottesville

first: Uma Devi

last: Paila

address: 1335 Lee St

institute: University of Virginia

data_processing:
The raw fastq files were generated with bcl2fastq2_v2.19.0, and quality control checks were done using FastQC software.
The reads were mapped to the mouse reference genome “GRCm39” and alignments and quantification of mRNA was performed with the STAR aligner v2.7
Differential expression analysis was done with DESeq2 in R v4.1, and significant genes were based on the p-adjusted values (Benjamini and Hochberg method for controlling FDR) of less than or equal to 0.05.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file of raw counts for all samples

source_name: P7, RETINA

extract_protocol:
Eyes from P7 pups of control (group 1), BMP9/10 Abs-treated (group 2), and BMP9/10 Abs + CDK4/6i (group 3) treated animals were dissected out and primary retinal ECs were FACS-isolated for bulk RNA sequencing. Six to nine retinas/group were pooled for 1 experiment and each experiment was repeated 3 times (N=3). mRNA samples from retinal ECs from groups 1, 2 and 3 were isolated using RNeasy Plus Micro Kit (QIAGEN, cat# 74034).
RNA libraries were prepared as per the (HiSeq4000) manufacturer's protocols. Next-generation whole transcriptome Illumina sequencing was performed at Yale Center for Genome Analysis.

value: P7, RETINA

value: Endothelial

value: BMP9-10 Abs + CDK4/6i treated


title: Uninjured DRG from Fmn2-/- mice, rep 1


title: Injured DRG from WT mice, rep 3

value: WT


title: Uninjured DRG from Fmn2-/- mice, rep 2


title: R2-only_FL_H3K4Me3_1

description: genome-wide R2-only_FL_H3K4Me3_1 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.

value: Primary erythroid cells derived from FL


title: Injured DRG from WT mice, rep 1


title: Injured DRG from WT mice, rep 2


title: Retinal ECs, BMP9-10 Abs + CDK4/6i treated, replicate 2


title: Retinal ECs, BMP9-10 Abs + CDK4/6i treated, replicate 1


title: Uninjured DRG from WT mice, rep 3


title: Retinal ECs, BMP9-10 Abs-treated, replicate 3

value: BMP9-10 Abs-treated


title: Uninjured DRG from WT mice, rep 1


title: Retinal ECs, BMP9-10 Abs-treated, replicate 2


title: R2-only_FL_tiled-C_3

description: sequences enriched from a 3C library for their interactions within the 3.3Mb tiled region surrounding the alpha-globin locus

data_processing:
Hi-C Pro to align reads, call interactions and ICE normalize interactions within the all-vs-all matrix.
Custom script to isolate interactions in which both participating fragments map to the tiled locus.
Custom R scripts to produce heatmaps and "virtual capture" plots.
Assembly: mm9
Supplementary files format and content: All-vs-all chromatin interaction matrices, restricted to the tiled locus (ICE-normalised).

extract_protocol:
To isolate foetal liver erythroid cells, HetXHet crosses were established. Pregnant mothers were sacrificed at embryonic day 12.5. Foetuses (WT and mutant) were isolated and the foetal liver extracted. Erythroid cells were disaggregated and collected for further processing.
The protocol used for generation of the 3C libraries was similar to previous methods with minor modifications. Briefly, cells were crosslinked with 2% formaldehyde (10 minutes, room temperature); quenched with cold glycine; washed in phosphate buffered saline; resuspended in cold lysis buffer (tris 10mM, NaCl 10mM, NP40 0.2%, complete proteinase inhibitor (Roche)) and snap frozen to -80.  Cells were thawed on ice and cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37C for 1h at 1400rpm on a Comfort Thermomixer (Eppendorf) followed by a further incubation of 1h following the addition of triton X100 (final concentration 1.67%). An overnight digestion was performed using Dpn II (500U /ml (NEB) at 37C / 1400 rpm). The digested chromatin was ligated overnight (T4 Ligase final concentration 10U/ml) at 16 degrees at 1400 rpm on the Thermomixer.  The samples were then decrosslinked overnight at 65C with Proteinase K (Roche) followed by a 30 min incubation at 37C with RNAse (Roche). Phenol/Chloroform extraction was then performed followed by an Ethanol precipitation and a wash with 70% Ethanol. Digestion efficiencys were assessed by gel electrophoresis (1% agarose).  DNA content of the Dpn II 3C libraries were quantitated using a Qubit fluorometer (Life technologies) and each library was sheared using a Covaris ME220. Following shearing, DNA was purified using AMPureXP beads (Agencourt) and DNA quality assessed on a Bioanalyser 2100 using a DNA High Sensitivity Chip (Agilent). DNA end repair and adapter ligation was performed using the NEB Ultra II DNA sample preparation reagent kit, using the standard protocol.  Biotinylated capture oligonucleotides were designed to corrsponding to every digestion fragment throughout the 3.3Mb tiled region surrounding the alpha globin locus.  The quality of the resultant captured library was assessed by Agilent tapestation or bioanalyser (D1000). The resulting libraries were sequenced using Illumina Next-Seq.
The experimental strategy was to generate very high complexity randomly sonicated 3C libraries with ligated Illumina sequencing adaptors (ideally with several hundred thousand fold coverage).  Oligonucleotide capture technology (with probes corresponding to every restriction-ligation junction throughout the 3.3Mb tiled region, surrounding the alpha-globin locus) was then used to pull down the restricion fragments with one or more fragments corresponding to the 3.3Mb tiled region.

value: E12.5 foetal liver cells


title: WT_FL_H3K4Me3_1

description: genome-wide WT_FL_H3K4Me3_1 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.


title: R2-only_FL_tiled-C_2


title: Retinal ECs, control, replicate 3

value: control


title: R2-only_FL_tiled-C_1


title: R2-only_FL_PAM_3

data_processing:
Mapping: STAR
Duplicate removal: samtools rmdup
Assembly: mm9
Supplementary files format and content: BAM

extract_protocol:
To isolate foetal liver erythroid cells, HetXHet crosses were established. Pregnant mothers were sacrificed at embryonic day 12.5. Foetuses (WT and mutant) were isolated and the foetal liver extracted. Erythroid cells were disaggregated and collected for further processing.
For RNA-seq libraries, 1-2 μg of total RNA was depleted of rRNA using the ribo-Zero rRNA Removal Kit (Illumina) according to the manufacturer’s instructions. To enrich for mRNA, poly(A)+ RNA was isolated, strand-specific cDNA was synthesised, and the resulting libraries prepared for Illumina sequencing using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs: E7490) and the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs: E7760) following the manufacturer’s instructions. Poly(A)+ and Poly(A)- RNA-seq libraries were sequenced on the Illumina Nextseq platform using a 75-cycle paired-end kit (NextSeq 500/550 High Output Kit v2.5: 20024906).

value: R2-only mice derived from C57Bl8 mouse strain

value: Foetal liver cells (E12.5)


title: WJL3490_RLF_N029_JoinT

state: CA California

address: 1291 Welch Rd, CCSR Room 1240

institute: Stanford University

data_processing:
Library strategy: LAM-HTGTS (linear amplification mediated high-throughput genomic translocations sequencing)
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203) and Liang et al., 2021 PNAS (PMC8166026).
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (https://expressionanalysis.github.io/ea-utils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2.
Assembly: The cross library contamination in the co-tagged PCR was filtered by the inner barcodes from I7-nested primers.
Supplementary files format and content: mm9
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step being omitted, using primers associated with the target locus and Illumina NovoSeq  sequencing

tag: cell line

value: vAbl-ProB

value: pro-B cells


title: WJL3489_RLF_N029_JoinT


title: WJL3488_RLF_N029_JoinT


title: WJL3486_RLF_N029_JoinT


title: WJL3487_RLF_N029_JoinT


title: WJL3485_RLF_N029_JoinT


title: Retina ECs, control, replicate 2


title: WJL3484_RLF_N029_JoinT


title: WT_FL_H3K4Me3_2

description: genome-wide WT_FL_H3K4Me3_2 ChIPmentation in Primary erythroid cells derived from FL derived from C57BL/6 mice.


title: Injured DRG from Fmn2-/- mice, rep 3

value: L4/5 DRGs


title: R2-only_FL_PAM_2


title: Retinal ECs, control, replicate 1


title: Uninjured DRG from WT mice, rep 2


title: WJL3481_RLF_N029_JoinT


title: WJL3482_RLF_N029_JoinT


title: WJL3480_RLF_N029_JoinT


title: WJL3479_RLF_N029_JoinT


title: YRG cells, SETDB-sg2, aIFNGR treated

city: New Haven

first: Meaghan

last: McGeary

state: CT

address: 300 Cedar St.

department: Immunobiology

institute: Yale School of Medicine

data_processing:
Reads were aligned using BWA (Li, 2013) (version 0.7.17) to mm10.
Gene expression values were counted using HTseq (Anders et al., 2015) (version 0.13.5) and differential expression was performed by edgeR (McCarthy et al., 2012) (version 3.36.0).
For analysis of transposable elements, RepEnrich was used to align to RepeatMasker (mm10) reference and generate counts for each element. Simple repeats were filtered out of results, and differential expression was performed for ERV and gene expression using edgeR (McCarthy et al., 2012)
Assembly: mm10; RepeatMasker
Supplementary files format and content: RNAseq counts files: all_counts_expt1.txt and blockade_all_counts.txt; ERV analysis TE_only.txt

source_name: cell line

growth_protocol: Cell lines were grown in Complete Media (DMEM/F12 (Gibco), 1X NEAA (Gibco), 1X PenStrep (Gibco), 10% FBS (Gibco) at 37C in 5% CO2, maintained at low passages and passaged using 0.25X Trypsin EDTA (Invitrogen).

extract_protocol:
1x106 cells were pelleted, and RNA isolated using RNeasy kit, supplemented with QIAshredder and DNase treatment (Qiagen).
TruSeq stranded library preparation was performed by the YCGA according to manufacturer protocol.

treatment_protocol: 1x106 cells were plated in complete media and incubate in culture for 24 hours to allow them to adhere. Cells were then treated with PBS or aIFNAR (listed above) for 72 hours (with treated media replaced every 36 hours)

value: cell line

value: melanoma

value: aIFNGR


title: WT_FL_PAM_2

value: WT mice derived from C57Bl8 mouse strain


title: YRG cells, SETDB1-sg2, aIFNAR treated

value: aIFNAR


title: WJL3478_RLF_N029_JoinT


title: WT_FL_PAM_1


title: R2-only_FL_PAM_1


title: Retinal ECs, BMP9-10 Abs-treated, replicate 1

value: P7, RETINA

value: Endothelial


title: WJL3476_RLF_N029_JoinT


title: WJL3475_RLF_N029_JoinT


title: R2-only_FL_PAP_3


title: WJL3483_RLF_N029_JoinT


title: R2-only_FL_PAP_2


title: YRG cells, SETDB1-sg2, PBS treated

value: PBS


title: YRG cells, SETDB-sg1, aIFNGR treated


title: WJL3471_RLF_N029_JoinT


title: WJL3470_RLF_N029_JoinT

value: + Lig4


title: YRG cells, SETDB1-sg1, aIFNAR treated


title: WJL3469_RLF_N029_JoinT


title: R2-only_FL_PAP_1


title: WJL3472_RLF_N029_JoinT


title: WJL3466_RLF_N029_JoinT


title: WJL3477_RLF_N029_JoinT


title: WJL3464_RLF_N029_JoinT


title: YRG cells, control, aIFNAR treated


title: WJL3465_RLF_N029_JoinT


title: R2-R4_EB_ATAC2

description: ATAC performed on R2-R4 CD71+ EB-derived erythroid cells, originally derived from 129/Ola mouse embryonic stem cells

data_processing:
Trim_galore (to remove sequencing adaptors)
Alignment to the genome Bowtie2 standard parameters with -k set to 2
Removal of PCR duplicates;
Assembly: mm9

growth_protocol:
To produce CD71+ erythroid cells in vitro from differentiated mESCs (WT or mutant): 24h prior to differentiation, mESCs were induced by passaging into IMDM base media, trypsinised and plated in differentiation media (IMDM suplemented serum and other reagents and growth factors) in either triple vent petri dishes (Thermo Fisher) or flat-bottom 96-well plates (Thermo Fisher) at 3x104 cells in 10 cm dishes or 250 cells per well of a 96-well plate for up to seven days without disruption. EBs were harvested and disaggregated in 0.25% trypsin for 3 minutes at 37°C. CD71-positive cells were isolated by magnetic column separation (LS Column, Miltenyi), according to the manufacturer’s instructions. Briefly, cells (from disaggregated EBs) were labelled with anti-mouse CD71-FITC (eBioscience 11-0711-85; 1:200) in staining buffer (PBS with 10% FCS; 500 ul per 10^7 cells) for 20 minutes at 4°C, washed, then incubated with MACS anti-FITC separation microbeads (Miltenyi; 10 ul  per 10^7 cells, following the manufacturer’s instructions) and bead-labelled cells were retained by LS columns. Cells were then processed for ATAC-Seq as in (Buenrostro et al, 2013).
To isolate foetal liver erythroid cells, HetXHet crosses were established. Pregnant mothers were sacrificed at embryonic day 12.5. Foetuses (WT and mutant) were isolated and the foetal liver extracted. Erythroid cells were disaggregated and collected for further processing.

extract_protocol:
To produce CD71+ erythroid cells in vitro from differentiated mESCs (WT or mutant): 24h prior to differentiation, mESCs were induced by passaging into IMDM base media, trypsinised and plated in differentiation media (IMDM suplemented serum and other reagents and growth factors) in either triple vent petri dishes (Thermo Fisher) or flat-bottom 96-well plates (Thermo Fisher) at 3x104 cells in 10 cm dishes or 250 cells per well of a 96-well plate for up to seven days without disruption. EBs were harvested and disaggregated in 0.25% trypsin for 3 minutes at 37°C. CD71-positive cells were isolated by magnetic column separation (LS Column, Miltenyi), according to the manufacturer’s instructions. Briefly, cells (from disaggregated EBs) were labelled with anti-mouse CD71-FITC (eBioscience 11-0711-85; 1:200) in staining buffer (PBS with 10% FCS; 500 ul per 10^7 cells) for 20 minutes at 4°C, washed, then incubated with MACS anti-FITC separation microbeads (Miltenyi; 10 ul  per 10^7 cells, following the manufacturer’s instructions) and bead-labelled cells were retained by LS columns. Cells were then processed for ATAC-Seq as in (Buenrostro et al, 2013).
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013). 60000-80000 cells were used per biological replicate. Cells were lysed and nuclei were isolated prior to transposition with Tn5 transposase (Nextera, Illumina) for 30 minutes at 37°C. DNA was purified using a MinElute kit (Qiagen). Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013. ATAC-Seq libraries profiles were visualized using D1000 tape on the Tapestation (Agilent). Due to the broad range of DNA fragment sizes found in these libraries, quantitation with the Qubit for DNA concentration was found to be highly variable and was omitted. The libraries were quantified using the universal library quantification kit (KAPA Biosystems). Samples were sequenced using 40 bp paired end reads (NextSeq platform).
The strategy was to survey regions of open chromatin in our cell population of interest (primary mouse derived erythroid cells or CD71+ EB-derived cells) as they mark regulatory genomic regions. The modified Tn5 can in one step identify open chromatin fragments, cut, and ligate adaptors. The fragments can then be multiplexed and sequenced

value: R2-R4 CD71+ EB-derived erythroid cells, originally derived from ESC


title: WJL3468_RLF_N029_JoinT


title: WJL3463_RLF_N029_JoinT


title: YRG cells, control, aIFNGR treated


title: YRG cells, control, PBS treated


title: YRG cells, SETDB1-sg2, untreated


title: WJL3474_RLF_N029_JoinT


title: WJL3473_RLF_N029_JoinT


title: WT_FL_PAP_2


title: R2-R4_EB_ATAC1


title: YRG cells, SETDB1-sg1, PBS treated


title: YRG cells, SETDB1-sg1, untreated


title: R1R2R3-R4_EB_ATAC2

description: ATAC performed on R1R2R3-R4 CD71+ EB-derived erythroid cells, originally derived from 129/Ola mouse embryonic stem cells

value: R1R2R3-R4 CD71+ EB-derived erythroid cells, originally derived from ESC


title: WJL3458_RLF_N029_JoinT


title: WJL3459_RLF_N029_JoinT


title: WJL3456_RLF_N029_JoinT


title: WJL3457_RLF_N029_JoinT


title: WJL3455_RLF_N029_JoinT


title: WT_FL_PAP_1


title: R2R4-R1_EB_ATAC2

description: ATAC performed on R2R4-R1 CD71+ EB-derived erythroid cells, originally derived from 129/Ola mouse embryonic stem cells

value: R2R4-R1 CD71+ EB-derived erythroid cells, originally derived from ESC


title: R1R2R3-R4_EB_ATAC1


title: WJL3454_RLF_N029_JoinT


title: miRNA-seq_92.W

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
Overall quality of the next-generation sequencing data was evaluated automatically and manually with fastQC v0.11.9 (Andrews 2010) and multiQC v1.10 (Ewels et al. 2016).
Reads from all passing samples were adapter trimmed and quality filtered using cutadapt v3.3 (Martin 2011) and filtered for a minimum length of 17nt.
Mapping steps were performed with bowtie v1.3.0 (Langmead et al. 2009) and miRDeep2 v2.0.1.2 (Friedländer et al. 2012), whereas reads were mapped first against the genomic reference GRCm38.p6 provided by Ensembl (Zerbino et al. 2018) allowing for two mismatches and subsequently miRBase v22.1 (Griffiths-Jones 2004), filtered for miRNAs of mmu only, allowing for one mismatch.
Assembly: GRCm39 Assembly GCA_000001635.9; miRBase v22.1
Supplementary files format and content: XLS file containing read counts of miRDeep2 mapped miRNAs

source_name: Whole kidney, biol rep 4

extract_protocol: Realseq Libaray preperation kit according to manufacturer's specification

value: Kidney

value: WT

value: male

tag: laser microdissected

value: No

tag: microvascular compartment

value: Whole kidney

tag: disease state

value: Cecal ligation & puncture (CLP) sepsis

tag: time


title: WJL3453_RLF_N029_JoinT

value: vAbl-ProB

value: pro-B cells


title: WJL3451_RLF_N029_JoinT


title: WJL3462_RLF_N029_JoinT


title: R3RMR4-only_EB_ATAC2

description: ATAC performed on R3RMR4-only CD71+ EB-derived erythroid cells, originally derived from 129/Ola mouse embryonic stem cells

value: R3RMR4-only CD71+ EB-derived erythroid cells, originally derived from ESC


title: miRNA-seq_50.W

source_name: Whole kidney, biol rep 2

tag: Sex


title: miRNA-seq_88.W

source_name: Whole kidney, biol rep 3


title: WJL3452_RLF_N029_JoinT


title: WJL3461_RLF_N029_JoinT


title: WJL3460_RLF_N029_JoinT


title: WJL3449_RLF_N029_JoinT


title: WJL3448_RLF_N029_JoinT


title: R3RMR4-only_EB_ATAC1


title: miRNA-seq_32.W

source_name: Whole kidney, biol rep 1


title: WJL3447_RLF_N029_JoinT


title: R2R3RMR4-only_EB_ATAC1

description: ATAC performed on R2R3RMR4-only CD71+ EB-derived erythroid cells, originally derived from 129/Ola mouse embryonic stem cells

value: R2R3RMR4-only CD71+ EB-derived erythroid cells, originally derived from ESC


title: miRNA-seq_88.V

source_name: Post-capillary venules, biol rep 3

value: Yes

value: Post-capillary venules


title: R1R3RMR4-only_EB_ATAC1

description: ATAC performed on R1R3RMR4-only CD71+ EB-derived erythroid cells, originally derived from 129/Ola mouse embryonic stem cells

value: R1R3RMR4-only CD71+ EB-derived erythroid cells, originally derived from ESC


title: WJL3446_RLF_N029_JoinT

value: + Lig4


title: miRNA-seq_92.V

source_name: Post-capillary venules, biol rep 4


title: YRG cells, control, untreated

value: cell line

value: YRG-WT

value: melanoma


title: WJL3444_RLF_N029_JoinT


title: WJL3441_RLF_N029_JoinT


title: WJL3442_RLF_N029_JoinT


title: miRNA-seq_50.V

source_name: Post-capillary venules, biol rep 2

value: Kidney


title: R2R4-R1_EB_ATAC1

source_name: EB derived Erythroid cells

value: R2R4-R1 CD71+ EB-derived erythroid cells, originally derived from ESC


title: WJL3450_RLF_N029_JoinT

source_name: vAbl-ProB


title: R1R2RMR4-only_EB_ATAC2

description: ATAC performed on R1R2RMR4-only CD71+ EB-derived erythroid cells, originally derived from 129/Ola mouse embryonic stem cells

value: R1R2RMR4-only CD71+ EB-derived erythroid cells, originally derived from ESC


title: miRNA-seq_32.V

source_name: Post-capillary venules, biol rep 1

value: WT

value: male


title: WJL3440_RLF_N029_JoinT


title: WJL3438_RLF_N029_JoinT


title: WJL3436_RLF_N029_JoinT


title: WJL3437_RLF_N029_JoinT


title: R1R2RMR4-only_EB_ATAC1


title: WJL3427_RLF_N029_JoinT

value: ATMi


title: miRNA-seq_88.P

source_name: Peritubular capillaries, biol rep 3

value: Peritubular capillaries

value: Cecal ligation & puncture (CLP) sepsis


title: R1R3RMR4-only_EB_ATAC2


title: miRNA-seq_50.P

source_name: Peritubular capillaries, biol rep 2


title: WJL3426_RLF_N029_JoinT

value: vAbl-ProB

value: pro-B cells


title: WJL3425_RLF_N029_JoinT


title: WJL3424_RLF_N029_JoinT


title: R1R2R3R4-only_EB_ATAC1

description: ATAC performed on R1R2R3R4-only CD71+ EB-derived erythroid cells, originally derived from 129/Ola mouse embryonic stem cells

value: R1R2R3R4-only CD71+ EB-derived erythroid cells, originally derived from ESC


title: WJL3445_RLF_N029_JoinT


title: R1R2R3RM-only_EB_ATAC2

description: ATAC performed on R1R2R3RM-only CD71+ EB-derived erythroid cells, originally derived from 129/Ola mouse embryonic stem cells

value: R1R2R3RM-only CD71+ EB-derived erythroid cells, originally derived from ESC


title: R1R2R3RM-only_EB_ATAC1


title: miRNA-seq_32.P

source_name: Peritubular capillaries, biol rep 1

value: Yes


title: miRNA-seq_88.G

source_name: Glomeruli, biol rep 3

value: Glomeruli


title: WJL3421_RLF_N029_JoinT

value: Polθi #2


title: miRNA-seq_92.P

source_name: Peritubular capillaries, biol rep 4


title: WJL3422_RLF_N029_JoinT


title: WJL3420_RLF_N029_JoinT


title: WJL3417_RLF_N029_JoinT


title: WJL3423_RLF_N029_JoinT


title: WJL3418_RLF_N029_JoinT


title: WJL3419_RLF_N029_JoinT


title: R1R2R4-only_ATAC2

description: ATAC performed on R1R2R4-only CD71+ EB-derived erythroid cells, originally derived from 129/Ola mouse embryonic stem cells

value: R1R2R4-only CD71+ EB-derived erythroid cells, originally derived from ESC


title: R1R2R3R4-only_EB_ATAC2


title: miRNA-seq_92.G

source_name: Glomeruli, biol rep 4


title: R1R2R4-only_ATAC1


title: WJL3416_RLF_N029_JoinT

value: Polαi #2


title: WJL3415_RLF_N029_JoinT


title: WJL3413_RLF_N029_JoinT

value: Polαi #1


title: miRNA-seq_50.G

source_name: Glomeruli, biol rep 2

value: Kidney


title: WJL3414_RLF_N029_JoinT


title: WJL3412_RLF_N029_JoinT


title: miRNA-seq_88.A

source_name: Arterioles, biol rep 3

value: Arterioles


title: WJL3411_RLF_N029_JoinT


title: R1R2R3-only_ATAC2

description: ATAC performed on R1R2R3-only CD71+ EB-derived erythroid cells, originally derived from 129/Ola mouse embryonic stem cells

value: R1R2R3-only CD71+ EB-derived erythroid cells, originally derived from ESC


title: R1R2RM-only_ATAC1

description: ATAC performed on R1R2RM-only CD71+ EB-derived erythroid cells, originally derived from 129/Ola mouse embryonic stem cells

value: R1R2RM-only CD71+ EB-derived erythroid cells, originally derived from ESC


title: WJL3410_RLF_N029_JoinT


title: R1R2R3-only_ATAC1


title: miRNA-seq_32.G

source_name: Glomeruli, biol rep 1

value: WT

value: male


title: miRNA-seq_92.A

source_name: Arterioles, biol rep 4

value: Cecal ligation & puncture (CLP) sepsis


title: WJL3409_RLF_N029_JoinT

value: vAbl-ProB


title: R1R2RM-only_ATAC2


title: miRNA-seq_32.A

source_name: Arterioles, biol rep 1


title: R1R2-only_ATAC2

description: ATAC performed on R1R2-only CD71+ EB-derived erythroid cells, originally derived from 129/Ola mouse embryonic stem cells

value: R1R2-only CD71+ EB-derived erythroid cells, originally derived from ESC


title: WJL3408_RLF_N029_JoinT

value: pro-B cells


title: WJL3406_RLF_N029_JoinT


title: miRNA-seq_46.W

source_name: Whole kidney, biol rep 4

value: No

value: Whole kidney

value: Sham-operated


title: miRNA-seq_50.A

source_name: Arterioles, biol rep 2

value: Yes


title: WJL3404_RLF_N029_JoinT


title: WJL3407_RLF_N029_JoinT


title: miRNA-seq_28.W

source_name: Whole kidney, biol rep 3


title: R2-only_EB_ATAC2

description: ATAC performed on R2-only CD71+ EB-derived erythroid cells, originally derived from 129/Ola mouse embryonic stem cells

source_name: EB derived Erythroid cells

value: R2-only CD71+ EB-derived erythroid cells, originally derived from ESC


title: R2-only_EB_ATAC1


title: WJL3401_RLF_N029_JoinT

source_name: vAbl-ProB


title: WJL3402_RLF_N029_JoinT


title: WJL3403_RLF_N029_JoinT


title: miRNA-seq_27.W

source_name: Whole kidney, biol rep 2


title: miRNA-seq_26.W

source_name: Whole kidney, biol rep 1


title: WJL3397_RLF_N029_JoinT

value: Dox


title: miRNA-seq_46.V

source_name: Post-capillary venules, biol rep 4

value: Post-capillary venules


title: WJL3399_RLF_N029_JoinT


title: WJL3396_RLF_N029_JoinT


title: R1-only_EB_ATAC2

description: ATAC performed on R1-only CD71+ EB-derived erythroid cells, originally derived from 129/Ola mouse embryonic stem cells

value: R1-only CD71+ EB-derived erythroid cells, originally derived from ESC


title: WJL3395_RLF_N029_JoinT


title: WJL3405_RLF_N029_JoinT

value: Polαi #2


title: SEKO_EB_ATAC2

description: ATAC performed on SE knockout CD71+ EB-derived erythroid cells, originally derived from 129/Ola mouse embryonic stem cells

value: SE knockout CD71+ EB-derived erythroid cells, originally derived from ESC


title: WJL3398_RLF_N029_JoinT


title: SEKO_EB_ATAC1


title: WJL3394_RLF_N029_JoinT


title: R1R2-only_ATAC1


title: WJL3393_RLF_N029_JoinT


title: miRNA-seq_27.V

source_name: Post-capillary venules, biol rep 2

value: Kidney


title: miRNA-seq_26.V

source_name: Post-capillary venules, biol rep 1

value: WT


title: WJL3390_RLF_N029_JoinT


title: WJL3392_RLF_N029_JoinT


title: WT_EB_ATAC2

description: ATAC performed on WT CD71+ EB-derived erythroid cells, originally derived from 129/Ola mouse embryonic stem cells

value: WT CD71+ EB-derived erythroid cells, originally derived from ESC


title: WJL3389_RLF_N029_JoinT


title: WT_EB_ATAC3


title: WJL3400_RLF_N029_JoinT


title: WJL3388_RLF_N029_JoinT


title: WT_EB_ATAC1


title: R1-only_EB_ATAC1


title: miRNA-seq_28.P

source_name: Peritubular capillaries, biol rep 3

value: male

value: Peritubular capillaries


title: WJL3387_RLF_N029_JoinT

value: vAbl-ProB


title: WJL3386_RLF_N029_JoinT

value: pro-B cells


title: R2-only_FL_ATAC3

description: ATAC performed on E12.5 foetal liver cells from R2-only mice derived from C57Bl8 mouse strain

source_name: Primary mouse erythroid cells (E12.5 foetal liver)

growth_protocol:
To isolate foetal liver erythroid cells, HetXHet crosses were established. Pregnant mothers were sacrificed at embryonic day 12.5. Foetuses (WT and mutant) were isolated and the foetal liver extracted. Erythroid cells were disaggregated and collected for further processing.
To isolate foetal liver erythroid cells, HetXHet crosses were established. Pregnant mothers were sacrificed at embryonic day 12.5. Foetuses (WT and mutant) were isolated and the foetal liver extracted. Erythroid cells were disaggregated and collected for further processing.

value: E12.5 foetal liver cells from R2-only


title: WJL3385_RLF_N029_JoinT


title: WJL3384_RLF_N029_JoinT


title: miRNA-seq_27.P

source_name: Peritubular capillaries, biol rep 2


title: miRNA-seq_28.V

source_name: Post-capillary venules, biol rep 3


title: R2-only_FL_ATAC2


title: WJL3382_RLF_N029_JoinT

value: ATMi


title: miRNA-seq_26.P

source_name: Peritubular capillaries, biol rep 1

value: Sham-operated


title: WJL3391_RLF_N029_JoinT


title: WJL3383_RLF_N029_JoinT


title: WJL3380_RLF_N029_JoinT

value: CTR


title: WJL3381_RLF_N029_JoinT


title: R2-only_FL_ATAC1


title: WJL3379_RLF_N029_JoinT


title: miRNA-seq_46.G

source_name: Glomeruli, biol rep 4

value: Yes

value: Glomeruli


title: WT_FL_ATAC3

description: ATAC performed on E12.5 foetal liver cells from WT C57Bl8 mouse strain

value: E12.5 foetal liver cells from WT


title: miRNA-seq_28.G

source_name: Glomeruli, biol rep 3


title: WJL3378_RLF_N029_JoinT


title: miRNA-seq_27.G

source_name: Glomeruli, biol rep 2


title: WJL3377_RLF_N029_JoinT


title: miRNA-seq_46.P

source_name: Peritubular capillaries, biol rep 4


title: WT_FL_ATAC1


title: WJL3376_RLF_N029_JoinT


title: WJL3375_RLF_N029_JoinT


title: miRNA-seq_26.G

source_name: Glomeruli, biol rep 1


title: WJL3374_RLF_N029_JoinT


title: miRNA-seq_46.A

source_name: Arterioles, biol rep 4

value: Arterioles


title: shMib2.2, scRNAseq

city: Houston

first: xinfang

last: yu

state: TX

address: one baylor plaza alkek building N720

institute: BAYLOR COLLEGE OF MEDICINE

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Count gene expression or feature barcode reads from a single sample and GEM well
Read 1: contains the 16bp barcode and the 10bp UMI. Read 2 contains the cDNA information.
Assembly: mm10
Supplementary files format and content: matrix files

source_name: Skin

extract_protocol:
Pooled fresh tumors were collected from three mice in shCtrl, shMIB2#1, and shMIB2#2 groups. Prepare enzyme mix by adding 2.35 mL of RPMI 1640, 100 µL of Enzyme D, 50 µL of Enzyme R, and 12.5 µL of Enzyme A into a gentleMACS C Tube. Cut the tumor into small pieces of 2–4 mm. Single-cell suspensions were prepared using Tumor Dissociation Kit (130-096-730, Miltenyi Biotec) by Miltenyi Biotec gentleMACS Octo Dissociator (130-096-427, Mitenyi Biotec). Resuspend sample and apply the cell suspension to a MACS SmartStrainer (70 µm) placed on a 15 mL tube. Use Red Blood Cell Lysis Solution (10×) (# 130-094-183) to remove erythrocytes or dead cells. Resuspended into single cells with 0.4% BSA for 10x genomics processing.
Library was performed according to the manufacter’s instructions (Chromium Single Cell V(D)J Reagent Kits (v1.1 Chemistry), 10x Genomics). Briefly, GEMs are generated by combining barcoded Single Cell 5’ Gel Beads, a Master Mix with cells, and Partitioning Oil on Chromium Next GEM Chip G. Immediately following GEM generation, the poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. Silane magnetic beads are used to purify the 10x Barcoded first-strand cDNA from the post GEM-RT reaction mixture, which includes leftover biochemical reagents and primers. The final libraries contain the P5 and P7 priming sites used in Illumina sequencing.

value: Skin

value: murine melanoma

tag: age

value: 6-8 weeks old


title: WJL3373_RLF_N029_JoinT

last: Wang

source_name: vAbl-ProB

tag: total reads


title: WJL3372_RLF_N029_JoinT


title: shMib2.1, scRNAseq

description: 10x Genomics


title: WJL3371_RLF_N029_JoinT


title: miRNA-seq_28.A

source_name: Arterioles, biol rep 3

value: Kidney

value: WT


title: WJL3370_RLF_N029_JoinT


title: miRNA-seq_27.A

source_name: Arterioles, biol rep 2

value: male


title: WJL3368_RLF_N029_JoinT


title: shCtrl, scRNAseq

description: 10x Genomics

value: shCtrl


title: WJL3367_RLF_N029_JoinT

value: vAbl-ProB


title: WT_FL_ATAC2


title: WJL3369_RLF_N029_JoinT

value: pro-B cells


title: miRNA-seq_26.A

source_name: Arterioles, biol rep 1


title: miRNA-seq_82.W

source_name: Whole kidney, biol rep 4

value: No

value: Whole kidney

value: Cecal ligation & puncture (CLP) sepsis


title: WJL3365_RLF_N029_JoinT

value: ATMi


title: WJL3366_RLF_N029_JoinT

value: CTR


title: shLINE_Orf1_2+LINE-1

city: La Jolla

first: Fred

middle: H

last: Gage

address: 10010 N Torrey Pines Rd

department: Laboratory of Genetics

institute: Salk Institute

data_processing:
mm10 a
Reads were first trimmed using the dynamictrim function from SolexaQA++.
Template-switch oligo (TSO) sequences were removed using cutadapt and requiring that sequences with at least 30bp were retained for downstream counting.
Trimmed reads were then aligned to the mouse genome using the rsem-calculate-expression function from RSEM.
Transcripts per million (TPM) were log2 + 1 normalized for visualization and differential expression calculations using a mixed effects model
Assembly: mm10
Supplementary files format and content: tab-delimited file for differential gene expression

source_name: Mouse neural progenitor cells

growth_protocol: mouse NPCs were maintained in the presence of FGF2 and EGF with heparin

extract_protocol:
RNAs were extracted using TRIZOL, and the quality of RNA were assessed with a TAPE station.
Libraries were prepared with SMRT-seq2 protocol

treatment_protocol: Plasmids haboring shRNAs and EGFP were neurofected, and GFP+ cells were collected using FACS sorting 3 days after the treatment

value: Mouse neural progenitor cells

value: wild type

value: shLINE_Orf1 + LINE-1


title: shLINE_Orf1_3+LINE-1


title: shLINE_Orf1_1+LINE-1


title: miRNA-seq_56.W

source_name: Whole kidney, biol rep 3


title: WJL3363_RLF_N029_JoinT


title: WJL3362_RLF_N029_JoinT


title: WJL3361_RLF_N029_JoinT


title: miRNA-seq_55.W

source_name: Whole kidney, biol rep 2


title: shLINE_MdV_I_3


title: WJL3360_RLF_N029_JoinT


title: shLINE_MdV_I_2


title: miRNA-seq_22.W

source_name: Whole kidney, biol rep 1


title: WJL3358_RLF_N029_JoinT


title: WJL3359_RLF_N029_JoinT


title: shLINE_MdV_I_1


title: miRNA-seq_82.V

source_name: Post-capillary venules, biol rep 4

value: Yes

value: Post-capillary venules


title: WJL3357_RLF_N029_JoinT


title: WJL3356_RLF_N029_JoinT


title: shLINE_Orf2_3


title: WJL3364_RLF_N029_JoinT


title: WJL3355_RLF_N029_JoinT


title: miRNA-seq_55.V

source_name: Post-capillary venules, biol rep 2


title: WJL3353_RLF_N029_JoinT


title: WJL3354_RLF_N029_JoinT


title: WJL3352_RLF_N029_JoinT


title: miRNA-seq_56.V

source_name: Post-capillary venules, biol rep 3


title: WJL3349_RLF_N029_JoinT


title: shLINE_Orf2_1


title: WJL3351_RLF_N029_JoinT


title: shLINE_Orf2_2


title: miRNA-seq_22.V

source_name: Post-capillary venules, biol rep 1


title: shLINE_Orf1_3


title: WJL3350_RLF_N029_JoinT


title: miRNA-seq_82.P

source_name: Peritubular capillaries, biol rep 4

value: Peritubular capillaries


title: shLINE_Orf1_2


title: shControl_3

value: shControl


title: WJL3346_RLF_N029_JoinT


title: WJL3345_RLF_N029_JoinT


title: miRNA-seq_56.P

source_name: Peritubular capillaries, biol rep 3

value: Kidney

value: WT


title: WJL3348_RLF_N029_JoinT


title: miRNA-seq_55.P

source_name: Peritubular capillaries, biol rep 2

value: male


title: shLINE_Orf1_1


title: WJL3344_RLF_N029_JoinT

value: vAbl-ProB


title: WJL3342_RLF_N029_JoinT

value: pro-B cells


title: WJL3341_RLF_N029_JoinT


title: miRNA-seq_22.P

source_name: Peritubular capillaries, biol rep 1


title: shControl_1


title: miRNA-seq_82.G

source_name: Glomeruli, biol rep 4

value: Glomeruli


title: shControl_2


title: miRNA-seq_56.G

source_name: Glomeruli, biol rep 3


title: WJL3330_RLF_N029_JoinT

source_name: vAbl-ProB


title: WJL3340_RLF_N029_JoinT


title: WJL3328_RLF_N029_JoinT


title: MUT 19

city: Bethesda

first: David

middle: A

last: Talmage

state: MD

address: 35 Convent Dr, Room 3B-101

department: NINDS

institute: National Institutes of Health

description:
Sequencing batch 2
LL019

data_processing:
QC inspection using FastQC, MultiQC, and Fastx_Screen
Adaptor sequences clipped, low quality and/or nucleotide biased positions in sequences were trimmed using Trimmomatic and QC was repeated
Alignment to ref. genome using HISAT2 and QC of alignment using RSeqC
Transcript assembly using StringTie, QC using gffcompare
Gene and isoform level enumeration using IsoformSwitchAnalyzeR
within sample normalization (cpm), cross-sample normalization CyclicLowess, PCA for outlier detection
Sequence batch correction using Limma, filter and floor values to 2.25
ANCOVA for differential gene expression
Genome_build: mm10
Supplementary_files_format_and_content: Gene level enumeration text file, ANCOVA adjusted expression text file

source_name: Dentate Gyrus

extract_protocol:
Rneasy Micro Kit (Qiagen)
NEBNext Library Prep Kit

value: Dentate Gyrus

value: mutant

value: Male

value: postnatal day 70


title: WJL3329_RLF_N029_JoinT


title: miRNA-seq_55.G

source_name: Glomeruli, biol rep 2

value: Cecal ligation & puncture (CLP) sepsis


title: WJL3326_RLF_N029_JoinT

value: Polθi #2


title: WJL3325_RLF_N029_JoinT


title: WJL3331_RLF_N029_JoinT

value: ATMi


title: miRNA-seq_22.G

source_name: Glomeruli, biol rep 1

value: Yes


title: MUT 15

description:
Sequencing batch 2
LL015

value: Female


title: WJL3327_RLF_N029_JoinT


title: WJL3323_RLF_N029_JoinT


title: WJL3324_RLF_N029_JoinT


title: WJL3322_RLF_N029_JoinT


title: miRNA-seq_82.A

source_name: Arterioles, biol rep 4

value: Arterioles


title: MUT 14

description:
Sequencing batch 2
LL014


title: miRNA-seq_56.A

source_name: Arterioles, biol rep 3


title: MUT 60

description:
Sequencing batch 1
LL60


title: WJL3321_RLF_N029_JoinT


title: MUT 53

description:
Sequencing batch 1
LL53


title: miRNA-seq_55.A

source_name: Arterioles, biol rep 2


title: MUT 51

description:
Sequencing batch 1
LL51


title: WJL3320_RLF_N029_JoinT

value: Polαi #2


title: WJL3319_RLF_N029_JoinT


title: WJL3318_RLF_N029_JoinT


title: WJL3317_RLF_N029_JoinT

value: Polαi #1


title: WT 13

description:
Sequencing batch 2
VV013

value: WT


title: miRNA-seq_22.A

source_name: Arterioles, biol rep 1

value: Kidney

value: male


title: WJL3314_RLF_N029_JoinT

value: vAbl-ProB

value: pro-B cells


title: WT 12

description:
Sequencing batch 2
VV012

value: Dentate Gyrus


title: WJL3316_RLF_N029_JoinT


title: miRNA-seq_76.W

source_name: Whole kidney, biol rep 4

value: No

value: Whole kidney

value: Sham-operated


title: miRNA-seq_75.W

source_name: Whole kidney, biol rep 3


title: WJL3315_RLF_N029_JoinT


title: WT 11

description:
Sequencing batch 2
VV011

value: postnatal day 70


title: WJL3312_RLF_N029_JoinT


title: miRNA-seq_17.W

source_name: Whole kidney, biol rep 1


title: miRNA-seq_19.W

source_name: Whole kidney, biol rep 2


title: WJL3313_RLF_N029_JoinT


title: WT 58

description:
Sequencing batch 1
VV58


title: WJL3311_RLF_N029_JoinT


title: WJL3308_RLF_N029_JoinT


title: miRNA-seq_76.V

source_name: Post-capillary venules, biol rep 4

value: Post-capillary venules


title: WJL3309_RLF_N029_JoinT


title: WJL3306_RLF_N029_JoinT


title: WJL3310_RLF_N029_JoinT


title: WT 55

description:
Sequencing batch 1
VV55


title: WJL3303_RLF_N029_JoinT


title: RNA-seq FL bud E10-E10.25 Hand2_del replicate 3

city: Basel

first: Aimee

last: Zuniga

address: Mattenstrasse, 28 4058

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

description: Total RNA extracted from forelimb buds of Hand2-deficient mouse (Prrx1-Cre;Hand2Δ/Δc) at E10-10.25 stage.

data_processing:
Raw single-end sequencing reads of 85bp read length from Tbx3 and Hand2 samples of mouse forelimb buds were subjected to quality check using FastQC v0.11.4 (FastQC: a quality control tool for high throughput sequence data)
High-quality sequencing reads were aligned on reference genome and transcriptome (ensembl release-91) of mouse (mm10) using a fast accurate aligner STAR v2.5.2 (Dobin A et al., 2012).
Subsequently, rsem-calculate-expression utility of RSEM v1.3.0 (Li, Bo, and Colin N. Dewey, 2011) was used to quantify expression levels of genes and transcripts across all the samples.
Genome_build: mm10
Supplementary_files_format_and_content: .txt, rsem quantifications

source_name: forelimb buds

extract_protocol:
Samples were defrosted and total RNA extracted using QIAGEN RNeasy kit according to manufactures instructions. The RNA quality was evaluated using the Fragment Analyzer in combination with the High Sensitivity RNA Analysis kit (Advanced Analytical). Only samples with a RIN ≥8.0 were used for library construction.
RNA-seq libraries were constructed using the using the Clontech SMARTer kit and 85bp single end reads were sequenced on the Illumina NextSeq 500.

treatment_protocol: For both Hand2 and Tbx3 samples, three replicates were analyzed per genotype. One replicate consists of one pair of forelimb buds, which were flash frozen in liquid nitrogen and stored at -80°C until RNA extraction.

value: Swiss albino

value: forelimb buds

tag: developmental stage


title: WJL3305_RLF_N029_JoinT


title: miRNA-seq_75.V

source_name: Post-capillary venules, biol rep 3

value: Yes


title: miRNA-seq_19.V

source_name: Post-capillary venules, biol rep 2


title: WJL3302_RLF_N029_JoinT

value: Dox


title: RNA-seq FL bud E10-E10.25 Hand2_del replicate 1


title: WJL3301_RLF_N029_JoinT


title: WJL3300_RLF_N029_JoinT