title: MUT colon basal, 123-853

description: MUT colon basal

value: whole colon


title: TKO_YT13_Rest_NE

status: Public on Feb 07 2022

type: SRA

city: Stanford

first: Julien

last: Sage

state: California

address: 265 Campus Drive

country: USA

institute: Stanford

library_source: transcriptomic

data_processing:
RNA quantification done by salmon version 0.8.2
Differential expression analysis with DESeq2 version 1.28.1
Genome_build: mm10
Supplementary_files_format_and_content: quant.sf files are tab delimited text files

molecule: polyA RNA

organism: Mus musculus

source_name: Cell lines

extract_protocol:
Cells were flash frozen on dry ice and sent to Novogene for total RNA isolation and quality control.
Library preparation and sequencing were performed by Novogene using Illumina’s sequencing platform.

tag: derived from pooled tumors from a mouse or single tumor

value: Pooled

tag: cancer type

value: Small cell lung cancer

tag: genotype

value: Rest floxed

tag: cell population

value: NE


title: B6 #5

type: RNA

first: Andy

middle: P

last: Tsai

address: 290 Jane Stanford Way E365

institute: Stanford University

description: nCounter® Neuroinflammation Panels

hyb_protocol: NanoString nCounter® Neuroinflammation Panels

data_processing: Data were processed and normalized using NanoString nSolver 4.0 analysis software

label: NanoString

molecule: total RNA

source_name: mouse cortex

extract_protocol: Total RNAs were prepared with Purelink RNA Mini Kit and subjected to NanoString analysis

tag: Sex

value: male

tag: age

value: 1 month

tag: tissue

value: brain

tag: brain region

value: cortex


title: MUT colon basal, 123-852

city: Durham

first: Leping

last: Li

state: NC

address: 111 TW Alexander Dr.

department: Biostatistics and Computational Biology

institute: NIEHS

description: MUT colon basal

data_processing:
The quality of reads was evaluated using FastQC (v0.11.5). Reads were aligned using STAR (version 020201).
The STAR index was built using mouse genome (mm10, GENCODE release vM25).
Transcript expression was quantified using the subread package (49) (version 1.6.2) to generate raw counts for 55,293 genes.
Genome_build: mm10, GENCODE release vM25
Supplementary_files_format_and_content: counts text file

extract_protocol:
RNA was extracted using RNeasy mini kit (QIAGEN) and were of sufficient quality. Single-ended (75 base pairs) sequencing was carried out in house using Illumina Nextseq to at least 30 million reads per sample.
Illumina Tru-Seq RNA
Quantification Method:  Qubit fluorometer or Bioanalyzer
Sequencing Format:  Single
Read Length:  75 nt

treatment_protocol: For the AOM model, 2-month-old Dnase1l3 WT and KO mice were injected intraperitoneally with AOM (8 mg/kg, body weight). Colon tissues were isolated 9 hours, or five days after injection. RNA was extracted from the whole colon tissue of Dnase1l3 WT and KO mice at basal condition, after one cycle of AOM/DSS, after three cycles of AOM/DSS and from final tumors from Dnase1l3 WT and KO mice after the three cycles of AOM/DSS.

value: DNase MUT

tag: treatment

value: basal condition

tag: group

value: basal control


title: TKO_YT12_Rest_nonNE

value: nonNE


title: B6 #6

description: nCounter® Neuroinflammation Panels

scan_protocol: NanoString nCounter® Neuroinflammation Panels


title: P2KO HOM #37

description: nCounter® Neuroinflammation Panels

label_protocol: NanoString nCounter® Neuroinflammation Panels


title: WT colon basal, 135-927

description: WT colon basal

value: DNase WT


title: B6 #7

description: nCounter® Neuroinflammation Panels


title: TKO_YT11_Rest_NE


title: WT colon basal, 134-920

description: WT colon basal


title: P2KO HOM #34

description: nCounter® Neuroinflammation Panels


title: BisRNA-seq_Py_S_rep2

city: shanghai

first: meng

last: liu

address: 1239,SiPing Road

country: China

institute: TongJi University

description:
Py_S_2
mRNA
m5C.Py.txt

data_processing:
Library strategy: RNA-BisSeq
Raw sequencing data were filtered to remove low-quality reads and adapter contaminations with cutadapt. Reads with average quality score >= 20 and length >=50bp were kept. Clean reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) or to the Plasmodium yoelii 17X genome (Py17x v45, obtained from PlasmoDB) using software meRanGs suit meRanGh align. Only unambiguously aligned reads were used to call m5C sites using meRanCall suit from meRanGh(40) (FDR < 0.01). Analysis of the Dhfr spike-in revealed C-T conversion around 98% (Dataset S1). Candidate cytosine positions were covered by at least 20 reads, methylated cytosine depth greater than 5 and m5C methylation level greater than 0.1. m5C sites detected in both two replicates were considered as valid m5C sites and used for further analysis.
Genome_build: Pf 3D7 v32 and Py17x v45
Supplementary_files_format_and_content: *.txt: Tab-delimited text files containing m5c level of genes at different stages in Plasmodium.

organism: Plasmodium yoelii

growth_protocol: P. falciparum parasite-infected red blood cells were cultured in T75 flask at 2% hematocrit in the presence of 5% O2 and 5% CO2 (rest N2) in RPMI 1640 supplemented with 25mM Hepes, 50mg/l Hypoxanthine, 0.21% NaHCO3, 0.5% Albumax I and 20mg/l Gentamicin; P. yoelii parasite-infected ICR mice (female, 5 to 6 weeks old) were housed in the Animal Care Center of Xiamen University and kept at room temperature under a 12 h light/dark cycle at a constant relative humidity of 45%.

extract_protocol:
The parasite pellets were washed twice with precooling 1 X PBS and then resuspended in 1 mL TRIzol (Invitrogen). Total RNA was extracted using the Direct-zol RNA Kit (Zymo Research) according to the manufacturer’s instructions. mRNA enrichment from the total RNA was performed using the Dynabeads™ mRNA Purification Kit (invitrogen) as per the manufacturer’s instructions.
RNA bisulfite treatment and purification of converted RNA was performed using the Methylamp™ RNA Bisulfite Conversion Kit (Epigentek Group Inc.) according to the manufacturer’s instructions. One ug mRNAs along with 5 ng Dhfr RNA (1:2000) as methylation conversion control were used and as input RNA. The converted RNA was subsequently used for fragmentation and library construction using the KAPA Stranded mRNA-Seq Kit (KAPA) according to the instructions provided by the manufacturer.

treatment_protocol: Phenylhydrazine (80 μg/g mouse body weight) was used to treat with the ICR mouse through intraperitoneal injection; For P. falciparum, 50 mM N-acetyl-D-glucosamine was added to the cultures for three consecutive days to kill the asexual-stage parasites after sexual commitment. P. falciparum schizont-stage parasite cultures were synchronized by repeated sorbitol and percoll-sorbitol treatments ((Lambros and Vanderberg, 1979).

tag: strain

value: Py 17xnl

value: Wild type

tag: host

value: Mouse

tag: developmental stage

value: Schizont

value: Whole body


title: BisRNA-seq_Py_S_rep1

description:
Py_S_1
mRNA
m5C.Py.txt


title: WT colon AOM/DSS early, 115-805

description: WT colon AOM/DSS early

value: whole colon

value: one cycle of AOM/DSS

value: early stage of AOM/DSS with 5 days recovery


title: TKO_YT18_Rest_nonNE

value: Single

value: Small cell lung cancer

value: Rest floxed


title: TKO_YT10_WT_nonNE

value: Wildtype


title: WT colon basal, 134-918

description: WT colon basal


title: MUT colon basal, 134-915

description: MUT colon basal

value: DNase MUT


title: P2KO HOM #47

description: nCounter® Neuroinflammation Panels

value: male

value: 1 month

value: brain

value: cortex


title: BisRNA-seq_Py_S-KO_rep2

description:
Py_S-KO_2
mRNA
m5C.Py.txt

value: Py 17xnl

value: PyNsun2 KO


title: Single Cell Chip A

first: Michelle

last: Monje

state: CA

address: 265 campus drive, SIM1 G3035

department: Neurology

data_processing:
Raw sequencing data were processed using the Cell Ranger software version 6.0.0 or higher (10X Genomics). Sequencer's base call files (BCLs) were demultiplexed into FASTQ files using the cellranger mkfastq pipeline. To optimize CAR sequence detection in the scRNA-seq data, we probed the FASTQ files using SeqKit38 in 50-basepair segments from the GD2 CAR plasmid sequence. Once we identified the segments with the most hits, we created a custom reference by appending these segments to the GRCh38 5.0.0 human genome reference with the cellranger mkref pipeline. FASTQ files were aligned to this custom reference using the cellranger count pipeline.
Unique molecular identifier (UMI) count matrices from Cell Ranger were analyzed using Seurat39. Dead cells and cell debris with >15% of UMI counts mapping to mitochondrial genes or <300 genes detected were excluded from the analysis. Cell doublets containing >10,000 genes or >50,000 UMI counts were also excluded. Next, scRNA-seq data were subsampled to 5,000 cells per sample, and all data were normalized together to the sequencing depth using the SCTransform pipeline40. Data between patients were integrated using reciprocal principal component analysis (RPCA). PCA was performed using all variable genes with the exception of TCR and BCR genes to prevent clonotypes from driving the final layout. In addition, a set of curated genes relevant to T-cell function or cell type identification were included into the list of variable genes. UMAP embedding was performed using the first 50 principal components. Cell types were assigned to all cells based on canonical lineage marker expression. Cell type doublets (so-called “lineage doublets”) were identified as cells expressing markers of more than one lineage: T cells (CD2, CD3E, CD3D, CD3G, CD247, CD7, GD2 CAR), B cells (CD19, CD22, PAX5), microglia/myeloid cells (CD14, CD68, CD163, CSF1R, AIF1), or astrocytes (GFAP). Differential expression analysis was performed on SCT counts modeled as a negative binomial distribution using the FindMarkers pipeline.
Genome_build: GRCh38 5.0.0
Supplementary_files_format_and_content: processed data files include a matrix.mtx, barcodes.tsv and genes.tsv needed for downstream analysis of the 10X data.

organism: Homo sapiens

source_name: Single Cell Chip A

extract_protocol: Reverse transcription inside GEMs was performed using a C1000 Touch Thermal Cycler (Bio-Rad). Barcoded complementary DNA (cDNA) was recovered through post-GEM-RT cleanup and PCR amplification. Recovered cDNA was amplified and used to construct 5’ whole transcriptome libraries. Quality of cDNA and each library was assessed using Agilent 2100 Bioanalyzer. The libraries were indexed using a Chromium i7 Sample Index Kit, pooled, and sequenced on NovaSeq 6000 System (Illumina) by Novogene.

treatment_protocol: Single-cell RNA-sequencing (scRNA-seq) was performed using 5’ v2 Single Cell Immune Profiling technology (10X Genomics) according to the manufacturer’s protocol. Briefly, cells from CSF samples collected at indicated time points before and after CAR T-cell administration, as well as sorted CAR+ and CAR- cells from the CAR T-cell infusion products, were counted, resuspended to 700-1,200 cells/µL, and captured using Single Cell Chip A on the 10x Chromium Controller (10X Genomics) to generate Gel Bead-In Emulsions (GEMs).

tag: disease

value: CSF


title: BisRNA-seq_Py_S-KO_rep1

description:
Py_S-KO_1
mRNA
m5C.Py.txt

value: Mouse

value: Schizont


title: WT colon basal, 123-851

description: WT colon basal

value: DNase WT

value: whole colon

value: basal condition

value: basal control


title: PRPF39 size-matched input, rep2

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Raw reads were processed using the eCLIP pipeline v0.7.0
Sequenced reads were reformatted to include randomers in read headers with umi_tools (1.0.0). Args: --random-seed 1 --bc-pattern NNNNNNNNNN
Reads were then trimmed with cutadapt (1.14). Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -a InvRNA1/Ril19.fasta (fasta sequences can be found at: https://github.com/YeoLab/eclip/tree/master/example/inputs/)
Reads were then trimmed again with cutadapt (1.14) to remove double-ligation events. Args: --match-read-wildcards -O 5 --times 1 -e 0.1 --quality-cutoff 6 -m 18  -a InvRNA1/Ril19.fasta (fasta sequences can be found at: https://github.com/YeoLab/eclip/tree/master/example/inputs/)
Trimmed and filtered reads were then mapped with STAR (2.7.6a) against a repeat element database (RepBase 18.05). Args: --runThreadN 16 \  --genomeDir human_repbase \  --readFilesIn path/to/read1 \  --outFileNamePrefix out_prefix \  --outReadsUnmapped Fastx \  --outSAMtype BAM Unsorted \  --outSAMattributes All \  --outSAMunmapped Within \  --outSAMattrRGline ID:foo \  --outFilterType BySJout \  --outFilterMultimapNmax 30 \  --outFilterMultimapScoreRange 1 \  --outFilterScoreMin 10 \  --alignEndsType EndToEnd
Unmapped reads filtered of repeat elements were then mapped with STAR (2.7.6a) against a human genome (GRCh38). Args: --runThreadN 16 \  --genomeDir genomedir \  --readFilesIn /path/to/read1 \  --outFileNamePrefix out_prefix \  --outReadsUnmapped Fastx \  --outSAMtype BAM   Unsorted \  --outSAMattributes All \  --outSAMunmapped Within \  --outSAMattrRGline ID:foo \  --outFilterType BySJout \  --outFilterMultimapNmax 1 \  --outFilterMultimapScoreRange 1 \  --outFilterScoreMin 10 \  --alignEndsType EndToEnd
Aligned reads were sorted with samtools (1.6)
Sorted reads were collapsed with umi_tools (1.0.0). Args: --random-seed 1 --method unique
BAM files were used to identify peak clusters with Clipper (1.2.2). Args: --species GRCh38_v29e --bam path/to/input.bam --timeout 3600000 --maxgenes 1000000 --save-pickle --outfile path/to/output.bam
Peak clusters were normalized using BAM files for IP against BAM files for INPUT with overlap_peakfi_with_bam.pl, included in eclip 0.1.5+.
Overlapping normalized peak regions were merged with compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat.pl, included within eclip-0.1.5+
Normalized peaks were filtered using a manually curated list blacklist file containing known artifacts/regions of nonspecific binding
Filtered peak files were ranked by entropy score (make_informationcontent_from_peaks.pl included within the merge_peaks pipeline) and used as inputs to IDR (2.0.2) to determine reproducible peaks.
Genome_build: GRCh38
Supplementary_files_format_and_content: BigWig files contain RPM-normalized read densities

growth_protocol: HepG2 cells were thawed and maintained in DMEM supplemented with 10% FBS at 37deg C with 5% CO2. Cells were maintained at 50-75% confluency and split 1:8-1:16

extract_protocol:
HepG2 replicates were treated with 400mJ of UV using the CL-1000 UV Crosslinker, harvested in ice cold PBS and pelleted by centrifugation. Cell pellets were flash frozen in liquid nitrogen and stored in -80 degrees until ready to IP with PRPF39 bound Dynabeads. Subsequent protocol was followed exactly as detailed in Blue et al 2021. Sequencing was performed on Illumina Novaseq 6000 single-end reads and data processed through Dr. Yeo's seCLIP pipeline.
Libraries were constructed as per the (s)eCLIP protocol using Illumina 50x forward and 70x reverse primers.
seCLIP

treatment_protocol: PBS washed HepG2 cells were crosslinked(254 nm; 400 mJ/cm2) and processed through the eCLIP protocol as previously described (van Nostrand et al, 2016). PRPF39 antibody employed for immunoprecipitation was Thermo Fisher Sceintific, PA5-21627

tag: antibody catalog

tag: antibody lot

tag: antibody manufacturer

value: Thermo Fisher Scientific

tag: antibody

value: polyclonal, IgG, affinity purified

tag: rnase i fragmentation condition

value: 10 ul 1:25 RNase I @ 37deg C for 5 minutes

tag: inline barcode1


title: TKO_YT8_WT_nonNE

tag: derived from pooled tumors from a mouse or single tumor

value: Single

tag: cancer type

value: Small cell lung cancer

tag: genotype

value: Wildtype

tag: cell population

value: nonNE


title: BisRNA-seq_Py_G_rep2

description:
Py_G_2
mRNA
m5C.Py.txt

value: Wild type

value: Gametocyte

tag: tissue

value: Whole body


title: TKO_YT9_WT_NE

value: NE


title: CD45 population - Dnase1l3 KO

description: CD45+ SingleCell Dnase1l3 KO

data_processing:
Raw sequencing data were demultiplexed, aligned, and counted with Cell Ranger pipelines (10X genomics). First, we used cellranger mkfastq command to generate FASTQ files. Then, we extracted expression data at a single-cell resolution using cellranger command count. Lastly, we used cellranger aggr to combine sequencing data from multiple libraries with mapped sequencing depth. We obtained four expression files for cDC and CD45+ populations isolated from Dnase1l3 KO and WT mice.
Genome_build: mm10
Supplementary_files_format_and_content: counts text files

source_name: KO CD45

extract_protocol:
Tumor associated DCs were isolated and enriched as described above. Cell surface antigens were stained with following fluorochrome-conjugated Abs together with eFluor780-conjugated Live/Dead dye (ThermoFisher Scientific). Alexa Fluor 488-anti-mouse CD3e (145-2C11, BL 100321; 2.5 µg/mL), PerCP-Cy5.5-anti-mouse CD11c (N418, eBio 45-0114-82; 1 µg/mL), Alexa Fluor 488-anti-mouse CD19 (6D5, BL 115521; 2.5 µg/mL), APC-anti-mouse CD26 (H194-112, BL 137807;  1 µg/mL), eFluor450-anti-mouse MHC class-II I-Ab (AF6-120.1, eBio 48-5320-82; 1 µg/mL), BV510-anti-mouse Ly-6G (1A8, BL 127633; 1 µg/mL), BV711-anti-mouse CD45.2 (104, BL 109847; 1 µg/mL), PE-anti-mouse CD88 (20/70, BL 135806; 0.5 µg/mL), PE-Dazzle594-anti-mouse F4/80 (BM8, BL 123146; 1 µg/mL). Among stained cells, conventional DCs (CD11c+ CD26+ CD45.2+ CD88– I-A+ Ly-6G– Live/Dead–) were purified using a cell sorter FACS ARIA-II (BD Biosciences). The cells were counted and examined for viability using a TC-20 cell counter (Bio-Rad). 8000-9900 live cells at 2×105 cells/mL concentration with 70% or higher viability were loaded into the Single Cell Chip followed by forming single cell emulsion in Chromium Controller (10x Genomics). The cDNA for antibody derived transcripts (ADT) and gene derived transcripts was generated and amplified according to manufacturer’s instructions (10x Genomics and BioLegend).
The Gene Expression library and the ADT Library were prepared using the Chromium single cell 3′ v2 library and gel bead kit v2 (10x Genomics) and additional reagents recommended in the protocol of Total A-seq (BioLegend). The two libraries were mixed at 10:1 molar ratio (Gene Expression library to ADT library)
Quantification Method:  NextSeq 500 (Illumina) with paired-end sequencing (Read 1: 30; Read 2: 100). The data were processed using RTA version 2.4.11. A total of 2.1-2.4×108 reads were obtained for the four samples.
Sequencing Format:  Paired

treatment_protocol: For the MC38 cancer cell allograft model, we performed analysis at two time points – early and late. For the late time point experiment, 8- to 12-week-old female Dnase1l3 WT and KO mice were injected subcutaneously with 1 x 10^5 MC38 cells into each flank. Mice were monitored twice weekly for 21 days. Tumor length and width were measured by caliper, and tumor volume was calculated using the formula V=length*width2/2. Mice were sacrificed at day 21 after the injection of the tumor cells or when their total tumor volume reached the volume of 2,000 mm3. For the early time point, 8- to 12-week-old female WT and KO mice were the injected subcutaneously with 5 x 10^5 MC38 cells into the back. Mice were monitored twice weekly for tumor growth and health status. Mice were sacrificed at day 8 for the analysis of the immune cell populations in tumors and tumor draining lymph nodes.

value: DNase1l3 KO

tag: cell type


title: BisRNA-seq_Py_G_rep1

description:
Py_G_1
mRNA
m5C.Py.txt

value: Py 17xnl

value: Mouse


title: PRPF39 clip, rep2


title: Half-life_Py_G_5h_Rep2

description:
mRNA
Halflife.Py.txt

data_processing:
Raw sequencing data were filtered to remove low-quality reads and adapter contaminations with cutadapt (v1.18). Reads with average quality score >= 20 and length >=50bp were kept. Clean reads were mapped to the Plasmodium yoelii 17X genome (Py17x v45, obtained from PlasmoDB) with ERCC spike in sequence using hisat2 (v2.1.0) with strand specific mode (--rna-strandness RF). Uniquely mapped reads were used to calculate read count for each transcript using software featureCounts. To remove low abundance transcripts, transcripts with at least 5 read counts at 0h were kept for downstream half-life analysis. The read count of each transcript in a time point is normalized with the sum of reads mapping to all spike-in transcripts. Half-lives of transcripts were calculated using R package MINPACK(53).
Genome_build: Py17x v45
Supplementary_files_format_and_content: Halflife.Py.txt: Tab-delimited text file containing half-lives of genes in P. yoelii.

growth_protocol: P. yoelii parasite-infected ICR mice (female, 5 to 6 weeks old) were housed in the Animal Care Center of Xiamen University and kept at room temperature under a 12 h light/dark cycle at a constant relative humidity of 45%.

extract_protocol:
The total RNA was extracted by Direct-zol RNA Kit (Zymo Research) as per the manufacturer’s instructions.
Before construction of the library with KAPA Stranded mRNA-Seq Kit Illumina platform (KK8421), ERCC RNA Spike-In Control Mixes (ambion) was added proportional to total RNA of each sample (0.1 µL per sample).

treatment_protocol: ICR mice blood with 4%-6% gametocytemia was gained in anticoagulant tubes with heparin and immediately added to gametocyte culture medium (RPMI 1640 medium) in a blood/medium volume ratio of 1:10. Then actinomycin D (Sigma-Aldrich) was added at 20 μg/ml, and samples were collected 0, 1, 3, and 5 hour later.

tag: time point


title: PRPF39 size-matched input, rep1


title: TKO_YT6_WT_NE


title: CD45 population - Dnase1l3 WT

description: CD45+ SingleCell Dnase1l3 Wildtype

source_name: WT CD45

value: DNase1l3 Wildtype

value: whole colon


title: Half-life_Py_G_5h_Rep1

description:
mRNA
Halflife.Py.txt

tag: strain


title: DC population - Dnase1l3 WT

description: DC SingleCell Dnase1l3 Wildtype

source_name: WT DC

value: DC


title: YT_KD12_shAscl1_no2

source_name: Cell line

extract_protocol:
RNA was isolated using Allprep DNA/RNA microkit (Qiagen 80204).
Library preparation and sequencing were performed by Novogene using Illumina’s sequencing platform.

tag: cell line

tag: disease state

tag: treatment

value: Ascl1 knockdown

tag: bioreplicate


title: TKO_YT7_WT_nonNE


title: TKO_YT5_WT_nonNE

value: Pooled


title: Half-life_Py_G_3h_Rep2

description:
mRNA
Halflife.Py.txt

tag: host

tag: developmental stage


title: SMS-CTR SIX1 KD6 rep 2

city: Aurora

first: Heide

middle: L

last: Ford

state: CO

address: 12800 East 19th Ave Rm 6401I

department: Pharmacology

institute: University of Colorado Anschutz Medical Campus

data_processing:
Read QC was performed using FastQC and reads trimmed by BBDuk
Reads were aligned to the hg38 reference genome and counted by STAR
Differential gene analysis performed using edgeR
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: SMS-CTR

extract_protocol:
Total RNA was isolated from SMS-CTR cells using the Zymo Direct-zol RNA Miniprep Kit and RNA integrity confirmed using TapeStation analysis
RNA libraries were prepared for sequencing using the Nugen Universal Plus mRNA-seq library prep kit

value: Fusion Negative Rhabdomyosarcoma

value: SIX1 KD

value: SMS-CTR


title: SMS-CTR SIX1 KD6 rep 1


title: YT_KD11_shAscl1_no1

value: Small cell lung cancer


title: TKO_YT4_WT_nonNE

value: Wildtype

value: nonNE


title: Half-life_Py_G_3h_Rep1

description:
mRNA
Halflife.Py.txt

value: Wild type

value: Gametocyte


title: YT_KD10_shGFP

value: shGFP

value: control


title: SMS-CTR SIX1 KD5 rep 2


title: Half-life_Py_G_1h_Rep2

description:
mRNA
Halflife.Py.txt

value: Py 17xnl

value: Whole body


title: YT_KD9_shAscl1_no2


title: Half-life_Py_G_1h_Rep1

description:
mRNA
Halflife.Py.txt

value: Mouse


title: SMS-CTR SIX1 KD5 rep 1


title: TKO_YT1_WT_NE

value: NE


title: PRPF39 clip, rep1

tag: antibody catalog

tag: antibody lot

tag: antibody manufacturer

value: Thermo Fisher Scientific

tag: antibody

value: polyclonal, IgG, affinity purified

value: 10 ul 1:25 RNase I @ 37deg C for 5 minutes


title: YT_12_Hes1neg

source_name: tumors

extract_protocol:
RNA was isolated using Allprep DNA/RNA microkit (Qiagen 80284).
Libraries were prepared using TRIO RNA-seq kit (Nugen 0507-32) according to manufacturer's protocol.

tag: mouse number

tag: cancer type

tag: hes1-gfp status

value: negative

value: tumor


title: YT_KD8_shAscl1_no1

tag: genotype

value: Ascl1 knockdown


title: Half-life_Py_G_0h_Rep2

description:
mRNA
Halflife.Py.txt

tag: tissue


title: SMS-CTR SCRAMBLE rep 4

tag: cell type

value: Fusion Negative Rhabdomyosarcoma

value: SMS-CTR


title: DC population - Dnase1l3 KO

description: DC SingleCell Dnase1l3 KO

source_name: KO DC

value: DNase1l3 KO

value: whole colon

value: DC


title: Half-life_Py_G_0h_Rep1

description:
mRNA
Halflife.Py.txt

tag: strain

value: Wild type

value: Gametocyte

tag: time point


title: YT_KD7_shGFP

tag: cell line

tag: disease state

value: Small cell lung cancer

value: shGFP

value: control


title: YT_11_Hes1pos

value: positive


title: SMS-CTR SIX1 KD5 rep 3

value: SIX1 KD


title: SMS-CTR SCRAMBLE rep 3


title: YT_10_Hes1neg

value: LJS NT


title: YT_KD6_shAscl1_no2

tag: treatment

tag: bioreplicate


title: TKO_YT3_WT_NE

tag: derived from pooled tumors from a mouse or single tumor

value: Pooled

value: Wildtype

tag: cell population

value: NE


title: TKO_YT2_WT_nonNE

value: nonNE


title: SMS-CTR SCRAMBLE rep 2

value: Fusion Negative Rhabdomyosarcoma


title: RNA-seq_Py_S_rep2

description:
Py_S_2
mRNA
Fpkm.Py.txt

data_processing:
Low-quality and adaptor sequences were trimmed using cutadapt (v1.18)(42) with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20,20. RNA sequencing reads were aligned using hisat2 (v2.1.0)(43) with strand specific mode (--rna-strandness RF) to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) or to the Plasmodium yoelii 17X genome (Py17x v45, obtained from PlasmoDB). Mapped reads were subsequently assembled into transcripts guided by the PlasmoDB gff annotation files (Pf3D7 v32/ Py17x v45) using featureCounts (v1.6.1)(44) with parameters: -M -p -B -C -s 2. Read counts were obtained using featureCounts (v1.6.1).
Genome_build: Pf 3D7 v32 and Py17x v45
Supplementary_files_format_and_content: *.txt: Tab-delimited text files for gene expression.

extract_protocol:
Parasites were harvested and total RNA was isolated using TRIzol (Life) according to the manufacturer’s manual and further purified using the Direct-zol RNA Kit (ZYMO RESEARCH) for removal of gDNA. Residual gDNA was digested with TURBO DNA-freeTM DNaseI (Ambion) and the RNA was quantified by NanoDrop.
The poly(A) RNA isolation, mRNA enrichment and library construction were performed as described using 15 cycles of library amplification. The mRNA was enriched by poly(A) selection with the KAPA mRNA Capture Beads (KAPA), and fragmented to about 300–400 nucleotides (nt) in length, then all subsequent steps were performed in accordance with an KAPA Stranded mRNA-Seq Kit Illumina platform (KAPABIOSYSTEMS KK8421-96 libraries).

treatment_protocol: Phenylhydrazine (80 μg/g mouse body weight) was used to treat with the ICR mouse through intraperitoneal injection; For P. falciparum, 50 mM N-acetyl-D-glucosamine was added to the cultures for three consecutive days to kill the asexual-stage parasites after sexual commitment. P. falciparum schizont-stage parasite cultures were synchronized by repeated sorbitol and percoll-sorbitol treatments (Lambros and Vanderberg, 1979).

value: Py 17xnl

tag: host

value: Mouse

tag: developmental stage

value: Schizont

value: Whole body


title: YT_9_Hes1pos

value: tumor


title: Tbx5G125R_Right_Atrium_2

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

description: Tbx5G125R_Whole tissue_RNA_RA_DE.xlsx

data_processing:
Reads were mapped to mm10 build of the mouse transcriptome using STAR (Dobin et al. 2013).
Differential expression analysis was performed using the DESeq2 package based on a model using the negative binomial distribution (Love, Huber, and Anders 2014).
Genome_build: mm10
Supplementary_files_format_and_content: G125R-whole-tissue-atrial-RNA-seq-counts.xlsx (Excel file with normalized (DESeq2) count data per gene & differential expression analysis).

source_name: right atrium whole tissue

growth_protocol: Murine atrial tissue was obtained between 8-12 weeks of age

extract_protocol:
RNA was extracted using ReliaPrep RNA Tissue Miniprep System (Promega)
Truseq RNA library Prep Kit v2 (Part# 15031048 Rev.E, Illumina) input 300ng

treatment_protocol: Atrial tissue was

tag: Sex

value: Female

tag: age

value: 8-12 week

value: Right atrium


title: SMS-CTR SCRAMBLE rep 1

value: control

value: SMS-CTR


title: YT_KD5_shAscl1_no1

value: Small cell lung cancer

value: Ascl1 knockdown


title: YT_6_Hes1neg

tag: mouse number

tag: cancer type

value: negative


title: YT_KD4_shGFP

value: shGFP

tag: genotype


title: RNA-seq_Py_S_rep1

description:
Py_S_1
mRNA
Fpkm.Py.txt

value: Wild type

tag: tissue


title: RNA-seq_Py_S_KO_rep2

description:
Py_S_KO_2
mRNA
Fpkm.Py.txt

value: PyNsun2 KO


title: HCT116 KIF-si rep2

city: Hangzhou

first: Wei

last: Zhuo

state: Zhejiang

address: 866 Yuhangtang Road

department: School of Medicine

institute: Zhejiang University

description: Gene expression after transfection with  siRNA targeting KIF26B for 48 h

data_processing:
Clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: HCT116 cells transfected with siRNA  targeting KIF26B for 48 h

growth_protocol: HCT116 CRC cell line was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA), and cultured in Maccoy 5A (Genom, China) with 10 % fetal bovine serum.

extract_protocol:
Total RNA was extracted from each cell sample using the Trizol  method
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HCT116 colorectal cancer cells were transfected with siRNA control or siRNAs targeting KIF26B for 48h.

value: colorectal cancer


title: YT_5_Hes1pos

tag: hes1-gfp status

value: positive


title: YT_KD3_shAscl1_no2


title: HCT116 KIF-si rep1

source_name: HCT116 cells transfected with siRNA targeting KIF26B for 48 h


title: YT_2_Hes1neg


title: RNA-seq_Py_S_KO_rep1

description:
Py_S_KO_1
mRNA
Fpkm.Py.txt

tag: strain

value: Py 17xnl

value: Mouse


title: RNA-seq_Py_G_rep2

description:
Py_G_2
mRNA
Fpkm.Py.txt

value: Gametocyte

value: Whole body


title: YT_KD2_shAscl1_no1


title: HCT116 NC rep2

description: Gene expression after transfection with  siRNA control for 48 h

source_name: HCT116 cells transfected with siRNA control for 48 h


title: YT_1_Hes1pos

value: tumor


title: YT_KD1_shGFP


title: RNA-seq_Py_G_rep1

description:
Py_G_1
mRNA
Fpkm.Py.txt


title: Fresh5

status: Public on Feb 06 2022

city: Washington

first: Jiaxiang

last: Tao

state: DC

address: 3970 Reservoir Road NW

department: Oncology

institute: Georgetown University

data_processing:
Illumnia's bcll2fastq/2.20.0 was used to generate Fastq files. Default parameters were used.
Reads were processed using the nf-core RNA-seq v1.4.2 bioinformatics pipeline (https://nf-co.re/rnaseq/1.4.2). (Mapped with mm10 genome and annotated with GENCODE M23)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Mouse MuSCs

growth_protocol: FACS-sorted MuSCs werecultrued on the Matrigel-fibronactin-coated plastic-bottom plate, with growth media 1% PS, 0.01% of Fungin, Plasmocin, 0.1% of chicken embryo extract, 10 ng/mL FGF, 5% of HS and 20% of FBS in DMEM.

extract_protocol:
TriZol was directly added to the cell culture, after removing the media and compression pillar (for the compressed samples)
Libraries were prepared according to Illumina's instructions. Purified RNA samples were reverse-transcribed to cDNA and amplified using SMART-seq v4 Ultra Low Input Kit for Sequencing.

treatment_protocol: Compression pillar was appplied to the cell culture 2 days post-culturing (for the compressed cells). Others were untreated

tag: cell type

value: FACS-sorted MuSCs from Pax7-ZsGreen mice's hindlimb

value: Freshly isolated


title: Fresh4


title: 2dU3

value: 2-day culturing, uncompressed


title: 2dU2


title: Control6

value: 5-day culturing, uncompressed


title: Fresh1


title: 2dU1


title: Compressed4

value: 2-day culturing, uncompressed+3-day culturing under compression


title: Compressed5


title: Compressed10


title: Control2


title: Control1


title: SmoKO

city: Los Angeles

first: Maxwell

last: Serowoky

address: 1425 San Pablo St.

department: Stem Cell

institute: USC

data_processing:
Reads were aligned to mm10 genome using 10x Genomics’ Cell Ranger v3.0.2 pipeline and default parameters. Cell Ranger outputs (barcodes, features, matrix) were used for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes contains cellular barcodes list
Supplementary_files_format_and_content: features contains features list (genes)
Supplementary_files_format_and_content: matrix contains count matrix

source_name: Rib repair callus

extract_protocol:
Repair calluses were dissected from control (Sox9:CreER;Smoflox/+) and Sox9:CreER;Smoflox/flox mice at 4 dpi. Care was taken to excise repair callus leaving the majority of adjacent skeletal muscle behind. Calluses were digested at 37C for 60 minutes on a shaker at 50 rpm in digest buffer (3 mg/mL Collagenase II (Worthington: LS004176), 1 U/mL Dispase (Corning: #354235), in EM (STEMCELL Technologies: #36453)). Cells were then filtered through 40 micron filter tips (Sigma: BAH136800040), spun at 300g for 5 min, and resuspended for dead cell removal using the Dead Cell Removal Kit (Miltenyi Biotec: #130-090-101). Cells were then resuspended in 1xPBS for loading into the 10x Chromium platform. Six calluses were dissected, digested, and pooled by genotype (3 animals for each genotype) for generation of single-cell libraries. Libraries were sequenced on an Illumina NextSeq machine.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: reparative skeletal

tag: treatment/timepoint

value: 4 days after large-scale rib resection injury


title: CTCF(Δ5|6:6|7) MN dual positive rep1

city: New York

first: Danny

last: Reinberg

state: New York

address: 522 First Avenue, 2nd floor, Room 211

department: Biochemistry

institute: New York University School of Medicine

description:
Hoxa5-P2A-mCherry/Hoxa7-P2A-eGFP reporter_sorted
E11_screens.count.txt

library_source: genomic

data_processing:
Overall processing by using MaGeCK tools (Li et al., 2014 and Li et al., 2015)
Alignment to CRISPR library and counts were obtained by using "count" function within the MaGeCK tools
Relevant comparisons were made by using "test" function within the MaGeCK tools
Supplementary_files_format_and_content: Count files in "txt" format

molecule: genomic DNA

source_name: Motor neurons

growth_protocol: ESCs were cultured in standard medium supplemented with LIF and 2i conditions (1 mM MEK1/2 inhibitor (PD0325901, Stemgent) and 3 mM GSK3 inhibitor (CHIR99021, Stemgent)). For motor neuron (MN) differentiation, the previously described protocol in Narendra et. al. (2015) was applied. Briefly, ESCs were differentiated into embryoid bodies in 2 days, and further patterning was induced with addition of 1 μM all-trans-retinoic acid (RA, Sigma) and 0.5 μM smoothened agonist (SAG, Calbiochem).

extract_protocol:
Cells were harvested, and genomic DNA was isolated as described before (Sanjana et al., 2014 and Shalem et al., 2014).
CRISPR libraries were prepared at each time point, and/or sorted population according to previously described protocol mainly consisting of two-step PCRs (Sanjana et al., 2014 and Shalem et al., 2014)
CRISPR knock-out

value: ESC-derived cervical motor neurons

value: CRISPR custom library expressing


title: CTCF(Δ5|6:6|7) MN dual positive rep2


title: CTCF(Δ5|6:6|7) MN mcherry positive rep2


title: Control


title: CTCF(Δ5|6:6|7) MN mcherry positive rep1


title: WT E14 MN mcherry positive rep1

description:
Hoxa5-P2A-mCherry/Hoxa7-P2A-eGFP reporter_sorted
1G5_screens.count.txt


title: WT E14 MN libB dual positive rep2

description:
Hoxa5-P2A-mCherry/Hoxa7-P2A-eGFP reporter
libB_sc2_counts.txt

value: GeCKO v2 library B expressing


title: HCT116 NC rep1

value: colorectal cancer

tag: cell line


title: WT E14 MN dual positive rep1


title: WT E14 MN libA dual positive rep2

description:
Hoxa5-P2A-mCherry/Hoxa7-P2A-eGFP reporter
libA_sc2_counts.txt

value: GeCKO v2 library A expressing


title: WT E14 MN libB mcherry positive rep2


title: WT E14 MN libB dual positive rep1

description:
Hoxa5-P2A-mCherry/Hoxa7-P2A-eGFP reporter
libB_sc1_counts.txt


title: WT E14 MN libA mcherry positive rep2


title: PK-15 cell line (WT)  rep3

city: changchun

first: Hongming

last: Yuan

state: Jilin province

address: Lvyuan road

institute: Jilin University

data_processing:
The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina platform and 150 bp paired-end reads were generated.
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Different expression genes and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were analyzed by iDEP (http://bioinformatics.sdstate.edu/idep/)
Genome_build: susScr11

organism: Sus scrofa

source_name: cell line

extract_protocol:
RNA purity was checked using the kaiaoK5500®Spectrophotometer (Kaiao, Beijing, China). RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina platform and 150 bp paired-end reads were generated.

value: wild type


title: WT E14 MN libB mcherry positive rep1


title: PK-15 cell line (WT)  rep1


title: PK-15 cell line (WT)  rep2


title: PK-15 cell line ZC3H11A-/- rep3


title: 1702-0235-L

city: Jeonju

first: Devender

last: Arora

address: 1500, Kongjwipatjwi-Ro, Iseo-Myeon, Wanju-gun

country: South Korea

institute: NIAS

data_processing:
For WGS data the sequence reads were first checked for quality and and alignment were subjected to the filtration of duplicate reads using SAMtools subsequently mapped against sus scrofa11.1 using BWA. Subsequently, we followed GATK best practice analysis for post data interpertation. SNPs were separated using variant calling and subsequently various filter parameter were applied. The VCF file later imputed using Beagle and phased data is presented.
For RNAseq data Sequence reads were first checked for quality and trimmed using trimmoatic tool and all quality-filtered PE reads were aligned to the Sscrofa genome (Sscrofa11.1) retrieved from the University of California Santa Cruz (UCSC) browser using Hisat2 . Later Bam were used as input with reference GTF file in subread package featureCounts and count data was generated.
Genome_build: sscrofa11.1
Supplementary_files_format_and_content: E_chr.vcf.gz and L_chr.vcf.gz (WGS samples)
Supplementary_files_format_and_content: blood_ETvsL.txt (RNA-seq samples)

source_name: Blood

extract_protocol:
Total DNA from minipig blood sample was subjected to whole genome sequencing using the Illumina Paired-end sequencing on an Illumina platform.
Blood sample taken from post-harvest minipig (N=4) similarly RNAseq data was generated for minipig (N=4) pair-end data after isolation blood samples  using TRIzol (Invitrogen) and a RNeasy RNA Purification Kit with DNase treatment (Qiagen), according to the instruction manual.  One microliter of cleaned total RNA was consumed to check RNA quality using BioAnalyzer 2011 with an RNA chip (RIN > 7 and 28S:18S ratio > 1.0). The library was constructed with random cDNA fragments and acquired adapter-fragments of the cDNA using the TruSeq Stranded Total RNA Sample Prep Kit (Illumina, San Diego, CA, USA), following the manufacturers instructions. The constructed library was used to perform sequencing on the Illumina platform and paired-end reads were generated.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

value: Blood

value: 22 months

tag: disease state

value: Normal

value: Male


title: 1702-0276-L


title: WT E14 MN libA mcherry positive rep1

description:
Hoxa5-P2A-mCherry/Hoxa7-P2A-eGFP reporter
libA_sc1_counts.txt


title: WT E14 libAB MN rep2

description:
Hoxa5-P2A-mCherry/Hoxa7-P2A-eGFP reporter
libAB_screen12.count.txt

value: GeCKO v2 library expressing


title: PK-15 cell line ZC3H11A-/- rep2


title: WT E14 libAB MN rep1


title: WT E14 libAB ESC rep2

source_name: Embryonic stem cells

value: Embryonic stem cells


title: WT E14 libAB ESC rep1


title: PK-15 cell line ZC3H11A-/- rep1


title: 1703-0326-L


title: 1702-0242-L


title: Maz KO MN, MAZ ChIP, rep1

description: Hoxa5-P2A-mCherry/Hoxa7-P2A-eGFP reporter

data_processing:
Sequence reads were mapped to mm10 reference genome with Bowtie 2.
After normalization with the spike-in Drosophila read counts, normalized ChIP-seq read densities were visualized in Integrative Genomics Viewer (IGV).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

growth_protocol: mESCs were cultured in standard medium supplemented with LIF and 2i conditions (1 mM MEK1/2 inhibitor (PD0325901, Stemgent) and 3 mM GSK3 inhibitor (CHIR99021, Stemgent)). For motor neuron (MN) differentiation, the previously described protocol in Narendra et. al. (2015) was applied. Briefly, ESCs were differentiated into embryoid bodies in 2 days (Day 0) in ANDFK medium (Advanced DMEM/F12 : Neurobasal (1:1) Medium, 15% Knockout Serum Replacement, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol). Medium was exchanged on Day 2 of differentiation, and further patterning of embryoid bodies was induced by supplementing the ANDFK media on Day 2 with 1 μM all-trans-Retinoic acid (RA, Sigma) and 0.5 μM smoothened agonist (SAG, Calbiochem).

extract_protocol:
In the case of samples containing DSG, they were crosslinked with 2mM DSG in 1X PBS for 30min at RT, and followed by 1% formaldehyde in DMEM for 10min. For the rest of the samples, crosslinking was performed with 1% formaldehyde in DMEM for 10min. Cells were lysed as described in Oksuz et al., 2018 using buffers in the following order: LB1 (50 mM HEPES, pH 7.5 at 4 C, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton X) for 10 min at 4 C, LB2 (10 mM Tris, pH 8 at 4 C, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 10 min at RT, and LB3 (10 mM Tris, pH 7.5 at 4 C, 1 mM EDTA, 0.5 mM EGTA, and 0.5% N-Lauroylsarcosine sodium salt). Chromatin was sonicated to an average size of ~250 bp using a Diagenode Bioruptor. ChIP was performed by using antibodies listed. Chromatin from Drosophila (1:100 ratio to ESC or MN derived chromatin), and Drosophila-specific H2Av antibody were used as spike-in control in each sample.
Libraries were prepared according to manufacturer’s instructions (Illumina) as described in Narendra et al., 2015. Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), ligated to custom adapters, and fragments of 300±100 bp were size-selected. These fragments were amplified through ligation-mediated PCR amplification (LM-PCR) by using Q5 polymerase (NEB M0530).

value: Maz -/-

tag: chip antibody

value: MAZ (Abcam, ab85725)


title: WT E14 MN, MAZ ChIP, rep1


title: 0384-L-blood


title: 0385-L-blood


title: CTCF (Δ5|6:6|7) MN, MAZ ChIP, rep1

value: CTCF (delta5|6:6|7)


title: Maz KO ESC, MAZ ChIP, rep1


title: 0377-L-blood


title: 0355-L-blood


title: 0355-L-blood_D

data_processing:
Library strategy: WGS
For WGS data the sequence reads were first checked for quality and and alignment were subjected to the filtration of duplicate reads using SAMtools subsequently mapped against sus scrofa11.1 using BWA. Subsequently, we followed GATK best practice analysis for post data interpertation. SNPs were separated using variant calling and subsequently various filter parameter were applied. The VCF file later imputed using Beagle and phased data is presented.
For RNAseq data Sequence reads were first checked for quality and trimmed using trimmoatic tool and all quality-filtered PE reads were aligned to the Sscrofa genome (Sscrofa11.1) retrieved from the University of California Santa Cruz (UCSC) browser using Hisat2 . Later Bam were used as input with reference GTF file in subread package featureCounts and count data was generated.
Genome_build: sscrofa11.1
Supplementary_files_format_and_content: E_chr.vcf.gz and L_chr.vcf.gz (WGS samples)
Supplementary_files_format_and_content: blood_ETvsL.txt (RNA-seq samples)


title: WT E14 ESC, MAZ ChIP, rep1


title: WT E14 ESC, Input

value: Input


title: 0385-blood_D


title: 0384-L-blood_D


title: WT E14 MN, Input


title: 0377-blood_D


title: WT E14 MN libA dual positive rep1


title: MAZ HoxA(Δ5|6) ESC, rep2

extract_protocol:
Cells were crosslinked with 2mM DSG in 1X PBS for 30min at RT, and followed by 1% formaldehyde in DMEM for 10min. Cells were lysed as described in Oksuz et al., 2018 using buffers in the following order: LB1 (50 mM HEPES, pH 7.5 at 4 C, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton X) for 10 min at 4 C, LB2 (10 mM Tris, pH 8 at 4 C, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 10 min at RT, and LB3 (10 mM Tris, pH 7.5 at 4 C, 1 mM EDTA, 0.5 mM EGTA, and 0.5% N-Lauroylsarcosine sodium salt). Chromatin was sonicated to an average size of ~250 bp using a Diagenode Bioruptor. ChIP was performed by using antibodies listed. Chromatin from Drosophila (1:100 ratio to ESC or MN derived chromatin), and Drosophila-specific H2Av antibody were used as spike-in control in each sample.
Libraries were prepared according to manufacturer’s instructions (Illumina) as described in Narendra et al., 2015. Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), ligated to custom adapters, and fragments of 300±100 bp were size-selected. These fragments were amplified through ligation-mediated PCR amplification (LM-PCR) by using Q5 polymerase (NEB M0530).

value: MAZ HoxA(delta5|6)


title: 1702-0276-ET_D


title: CTCF (Δ5|6:6|7) ESC, MAZ ChIP, rep1


title: MAZ HoxD(Δ4|8) MN set2

value: ESC-derived cervical motor neurons

value: MAZ HoxD(delta4|8)


title: 1702-0242-ET_D


title: 1703-0326-ET_D


title: WT E14 MN set2


title: WT E14 ESC set2


title: MAZ HoxD(Δ4|8) ESC set2


title: WT E14 ESC rep1 (Sample 1)

extract_protocol:
Cells were lysed as described in Oksuz et al., 2018 using buffers in the following order: LB1 (50 mM HEPES, pH 7.5 at 4 C, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton X) for 10 min at 4 C, LB2 (10 mM Tris, pH 8 at 4 C, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 10 min at RT, and LB3 (10 mM Tris, pH 7.5 at 4 C, 1 mM EDTA, 0.5 mM EGTA, and 0.5% N-Lauroylsarcosine sodium salt). Chromatin was sonicated to an average size of ~250 bp using a Diagenode Bioruptor. ChIP was performed by using antibodies listed. Chromatin from Drosophila (1:100 ratio to ESC or MN derived chromatin), and Drosophila-specific H2Av antibody were used as spike-in control in each sample.
Libraries were prepared according to manufacturer’s instructions (Illumina) as described in Narendra et al., 2015. Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), ligated to custom adapters, and fragments of 300±100 bp were size-selected. These fragments were amplified through ligation-mediated PCR amplification (LM-PCR) by using Q5 polymerase (NEB M0530).

value: H3K27me3 (Cell Signalling, #9733)


title: CTCF (delta5|6:6|7) ESC rep1 (Sample 4)


title: CTCF-(Δ5|6:6|7)-MN-rep2

value: CTCF (Millipore, #07-729)


title: CTCF-(Δ5|6:6|7)-ESC-rep2


title: S1319N

city: Seoul

first: Yun-Suhk

last: Suh

address: 101 Daehang-ro, Jongo-Gu

institute: Seoul National University College of Medicine

description: surgical specimen

data_processing:
Read alignment and processing were performed using STAR aligner with the Homo sapiens GRCh37 Ensembl v74 gene assembly.
The mRNA expression was quantified for downstream analysis by expected read count based on effective gene length using RNA-Seq by Expectation Maximization (RSEM).
the quantified mRNA expression was normalized either between the tumor and normal samples in each molecular subtype or between the molecular subtypes of the tumor samples, according to the comparative conditions of DESeq
Genome_build: Homo sapiens GRCh37 Ensembl v74 gene assembly
Supplementary_files_format_and_content: format: mRNA expression quanficiation matrix for genes per individual sample, content: ensembl gene ID, transcript ID, gene length, effective length, expected count, TPM and FPKM for each gene.
Supplementary_files_format_and_content: format: mRNA expression quanficiation matrix for isoform transcripts per individual sample, content: included ensembl transcript ID, gene ID,  gene length, effective length, expected count, TPM and FPKM for each isoform.

source_name: gastric mucosa

growth_protocol: snap frozen status at -80

extract_protocol:
RNA of all fresh frozen tumors and corresponding normal gastric mucosa were extracted using the TRIzol® Reagent in accordance with the protocol provided by the manufacturer (User Manual TRIzol® Reagent, Invitrogen). In brief, 1 mL of TRIzol was added to every 4 mm3 of fresh tissue, followed by the addition of 200 μL of chloroform in each tube. The RNA in the aqueous phase was precipitated with 0.5 ml of isopropanol and washed with 1 ml of 75% ethanol. The resulting RNA pellet was then resuspended in 50 μL of DEPC-treated water and quantified using a NanoDropTM 1000 (Thermo Scientific) to determine the sample concentration and purity. The use of degraded RNA can result in low yield, overrepresentation of the 5' ends of the RNA molecules, or failure of the whole transcriptome sequencing library preparation. Total RNA integrity was evaluated following isolation using an Agilent Technologies 2100 Bioanalyzer, and samples with an RNA Integrity Number greater than 5.0. RNA was quantified with rRNA ratio≧1.5, and amount of RNA≧1.2 µg.
The Illumina TruSeq RNA Library Preparation Kit v2 was used for the mRNA-focused sequencing library

treatment_protocol: No previous treatment

tag: tumor or normal

value: paired normal


title: S1319T

description: surgical specimen

value: adenocarcinoma


title: S1308T

description: surgical specimen


title: S1308N

description: surgical specimen


title: 1702-0235-ET_D

value: Blood


title: S1286N

description: surgical specimen


title: 14SE440_iBAT_RT_mRNA

city: Bellaterra

first: Jordi

last: Rodo

state: Barcelona

address: Carrer de la Vall Moronta, edifici H

country: Spain

institute: CBATEG, UAB

description: FBosch_April2020_mRNA_14SE440_iBAT_RT.rma-gene-full.chp Signal

hyb_protocol: The GeneTitan Hybridization Wash and Stain kit for WT array plates (Affymetrix, Thermo Fisher Scientific, Waltham, MA, USA) were then used following the manufacturer’s instructions. This procedure was performed by Progenika Biopharma (Progenika Biopharma, Grifols, Barcelona, CAT, ES).

data_processing: The Transcriptome Analysis Console (TAC) software version 4.0.2.15 was used to perform quality control, data normalization (using RMA) and statistical tests. Data were annotated using the “MoGene-2_1-st-v1 Transcript Cluster Annotations, Release 36” from the 7/6/2016.

label: biotin

source_name: Interscapular Brown Adipose Tissue_22ºC

label_protocol: 300ng of RNA were used to synthesize cDNA with the GeneChip WT PlusReagent kit following the manufacturer’s instructions. From the obtained cDNA, 5.5 μg were fragmented using UDG (Uracil DNA Glycosylase) and APE1 (Apurinic/apyrimidinic endonuclease 1). Fragmented cDNA was then labeled with terminal transferase using the WT Terminal Labeling kit (Affymetrix, Thermo Fisher Scientific, Waltham, MA, USA). All these procedures were performed by Progenika Biopharma (Progenika Biopharma, Grifols, Barcelona, CAT, ES).

extract_protocol: Mice were anesthetized by inhalation anesthesia and euthanized by decapitation. Tissue samples were obtained in the morning and were immediately frozen in liquid nitrogen (N2) and then stored at -80 ºC. Tissue was homogenized in 1 mL of QIAzol (Qiagen, Hilden, NW, DE) for adipose depots. Next, the Rneasy Mini Kit (Qiagen, Hilden, NW, DE) was used to extract total RNA.

treatment_protocol: Male mice of the strain C57Bl/6JOlaHsd of 8 weeks of age were divided into two groups that were either exposed during 4 days to 4ºC in a humidity and temperature-controlled refrigerator room or housed at 22 ºC. Each mouse was housed individually, and the bedding of the cage was removed to keep mice from nesting to help regulate body temperature. Day and night cycles were maintained with 12 hours of light and 12 hours of darkness.

tag: age (weeks)

value: male

tag: temperature (degree celsius)

value: Interscapular Brown Adipose tissue


title: 14SE444_iBAT_RT_mRNA

description: FBosch_April2020_mRNA_14SE444_iBAT_RT.rma-gene-full.chp Signal

scan_protocol: This procedure was performed by Progenika Biopharma (Progenika Biopharma, Grifols, Barcelona, CAT, ES).


title: S1256T

description: surgical specimen


title: S1250N

description: surgical specimen


title: 14SE434_iWAT_RT_mRNA

description: FBosch_April2020_mRNA_14SE434_iWAT_RT.rma-gene-full.chp Signal

source_name: Inguinal White Adipose Tissue_22ºC

value: Inguinal White Adipose tissue


title: S1256N

description: surgical specimen


title: S1230T

description: surgical specimen


title: S1230N

description: surgical specimen


title: 14SE436_iBAT_Cold_mRNA

description: FBosch_April2020_mRNA_14SE436_iBAT_Cold.rma-gene-full.chp Signal

source_name: Interscapular Brown Adipose Tissue_4ºC

tag: treatment

value: Cold


title: S1286T

description: surgical specimen


title: S1221T

description: surgical specimen


title: S1221N

description: surgical specimen


title: 14SE439_iBAT_Cold_mRNA

description: FBosch_April2020_mRNA_14SE439_iBAT_Cold.rma-gene-full.chp Signal

tag: Sex


title: 14SE432_iWAT_RT_mRNA

description: FBosch_April2020_mRNA_14SE432_iWAT_RT.rma-gene-full.chp Signal


title: S824T

description: surgical specimen


title: 14SE438_iBAT_Cold_mRNA

description: FBosch_April2020_mRNA_14SE438_iBAT_Cold.rma-gene-full.chp Signal


title: 14SE443_iBAT_RT_mRNA

description: FBosch_April2020_mRNA_14SE443_iBAT_RT.rma-gene-full.chp Signal


title: 14SE430_iWAT_RT_mRNA

description: FBosch_April2020_mRNA_14SE430_iWAT_RT.rma-gene-full.chp Signal


title: 14SE427_iWAT_Cold_mRNA

description: FBosch_April2020_mRNA_14SE427_iWAT_Cold.rma-gene-full.chp Signal

source_name: Inguinal White Adipose Tissue_4ºC


title: 14SE429_iWAT_Cold_mRNA

description: FBosch_April2020_mRNA_14SE429_iWAT_Cold.rma-gene-full.chp Signal


title: S1250T

description: surgical specimen


title: 14SE433_iWAT_RT_mRNA

description: FBosch_April2020_mRNA_14SE433_iWAT_RT.rma-gene-full.chp Signal


title: 14SE428_iWAT_Cold_mRNA

description: FBosch_April2020_mRNA_14SE428_iWAT_Cold.rma-gene-full.chp Signal


title: 14SE437_iBAT_Cold_mRNA

description: FBosch_April2020_mRNA_14SE437_iBAT_Cold.rma-gene-full.chp Signal


title: 14SE426_iWAT_Cold_mRNA

description: FBosch_April2020_mRNA_14SE426_iWAT_Cold.rma-gene-full.chp Signal


title: 14SE442_iBAT_RT_mRNA

description: FBosch_April2020_mRNA_14SE442_iBAT_RT.rma-gene-full.chp Signal


title: 14SE423_eWAT_RT_mRNA

description: FBosch_April2020_mRNA_14SE423_eWAT_RT.rma-gene-full.chp Signal

source_name: Epididymal White Adipose Tissue_22ºC

value: Epididymal White Adipose tissue


title: 14SE422_eWAT_RT_mRNA

description: FBosch_April2020_mRNA_14SE422_eWAT_RT.rma-gene-full.chp Signal


title: S798T

description: surgical specimen


title: S824N

description: surgical specimen


title: S798N

description: surgical specimen


title: 14SE424_eWAT_RT_mRNA

description: FBosch_April2020_mRNA_14SE424_eWAT_RT.rma-gene-full.chp Signal


title: S715N

description: surgical specimen


title: S715T

description: surgical specimen


title: WT E14 ESC, MAZ ChIP, rep2

description: Hoxa5-P2A-mCherry/Hoxa7-P2A-eGFP reporter

value: Embryonic stem cells

value: wild type

tag: developmental stage


title: S567T

description: surgical specimen


title: S673N

description: surgical specimen


title: S673T

description: surgical specimen


title: WT E14 MN

extract_protocol:
Cells were lysed as described in Oksuz et al., 2018 using buffers in the following order: LB1 (50 mM HEPES, pH 7.5 at 4 C, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton X) for 10 min at 4 C, LB2 (10 mM Tris, pH 8 at 4 C, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 10 min at RT, and LB3 (10 mM Tris, pH 7.5 at 4 C, 1 mM EDTA, 0.5 mM EGTA, and 0.5% N-Lauroylsarcosine sodium salt). Chromatin was sonicated to an average size of ~250 bp using a Diagenode Bioruptor. ChIP was performed by using antibodies listed. Chromatin from Drosophila (1:100 ratio to ESC or MN derived chromatin), and Drosophila-specific H2Av antibody were used as spike-in control in each sample.
Libraries were prepared according to manufacturer’s instructions (Illumina) as described in Narendra et al., 2015. Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), ligated to custom adapters, and fragments of 300±100 bp were size-selected. These fragments were amplified through ligation-mediated PCR amplification (LM-PCR) by using Q5 polymerase (NEB M0530).
instrument model: HiSeq4000/Nextseq500

value: RAD21 (Abcam, ab992)


title: S538T

description: surgical specimen


title: Maz KO MN, CTCF ChIP, rep1

value: Maz -/-


title: S566N

description: surgical specimen


title: Maz KO MN, CTCF ChIP, rep3


title: Maz KO ESC, CTCF ChIP, rep3


title: WT E14 MN, MAZ ChIP, rep2

value: MAZ (Abcam, ab85725)


title: Maz KO MN, CTCF ChIP, rep2

value: ESC-derived cervical motor neurons


title: S538N

description: surgical specimen


title: 14SE416_eWAT_Cold_mRNA

description: FBosch_April2020_mRNA_14SE416_eWAT_Cold.rma-gene-full.chp Signal

source_name: Epididymal White Adipose Tissue_4ºC


title: S566T

description: surgical specimen


title: WT E14 ESC, CTCF ChIP, rep1


title: Maz KO ESC, CTCF ChIP, rep2


title: 14SE419_eWAT_Cold_mRNA

description: FBosch_April2020_mRNA_14SE419_eWAT_Cold.rma-gene-full.chp Signal


title: Maz KO ESC, CTCF ChIP, rep1


title: S1246T

description: surgical specimen


title: 14SE418_eWAT_Cold_mRNA

description: FBosch_April2020_mRNA_14SE418_eWAT_Cold.rma-gene-full.chp Signal


title: 14SE417_eWAT_Cold_mRNA

description: FBosch_April2020_mRNA_14SE417_eWAT_Cold.rma-gene-full.chp Signal


title: CTCF (delta5|6:6|7) MN rep1  (Sample 12)

value: CTCF (delta5|6:6|7)

value: H3K4me3 (Abcam, ab8580)


title: S567N

description: surgical specimen


title: MAZ HoxD(delta4|8) MN rep1 (Sample 11)

value: MAZ HoxD(delta4|8)


title: S1246N

description: surgical specimen

value: paired normal


title: S1201T

description: surgical specimen

value: adenocarcinoma


title: MAZ HoxA(delta5|6) MN rep1 (Sample 10)

value: MAZ HoxA(delta5|6)


title: CTCF (delta5|6:6|7) MN rep1  (Sample 8)

value: H3K27me3 (Cell Signalling, #9733)


title: S1175T

description: surgical specimen


title: S1201N

description: surgical specimen


title: WT E14 MN rep1 (Sample 9)


title: MAZ HoxA(delta5|6) MN rep1 (Sample 6)


title: S1324N

description: surgical specimen


title: S1324T

description: surgical specimen


title: S1175N

description: surgical specimen


title: S1158T

description: surgical specimen


title: S1176N

description: surgical specimen


title: MAZ HoxD(delta4|8) MN rep1 (Sample 7)


title: WT E14 MN rep1 (Sample 5)


title: MAZ HoxA(delta5|6) ESC rep1 (Sample 2)


title: MAZ HoxD(delta4|8) ESC rep1 (Sample 3)


title: MAZ-HoxD(Δ4|8)-MN-rep2

value: CTCF (Millipore, #07-729)


title: S1124N

description: surgical specimen


title: S1078T

description: surgical specimen


title: S1158N

description: surgical specimen


title: S1124T

description: surgical specimen


title: MAZ-HoxA(Δ5|6)-MN-rep2


title: WT-E14-MN-rep2


title: S1078N

description: surgical specimen


title: WT-E14-ESC-rep2


title: S0975T

description: surgical specimen


title: MAZ-HoxD(Δ4|8)-MN-rep1


title: S0975N

description: surgical specimen


title: S1176T

description: surgical specimen


title: MAZ-HoxA(Δ5|6)-MN-rep1


title: CTCF-(Δ5|6:6|7)-MN-rep1


title: S0969T

description: surgical specimen


title: WT-E14-MN-rep1


title: MAZ-HoxD(Δ4|8)-ESC-rep1


title: S0969N

description: surgical specimen


title: MAZ-HoxA(Δ5|6)-ESC-rep1


title: CTCF-(Δ5|6:6|7)-ESC-rep1


title: S801T

description: surgical specimen


title: S801N

description: surgical specimen


title: MAZ-HoxD(Δ4|8)-ESC-rep2


title: WT-E14-ESC-rep1


title: S570T

description: surgical specimen


title: S451T

description: surgical specimen


title: S570N

description: surgical specimen


title: RNA-seq_Maz_KO_MN_rep3

description: Hoxa5-P2A-mCherry/Hoxa7-P2A-eGFP reporter cells

data_processing:
Reads were aligned to mm10 reference genome using tophat 2.0.9 and bowtie2 2.1.0
Reads were assigned to the UCSC mm10 gene annotation
Counts were obtained by using featureCounts v1.6.2
Normalized differential expression (taking into account biological replicates) was calculated by using Deseq2.
Genome_build: mm10
Supplementary_files_format_and_content: counts in txt format

extract_protocol:
RNA was purified from cells with RNAeasy Plus Mini kit (Qiagen), and 1ug RNA was used for library preparation.
RNA was used to prepare automated TruSeq (Illumina) stranded RNAseq libraries by using RiboZero Gold library prepation according to manufacturer's protocols by NYU Genome Technology Center.


title: S1058N

description: surgical specimen


title: S451N

description: surgical specimen


title: RNA-seq_WT_E14_MN_rep3


title: S0950T

description: surgical specimen


title: S0950N

description: surgical specimen


title: MAZ-HoxA(Δ5|6)-ESC-rep2


title: RNA-seq_WT_E14_MN_rep2


title: S439N

description: surgical specimen


title: RNA-seq_WT_E14_MN_rep1


title: RNA-seq_Maz_KO_ESC_rep3


title: RNA-seq_Maz_KO_ESC_rep1


title: S439T

description: surgical specimen


title: RNA-seq_Maz_KO_ESC_rep2


title: S1058T

description: surgical specimen


title: RNA-seq_Maz_KO_MN_rep2


title: RNA-seq_WT_E14_ESC_rep3


title: RNA-seq_Maz_KO_MN_rep1


title: S1339N

description: surgical specimen


title: S1318N

description: surgical specimen


title: S1318T

description: surgical specimen


title: RNA-seq_WT_E14_ESC_rep2


title: S1298N

description: surgical specimen


title: JQ1-3

city: Chicago

first: Yongzhan

last: zhang

state: Illinois

address: 303 East Superior Street

department: Department of Pediatrics, Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

data_processing:
Total RNA-sequencing (RNA-seq) reads were trimmed from the 3′ end until the final base had a quality score > 30, using Trimmomatic version 0.33
Processed reads were aligned to the human reference genome UCSC hg19 using STAR (38) and were counted using HTSeq
Data normalization and differential gene expression was analyzed using DESeq2 (40) with default settings
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: AT/RT cell

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 0.3 μM JQ1


title: RNA-seq_WT_E14_ESC_rep1


title: S1298T

description: surgical specimen


title: JQ1-2


title: S1274N

description: surgical specimen


title: S1274T

description: surgical specimen


title: GSK126-3

value: 6 μM GSK126


title: GSK126-2


title: S1241N

description: surgical specimen


title: GSK126-1


title: S1241T

description: surgical specimen


title: S1339T

description: surgical specimen


title: S1055N

description: surgical specimen


title: GSK126_plus_JQ1-3

value: 6 μM GSK126 and 0.3 μM JQ1


title: GSK126_plus_JQ1-2


title: GSK126_plus_JQ1-1


title: DMSO-3


title: DMSO-2


title: S1055T

description: surgical specimen


title: DMSO-1


title: S0911N

description: surgical specimen


title: S0911T

description: surgical specimen


title: S0714N

description: surgical specimen


title: WT E14 MN, CTCF ChIP, rep1


title: S0441N

description: surgical specimen


title: JQ1-1


title: MVV vector in HEK293T cells

city: London

first: Peter

last: Cherepanov

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Paired-end reads were cropped to remove linker and virus LTR sequences.
Cropped paired reads were aligned to human genome hg38 using BWA MEM.
High-quality alignemnts were selected with samtools view -F 4 -F 256 -q 1.
The remaining alignements were parsed to select unique integration sites and extract coordinates of the central base pair step for each site.
Genome_build: hg38
Supplementary_files_format_and_content: bed

source_name: HEK293T cells infected with MVV vector

growth_protocol: Cells were cultured at 37°C in 5% CO2 atmosphere in Dulbecco's modified Eagle medium (DMEM, Life Technologies) supplemented with 10% heat-inactivated fetal bovine serum (FBS) and antibiotic/antimycotic solution (Sigma-Aldrich).

extract_protocol: Genomic DNA isolated from cells 5 days post-infection with MVV vector was processed for linker-mediated PCR, and the amplified viral LTR-chromosome junctions were sequenced. To this end, genomic DNA, digested with MseI overnight at 37°C, was ligated to a double-stranded DNA linker containing 5'-TA overhang overnight at 12°C. Customized DNA linkers were used in conjunction with barcoded primers to aid in multiplexing and prevent crosstalk between samples. The first round and the nested MVV U5 primers were 5'-CTAATTCCGTGCAACACCG and 5'-AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TNN NNN NCA ACA CCG GAG CGG ATC, respectively (underlined sequence represents the 6 nucleotides barcode specific to LTR primer for multiplexing). The nested PCR primers contained Illumina adaptor sequences appended at the 5' ends. The PCR products, multiplexed on a single lane of a flow cell, were subjected to 150-bp paired-end sequencing on a HiSeq-4000 Illumina instrument.

tag: infection protocol

value: Cells were infected with MVV vector and processed for linker-mediated PCR 5 days post infection.

value: Human embryonic kidney cells


title: MVV vector in LKO cells

source_name: LKO cells infected with MVV vector

value: LKO is a LEDGF-null cell line, generated via TALEN-mediated PSIP1 gene disruption in HEK293T cells


title: S0441T

description: surgical specimen


title: MVV vector in LHKO cells

source_name: LHKO cells infected with MVV vector

value: LHKO was derived by using CRISPR-Cas9 guide RNAs targeting exon 2 (5'-ACCCAACAAGTACCCCATCTTTTTC) and exon 15 (5'-CGACCGGCAGGAGCGCGAGAGGG), resulting in deletion of most of HDGFL2 gene.


title: S110N

description: surgical specimen


title: S0437N

description: surgical specimen


title: S0437T

description: surgical specimen


title: TTP-3

city: Shanghai

first: Huanqiang

last: Zhao

address: Fangxie Road 419, Huangpu District

institute: Fudan university

data_processing:
The low quality reads and those with adaptor contamination or undetermined bases were removed using Cutadapt, and the sequence quality was estimated by FastQC.
The reads were then mapped to the human genome using Bowtie2 and TopHat2, and the reads spanning circRNA back-splicing junctions in the unmapped reads were identified by Tophat-Fusion
The CIRCexplorer2 and CIRI pipelines were used with default parameters for de novo circRNA assembly, and back splicing reads were identified in unmapped reads by Tophat-Fusion
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw back splice counts for every circRNA and every sample

source_name: Third trimester placenta

extract_protocol:
Total RNA was isolated from the placentas using TRIZOL (Invitrogen, Carlsbad, CA, USA). The concentration and quality of the RNA samples were determined using NanoDrop ND-1000, and RNA integrity was evaluated by Agilent 2100 instrument with RIN number >7.0. To enrich for circRNAs, the rRNAs were first depleted using the Ribo-Zero™ rRNA Removal Kit (Illumina, San Diego, USA), followed by the removal of linear RNAs with RNase R (Epicentre Inc, Madison, WI, USA).
The enriched circRNAs were fragmented into small pieces, reverse-transcribed to cDNAs, and synthesized to U-labeled second-stranded DNAs. The blunt ends of the cDNA were ligated to A-base and thereafter to the indexed adapters. After library size selection with AMPureXP beads (Beckman, Brea, CA), the ligated cDNA products were incubated with the heat-labile UDG enzyme to remove the second-strand cDNA. The first-strand cDNA was amplified by PCR to construct the library, which was then sequenced on an Illumina Hiseq 4000 platform (LC Bio, Hangzhou, China) on a 150 bp paired-end run.

tag: maternal age

value: 27 years

tag: previous nulliparity

value: Yes

tag: gestational age

value: 39.6 weeks

value: Third trimester

value: placenta

tag: fraction

value: circular RNA


title: S0970N

description: surgical specimen

value: paired normal


title: S0970T

description: surgical specimen

value: adenocarcinoma


title: TTP-2

value: 31 years

value: No

value: 38.6 weeks

tag: tissue


title: S0354N

description: surgical specimen


title: S0354T

description: surgical specimen


title: S0348N

description: surgical specimen


title: STP-3

source_name: Second trimester placenta

value: 28 years

value: 18.6 weeks

value: Second trimester


title: TTP-1

value: 32 years

value: 39.4 weeks


title: STP-1

value: 22 years

value: 18.9 weeks


title: S0348T

description: surgical specimen


title: S0714T

description: surgical specimen


title: Group 3 PEA exposed

city: Valparaiso

first: Kathleen

last: Whitlock

state: Valparaiso

address: Pasaje Harrington 269

department: Centro Interdisciplinario de Neurociencia de Valparaíso (CINV)

country: Chile

institute: Universidad de Valparaiso

data_processing:
The quality of the sequencing reaction was analyzed with the FastQC software (v0.11.9) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed with Trim_galore (v0.6.4) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
Reads were aligned to the Zv9 reference genome using Bowtie2 software with standard settings (doi:10.1038/nmeth.1923)
The gene abundance was determined using the HTseq software (v0.11.2) (https://htseq.readthedocs.io/en/master/) (doi:10.1093/bioinformatics/btu638) to calculate the raw reads number for each gene
Differential gene expression was estimated using DESeq2 (v1.24) (10.1186/s13059-014-0550-8) within SARTools R package (v1.6.9) (http://dx.doi.org/10.1371/journal.pone.0157022)
Genome_build: zv9
Supplementary_files_format_and_content: Defferential gene expression report was generated using DESeq2 (v1.24) and include the normalized results of comaparison between control and PEA exposed group for all transcripts

organism: Danio rerio

source_name: Adult Olfactory epithelium

growth_protocol: The fish were maintained at 28 ÅãC on a light–dark cycle of 14 and 10 h, respectively

extract_protocol:
Ten adult fish head per each experimental group was used and collected in RNA-later solution. Adult fish olfactory epithelium were dissected in RNA-later solution and the total RNA was harvested using TRIZOL.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Zebrafish embryos were collected and separated into experimental (PEA exposed) and control groups. Fish were exposed every day for 3 weeks of development as described previously (Calfun et al. 2016), after which the fish were transferred to a recirculating system . Experimental groups were exposed 1.0 106 M βPEA (SAFC, W285811) and for control group only distilled water was added. All fish were maintained at 28ºC until sacrificed at 6 months, where the Olfactory epithelium were collected. The PEA exposure experiment was performed in biological triplicates

tag: strain

value: New wild type (AB derived line)

value: Adult Olfactory epithelium

tag: age

value: Six months

value: Phenyl ethyl alcohol (PEA)


title: S0257N

description: surgical specimen


title: FTP-2

source_name: First trimester placenta

value: 23 years

value: Yes

value: 6.6 weeks

value: First trimester

value: placenta

value: circular RNA


title: FTP-3

value: 28 years

value: No

value: 6.1 weeks


title: Group 2 Control

value: Untreated


title: S110T

description: surgical specimen

value: adenocarcinoma


title: S0250N

description: surgical specimen

value: paired normal


title: MAZ HoxA(Δ5|6) MN, rep2

source_name: Motor neurons

tag: cell type

value: ESC-derived cervical motor neurons

tag: genotype

value: MAZ HoxA(delta5|6)

value: MAZ (Abcam, ab85725)


title: FTP-1

value: 26 years

value: 7 weeks


title: STP-2

value: 30 years

value: 20 weeks

value: Second trimester


title: Group 1 PEA exposed

value: New wild type (AB derived line)

value: Adult Olfactory epithelium

value: Six months

value: Phenyl ethyl alcohol (PEA)


title: S0257T

description: surgical specimen


title: WT E14 MN, rep1

value: wild type

tag: chip antibody


title: MAZ HoxA(Δ5|6) ESC, rep1

source_name: Embryonic stem cells

value: Embryonic stem cells


title: WT E14 ESC, rep2


title: plasma microRNA rep24

first: Issam

last: Awad

state: IL

address: 5841 S. Maryland Avenue

department: Department of Neurology

institute: The University of Chicago

description: processed data file contains all the samples

data_processing:
All analyses were completed using the sRNAToolbox tools (Aparicio-Puerta et al 2019) with miRBase(v22.1), and DESeq2 packages (v1.30.1) in R statistical environment (v4.0.5).
Differential miRNA analyses were completed between (1) CCM + DVA to DVA only and then (2) DVA only to healthy controls. The differentially expressed miRNAs were identified having P < 0.05, FDR-corrected.
Genome_build: hg38
Supplementary_files_format_and_content: csv (comma-separated values) file of raw read counts

source_name: plasma

extract_protocol:
Total plasma RNA was extracted from the plasma of individuals using the miRNeasy Serum/Plasma Kit (Qiagen, Hilden, Germany) following the manufacturer isolation protocol.
Illumina small RNA-Seq kits (Clontech, Mountain View, CA, USA) were then used to generate cDNA libraries.
Sequencing of the plasma miRNomes was completed with the Illumina HiSeq 4000 platform (Illumina, San Diego, CA, USA), with single-end 50bp reads.

tag: group

value: DVA

tag: batch

tag: sample type

value: plasma microRNA


title: S0250T

description: surgical specimen

source_name: gastric mucosa

tag: tumor or normal

value: adenocarcinoma


title: plasma microRNA rep23


title: 14SE420_eWAT_RT_mRNA

description: FBosch_April2020_mRNA_14SE420_eWAT_RT.rma-gene-full.chp Signal

tag: age (weeks)

tag: Sex

value: male

tag: temperature (degree celsius)

value: Epididymal White Adipose tissue


title: plasma microRNA rep25

value: Healthy


title: plasma microRNA rep22


title: MAZ HoxA(Δ5|6) MN, rep1

value: ESC-derived cervical motor neurons

value: MAZ HoxA(delta5|6)

tag: developmental stage

value: MAZ (Abcam, ab85725)


title: Group 3 Control

tag: treatment

value: Untreated


title: CTCF (Δ5|6:6|7) MN rep3

data_processing:
Library strategy: 4C-seq
4C-seq data was analyzed using the 4C-ker (version 0.0.0.9000) pipeline as described by Raviram et al., 2016. 4C-seq reads were mapped to mm10 reduced reference genome.
Undigested and self-ligated fragments were removed based on the viewpoint.
Near-bait analysis were generated in R by using 4C-ker tools. Normalized 4C-seq read densities were visualized in Integrative Genomics Viewer (IGV).
Genome_build: mm10
Supplementary_files_format_and_content: BedGraph

extract_protocol:
Cells were processed for 4C-seq as described in Narendra et al., 2015; following the protocol details as published in van de Werken et al., 2012. Cells were trypsinized, counted, and 1 x 107 cells were crosslinked with the Crosslinking Solution (2% formaldehyde and 10% FBS in 1X PBS) for 10 min at room temperature. After the reaction was quenched with glycine, the cells were lysed on ice with 1ml Lysis Buffer (50mM Tris pH 7.3, 150mM NaCl, 5mM EDTA, 0.5% NP-40, and 1% Triton X-100) for 15 min. Nuclei were spun down and frozen at -80 oC. Upon thawing on ice, nuclei were resuspended in 360ul H2O. The primary restriction enzyme was DpnII. The secondary restriction enzyme was Csp6I. 1ug 4C template DNA obtained was amplified using inverse primers containing barcoded illumina sequencing adapters on either end.
Libraries were prepared according to manufacturer’s instructions (Illumina) as described in Narendra et al., 2015. 4C-seq libraries were constructed by attaching barcoded Illumina adapters to the 5’ end of the primer. PCR reactions were performed using the Expand Long Template PCR System (Roche) and about 100-700bp DNA was gel purified and quantified prior to sequencing.

value: CTCF (delta5|6:6|7)


title: Input_Sample1

city: Houston

first: MURUGESAN

last: PALANIAPPAN

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
DNA libraries were sequenced on a Illumina HiSeq 2500.
Sequences (50-nt reads) were aligned to the mouse genome (mm9) using the BWA algorithm with default settings.
Aligns were extended in silico at their 3'-ends to a length of 150bp and assigned to 32-nt bins along the genome.
The resulting histograms were stored as bigWIG (BW) files.
Peak locations were determined using the Model-based Analysis of ChIP-seq Algorithm (MACS v1.4.2) with a cutoff of p-value 1e-5.
Signal maps and peak locations were used as input data to Active Motif's proprietary analysis program, which provided detailed information on sample comparison, peak metrics, peak locations, and gene annotations.
Genome_build: mm9
Supplementary_files_format_and_content: bigWIG (BW) files

source_name: p53 null mammary glands  treated with E8h

growth_protocol: Mammary epithelium from p53 null mice was transplanted into the cleared fat pad of syngeneic wild type Balb/c mice. At 8 weeks after transplantation mice received a tamoxifen (5mg) or sham pellet subcutaneously for 13 weeks.  At 4 weeks after tamoxifen removal, all mice were injected with 17β-estradiol (100ug) for 8  hours.

extract_protocol:
Mammary glands were treated with a TissueTearer followed by dounce-homogenization in lysis buffer.  Lysates were sonicated and ERα-DNA complexes were isolated using a ERα antibody.
ChIP and input DNA were amplified using the Illumina ChIP-Seq DNA Sample Prep Kit.

treatment_protocol: All mice were treatedwith 17β-estradiol (100ug) for 8 h

tag: host strain background

value: BALB/c

tag: host strain genotype/variation

tag: transplanted with

value: Mammary epithelium from p53 null mice

tag: injected with

value: 17β-estradiol (100ug) for 8  hrs

value: 33 weeks

value: Mammary gland


title: CTCF (Δ5|6:6|7) MN rep2


title: Group 2 PEA exposed

tag: strain

value: New wild type (AB derived line)

tag: tissue

value: Adult Olfactory epithelium

tag: age

value: Six months

value: Phenyl ethyl alcohol (PEA)


title: WT E14 ESC, rep1

tag: cell type

value: Embryonic stem cells

tag: genotype

value: wild type

tag: chip antibody


title: CTCF (Δ5|6:6|7) MN rep1


title: Tam_ERα_ChIP-seq_Sample2

source_name: p53 null mammary glands  Tam treated with E8h

tag: treated with

value: tamoxifen (5mg) pellet subcutaneously for 13 weeks

value: ERα (Santa Cruz, sc-542)


title: MAZ HoxA(Δ5|6) MN rep3

value: ESC-derived cervical motor neurons

value: MAZ HoxA(delta5|6)


title: Group 1 Control

value: Untreated


title: plasma microRNA rep21

tag: group

value: Healthy

tag: batch

tag: sample type

value: plasma microRNA


title: Tam_ERα_ChIP-seq_Sample1

value: BALB/c

value: Mammary epithelium from p53 null mice


title: MAZ HoxA(Δ5|6) MN rep1


title: WT E14 MN rep2


title: Sham_ERα_ChIP-seq_Sample2

source_name: p53 null mammary glands  Sham treated with E8h

value: sham pellet subcutaneously for 13 weeks

value: 17β-estradiol (100ug) for 8  hrs

value: 33 weeks


title: Sham_ERα_ChIP-seq_Sample1

value: Mammary gland


title: plasma microRNA rep19

value: DVA


title: CTCF (Δ5|6:6|7) ESC rep3

value: CTCF (delta5|6:6|7)


title: plasma microRNA rep18


title: MAZ HoxA(Δ5|6) MN rep2


title: E180117

city: Heidelberg

first: Christian

last: Arnold

state: Baden-Württemberg

address: Meyerhofstraße 1

country: Germany

institute: EMBL

data_processing:
Adaptor trimming with Trimmomatic v0.38 (parameters: ILLUMINACLIP::1:30:4:1:true TRAILING:3 MINLEN:20)
Alignment with Bowtie2 v2.3.4.3 (parameters: -X2000 --very-sensitive -t)
Post-alignment processing (using samtools v1.9, Picard tools v2.18.16-SNAPSHOT): (0) cleaning the BAM file with Picard CleanSam, FixMateInformation, AddOrReplaceReadGroups and ReorderSam,  (1) removing mitochondrial reads and reads from non-assembled contigs or alternative haplotypes, (2) marking and removing duplicate reads with MarkDuplicates, (3) filtering reads with a mapping quality below 10 (-F 4 -q 10), (4) adjusting read start sites as described previously by 4 and -5 base pairs, and (5) removing reads with insertions or deletions using samtools, followed by final cleaning and sorting using Picard SortSam, CleanSam, and FixMateInformation
Peak calling with MACS2 (parameters: -q 0.01 -g hg19 --nomodel --keep-dup all) followed by filtering using bedtools subtract v2.27.1 against the publicly available blacklist regions
Genome_build: hg19
Supplementary_files_format_and_content: We provide the individual peak files as well as the main consensus peak set along with raw read counts for each sample

source_name: AML cells

extract_protocol:
Briefly 50,000 cells from frozen samples were collected, then placed into lysis buffer (10 mM Tris·Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween 20), followed by Tn5 transposase-mediated tagmentation and adaptor incorporation at sites of accessible chromatin carried out using the Nextera DNA Library Prep kit (FC-121-1030, Illumina) at 37°C for 30 min.
Library amplification was performed using NEB Nex High-Fidelity 2x PCR Master Mix (M0541L, NEB) and primer combinations provided in Nextera DNA Library Prep kit.  The library was optimized for enrichment for 100-1000 bps fragments using SPRI beads based size-selection and the quality of the purified DNA library was analyzed on a Bioanalyzer (2100 Expert software, Agilent Technologies) using High Sensitivity DNA Chips (5067-4626; Agilent Technologies Inc.). The appropriate concentration of sample was determined using the Qubit Fluorometer (Molecular Probes). Ten 40nM samples were pooled and run on a NextSeq 500/550 High Output Kit (20024907; Illumina, Inc. San Diego, CA) and the NextSeq 500 Illumina Sequencer to obtain paired end reads of 75 bp.

value: primary AML cells


title: MAZ HoxA(Δ5|6) ESC rep3

value: Embryonic stem cells


title: CTCF (Δ5|6:6|7) ESC rep2


title: plasma microRNA rep17


title: MAZ HoxA(Δ5|6) ESC rep2


title: E180029


title: MAZ HoxA(Δ5|6) ESC rep1


title: plasma microRNA rep16


title: plasma microRNA rep20


title: plasma microRNA rep15


title: WT E14 ESC rep3

value: wild type


title: plasma microRNA rep14

value: Sporadic


title: E180013


title: E180015


title: WT E14 ESC rep2


title: WT E14 ESC rep1


title: MAZ HoxA(Δ5|6) MN double pos (Sample 12)

description: Hoxa5-P2A-mCherry/Hoxa7-P2A-eGFP reporter sorted for mCherry and GFP

data_processing:
Library strategy: CUT&RUN
Sequence reads were mapped to mm10 reference genome with Bowtie 2.
After normalization with the total read counts, normalized CUT&RUN read densities were visualized in Integrative Genomics Viewer (IGV).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
CUT&RUN was performed as described previously by Skene and Henikoff, 2017 and Meers et al., 2019. 100K to 200K cells were sorted for double-positive (Hoxa5-P2A-mCherry and Hoxa7-P2A-EGFP) populations. Wild-type MNs were treated similarly and collected through FACS. The cells were re-counted after sorting and the published protocol by Skene et al., 2018 detailed in “https://www.protocols.io” by Janssens, D. and Henikoff, S. was followed.
Libraries were prepared according to manufacturer’s instructions (Illumina) as published in the protocol by Skene et al., 2018, detailed in “https://www.protocols.io” by Janssens, D. and Henikoff, S.

value: ESC-derived cervical motor neurons sorted for mCherry and GFP

tag: cut&run antibody

value: H3K4me3 (Abcam, ab8580)


title: WT E14 MN rep1

value: ESC-derived cervical motor neurons

tag: developmental stage


title: plasma microRNA rep13


title: E180007


title: WT E14 MN (Sample 11)


title: plasma microRNA rep12


title: WT E14 MN (Sample 9)

value: H3K27me3 (Cell Signalling, #9733)


title: CTCF (Δ5|6:6|7) ESC rep1


title: plasma microRNA rep11

value: plasma microRNA


title: E170001


title: MAZ HoxA(Δ5|6) MN double pos (Sample 10)

value: MAZ HoxA(delta5|6)


title: MAZ HoxA(Δ5|6) MN double pos (Sample 8)

value: RAD21 (Abcam, #ab992)


title: WT E14 MN (Sample 7)


title: 14H007


title: WT E14 MN (Sample 5)

value: CTCF (Millipore, #07-729)


title: 14H001


title: plasma microRNA rep10


title: MAZ HoxA(Δ5|6) MN double pos (Sample 6)


title: WT E14 MN (Sample 3)


title: MAZ HoxA(Δ5|6) MN double pos (Sample 2)

value: IgG rabbit (Sigma, #I8140)


title: plasma microRNA rep9


title: plasma microRNA rep8


title: WT E14 MN (Sample 1)


title: 13H110


title: 13H073


title: Macrophage Raw264.7 sh-Etv5 rep3

city: Guangzhou

first: Rendong

last: Hu

address: Guangzhou Higher Education Mega Centre, Panyu District

institute: South china university of technology

data_processing:
Illumina NovaSeq 6000 used for basecalling.The accuracy of base recognition was higher than 99%,
After the RNA samples were qualified, the eukaryotic mRNA was enriched with oligo (DT) magnetic beads (in the case of prokaryotes, the rRNA was removed by the kit to enrich the mRNA). After that, the fragment buffer was added to break the mRNA into short fragments. Using the mRNA as the template, random hexamers were used to synthesize a strand of cDNA. Then the buffer solution, dNTPs, DNA polymerase I and RNase H were added to synthesize the two strand cDNA. Then the double strand cDNA was purified by ampere XP beads. The purified double stranded cDNA was repaired at the end, added a tail and connected to the sequencing connector, and then ampure XP beads was used to select the fragment size. Finally, the PCR products were amplified by PCR and purified by ampure XP beads to obtain the final library. After the library was constructed, qubit 2.0 was used for preliminary quantification, and the library was diluted. Then, Agilent 2100 was used to detect the insert size of the library. After the insert met the expectation, Q-PCR method was used to accurately quantify the effective concentration of the library to ensure the quality of the library.
38.9G of Raw data was produced, and 36.55G of filtered Clean data was produced
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

source_name: Macrophage

growth_protocol: The mouse macrophage line RAW264.7 were cultured in DMEM (SH30022.01, Hyclone) medium supplemented with 10% FBS (FB15015, Clark), 100 U/ml penicillin and 100 µg/ml streptomycin (SV30010, Hyclone) and placed in a cell culture chamber at 37°C in a humidified atmosphere with 5% CO2. Logarithmic growth phase cells were used for all experiments.

extract_protocol:
Macrophages were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Raw264.7 cell line were infected with the lentivirus (sh-NC/sh-Etv5) in the presence of Lipofectamine 3000 Reagent (L3000001, Invitrogen). Gene or protein expression levels were detected 24 or 48 hours after infection.

tag: cell line

value: Macrophage line Raw264.7

tag: cell line established from

value: Abelson murine leukemia virus-induced tumor

value: post natal day 21

value: Etv5 knockdown


title: Macrophage Raw264.7 sh-Etv5 rep2


title: MAZ HoxA(Δ5|6) MN double pos (Sample 4)


title: plasma microRNA rep7


title: 12H010

value: primary AML cells


title: Macrophage Raw264.7 sh-Etv5 rep1


title: plasma microRNA rep6


title: Macrophage Raw264.7 sh-NC rep3

value: control


title: Macrophage Raw264.7 sh-NC rep1


title: 11H160


title: 11H142


title: Macrophage Raw264.7 sh-NC rep2


title: MAZ_HoxA(Δ5|6)_MN_rep1

data_processing:
Align to mm10 reference genome using tophat 2.1.1 and bowtie2 2.3.1
Reads were assigned to the UCSC mm10 gene annotation
Counts were obtained by using featureCounts v1.6.1
Normalized differential expression (taking into account biological replicates) was calculated by using Deseq2.
Genome_build: mm10
Supplementary_files_format_and_content: counts in txt format

value: MAZ HoxA(delta5_6)


title: 11H027


title: MAZ_HoxA(Δ5|6)_MN_rep2


title: 11H008


title: MAZ_HoxA(Δ5|6)_MN_rep3


title: WT_E14_MN_rep3

value: wild type


title: WT_E14_MN_rep2


title: MAZ_HoxA(Δ5|6)_ESC_rep3

value: Embryonic stem cells


title: WT_E14_MN_rep1


title: MAZ_HoxA(Δ5|6)_ESC_rep2


title: 10H166


title: plasma microRNA rep1

value: Sporadic


title: MAZ_HoxA(Δ5|6)_ESC_rep1


title: plasma microRNA rep3

value: Healthy


title: plasma microRNA rep2


title: 09H115


title: WT_E14_ESC_rep1


title: DAAO RV 7146

city: Boston

first: Fotios

last: Spyropoulos

state: USA

address: 75 Francis Street Thorn 1005

department: Pediatric Newborn Medicine

institute: Brigham and Women's Hospital/Harvard Medical School

data_processing:
Reads (Fastq files) obtained from paired-end sequencing were aligned were to the rat genome (Rnor 6.0) using STAR (v2.7.0a)
Quality control was performed on raw reads and alignment results using fastQC and Qualimap, respectively. Sample clustering was visualized using principal component analysis.
Differential expression analysis was performed using DESeq2 (v1.26.0) using standard parameters, comparing DAAO rats with their controls
Genome_build: Rnor 6.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Heart

extract_protocol:
Hearts were removed, snap frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. RNA quantification and sample integrity were then analyzed using a Nanodrop spectrophotometer and an Agilent 2100 bioanalyzer, respectively.
Library preparation and sequencing were performed by Novogene (Sacramento, CA) using an Illumina Platform PE150.

value: WI

value: Right ventricle free wall


title: WT_E14_ESC_rep3


title: plasma microRNA rep4

value: plasma microRNA


title: 09H083


title: WT_E14_ESC_rep2


title: DAAO RV 7143


title: plasma microRNA rep5


title: Hi-C_Maz_KO_MN_rep2

data_processing:
Overall processing by HiC-bench pipeline
Align to mm10 reference genome internally using bowtie2 2.3.5.1
Create contact matrix in hic format using Juicer 1.5
Genome_build: mm10
Supplementary_files_format_and_content: Contact matrix in hic format

extract_protocol:
Cells were harvested, and 1 M cells were fixed in 2% formaldehyde (Fisher Chemical) according to the ARIMA-HiC protocol.
Libraries were prepared according to ARIMA-HiC protocol by NYU Genome Technology Center.

value: ESC-derived cervical motor neurons

value: Maz -/-


title: 08H138


title: DAAO RV 7142


title: Hi-C_Maz_KO_MN_rep1


title: 08H082


title: DAAO RV 7138


title: Hi-C_WT_E14_MN_rep2


title: Hi-C_Maz_KO_ESC_rep2


title: 07H158


title: Hi-C_Maz_KO_ESC_rep1


title: DAAO RV 7137


title: CTL RV_7123


title: 07H062


title: Hi-C_WT_E14_ESC_rep1


title: Hi-C_WT_E14_ESC_rep2


title: DAAO RV 7135


title: 07H009


title: 07H005


title: CTL RV_7121


title: 06H143


title: 06H133


title: CTL RV_7118


title: CTL RV_7000


title: Hi-C_WT_E14_MN_rep1


title: CTL RV_7120


title: 14SE422_eWAT_RT_miRNA

hyb_protocol: The kit GeneAtlasTM Hybridization, Wash, and Stain Kit for miRNA Array Strips was used following the protocol by Progenika Biopharma (Progenika Biopharma, Grifols, Barcelona, CAT, ES).

data_processing: The Transcriptome Analysis Console (TAC) software version 4.0.2.15 was used to perform quality control, data normalization (using RMA+DABG) and statistical tests. Data were annotated using the “miRNA-4_1-st-v1 Transcript Cluster Annotations” from the 22/9/2016.

source_name: Epididymal White Adipose Tissue_22ºC

label_protocol: From 500ng of each sample, a Poly(A)-tail was first bound to the total RNA with a PolyA Polymerase, and then 3DNA dendrimers were biotin-labeled, following the Affymetrix FlashTagBiotin HSR (Affymetrix) protocol. Then a mix of RNA Spike controls included in the kit was added to the starting RNA to verify that the processing had proceeded as expected.

extract_protocol: Mice were anesthetized by inhalation anesthesia and euthanized by decapitation. Tissue samples were obtained in the morning and were immediately frozen in liquid nitrogen (N2) and then stored at -80 ºC. Tissues were homogenize using the lysis/binding buffer provided in the mirVana miRNA Isolation Kit (Thermo Fisher Scientific, Waltham, MA, USA). Then miRNAs were extracted using this mirVana kit.

tag: age(weeks)

tag: gender

value: Male

tag: temperature(degree celsius)


title: 14SE423_eWAT_RT_miRNA

tag: strain


title: 14SE416_eWAT_Cold_miRNA

source_name: Epididymal White Adipose Tissue_4ºC

tag: stimulus

value: Cold


title: 14SE420_eWAT_RT_miRNA


title: 26996


title: 14SE424_eWAT_RT_miRNA


title: 14SE419_eWAT_Cold_miRNA


title: DAAO LV 7143

tag: tissue

value: Left ventricle + septum tissue


title: 14SE442_iBAT_RT_miRNA

source_name: Interscapular Brown Adipose Tissue_22ºC


title: 14SE437_iBAT_Cold_miRNA

source_name: Interscapular Brown Adipose Tissue_4ºC


title: 14SE439_iBAT_Cold_miRNA


title: 14SE443_iBAT_RT_miRNA


title: 14SE444_iBAT_RT_miRNA


title: 14SE417_eWAT_Cold_miRNA


title: CTL RV_7005


title: 05H111

tag: cell type


title: 25963


title: 14SE434_iWAT_RT_miRNA

source_name: Inguinal White Adipose Tissue_22ºC


title: 14SE418_eWAT_Cold_miRNA


title: 04H112


title: 14SE432_iWAT_RT_miRNA


title: 14SE438_iBAT_Cold_miRNA


title: 14SE433_iWAT_RT_miRNA


title: 26774


title: 11244


title: DAAO LV 7135


title: CTL LV_7123


title: shLuc_ctrl_B

data_processing:
Adaptor trimming with cutadapt v1.18 (parameters: -m 30)
Alignment with STAR v2.6.1a_08-27 (parameters: --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignMatesGapMax 1000000 --alignIntronMin 20 --alignIntronMax 1000000 --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04. For gene annotation, we used the Gencode  v28 annotation. )
Gene counts with featureCounts v1.6.3 (parameters: -p -B -C -Q 10 -O -s 2 -t exon -g gene_id)
Differential gene expression DESeq2 v1.24.0 with the design formula ‘‘condition,’’ and size factor normalization to compare both the weak and the strong KD versus control. We computed and subsequently used the shrunken log2 fold-changes via lfcShrink from DESeq2 with the apeglm method.
Genome_build: hg38
Supplementary_files_format_and_content: We provide raw gene counts for each sample as well as the results of the DESEq2 analysis as described above. In addition, the final results from DESEq2 are provided, with base mean, shrunken log2 fold-change estimates, p-values, normalized read counts per sample, gene names & synonyms & Ensembl IDs

source_name: Cord Blood CD34+

growth_protocol: CD34+ cells were enriched from umbilical cord blood mononucleated cells (MNCs) through magnetic ultrabeads and grown and transduced in cytokine supplemented culture media.

extract_protocol:
RNA was isolated with Trizol reagent plus an additional purification step with RNAeasy Mini columns.
Ovation Human FFPE RNA-Seq Library Systems (Nugen)

treatment_protocol: GFP+ cells were sorted 72 hours post transduction and resuspended in Trizol.

tag: fluorescence

value: GFP

tag: individual

value: pooled

value: Cord Blood CD34+

tag: knockdown


title: 14SE430_iWAT_RT_miRNA


title: 14SE440_iBAT_RT_miRNA


title: CTL LV_7121


title: 04H055

value: primary AML cells


title: DAAO LV 7146


title: CTL LV_7120