title: MLL-r B-ALL

description:
Single-cell RNA-seq data of MLL-r B-ALL infant leukemia.
This Sample represents two replicates.
Library index for replicate 1: TCGCATAA
Library index for replicate 2: TTACCTCC

data_processing:
Raw sequencing files were processed using a standard inDropSeq pipeline available at https://github.com/indrops/indrops
The project yaml file to be used with the inDrops pipeline available at https://github.com/indrops/indrops can be provided upon request.
Quality control, normalization, graph-based clustering and identification of gene signatures were performed using CellRouter (https://github.com/edroaldo/cellrouter).
Prediction of multipotent cells was performed using StemID (https://github.com/dgrun/StemID). Cluster classification was performed using SingleCellNet (https://github.com/pcahan1/singleCellNet/).
We used scImpute to account for drop-out rates in single-cell RNA-seq data (https://github.com/Vivianstats/scImpute).
Genome_build: GRCh38
Supplementary_files_format_and_content: *.tsv, *.csv: Tab- or comma-delimited text files containing gene expression counts.

extract_protocol:
RNA was purified and processed for inDrop according to the protocol from Klein et al. (Cell, 2015, doi:10.1016/j.cell.2015.04.044).
RNA libraries were prepared for sequencing by the inDrop core facility at Harvard Medical School. We used library version v3 where R1 is the biological read. R2 carries the first half of the gel barcode, R3 carries the library index and R4 the second half of the gel barcode, the UMI and a fraction of the polyA tail. Library index for replicate1 is: TCGCATAA; library index for replicate2 is: TTACCTCC.

value: MLL-r B-ALL infant leukemia


title: M. tuberculosis Beijing-Like 323 Day 14 Post Infection Biological Replicate 1 - Technical Replicate 1

status: Public on Mar 24 2022

type: SRA

city: Bogota

first: Juan

middle: Manuel

last: Anzola

state: Bogota

department: Bioinformatics

country: Colombia

institute: CorpoGen

library_source: transcriptomic

data_processing:
1. Quality control using  MULTIQC
2. Adapters and low quality sequence were trimmed with TRIMMOMATIC
3. The mapping was done against the genome reference sequences using SMALT
4. A first mapping process was done against a mouse reference genome (Mus musculus assembly GRC m38.p6). Reads mapping to mouse were removed
5. The rest of the reads were subsequently mapped against MTB H37Rv and to the available BL-323 and BC-391 genomes
6. obtention of  differentially expressed genes was done using SUBREAD package
7. Differentially expressed genes were determined using the tool edgeR.
Assembly: CP010873 (strain 323) and CP017596 (strain 391)
Supplementary files format and content: EdgeR counts of reads mapping to genes in CP010873 and CP017596

molecule: total RNA

organism: Mycobacterium tuberculosis

source_name: Mus musculus

growth_protocol: Clinical isolates were cultured in Middlebrook 7H10 supplemented with 5% glycerol. For the infection of mice, an isolated colony was grown in 60 ml of Middlebrook 7H9 medium supplemented with 5% glycerol, 10% OADC, and 0.02% of Tyloxapol Premium (SIGMA / T8761) without the addition of antibiotics. When bacteria reached the mid-logarithmic growth phase (0.013 for BL-323 and 0.0325 for BC-391 at OD 680), the bacteria were centrifuged at 3,500 rpm, and aliquots of 1-ml were stored at -80ºC until use. For mice infection, each aliquot was evaluated for bacterial concentration by UFCs. For mice infection, 250,000 UFCs/mL in sterile saline solution were used.

extract_protocol:
Lungs stored at -80°C were removed and maintained in liquid nitrogen until processing. All the procedures were handled at 4ºC to avoid RNA degradation. Both mouse lungs were pulverized with liquid nitrogen, and aliquots of lung powder were stored to -80°C until used. To release the bacterial cells, mild-lysis buffer RLT Plus (Cat No: 1053393 Qiagen) supplemented with 10% β-mercaptoethanol was added. After centrifugation at 14,000 rpm/4ºC for 5 min, the bacterial enriched pellet was used for RNA extraction using the Quick-RNA Miniprep Kit (Zymo Research), following the manufacturer's instructions
Depletion of eukaryotic ribosomal subunits was carried out with the Ribo-Zero Kit (llumina® Ribo-Zero Plus rRNA Depletion Kit Cat: 20037135) following the manufacturer's instructions. Depleted RNA (500 ng of each sample) was used to construct libraries using the TruSeq® Stranded mRNA llumina® kit. The fragmentation time was adjusted to 14 min to obtain ~ 200-400 bp inserts, and the PCR enrichment was set to 15 cycles. To ensure good quality and quantity for the libraries, the concentration was verified by Qubit™ dsDNA HS (ThermoFisher Cat: Q32852), and the size of the libraries was verified using Agilent 2100 bioanalyzer System High Sensitivity DNA Kit (Cat: 5067-4626). The libraries with the correct insert size were subjected to bacterial ribosomal subunits depletion with an in-house subtractive hybridization
TruSeq® Stranded mRNA llumina®

treatment_protocol: The progressive pulmonary TB model [20, 21] was used for the transcriptomic assay of Beijing isolates. The bacterial aliquots were thawed and sonicated for 30 seconds at 20kHz to disaggregate the bacterial clumps and held at 4°C until inoculation. Male BALB/c mice, between 6-8 weeks old with ~22 gr weight were used. Mice were anaesthetized with 100% of Sevofluorane in a gas chamber and infected with both Beijing isolates by trachea exposure using a total of 250,000 bacteria

tag: tissue

value: Lungs

tag: strain

value: Balb/c


title: small RNA-seq: A549-AtRDR1 (+)Dox-siNC

city: Beijing

first: Li

last: Ding

state: Beijing

address: No.5, Yiheyuan Road

country: China

institute: Peking University

description:
smallRNA_siAGO2.csv
small_RNA_seq_A549-At-siNC

data_processing:
To analyze polyA(+) RNA-seq data, adapters of raw data were trimmed with Trimmomatic software. The quality of these data was evaluated by FastQC software. HISAT2 software with default parameters was used to align sequences to the human genome (hg38, UCSC) and the mouse genome (mm10, UCSC) based on the origin of the cell lines. Output files after sequence alignment were used to obtain gene count matrix with featureCounts software using corresponding UCSC RefSeq as gene annotations. For further analyses, gene counts in each sample were normalized to the total reads of the library to calculate reads per million (RPM).
Perl and python scripts were used to analyze small RNA-seq data. Adapters of sequences were trimmed and sequences with a length of 19-25nt were retained. To build the index of miRNA, we downloaded the mature miRNA sequences from miRBase, 3nt upstream and 3nt downstream of mature miRNA were added to the references. Each sequence was aligned to the reference using Bowtie software using the following parameters: -a -v 1 -3 3.In order to compare the miRNA expression in the line, the count of miRNAs was normalized. In RDR1 expression group, two ways were used to normalize miRNA data. Fly miRNA was added as spike-in in some samples. In non-spike-in method (including A549, HeLa, HepG2, HCT116 and NIH/3T3), the numbers of miRNAs were normalized to the numbers of total reads of the corresponding library to calculate RPM. In spike-in method (including H1299, Jurkat and RPE-1), the number of miRNAs was multiplied by a factor to make the count of fly miRNAs equal in all samples in a cell line. We used the top-10 highest expressed miRNAs as reference, which did not contain identical miRNAs in fly and human/mouse. Each of these 10 miRNAs was used to calculate a factor and the mean of these 10 factors was used as the factor for this sample for normalization. After normalization between samples within cell lines, the normalized reads of the sample with higher miRNA expression level was set at one million. In cell cycle inhibition, AGO2-CLIP and AGO2 knockdown experiments, miRNA expression was normalized with non-spike-in method. Some cell lines of RDR1 expression group were used in this analysis (A549, HeLa, HepG2). In order to be consistent with the previous analysis in RDR1 expression group, the normalized reads of the sample with higher miRNA expression level of RDR1 expression group was set at one million. In the miR-34c transfection assay, miRNA expression was normalized to the expression of endogenous miRNA, which was set at one million.
Assembly: hg38
Supplementary files format and content: Gene expression matrix; miRNA expression matrix

organism: Homo sapiens

extract_protocol:
TRIzol reagent (Invitrogen) was used to isolate total RNA according to the manufacturer’s instructions.
RNA-seq libraries preparation using the TruSeq Stranded mRNA Sample Prep Kits (Illumina), VAHTS Stranded mRNA-seq Library Prep Kits (Vazyme) and VAHTS Ribo-off Globin & rRNA Depletion Kits(Vazyme). Small RNA-seq libraries preparation using the NEBNext® Small RNA Library Prep Set for Illumina kits. Single-cell RNA-seq libraries preparation using the Chromium Next GEM Single Cell 3’ Kit v3.1 (10x Genomics).

tag: cell type and treatment

value: A549-AtRDR1 with Dox induction for 2 days and transfected with siNC for next 2 days

tag: genotype

value: WT

tag: cell line

tag: fraction

value: Gel-purified 15-50nt small RNAs


title: Aramis_igg2

city: Albany

first: Prashanth

last: Rangan

state: NY

address: 1400 Washington

department: Biological Sciences

country: USA

institute: RNA Institute

data_processing:
Sequenced reads were aligned to the M21017.1 NCBI Drosophila rRNA sequence record using HISAT2 (version 2.1.0)
Raw counts were generated using featureCounts (version 1.4.6.p5)
For total RNA IP experiments, expression was normalized to the matched inputs and a luciferase spike-in. Enrichment was assesed compared to the IgG control.
Genome_build: M21017.1 NCBI Drosophila rRNA sequence
Supplementary_files_format_and_content: tabular file (count table)

organism: Drosophila melanogaster

source_name: Ovaries

growth_protocol: Flies were fattened on yeast prior to dissection, ovaries were dissected in 1x PBS.

extract_protocol:
RNA was isolated using TRIzol (Invitrogen, 15596026), treated with DNase (TURBO DNA-free Kit, Life Technologies, AM1907).  mRNA-enriched libraries were obtained by treating total RNA with poly(A)tail selection beads following the manufacturer's instructions of the NEXTflex Rapid Directional RNAseq Kit (Bioo Scientific Corp, NOVA-5138-08)
Following the manufacturer's instructions of the NEXTflex Rapid Directional RNAseq Kit (Bioo Scientific Corp, NOVA-5138-08), except RNA was fragmented for 13 minutes

treatment_protocol: Samples in the characteristics "RIP antibody" field:  those with "IP" were subected to IP with an antibody against FLAG conjugated to the protein indicated, those with "IgG" were subjected to IP using control mouse IgG, and those with "Input" consisted of 10% of the total lysate reserved for RNA extraction using Trizol.

tag: group

value: Aramis

tag: dissection

value: dissected 1-3 days post-eclosion

tag: experiment

value: rRNA IP seq

tag: rip antibody

value: IgG

value: Ovaries


title: small RNA-seq: A549-AtRDR1 (+)Dox-siAGO2

description:
smallRNA_siAGO2.csv
small_RNA_seq_A549-At-siAGO2

source_name: A549-AtRDR1 stable cell line

value: A549-AtRDR1 with Dox induction for 2 days and transfected with siAGO2 for next 2 days

value: A549-AtRDR1 stable cell line


title: MZY-2018051001-1

city: Wuhan

first: Dong

last: Li

state: Hubei

address: No.1095 Jie Fang Avenue

institute: Tongji Hospital, Tongji Medical College,Huazhong University of Science and Technology

data_processing:
The raw reads were manufactured by removing containing adapter, poly‘N’, low quality and <17nt reads using FASTQC to acquire clean reads.
Mapping reads were got by mapping clean reads to reference genome of BWA
The miRDeep2 was used to recognize known mature miRNAs according to miRBase21 (www.miRBase.org) and to predict novel miRNAs.
The miRNA expression were counted by Reads Per Million (RPM) values
Assembly: hg19
Supplementary files format and content: text files include all detected miRNAs

source_name: Exosome

extract_protocol:
Blood were obtained from healthy volunteers or patients with SV who have not received any treatments for at least three months.Plasma exosomes and exosomal RNA of 15 samples were extracted and purified by exoRNeasy Maxi Kit.Appropriately 50ng exosomal RNA of each samples was used to establish small RNA libraries by NEBNext® Multiplex Small RNA Library Prep Set for Illumina
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age(years)

tag: gender

value: Female

tag: disease state

value: segmental vitiligo (SV) patient

tag: cell type

value: Exosome


title: Aramis_igg1


title: M. tuberculosis Beijing-Like 323 Day 14 Post Infection Biological Replicate 2 - Technical Replicate 2


title: Bam RNA-seq 2

data_processing:
Sequenced reads were aligned to the D. melanogaster genome (UCSC dm6) using HISAT2 (version 2.1.0)
Raw counts were generated using featureCounts (version 1.4.6.p5)
For RNA-seq samples differential gene expression was assayed by DEseq2 (version 1.24.0), using a false discovery rate of (FDR) of 0.05, and genes with >|1.5| log2(foldchange)  were considered significant.
Genome_build: UCSC dm6
Supplementary_files_format_and_content: tabular file (count table)

molecule: polyA RNA

value: mRNA-seq

value: UAS-Dicer2;NosGAL4 > bam RNAi


title: 2018072804-HG

value: Male


title: MLP

city: Boston

first: Edroaldo

last: Lummertz da Rocha

state: MA

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

description: processed data file: rawcounts.txt

data_processing:
Alignments were performed with TopHat2.
Counts were generated using featureCounts.
Normalization was performed with DESeq2.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: rawcounts.txt: Tab-separated text file containing gene expression counts.

source_name: Cells sorted by FACS

growth_protocol: Not applicable

extract_protocol:
RNA was isolated using RNeasy columns (Qiagen) and low input libraries prepared in collaboration with the Molecular Biology Core at the Dana-Farber Cancer Institute.
RNA-seq libraries were prepared by The Center for Cancer Computational Biology (CCCB), Dana-Farber Cancer Institute, Boston MA using NEB Ultra Directional RNA library prep kit for Illumina and sequenced using Illumina NextSeq 500 Single Read 75.

treatment_protocol: Not applicable

value: Sorted CD34+CD38-CD90-CD45RA+ leukemic multilymphoid progenitors (L-MLPs)


title: M. tuberculosis Beijing-Like 323 Day 3 Post Infection Biological Replicate 3 - Technical Replicate 4

value: Lungs

value: Balb/c


title: M. tuberculosis Beijing-Like 323 Day 3 Post Infection Biological Replicate 3 - Technical Replicate 3


title: MLP_1

description: processed data file: rawcounts.txt


title: Bam RNA-seq 1


title: 2018090601-FWJ


title: M. tuberculosis Beijing-Like 323 Day 3 Post Infection Biological Replicate 3 - Technical Replicate 2


title: GMP

description: processed data file: rawcounts.txt

value: Sorted CD34+CD38+CD90-CD45RA+ leukemic GMPs (L-GMPs)


title: 2018080104-MJS


title: Aramis RNA-seq 2

value: UAS-Dicer2;NosGAL4 > aramis RNAi


title: 2018072304-DJC


title: Aramis RNA-seq 1

value: dissected 1-3 days post-eclosion


title: M. tuberculosis Beijing-Like 323 Day 3 Post Infection Biological Replicate 3 - Technical Replicate 1


title: GMP_2

description: processed data file: rawcounts.txt


title: M. tuberculosis Beijing-Like 323 Day 14 Post Infection Biological Replicate 2 - Technical Replicate 1


title: GMP_1

description: processed data file: rawcounts.txt


title: M. tuberculosis Beijing-Like 323 Day 3 Post Infection Biological Replicate 2 - Technical Replicate 4


title: Array4

description:
Early passage Single-cell RNA-seq data of human MLL-r B-ALL PDX model.
processed data file: reads.Array4_R1.fastq_bq10_star_corrected.umi.dge.txt.gz
processed data file: scimpute_count_Leukemia.csv

data_processing:
Reads were first aligned to hg19, and individual reads were tagged according to the 12-bp barcode sequence and the 8-bp UMI contained in read 1 of each fragment. Following alignment, reads were binned and collapsed onto 12-bp cell barcodes that corresponded to individual beads using Drop-seq tools (http://mccarrolllab.com/dropseq). Barcodes were collapsed with a single-base error tolerance (Hamming distance = 1), with additional provisions for single insertions or deletions. An identical collapsing scheme (Hamming distance = 1) was then applied to UMIs to obtain quantitative counts of individual mRNA molecules.
Quality control, normalization, graph-based clustering and identification of gene signatures were performed using CellRouter (https://github.com/edroaldo/cellrouter).
Prediction of multipotent cells was performed using StemID (https://github.com/dgrun/StemID). Cluster classification was performed using SingleCellNet (https://github.com/pcahan1/singleCellNet/).
We used scImpute to account for drop-out rates in single-cell RNA-seq data (https://github.com/Vivianstats/scImpute).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt, *.csv: Tab- or comma-delimited text files containing gene expression counts.

source_name: Human MLL-r B-ALL purified from mouse spleen (PDX) by FACS, replicate 2

extract_protocol: RNA was prepared following the Seq-Well protocol (Gierahn et al., Nature Methods, 2018).

value: MLL-r B-ALL PDX model


title: LQ-N007-1

value: Healthy person


title: M. tuberculosis Beijing-Like 323 Day 14 Post Infection Biological Replicate 1 - Technical Replicate 3


title: M. tuberculosis Beijing-Like 323 Day 3 Post Infection Biological Replicate 2 - Technical Replicate 3


title: WX-N004-1


title: XD-2018050704-1


title: MLL-r B-ALL Replicate 1

description: CITE-seq data of MLL-r B-ALL infant leukemia

data_processing:
Raw sequencing files were processed using a DropEst pipeline
Quality control, normalization, graph-based clustering, gene signatures were performed using CellRouter
The project yaml file to be used with the indrops pipeline available at https://github.com/indrops/indrops can be provided upon request
Quality control, normalization, graph-based clustering and identification of gene signatures were performed using CellRouter (https://github.com/edroaldo/cellrouter)
Prediction of multipotent cells was performed using StemID (https://github.com/dgrun/StemID).
We used scImpute to account for drop-out rates in single-cell RNA-seq data (https://github.com/Vivianstats/scImpute)
Genome_build: GRCh38
Supplementary_files_format_and_content: .rds files containing gene expression counts

source_name: Peripheral blood

extract_protocol:
RNA was purified and proccessed for indrop according to the protocol from Klein et al (Cell, 2015, doi:10.1016/j.cell.2015.04.044)
RNA libraries were prepared for sequencing by the indrop core facility at Harvard Medical School. We used library version v3 where R1 is the biological read. R2 carries the first half of the gel barcode, R3 carries the library index and R4 the second half of the gel barcode, the UMI and a fraction of the polyA tail.

tag: replicate

value: Replicate 1

tag: library index

value: TTACCTCC

value: MLL-r B-ALL infant leukemia


title: Ago2&1_1 [ATAC-seq]

city: Zurich

first: Constance

last: Ciaudo

email: cciaudo@ethz.ch, ciaudobeyer@gmail.com

address: Otto-Stern-Weg 7

department: D-BIOL

country: Switzerland

institute: ETH

library_source: genomic

data_processing:
Trim Galore/cutadapt adapter trimming (--nextera –paired)
Bowtie2 read mapping
Filtering of PCR duplicates, mapping quality (mapq > 3) and fragment size ( < 150)
Genrich peak calling
Differential accessibility with CSAW_EdgeR, taking into account FRiP-based normalization
Genome_build: ENSEMBL GRCm38 v98
Supplementary_files_format_and_content: bigwig, narrowPeak (coverage files and called peaks)

molecule: genomic DNA

organism: Mus musculus

growth_protocol: mESCs have been grown in medium supplemented with Serum+LIF

extract_protocol:
Performed by Quick Biology Inc.: 50.000 cells were washed and lysed to generate a crude nuclei preparation, according to the protocol described in (M Ryan Corceset al., 2017)
Performed by Quick Biology Inc.: Tn5 transposase tagmentation simultaneously fragmented the genome and tagged the resulting DNA with Illumina sequencing adapters, according to the protocol described in (M Ryan Corceset al., 2017). DNA fragments were PCR amplified and subsequently purified using Qiagen MinElute PCR Purification Kit (Qiagen, Maryland, USA).

treatment_protocol: Two million cells per sample were trypsinized and resuspended in DMSO+10%FBS. Cells were frozen and sent to Quick Biology Inc.

value: Embryonic stem cells

tag: strain background

value: 129/Ola background

value: Blastocyst

value: Ago2&1 KO


title: Ago2&1_2 [ATAC-seq]

tag: tissue


title: M. tuberculosis Beijing-Like 323 Day 3 Post Infection Biological Replicate 2 - Technical Replicate 2

tag: strain


title: 34neg_regen

description: processed data file: rawcounts.txt

value: Sorted CD34- cells undergoing regeneration


title: TJ013-WXY

value: Female

value: Exosome


title: Ago2_2 [ATAC-seq]

value: Ago2 KO


title: 34neg_regen_2

description: processed data file: rawcounts.txt


title: M. tuberculosis Beijing-Like 323 Day 3 Post Infection Biological Replicate 2 - Technical Replicate 1

value: Lungs

value: Balb/c


title: 34neg_regen_1

description: processed data file: rawcounts.txt


title: TJ010-XYY

value: Male


title: M. tuberculosis Beijing-Like 323 Day 3 Post Infection Biological Replicate 1 - Technical Replicate 4


title: MLP_2

description: processed data file: rawcounts.txt

value: Sorted CD34+CD38-CD90-CD45RA+ leukemic multilymphoid progenitors (L-MLPs)


title: Ago2_1 [ATAC-seq]


title: TJ011-WTT


title: 34neg

description: processed data file: rawcounts.txt

value: Sorted CD34- cells


title: Ago1_2 [ATAC-seq]

value: Ago1 KO


title: M. tuberculosis Beijing-Like 323 Day 3 Post Infection Biological Replicate 1 - Technical Replicate 3


title: TJ016-WYF

value: Healthy person


title: 34neg_2

description: processed data file: rawcounts.txt


title: Ago1_1 [ATAC-seq]


title: TJ019-ZYH


title: M. tuberculosis Beijing-Like 323 Day 3 Post Infection Biological Replicate 1 - Technical Replicate 2


title: 34neg_1

description: processed data file: rawcounts.txt


title: WT_2 [ATAC-seq]

value: WT


title: M. tuberculosis Beijing-Like 323 Day 3 Post Infection Biological Replicate 1 - Technical Replicate 1


title: WT_1 [ATAC-seq]


title: TJ017-LYY


title: CUTRUN_NFIA_HUDEP2 clone 6_NFI-451

status: Public on Mar 23 2022

city: Philadelphia

first: KUNHUA

last: QIN

email: qink@chop.edu, kunhua.qin@gmail.com

state: PA

address: 3615 Civic Center Blvd, 315H

institute: Children's Hospital of Philadelphia

data_processing:
Library strategy: CUT&RUN-seq
CUT&RUN sequencing reads were analyzed by CUT-RUNTOOLS-2.0 (https://github.com/fl-yu/CUT-RUNTools-2.0).
Genome_build: hg38
Supplementary_files_format_and_content: BigWig

source_name: HUDEP2 clone 6

growth_protocol: HUDEP2 Cells were maintained in a medium containing StemSpan SFEM (9650, StemCell Technologies) supplemented with 50 ng/mL recombinant human stem cell factor (300-07, Peprotech), 3 IU/mL Epoetin alfa (Epogen, Amgen), 0.4 μg/mL dexamethasone (D9891, Sigma Aldrich), 1 μg/mL doxycycline (D9891, Sigma Aldrich) and 1% Pen-Strep (15140122, Invitrogen). Erythroid differentiation was induced by placing 2-5 million HUDEP-2 cells into 1x Iscove’s modified Dulbecco’s medium (IMDM, MT10016CV, Mediatech) supplemented with 1% L-glutamine, 330 μg/mL human holo-transferrin (T4132, Sigma Aldrich), 10 μg/mL recombinant human insulin solution (I9278, Sigma Aldrich), 2 IU/mL heparin, 5% inactivated fetal biovine serum (FBS), 3 IU/mL Epoetin alfa (Epogen, Amgen), 1 μg/mL doxycycline and 1% Pen-Strep.

extract_protocol:
0.5-1 million undifferentiated HUDEP2, HUDEP2 undergoing 2 days of differentiation, and primary cells undergoing 8 days of erythroid differentiation were used for CUT&RUN. We followed the experimental procedure published by Henikoff lab (dx.doi.org/10.17504/protocols.io.bcuhiwt6) with adaptations15. Antibody incubation was performed in 300μl PCR tubes for 2 hours in the cold room. pA/G-MNase and Spike-In DNA (#40366) were obtained from Cell Signaling. The following antibodies were used: IgG (#3900, Cell signaling), BCL11A (ab191401, Abcam), NFIA (PA5-52252, Thermo Fisher Scientific), NFIX (SAB1401263, Sigma Aldrich), GATA1(Ab11852, Abcam), H3K27Ac (MA5-23516, Invitrogen). All antibodies were used approximately 1μg in 100μl.
The concentration of the released DNA fragments was determined by Qubit and 15-30ng DNA was used for adapter ligation and library construction. The sequencing libraries were generated using the kit from NEB (Cat# E7645 and E6440S). We followed the experimental procedure posted by Nan Liu (dx.doi.org/10.17504/protocols.io.wvgfe3w) to size select the <120 bp fragment and facilitate the transcription faction binding site identification20. The multiplexed sequencing libraries were pair-end (2x50bp) sequenced on Illumina Nextseq 2000 platform.

treatment_protocol: We established the Cas12a stably expressing HUDEP-2 using pRG232 (#149723, Addgene) and puromycin selection. Control and NFIA&NFIX Cas12a gRNA oligos were subcloned into lentiviral pRG212 (#149722, Addgene) using BsmBI restriction site, and then introduced into HUDEP2 cells by lentivirual infection

value: HUDEP2 clone 6

tag: differentiation

value: undifferentiated

tag: antibody

value: NFIA

tag: biological replicate

tag: treatment

value: NFI-451 gRNA


title: CUTRUN_NFIA_K562_NFI+202

tag: cell line

value: NFI+202 gRNA


title: CUTRUN_NFIA_K562_NFI-451


title: CUTRUN_NFIA_HUDEP2 clone 6_NFI+202


title: CUTRUN_NFIA_K562_ctrl

value: no


title: CUTRUN_NFIA_HUDEP2D2_+23


title: CUTRUN_NFIA_HUDEP2D2_+58.4


title: CUTRUN_NFIA_Primary_Perpheral Blood_Invitrogen#535936

source_name: Primary_Peripheral Blood

value: Peripheral Blood


title: CUTRUN_NFIA_HUDEP2D2_+58


title: CUTRUN_NFIA_Primary_Perpheral Blood_Activemotif#39397


title: CUTRUN_NFIA_Primary_Fetal Liver_Rep2

source_name: Primary_Fetal Liver

value: Fetal Liver


title: CUTRUN_NFIA_Primary_Fetal Liver_Rep1


title: CUTRUN_NFIA_Primary_Perpheral Blood_Sigma#HPA008884


title: Mitf_control3

city: Taigu

first: Lijun

last: Zhao

state: Shanxi

address: No. 1 Mingxian South Road,Taigu,  Shanxi Province, China

department: College of Veterinary Medicine

institute: Shanxi Agricultural University

data_processing:
Remove the 3 'connector and garbage sequence: obtain clean data.
Length screening: the sequences with the base length between 18-25nt for plants and 18-26nt.
Comparison and analysis of various RNA databases: the remaining sequences (excluding miRNA) were compared with mRNA, RFam and Repbase databases and filtered.
MiRNA identification: Obtain valid data and identify miRNA by comparing precursor and genome.
Difference analysis of miRNA and  Prediction analysis of miRNA target genes.
Assembly: mm9
Supplementary files format and content: Overview_of_reads_from_raw_data_to_cleaned_sequences.xlsx: Reads conts from raw_data to cleaned_data.
Supplementary files format and content: All_Expressed_miRNA.xlsx: MiRNAs expressed in all samples
Supplementary files format and content: Mitf_oevsMitf_control.xlsx: Differential miRNA expression

source_name: melanocyte

growth_protocol: Melan-α cells and MITF-overexpression melan-α cells were cultured in medium RPMI 1640 +10%FBS.

extract_protocol:
Melan-α cells were  collected  and washed,TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA) Kits were used to prepare Small RNA sequencing libraries.
miRNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: MITF-overexpression melan-α cells were that melan-α cell were infected with lentivirus including mice MITF gene.

value: Mus skin

value: melan-alpha

tag: genotype

tag: source

value: Extracellular vesicle


title: Mitf_OE1


title: Mitf_OE3


title: Mitf_OE2


title: Mitf_control2


title: Mitf_control1


title: PSA-activated MHCII+ antigen presenting cells 3

city: Cleveland

first: Brian

middle: A

last: Cobb

state: OH

address: 10900 Euclid Avenue, WRB 5132

department: Pathology

institute: Case Western Reserve University School of Medicine

description:
PSA-activated MHCII+ APCs from adult mouse spleen
MD18

data_processing:
data QC Cutadapt/perl
Alignment Tophat v1.4.1
Assembly Cufflinks v2.2.1
Differential Expression Cufflinks v2.2.1 Cuffdiff module of Cufflinks and the q-value (False-Discover-Rate adjusted p-value) of 0.05 is used as the cutoff to define genes showing significant difference
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: MS Excel format containing RPKM values and statistical p values

source_name: spleen

growth_protocol: Cells were cultured in Gibco Advanced RPMI1640 media with 10% fetal bovine serum for the indicated number of days at 37C with 5% CO2

extract_protocol:
Qiagen RNeasy
RNA library is prepared according to Illumina's protocol1 and sequencing is conducted on Illumina HiSeq 2500. The 3' adaptor (TGGAATTCTCGGGTGCCAAGG) for sequencing is removed from the raw reads. After removing the 3' adaptor, reads with the length less than 10 nt are excluded. The remaining reads are aligned against genome using Tophat v1.4.12 and assembled using Cufflinks v2.2.13. The abundance is estimated in Fragments Per Kilobase of transcript per Million mapped reads (FPKM) as defined in Cufflinks. Differential expression analysis is conducted using the Cuffdiff module of Cufflinks and the q-value (False-Discover-Rate adjusted p-value) of 0.05 is used as the cutoff to define genes showing significant difference.

treatment_protocol: Cells were either untreated (no PSA, day zero, freshly isolated) or stimulated with 50 ug/ml PSA for 24 hours/1 day

value: antigen presenting cell MHCII+


title: PSA-activated MHCII+ antigen presenting cells 1

description:
PSA-activated MHCII+ APCs from adult mouse spleen
MD14


title: PSA-activated MHCII+ antigen presenting cells 2

description:
PSA-activated MHCII+ APCs from adult mouse spleen
MD16


title: resting MHCII+ antigen presenting cells

description:
resting MHCII+ APCs from adult mouse spleen
MC23


title: Sample 58

city: Ulm

first: Johannes

last: Doescher

state: Deutschland

address: Frauensteige 12

department: Otorhinolaryngology, Head and Neck Surgery

country: Germany

institute: University hospital of Ulm

data_processing:
Sequencing output basecalls were converted into FASTQ and demultiplexed using module bcl2fastq2/2.18 on IRIDIS HPS (UoS), adding the option --barcode-mismatches 0.
FASTQ files were parsed on HTG EdgeSeq parser (v 5.2.823).
Construction of  a gene expression count matrix for each gene and each patient. They were merged to form a single output file containing all genes and all counts.
HTG Reveal, a web-based, GDPR-compliant data analysis suite.
Quality control of RNA sequencing data was performed in line with recommendations from HTG, to satisfy cut-offs for sample quality, sufficient read depth and minimal expression variability across probes.
Differential expression was assessed using DESeq2 package (R version 4.1.1).
Principal component analyses were done with PCAtools package (R version 4.1.1)
Immune signature analysis was done on the software platform HTG REVEAL.
Genome_build: NA; known sequences designed by the product manufacturer.
Supplementary_files_format_and_content: Raw gene count matrix, csv

extract_protocol:
Tissues were lysed using HTG Lysis Buffer, followed by proteinase K digestion and dilution if necessary.
RNA samples were thawed, diluted and 35µl of each sample was plated in 24 wells and loaded onto the HTG EdgeSeq instrument. HTG fully automated nuclease target protection chemistry includes hybridization of mRNA to target-specific Nuclease Protection Probes (NPPs), addition of S1 nuclease to digest excess NPPs and non-hybridized RNA followed by heat denaturation of S1. The processed samples contain 5’ and 3’-end wing sequences and were used as a template for PCR reactions with primers complementary to the “wings” which also contain barcode sequences and common adaptors required for cluster generation and sequencing (P5, P7). Libraries were cleaned-up following a standard clean-up procure (AMPureXP, PEG8000) and quantified with qPCR using KAPA Library quantification (Roche) kit. Libraries were normalized accordingly, were pooled in a 3pM concentration and were loaded on the Illumina NextSeq500 for single read deep sequencing (Read1: 50bp, Index1: 6bp, Index2: 6bp).

value: Head and neck mucosa

tag: type

value: FFPE

tag: response

value: CR

tag: batch

value: three

tag: timepoint

value: post

tag: subject id

value: Patient 32


title: Sample 60

value: Patient 33


title: Sample 59

value: pre


title: Sample 57

value: four


title: Sample 55

value: Patient 31


title: Sample 54

value: RM

value: Patient 29


title: Sample 56


title: Sample 51

value: Patient 28


title: Sample 52


title: Sample 53


title: Sample 50

value: Patient 27


title: Sample 49


title: Sample 48

value: Patient 26


title: Sample 47


title: Sample 46

value: Patient 25


title: Sample 45


title: Sample 44

value: Patient 24


title: Sample 42

value: Head and neck mucosa

value: Patient 23


title: Sample 38

value: FFPE

value: two

value: Patient 21


title: Sample 43

value: three


title: Sample 39

value: Patient 22


title: Sample 35

value: CR

value: pre

value: Patient 20


title: Sample 37

value: RM


title: Sample 32

value: four

value: post

value: Patient 18


title: Sample 33

value: Patient 19


title: Sample 34


title: Sample 36


title: Sample 29

value: PR

value: Patient 17


title: Sample 30

value: Head and neck mucosa


title: Sample 31


title: Sample 26

value: Patient 15


title: Sample 27

value: FFPE

value: Patient 16


title: Sample 28


title: Sample 24

value: Patient 14


title: Sample 25

value: two


title: Sample 21

value: Patient 13


title: Sample 22

value: CR


title: Sample 20

value: Patient 12


title: Sample 18

value: Patient 11


title: Sample 17

value: pre


title: Sample 19


title: Sample 15

value: RM

value: one

value: Patient 9


title: Sample 14

value: post

value: Patient 8


title: Sample 13

value: Patient 7


title: Sample 12

value: Head and neck mucosa

value: PR

value: Patient 5


title: Sample 11

value: FFPE

value: Patient 4


title: Sample 41

value: three

value: Patient 23


title: Sample 10

value: Patient 3


title: Sample 8

value: Patient 10


title: Sample 6


title: Sample 7


title: Sample 40

value: four

value: Patient 22


title: Sample 3

value: pre


title: Sample 1

value: one

value: Patient 2


title: Sample 5

value: RM


title: Sample 4


title: Sample 2


title: RNA-seq_NFIA/X_gRNA2_rep1

data_processing:
The sequence reads were processed using the ENCODE3 long RNA-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL002LPE/).
Gene set Gencode v29 was used for mapping the reads to the human genome (hg38 assembly) using STAR, followed by RSEM for gene quantifications.
Genome_build: hg38 assembly
Supplementary_files_format_and_content: TSV Files

growth_protocol: Erythroid differentiation was induced by placing 2-5 million HUDEP-2 cells into 1x Iscove’s modified Dulbecco’s medium (IMDM, MT10016CV, Mediatech) supplemented with 1% L-glutamine, 330 μg/mL human holo-transferrin (T4132, Sigma Aldrich), 10 μg/mL recombinant human insulin solution (I9278, Sigma Aldrich), 2 IU/mL heparin, 5% inactivated fetal biovine serum (FBS), 3 IU/mL Epoetin alfa (Epogen, Amgen), 1 μg/mL doxycycline and 1% Pen-Strep.

extract_protocol:
RNA samples were harvested in TRIzol (ThermoFisher Scientific) and purified with the RNeasy Mini kit (Qiagen). For RNA-Seq, approximately 200 ng of RNA was then depleted for rRNA and globins using the Ribo-Zero removal reagents and protocol from the ScriptSeq Complete kit (Illumina Cat # BHMR1224), followed by purification using the RNeasy MinElute Clean Up kit (Qiagen Cat # 74202).
Sequencing libraries were then constructed from depleted RNA using the TruSeq Stranded Total RNA kit (Illumina Cat # 20020598) and PCR-amplified for 13 cycles. The size and quality of each library were then evaluated by Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA), and quantified using qPCR. Libraries were sequenced in paired-end mode on the NextSeq 500 to generate 2 x 76 bp reads using Illumina-supplied kits as appropriate.
The sequence reads were processed using the ENCODE3 long RNA-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL002LPE/). Gene set Gencode v29 was used for mapping the reads to the human genome (hg38 assembly) using STAR, followed by RSEM for gene quantifications.

treatment_protocol: For Cas9 mediated-genome editing in HUDEP-2 and fetal liver experiments, we used optimized SpCas9 gRNA scaffold viral vectors to introduce the gRNA into the spCas9 expressing cells as described previously. Cas9  gRNA oligos were subcloned into lentiviral pLRG2.1 (#108098, Addgene) and pLRCherry2.1 (#108099, Addgene)  using BsmBI restriction site.

tag: differeniation days

value: Day 5

tag: data file subset

value: RNASeq

value: NFIA/X DKO


title: RNA-seq_NFIA/X_gRNA2_rep2


title: RNA-seq_NFIA/X_gRNA1_rep2


title: RNA-seq_NFIA/X_gRNA1_rep1


title: RNA-seq_NFIX_gRNA2_rep2

value: NFIX KO


title: RNA-seq_NFIX_gRNA2_rep1


title: RNA-seq_NFIX_gRNA1_rep2


title: RNA-seq_NFIX_gRNA1_rep1


title: Sample 23

value: Head and neck mucosa

value: CR

value: two

value: Patient 14


title: RNA-seq_NFIA_gRNA2_rep2

value: NFIA KO


title: RNA-seq_NFIA_gRNA1_rep2


title: RNA-seq_NFIA_gRNA2_rep1


title: RNA-seq_Negative_gRNA_rep1

value: Control


title: RNA-seq_Negative_gRNA_rep2


title: RNA-seq_NFIA_gRNA1_rep1


title: Sample 16

value: FFPE

value: post

value: Patient 10


title: CUTRUN_NFIA_Primary_Perpheral Blood_Rep2

source_name: CD34+ derived primary erthroblasts

value: NFIA

value: no


title: CUTRUN_NFIX_Primary_Perpheral Blood_Rep2

value: NFIX


title: CUTRUN_H3K27Ac_Primary_Perpheral Blood


title: CUTRUN_NFIX_Primary_Perpheral Blood_Rep1


title: CUTRUN_IgG_Primary_Perpheral Blood_Rep2

value: IgG


title: CUTRUN_IgG_Primary_Perpheral Blood_Rep1


title: Sample 9

value: PR

value: one

value: Patient 2


title: CUTRUN_NFIA_K562_Rep1

value: undifferentiated


title: CUTRUN_NFIA_K562_Rep3


title: CUTRUN_NFIA_HUDEP2_clone6_Rep1


title: CUTRUN_NFIX_HUDEP2_WT


title: CUTRUN_NFIA_K562_Rep2


title: CUTRUN_NFIX_HUDEP2_KO

value: NFIX KO


title: CUTRUN_NFIA_HUDEP2_WT


title: ATAC_HUDEP2_Control_Rep2

data_processing:
Data were processed using CUT&RUNTOOLS2 with the default setting for CUT&Tag
Genome_build: hg38
Supplementary_files_format_and_content: BigWig

growth_protocol: HUDEP2 Cells were maintained in a medium containing StemSpan SFEM (9650, StemCell Technologies) supplemented with 50 ng/mL recombinant human stem cell factor (300-07, Peprotech), 3 IU/mL Epoetin alfa (Epogen, Amgen), 0.4 μg/mL dexamethasone (D9891, Sigma Aldrich), 1 μg/mL doxycycline (D9891, Sigma Aldrich) and 1% Pen-Strep (15140122, Invitrogen).

extract_protocol:
50,000 undifferentiated HUDEP-2 cells were washed with cold PBS and lysed in a modified Omni-ATAC-seq lysis buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% Tween-20 and 0.01% Digitonin) for 3 min. The lysates were washed 3 times with buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM MgCl2 and 0.1% Tween-20) and spin at 500g for 10min to harvest the nuclei. Transposition reaction was performed using Illumina Tagment DNA Enzyme and Buffer (Cat# 20034197) in the presence of 0.1% Tween-20 and 0.01% Digitonin. DNA was isolated using Qiagen MinElute Reaction Cleanup Kit.
Sequencing libraries were generated by using NEB High Fidelity 2x PCR Master Mix and amplified for 9 cycles using the following cycles: (1) 72°C, 5 min (2) 98°C, 30 sec (3) 98°C, 10 sec (4) 63°C, 30 sec (5) 72°C, 1 min (6) Repeat steps 3-5, 4x (7) Hold at 4°C. The amplified DNA fragments were cleaned and size-selected by SPRIselect beads. The libraries were pair-end (2x50bp) sequenced on Illumina Nextseq  platform

tag: biolobical replicate

tag: differeniation stage

value: Expansion


title: CUTRUN_NFIA_HUDEP2_KO


title: ATAC_HUDEP2_NFIKO_Rep1

value: NFIA&NFIX KO


title: ATAC_HUDEP2_Control_Rep1


title: ATAC_HUDEP2_NFIKO_Rep2


title: KO1_DK

city: Guangzhou

first: Jie

last: Chen

address: No. 58, Zhongshan 2nd Road, Yuexiu District, Guangzhou

institute: The First Affiliated Hospital of Sun Yat-sen University

description:
small RNA
TRAC-seq

data_processing:
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as Reads per kilo base per million mapped reads (RPKM) using edegR.
For Ribo-Seq data analysis, Adapter sequences were trimmed and low quality sequences (Q30) were discarded using trim_galore. The sequences with length of at least 25nt were further aligned to human rRNA and tRNA index constructed from Ensembl (Release 91) and GtRNAdb databases , respectively. The remaining reads were aligned to the UCSC canonical known gene transcripts of the mouse reference genome (mm10) using bowtie with a maximum one mismatch allowed.
For TRAC-Seq, after adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2. Then read count for each tRNA was calculated using the method in (Cozen et al., 2015).
scRNA-seq data generated from the 10× Genomics platform were processed using CellRanger (version 3.1.0) pipeline. Gene expression matrix was created by using Seurat (V3.1.5) pipeline.
Genome_build: hg38, GRCH38，mm10
Supplementary_files_format_and_content: matrix table with raw gene counts

source_name: HNSCC

growth_protocol: SCC15 cells were cultured in DMEM/F12 (Gibco, USA) with 10% fetal bovine serum (FBS, Gibco, USA), 1% streptomycin (Gibco, USA) . Cells were cultured in a water-saturated atmosphere under 5% CO2 at 37 °C in an incubator (Thermo Scientific, USA).

extract_protocol:
RNA was extracted according to TRIzol protocol. Small RNAs (<200nt) were first purified using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific).  HNSCC samples were harvested from the tongue of mice and single cell suspensions were prepared for 10× genomics processing.
Libraries were prepared according to Illumina's instructions accompanying the TrueSeq Stranded mRNA library preparation kit, TruSeq Ribo Profile (Mammalian) Library Prep Kit and the NEBNext® Small RNA Library Prep Set. scRNA-seq libraries were prepared using Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10X Genomics) according to manufacturer’s protocol.

treatment_protocol: SCC15 cells were  transfected with sgRNAs for knockout of METTL1. SCC15 cells with normal expression of METTL1 were used as control. Mettl1-/- and wild type mice were induced with 4NQO to establish murine HNSCC model.

tag: cell type

value: HNSCC cells

value: demethylated by ALKB


title: WT2_NV

description:
small RNA
TRAC-seq

value: demethylated by ALKB; NaBH4/Aniline induced reduction and cleavage

value: normal


title: WT1_NV

description:
small RNA
TRAC-seq


title: KO1_NK

description:
small RNA
TRAC-seq


title: KO2_NK

description:
small RNA
TRAC-seq


title: WT1_DV

description:
small RNA
TRAC-seq


title: WT2_DV

description:
small RNA
TRAC-seq


title: 18SD03290

city: LYON

first: Julie

last: CARAMEL

address: 28 Rue Laennec

country: France

institute: Cancer Research Center of Lyon

data_processing:
Raw sequencing reads were aligned on the human genome (GRCh38) with STAR (v2.7.3a), with the annotation of known genes from gencode v33.
Gene expression was quantified using Salmon (1.1.0) and the annotation of protein coding genes from gencode v33
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file with raw counts from salmon for each sample

extract_protocol:
RNA was extracted from FFPE sections with the RNeasy FFPE Kit (Qiagen)
RNA libraries were prepared with the TruSeq RNA exome kit (Illumina).

tag: tissue

value: Cutaneous tumor

value: melanoma


title: 14SD05148


title: 16SD08140


title: 15SD07985


title: 16SD01637


title: 14SD04701


title: 15SD06506


title: 16SD03279


title: 14SD04636


title: 16SD00980


title: 14SD08747


title: 16SD00829


title: CUTRUN_NFIA_Primary_Perpheral Blood_Rep1

tag: differentiation

tag: antibody

value: NFIA


title: 11SD09375


title: 16SD07609


title: CUTRUN_NFIA_HUDEP2_clone6_Rep3

tag: biological replicate

tag: treatment

value: no


title: 15SD01736


title: Control sample 2

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

country: Canada

institute: University Health Network

description: Control

data_processing:
Raw fastq files were aligned to hg19 using Tophat, and QC performed using fastqc
Counts were generated, and differential expression calculated using cufflinks
cummeRbund was used to investigate results and generate output files
Default parameters were used for all software
Splicing events were counted using rmats-turbo with gencode v34 gtf file
Genome_build: hg19
Supplementary_files_format_and_content: comma separated values file containing fragments per kilobase mapped for each sample and results of differential expression analysis using cufflinks.
Supplementary_files_format_and_content: tab separated values files containing retain intron (RI) and skipped exon (SE) outputs from rmats splicing analysis

source_name: OCI-AML-20 cell line

growth_protocol: OCI-AML-20 were cultured in IMDM media (Gibco/Wisent) with 2mM L-glutamine, 10% FBS (Wisent), 55uM β-mercaptoethanol (Gibco), 100ug/mL Primocin (InvivoGen), 100ng/mL SCF, 50ng/mL FLT3L, 40ng/mL THPO, 20ng/mL IL3, and 20ng/mL GM-CSF (Shenandoah Biotech or Custom Biologics) in 6-well plates (Greinier) seeded with confluent OP9

extract_protocol:
RNA was extracted using TRIzol (Invitrogen) and quality was assessed using a Bioanalyzer (Agilent Technologies).
Sample libraries were prepared using the Illumina TruSeq Stranded mRNA sample preparation kit.
Sequencing was performed using Illumina Next-Seq500 using 75-cycle paired-end protocol and multiplexing at the Princess Margaret Genomics Centre.

treatment_protocol: OCI-AML-20 were treated with GSK591 1uM or DMSO for 6 days

tag: agent

value: DMSO

tag: cell line


title: 15SD03482


title: CUTRUN_NFIA_HUDEP2_clone6_Rep2


title: Control sample 3

description: Control


title: 17SD00684


title: GSK591 sample 2

description: PRMT5 inhibitor


title: Huh7_P3

city: Maywood

first: Wei

last: Qiu

state: Illinois

address: 2160 S 1st Ave

department: Cancer Biology

institute: Loyola University Chicago

data_processing:
Sequencing was performed using the Illumina HiSeq 2000.
Sequenced reads were trimmed for adaptor sequence,  the pass filter reads were mapped to the genome (Enseml/GRch37)
Genome_build: Ensembl GRCh37
Supplementary_files_format_and_content: xlsx files, parental vs lenvatinib-resistant

source_name: HCC cell line  Huh7

extract_protocol:
Total RNA from HCC (Hep3B, Huh7) cells using QIAGEN RNeasy Mini Kit (Catalog no.74106)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DMSO or lenvatinib

value: HCC cell

tag: group

value: parental


title: Huh7_P2


title: Huh7_LR3

value: lenvatinib-resistant


title: KO2_DK

description:
small RNA
TRAC-seq

tag: genotype


title: GSK591 sample 3

description: PRMT5 inhibitor


title: Huh7_LR1


title: Hep3B_P3

source_name: HCC cell line  Hep3B


title: Hep3B_P1


title: Hep3B_LR1


title: Hep3B_LR2


title: Hep3B_P2


title: SIRPa_3

city: Minneapolis

first: Matous

last: Voboril

state: Minnesota

address: 2101 6th Street SE

department: Department of Lab Medicine & Pathology

institute: University of Minnesota

data_processing:
Raw reads were summarized with FastQC, and trimmed with Trimmomatic. Trimmed reads were aligned to the mm10 reference genome with HISAT2. Duplicate reads based on alignment position were marked with SAMTools. Alignments with duplicates marked were summarized with RNASeQC to quantify the proportion of positional duplicates, identify risosomal alignments, and quantify the proportion of "on-target" reads. Processed alignments were filtered of reads that have a mapping quality of less than 60, and sorted by query name rather than position.
Cleaned and name-sorted alignments were processed with the featureCounts tool from the subread package. Fragments were counted in a strand-specific manner.
Raw counts were imported into the edgeR package in R. Genes that are shorter than 200bp were pruned from the counts matrix before differential expression testing. The differential expression testing was peformed with a quasi-likelihood test in edgeR between all pairwise combinations of groups.
Assembly: mm10
Supplementary files format and content: Text files that contain normalized relative expression matrix and raw read counts matrix

source_name: Murine thymocytes

extract_protocol:
Thymi were harvested and digested in Collagenase D for 30 min, stained with antibody and sorted using a FACS ARIA II. RNA from sorted cells was isolated using the Qiagen Rneasy Micro kit per the manufacturer’s instructions.
RNA libraries were generated using Clontech Stranded Total RNA Pico Mammalian v2 and sequenced  on a NextSeq instruemnt (Illuminia)

tag: strain

value: thymic dendritic cells


title: SIRPa_2


title: SIRPa_1


title: Mut_off, adenine 500, rep 1

city: Houston

first: Anthony

middle: M

last: Mustoe

state: TX

address: 1 Baylor Plaza

department: Biochemistry and Molecular Biology

institute: Baylor College of Medicine

data_processing:
Fastq files were aligned and parsed using ShapeMapper2 (v.2.1.5; https://github.com/Weeks-UNC/shapemapper2)
Parsed mutation files were analyzed using DanceMapper (v1)
Genome_build: sequence files used for alignment are included as supplementary files
Supplementary_files_format_and_content: DanceMapper archives (.tgz) include bernouli mixture save files (.bm), normalized reactivites (reactivities.txt), pairmap analysis files (pairmap.bp, pairmap.txt, allcorrs.txt), and ringmap analysis files (rings.txt). A complete description of these files is provided in the DanceMapper documentation

organism: Vibrio vulnificus

source_name: in vitro transcript

growth_protocol: WT and mutant adenine riboswitch RNAs were in vitro transcribed with 5' and 3' structure cassettes.

extract_protocol: RNA was converted to cDNA using mutational profiling (MaP) reverse transcription, and libraries were prepared by 2-step PCR.

treatment_protocol: RNA was folded at 30 C in 300 mM bicine (pH 8.0), 100 mM NaCl, 5 mM MgCl2 with variable adenine and modified with DMS (or ethanol) for 10 minutes, quenched with 20% 2-mercaptoethanol, and ethanol precipitated.

value: DMS

tag: genotype/variation

value: Mut


title: Mut_on, etoh, rep 2

value: EtOH control


title: Mut_off, adenine 0, rep 1


title: Mut_on, etoh, rep 1


title: CD301b_3


title: CD301b_4


title: CD301b_1


title: RRBS_Sscr_sperm

city: Illkirch

first: Michael

last: Weber

address: 300 Bd Sebastien Brant

department: UMR7242 Biotechnology and Cell Signalling

institute: CNRS

data_processing:
Reads were trimmed with Trim Galore v0.4.4 to remove adapter sequences and low-quality ends with a Phred score below 20. Trim Galore was run in –non_directional and –rrbs mode to remove two additional bases artificially introduced at the MspI restriction sites.
Reads were aligned to the corresponding genome with Bismark v0.18.2 with default parameters.
A maximum of two mismatches and an insertion size for paired-end sequences of between 30 and 400 bp were allowed.
Methylation scores were extracted as the ratio of the number of Cs over the total number of Cs and Ts using the Bismark_methylation_extractor. CGs were filtered to have a minimum sequencing depth of 10X.
genome build: hg38, mm10, oryCun2, canFam3, bosTau8, susScr11, galGal6
processed data files format and content: We provide IGV files containing methylation scores for all CGs with at least 10X sequencing depth.

organism: Sus scrofa

source_name: Sperm

extract_protocol:
Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen).
100 ng of genomic DNA were digested 5 hours by MspI (Thermo Scientific), end-repaired and A-tailed with Klenow fragment exo- (Thermo Scientific), and ligated to methylated adapters with T4 DNA ligase (Thermo Scientific) in Tango 1X buffer. Size selection was performed by gel excision from a 3% agarose 0.5X TBE gel to select fragments ranging from 150 to 400 bp. DNA was purified using the MinElute gel extraction kit (Qiagen) and bisulfite-converted twice with the EpiTect bisulfite kit (Qiagen), following the manufacturer’s instructions. Final libraries were amplified using the Pfu Turbo Cx hotstart DNA polymerase (Agilent) with 12 to 14 PCR cycles. The libraries were purified using Agencourt AmpureXP beads (Beckman-Coulter).

tag: Sex

value: Male

tag: genome build

value: No treatment

value: Sperm


title: Mut_on, adenine 0, rep 2


title: Mut_on, adenine 500, rep 1


title: XCR1_3


title: Control sample 1

description: Control


title: Mut_on, adenine 0, rep 1


title: XCR1_1


title: WT, etoh, rep 1

value: WT


title: WT, etoh, rep 2


title: F hMet CORT vHPC 3

city: New York

first: Jordan

last: Marrocco

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
Illumina NextSeq 500
Quality control was performed on the reads obtained from the core and reads with a score of less than 15 were discarded.
The reads were then aligned to the GRCm genome using the STAR aligner with Ensembl annotation and quantified to the gene-level using featureCounts.
The read counts were analyzed using the R/Bioconductor framework (www.R-project.org).
Differentially expressed gene (DEG) expression analysis was conducted using the Limma-Voom package.
Genome_build: mm10
Supplementary_files_format_and_content: limmaVoom files contain logFC between VEH vs CORT animals and WT vs BDNF animals

source_name: Ventral Hippocampus

extract_protocol:
After rapid decapitation, brains were immediately dissected to separate the dorsal and the ventral hippocampus, which wer rapidly flash frozen and stored at -80 °C. RNA was extracted from the dorsal and the ventral hippocampal tissue using Qiagen Lipid Tissue Mini Kit.
A total of at least 200ng of RNA per replicate was prepared for sequencing by The Rockefeller University Genomics Core Facility using the Tru-Seq Stranded RNA-Seq library preparation kit (Illumina, USA). Three biological replicates were used per experimental group, comprising of RNA pooled from 2 animals each. cDNA libraries were sequenced on an Illumina NextSeq 500 in a single lane to obtain 75-bp single-end reads at an approximate sequencing depth of 35-40 million reads per sample.

treatment_protocol: At two months of age mice were randomly assigned to either vehicle- (1% ethanol) or CORT- (25mg/l, 1% ethanol) treated groups for 6 weeks of treatment.

value: Female

value: BDNF Val66Met

value: CORT

value: Ventral Hippocampus


title: F hMet CORT vHPC 2


title: GSK591 sample 1

description: PRMT5 inhibitor


title: F hMet CORT vHPC 1


title: WT, adenine 100, deep

description: Data from GSE135211  were resequenced and pooled


title: Hep3B_LR3


title: M hMet CORT vHPC 4


title: WT, adenine 500, rep 2


title: WT, adenine 0, deep


title: Mut_off, etoh, rep 1


title: M hMet CORT vHPC 3


title: M hMet CORT vHPC 2


title: WT, adenine 55.6, rep 2


title: M hMet CORT vHPC 1


title: WT, adenine 18.5, rep 2


title: WT, adenine 166.7, rep 2


title: WT, adenine 6.2, rep 2


title: Mut_on, adenine 500, rep 2


title: F hMet Veh vHPC 3

value: Vehicle


title: F hMet Veh vHPC 2


title: WT, adenine 2.1, rep 2


title: WT, adenine 0.7, rep 2


title: XCR1_2


title: M hMet Veh vHPC 4


title: WT, adenine 0.08, rep 2


title: F hMet Veh vHPC 1


title: WT, adenine 0.22, rep 2


title: M hMet Veh vHPC 3


title: WT, etoh, deep


title: F hMet CORT vHPC 4


title: WT, adenine 0, rep 2


title: WT, adenine 500, rep 1


title: F WT CORT vHPC 4

value: Wild Type


title: WT, adenine 18.5, rep 1


title: WT, adenine 166.7, rep 1


title: M hMet Veh vHPC 1


title: WT, adenine 55.6, rep 1


title: F WT CORT vHPC 2


title: F WT CORT vHPC 3


title: WT, adenine 6.2, rep 1


title: F WT CORT vHPC 1


title: M WT CORT vHPC 4


title: M WT CORT vHPC 3


title: WT, adenine 0.7, rep 1


title: Huh7_LR2

value: HCC cell


title: F hMet Veh vHPC 4


title: WT, adenine 0, rep 1


title: M WT CORT vHPC 2


title: SK-N-BE2 GNE987 10nm_Input

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

data_processing:
Raw Data of ChIP-Seq was aligned to the reference genome (UCSC hg38) using BWA-MEM (v0.7.17)
Peaks were identified using MACS2 (v2.2.7)
Genome_build: hg38
Supplementary_files_format_and_content: peak text files

source_name: Neuroblastoma cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols

value: Neuroblastoma cells

value: input


title: M WT CORT vHPC 1


title: SK-N-BE2 GNE987 10nm_H3K27ac


title: F WT Veh vHPC 4


title: H1KD_T47D_HiC_3

city: Barcelona

first: Albert

last: Jordan

address: Baldiri Reixac 4

department: Molecular Genomics

country: Spain

institute: IBMB-CSIC

description:
TADs_H1KD_123.txt.gz
ABcompartments_H1KD_123.txt.gz

data_processing:
Hi-C data was processed with TADbit. Sequencing reads from replicates 1, 2, and 3 were merged and mapped to the reference genome (GRCh37/hg19) applying an iterative strategy and using the GEM mapper.
Mapped reads were filtered to remove those resulting from unspecified ligations, errors or experimental artifacts Specifically, nine different filters were applied using the default parameters in TADbit: self-circles, dangling ends, errors, extra dangling-ends, over-represented, too short, too long, duplicated and random breaks.
Hi-C data were normalized with ICE Vanilla correction at the resolutions of 1 Mb, 500 kb, 100 kb, and 10 kb to remove Hi-C biases and artifacts. Filtered read-pairs were binned at the resolutions of 1 Mb, 500 kb, 100 kb, and 10 kb, applying biases from the normalization step and decay correction to generate interaction matrices.
TADs were identified at the resolution of 50 kb using TADbit with default parameters. The segmentation of the genome into A/B compartments at 100 kb resolution was performed with HOMER software.
Genome_build: hg19
Supplementary_files_format_and_content: TXT files include TADs coordinates (border strength and interactions density are also indicated) and A/B compartments coordinates.

source_name: Breast cancer cell line

growth_protocol: Cells were grown in RPMI 1640 medium, supplemented with 10% FBS, 2mM L-glutamine, 100 U/ml penicillin, and 100µg/ml streptomycin.

extract_protocol:
For the in situ Hi-C, adherent cells were crosslinked with 1% formaldehyde in PBS for 10 min at room temperature. Glycine 0.125M was added for 5 min at room temperature and for 15 min at 4ºC to stop the crosslink reaction. Before permeabilization, cells were treated for 5 min with trypsin. Nuclei digestion was performed with 400 units of MboI restriction enzyme. The ends of the restriction fragments were labeled using biotinylated nucleotides and ligated with T4 DNA ligase. After reversal of crosslinks, DNA was purifed and sheared (Diagenode BioruptorPico) to obtain fragments of around 300-500 bp and ligation junctions were pull-down with streptavidin beads.
Hi-C libraries were finally amplified, controlled for quality, and prepared for sequencing using standard Illumina protocols.

treatment_protocol: Initially, a cell line expressing the Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) was generated. This cell line was subsequently infected with viruses for expression of the H1 variants shRNA (pLVTHM). The inducible knocked-down cell lines were sorted in a FACSvantageSE (Becton Dickinson) for RedFP-positive and GFP-positive fluorescence after 3 days of Doxicycline treatment. Then cells were amplified in the absence of Dox until an experiment was performed. Doxicycline (Sigma) was added at 2.5 µg/ml when indicated and cells were treated for 6 days.

value: Breast cancer ductal carcinoma

tag: dox treatment

value: Treated


title: dfo_rep2

city: Providence

first: William

last: Fairbrother

state: RI

address: 70 Ship St, Box G

department: Molecular Biology, Cell Biology and Biochemistry

institute: Brown University

data_processing:
Reads originating from lariats were identified in the sequenced reads using the branchpoint detection algorithm described in Taggart et al (2012)
Transcript levels were quantified with Salmon
Assembly: hg19
Supplementary files format and content: sf - Transcript quantification output from Salmon
Supplementary files format and content: BED - each mapped lariat read is listed with the start and end coordinates being the 5' splice site and branchpoint (or vice versa if the the lariat maps to the negative strand); additionally, the read ID, inferred branchpoint nucleotide, and nearest 3' splice site are listed in the name field

source_name: Lymphoblast cells

growth_protocol: RPMI 1640 media with 15% FBS, 1% Pen-strep

extract_protocol:
Trizol extraction
Illumina TruSeq stranded total RNA human/mouse/rat kit

treatment_protocol: Two replicates were treated with 200 uM deferoxamine and cultured for 60 hours

value: 60hr DFO treated

value: Lymphoblast


title: H1KD_T47D_HiC_2


title: F WT Veh vHPC 3


title: WT_T47D_HiC_3

description:
TADs_WT_123.txt.gz
ABcompartments_WT_123.txt.gz

value: Untreated


title: WT_T47D_HiC_2


title: F WT Veh vHPC 2


title: HOMO_rep2

city: Shanghai

first: Mengzhu

last: Xue

address: No.100, Haike Road

institute: Shanghai Advanced Research Institute

description:
HOMO_2
Homodeficient
WT12HTZ12HOMO12.genesymbolTPM.txt

data_processing:
Fastqc was taken to check the RNA sequencing quality.
Reads were mapped to mm10 by RSEM, then TPM values were calculated to characterize gene expression profiles.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: WT12HTZ12HOMO12.genesymbolTPM.txt: Tab-delimited text file includes TPM values for each Sample.

source_name: mouse brain

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols, and Illumina TruSeq RNA Sample Prep Kit was used for library construction.

treatment_protocol: Dentate neuroepithelium cells were separated from E14 wild type, SOX11f/+ and SOX11f/f mice.

value: Dentate neuroepithelium cells

tag: developmental stage


title: HOMO_rep1

description:
HOMO
Homodeficient
WT12HTZ12HOMO12.genesymbolTPM.txt


title: HTZ_rep2

description:
HTZ_2
Haplodeficient
WT12HTZ12HOMO12.genesymbolTPM.txt


title: F WT Veh vHPC 1


title: M hMet Veh vHPC 2

value: Male


title: HTZ_rep1

description:
HTZ
Haplodeficient
WT12HTZ12HOMO12.genesymbolTPM.txt


title: M WT Veh vHPC 4


title: untreated_rep1


title: WT_rep2

description:
WT_2
Control
WT12HTZ12HOMO12.genesymbolTPM.txt

value: WT


title: M WT Veh vHPC 3


title: WT_rep1

description:
WT
Control
WT12HTZ12HOMO12.genesymbolTPM.txt


title: Huh7_P1

value: parental


title: colon tumor sample from CRC patient [T1020919]

type: genomic

first: Carmen

last: Sapienza

address: 3307 N Broad Street, Room 300 PAHB

department: Fels Cancer Institute for Personalized Medicine

institute: Temple University

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

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

data_processing:
GenomeStudios
matrix processed value definition: Average Beta
matrix signal intensities value definition: Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: colon mucosa biopsy

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from colon samples according to SOP

tag: age

value: F

tag: race

value: AA

tag: disease state

value: Tumor

tag: tissue type

value: colon tumor sample from CRC patient


title: colon tumor sample from CRC patient [T1021677]

value: M


title: DMSO-2

first: Yariv

last: Houvras

address: 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Reads were then aligned to the human genome (hg19) using Star v2.3
The Ensemble transcriptome was used to identify genes
Differential gene expression was analyzed using DESeq2
Assembly: hg19
Supplementary files format and content: DESeq2 was used to normalize gene expression and to identify differentially regulated genes

growth_protocol: TPC1 cells were grown in DMEM supplemented with 10% FBS

extract_protocol:
Total RNA was isolated using Qiagen RNAeasy extraction kit
RNA-seq libraries were prepared according to the Illumina TruSeq RNA protocol. cDNA libraries were then run on the HiSeq platform to obtain 50 bp single-end reads.

treatment_protocol: TPC1 cells were treated with 100microMolar of the RET inhibitor BLU6864 for the indicated time in hours

tag: cell type

value: Thyroid cancer

value: DMSO


title: colon tumor sample from CRC patient [T1020871]


title: DMSO-1


title: colon tumor sample from CRC patient [T1020511]


title: BLU6H-2 [re-analysis]


title: colon tumor sample from CRC patient [T1020308]


title: M WT Veh vHPC 1

value: Wild Type

value: Vehicle

tag: tissue

value: Ventral Hippocampus


title: colon tumor sample from CRC patient [T1019808]


title: colon tumor sample from CRC patient [T1019702]


title: BLU6H-1 [re-analysis]

tag: treatment


title: F hMet CORT dHPC 3

source_name: Dorsal Hippocampus

value: Female

value: BDNF Val66Met

value: CORT

value: Dorsal Hippocampus


title: colon tumor sample from CRC patient [T1019666]


title: BLU6H-2


title: dfo_rep1

value: 60hr DFO treated

value: Lymphoblast


title: colon tumor sample from CRC patient [T1019191]


title: untreated_rep2

value: Untreated


title: BLU6H-1


title: WT, adenine 2.1, rep 1

value: DMS

value: WT


title: colon tumor sample from CRC patient [T1018746]

value: F

value: CA

value: Tumor


title: colon tumor sample from CRC patient [T1018343]

value: M

value: AA

value: colon tumor sample from CRC patient


title: F hMet CORT dHPC 1


title: colon tumor sample from CRC patient [T1018361]


title: M hMet CORT dHPC 4

value: Male


title: BLU24H-1 [re-analysis]

value: Thyroid cancer


title: colon tumor sample from CRC patient [T1018214]


title: colon tumor sample from CRC patient [T1018133]


title: BGJ6H-2

treatment_protocol: TPC1 cells were treated with 100microMolar of BGJ398 for the indicated time in hours


title: colon tumor sample from CRC patient [T1018024]


title: colon tumor sample from CRC patient [T1017989]


title: M WT Veh vHPC 2

value: Wild Type

value: Vehicle

value: Ventral Hippocampus


title: BGJ6H-1


title: M hMet CORT dHPC 2

value: BDNF Val66Met

value: CORT

value: Dorsal Hippocampus


title: colon tumor sample from CRC patient [T1017724]


title: BGJ24H-2


title: colon tumor sample from CRC patient [T1016873]


title: colon tumor sample from CRC patient [T1016365]


title: F hMet CORT dHPC 4

value: Female


title: BGJ24H-1


title: colon tumor sample from CRC patient [T1016765]


title: M hMet CORT dHPC 1


title: colon tumor sample from CRC patient [T1015423]


title: colon tumor sample from CRC patient [T1019104]


title: F hMet Veh dHPC 3


title: colon tumor sample from CRC patient [T1014017]


title: colon tumor sample from CRC patient [T1019619]


title: COMBO24H-1

treatment_protocol: TPC1 cells were treated with 100microMolar of the indicated inhibitors, either the combination of BLU6864 and BGJ398 or BLU6864 alone for 24 hours


title: COMBO24H-2


title: F hMet CORT dHPC 2


title: colon tumor sample from CRC patient [T1013970]


title: colon tumor sample from CRC patient [T1016324]


title: BLU24H-2 [re-analysis]


title: F hMet Veh dHPC 2


title: colon tumor sample from CRC patient [T1011878]


title: F hMet Veh dHPC 1


title: BLU24H-2


title: colon tumor sample from CRC patient [T1011109]


title: colon tumor sample from CRC patient [T1010070]


title: BLU24H-1


title: M hMet CORT dHPC 3


title: colon tumor sample from CRC patient [T1009911]


title: M hMet Veh dHPC 4


title: TWNT-4 cells, siMPI 2

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
Trimmed reads by Trimmomatic (DOI: 10.1093/bioinformatics/btu170) were mapped to the Ensembl human reference genome GRCh38 using HISAT2 with default parameters.
To estimate gene expression, reads mapped at exons of ensemble annotated genes were calculated with the ‘union’ and ‘no stranded’ mode with by HTSeq (https://doi.org/10.1093/database/baw093, doi:10.1093/bioinformatics/btu638).
DESeq2 in Bioconductor was adopted to test differential gene expression.
Genome_build: GRCh38

source_name: TWNT-4 (human hepatic stellate cell)

growth_protocol: LX-2 human HSCs  were maintained in Dulbecco’s modified Eagle’s medium with 10% FBS, L-glutamine, and penicillin/streptomycin) and routinely tested for mycoplasma using the Venor GeM Mycoplasma Detection Kit (Sigma-Aldrich).

extract_protocol:
Cells were collected in TRIzol and total RNA was purified following the supplied protocol.
RNA quality was determined with the Agilent 2100 BioAnalyzer. cDNA libraries were prepared using the Illumina TruSeq RNA sample preparation version 2 protocol,  and DNA quality was checked with the Agilent 2100 BioAnalyzer. PolyA selection was carreid out.

treatment_protocol: Duplex siRNA (dsiRNA, negative control (NC), validated negative control that is not present in the human, mouse, or rat genomes) and MPI-targeted siRNA (siMPI)) were transfected according to the Life Technologies protocol for siRNA transfection, using Lipofectamine RNAiMAX Transfection Reagent (ThermoFisher Scientific, Waltham, MA) and Opti-MEM I Reduced Serum Medium (ThermoFisher Scientific, Waltham, MA).

value: MPI-targeted siRNA


title: colon tumor sample from CRC patient [T1008838]

city: Philadelphia


title: colon tumor sample from CRC patient [T1009706]


title: M hMet Veh dHPC 3


title: colon tumor sample from CRC patient [T1008446]


title: TWNT-4 cells, Control 2

value: Control siRNA


title: M hMet Veh dHPC 2


title: TWNT-4 cells, siMPI 1


title: colon tumor sample from CRC patient [T1008179]

value: F


title: F hMet Veh dHPC 4


title: M hMet Veh dHPC 1


title: colon tumor sample from CRC patient [T1007884]

value: CA


title: colon tumor sample from CRC patient [T1007888]

value: Tumor


title: TWNT-4 cells, Control 1


title: colon tumor sample from CRC patient [T1007544]

value: M


title: Patient 27 relapse

city: Helsinki

first: Katja

last: Eloranta

address: Tukholmankatu 8

department: Children's Hospital

country: Finland

institute: University of Helsinki

data_processing:
QuantSeq 3’ mRNA-Seq Integrated Data Analysis Pipeline on Bluebee® (Lexogen) was used for preliminary quality evaluation and alignment of the RNA sequencing data.
To filter out lowly expressed genes, sample read counts were transformed into count-per-million (CPM) values using edgeR (doi: 10.1093/bioinformatics/btp616) package (cut-off CPM > 0.4 in at least 8 samples)
Filtered data were normalized and transformed using the voomfunction from the limma package (doi: 10.1093/nar/gkv007).
Differential gene expression analyses were performed using the lmfit function (limma package) (doi: 10.1093/nar/gkv007)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with TMM normalized gene counts for every gene and every sample

source_name: Granulosa cell tumor tissue

extract_protocol:
Ten AGCT FFPE tissue sections of 5 µm thickness were mounted on objective slides, and areas with >80% AGCT cellularity based on hematoxylin and eosin slide review were scraped off into a microcentrifuge tube.Total RNA was extracted from the FFPE tissue using Maxwell RSC RNA FFPE kit
Single-indexed mRNA libraries were prepared from 100 ng of RNA with QuantSeq 3’ mRNA-Seq Library Prep Kit FWD

tag: tissue preparation

value: Formalin fixed paraffin embedded tissue

tag: sample type

value: Relapsed tumor

value: Granulosa cell tumor tissue


title: colon tumor sample from CRC patient [T1007546]

value: AA

value: colon tumor sample from CRC patient


title: colon tumor sample from CRC patient [T1006969]


title: colon tumor sample from CRC patient [T1015212]


title: F WT CORT dHPC 3

value: Wild Type


title: F WT CORT dHPC 4


title: Patient 25 relapse


title: colon tumor sample from CRC patient [T1005006]


title: Patient 29 relapse


title: F WT CORT dHPC 1


title: F WT CORT dHPC 2


title: colon tumor sample from CRC patient [T1005074]


title: colon tumor sample from CRC patient [T1005460]


title: colon tumor sample from CRC patient [T1005934]


title: colon tumor sample from CRC patient [T1004526]


title: Patient 28 relapse


title: colon tumor sample from CRC patient [T1003900]


title: M WT CORT dHPC 4

value: Male


title: colon tumor sample from CRC patient [T1003838]


title: colon tumor sample from CRC patient [T1003884]


title: Patient 22 relapse


title: colon tumor sample from CRC patient [T1003680]


title: M WT CORT dHPC 3


title: Patient 21 relapse


title: M WT CORT dHPC 2


title: colon tumor sample from CRC patient [T1003588 rep2]


title: colon tumor sample from CRC patient [T1003661]


title: colon tumor sample from CRC patient [T1003588 rep1]


title: Patient 20 relapse


title: M WT CORT dHPC 1


title: colon tumor sample from CRC patient [T1003077]


title: Patient 16 relapse


title: colon tumor sample from CRC patient [T1002980]


title: F WT Veh dHPC 4

value: Vehicle


title: Patient 27 primary (with a relapse)


title: colon tumor sample from CRC patient [T1002928]


title: F WT Veh dHPC 2


title: Patient 26 primary (with a relapse)

value: Primary tumor with relapse


title: F WT Veh dHPC 3

value: Dorsal Hippocampus


title: colon tumor sample from CRC patient [T1002915]


title: Patient 25 primary (with a relapse)


title: colon tumor sample from CRC patient [T1002746]


title: colon tumor sample from CRC patient [T1002878]


title: colon tumor sample from CRC patient [T1002335]


title: M WT Veh dHPC 4


title: F WT Veh dHPC 1

value: Female


title: colon tumor sample from CRC patient [T1002200]


title: Patient 24 primary (with a relapse)


title: colon tumor sample from CRC patient [T1001772]


title: Patient 23 primary (with a relapse)


title: colon tumor sample from CRC patient [T1001503]


title: colon tumor sample from CRC patient [T1001527]


title: M WT Veh dHPC 2


title: Patient 22 primary (with a relapse)


title: colon tumor sample from CRC patient [T1001323]


title: colon tumor sample from CRC patient [T1001383]


title: Patient 20 primary (with a relapse)


title: M WT Veh dHPC 1


title: colon tumor sample from CRC patient [T1001204]


title: colon tumor sample from CRC patient [T1001186]


title: colon tumor sample from CRC patient [T1002979]


title: EKO_OVA__R3 (Sample 12)

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

institute: University of Basel

data_processing:
Paired-end reads were aligned to the mouse genome (UCSC version mm10 analysis set) with STAR with default parameters except for allowing up 10 hits to genome (outFilterMultimapNmax 10), reporting only one location for hits with equal score (outSAMmultNmax 1), and for filtering reads without evidence in spliced junction table (outFilterType "BySJout").
The output was sorted and indexed with samtools. Read and alignment quality was evaluated using the qQCReport function of the Bioconductor package QuasR.
The featureCounts function from Bioconductor package Rsubread was used to count the number of read (5'ends) overlapping with the exons of each gene assuming an exon union model (gene annotation: ensembl genes v101)
Genome_build: mm10
Supplementary_files_format_and_content: TXT file (with tab separated values) with raw counts for ensembl  genes, 1.column is  ensembl Gene ID, 2. and remaining columns contain raw counts

source_name: Spleen-derived dendritic cell line Sp37A3

growth_protocol: Both DC cell lines were cultured in complete IMDM medium supplemented with murine GM-CSF and M-CSF

extract_protocol:
RNeasy Plus Micro Kit(Qiagen, Cat: 74034) was used to isolate RNA from cultured cells
TruSeq Stranded mRNA Library Kit (Cat# 20020595, Illumina) and the TruSeq RNA UD Indexes (Cat# 20022371, Illumina) were used to prepare the library.

treatment_protocol: DCs were unpulsed or pulsed with ovalbumin protein and stimulated with LPS, followed by 24 hours of processing time.

tag: genetic modification

value: SiglecE-knockout

value: OVA-pulsed, LPS-stimulated

tag: replicate


title: Patient 19 primary (with a relapse)


title: colon tumor sample from CRC patient [T1001125]


title: colon tumor sample from CRC patient [T1001063]

value: F


title: EKO_OVA__R2 (Sample 11)


title: colon tumor sample from CRC patient [T1002923]

value: CA


title: colon tumor sample from CRC patient [T1000979]

value: Tumor


title: Patient 18 primary (with a relapse)


title: EKO_OVA__R1 (Sample 10)


title: colon tumor sample from CRC patient [T1002971]

value: M


title: colon tumor sample from CRC patient [T1000168]


title: colon tumor sample from CRC patient [T1000822]


title: colon tumor sample from CRC patient [T1000048]


title: EKO_ut__R3 (Sample 9)

value: unpulsed, LPS-stimulated


title: Patient 16 primary (with a relapse)

value: Formalin fixed paraffin embedded tissue


title: normal colon tissue from non-CRC patient [Y89]

value: Healthy


title: normal colon tissue from non-CRC patient [Y81]


title: M WT Veh dHPC 3

tag: strain

tag: genotype


title: Patient 15 primary (with a relapse)

value: Granulosa cell tumor tissue


title: normal colon tissue from non-CRC patient [Y80]

tag: Sex


title: EKO_ut__R2 (Sample 8)


title: EKO_ut__R1 (Sample 7)


title: normal colon tissue from non-CRC patient [Y79]


title: Patient 21 primary (with a relapse)


title: Patient 14 primary

value: Primary tumor without relapse


title: normal colon tissue from non-CRC patient [Y77]


title: CtrV_OVA__R3 (Sample 6)

value: SiglecE-expressing


title: normal colon tissue from non-CRC patient [Y67]


title: Patient 17 primary (with a relapse)


title: Patient 13 primary


title: normal colon tissue from non-CRC patient [Y118]


title: CtrV_OVA__R2 (Sample 5)


title: normal colon tissue from non-CRC patient [Y113]


title: Patient 12 primary


title: CtrV_OVA__R1 (Sample 4)


title: normal colon tissue from non-CRC patient [Y109]


title: colon tumor sample from CRC patient [T1001153]

value: AA

value: colon tumor sample from CRC patient


title: Patient 11 primary


title: normal colon tissue from non-CRC patient [Y108]


title: normal colon tissue from non-CRC patient [Y103]


title: normal colon tissue from non-CRC patient [Y102]


title: CtrV_ut__R2 (Sample 2)


title: normal colon tissue from non-CRC patient [Plate Control 929 rep1]


title: normal colon tissue from non-CRC patient [929 Plate_Control_2]


title: Patient 9 primary


title: normal colon tissue from non-CRC patient [929 Plate_Control_1]


title: CtrV_ut__R1 (Sample 1)


title: normal colon tissue from non-CRC patient [309Y]


title: Patient 8 primary


title: KRC3968

first: Anirban

last: Maitra

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

data_processing:
Raw base call (BCL) files were demultiplexed and converted to FASTQ files, which were subsequently used to generate feature-barcode matrices using Cell Ranger RNA v3.1 (10x Genomics). PM sample was run through the Single cell RNA-seq app on BaseSpace. Briefly, reads were aligned against a reference genome using Spliced Transcripts Alignment to a Reference (STAR), followed by barcode tagging and BAM indexing. Count file was generated using gene UMI counter and with cells passing quality filter based on cells above background and passing knee filter.
Initial single-cell analysis was performed using Seurat v3. Cells containing less than 200 genes were removed, and log-normalized expression of 2,000 variable genes were used to reduce the data into two-dimensional space.
Cells from all 10 samples were combined using FindIntegrationAnchors and IntegrateData functions. Cell identities were manually assigned using highly expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: filtered_feature_bc_matrix

source_name: KRC tumor

extract_protocol:
Tumors and pancreas were enzymatically digested into a single-cell suspension:  a 10× digestion buffer was prepared in PBS: collagenase type I (450 units/mL, Worthington Biochemical), collagenase type II (150 units/mL, Worthington Biochemical), collagenase type III (450 units/mL, Worthington Biochemical), collagenase type IV (450 units/mL, Gibco, Thermo Fisher Scientific), elastase (0.8 units/mL, Worthington Biochemical), hyaluronidase (300 units/mL, MilliporeSigma), and DNAse type I (250 units/mL, MilliporeSigma). Tumors and pancreas were enzymatically digested into a single-cell suspension. Briefly, freshly dissected tissue was placed into a 10-cm tissue culture dish, and a sterile razor blade was used to cut the tissue into fine pieces. Samples were resuspended in PBS and washed twice by centrifuge at 480 g for 3 minutes and added to a 50-mL tube containing 1× digestion buffer (Worthington Biochemical) containing 1% FBS. The tube was incubated on a shaker at 37°C for 60 minutes. Then 35 mL of PBS was added, and cells were washed 3 times before filtering out debris using a 70-μm mesh filter (MilliporeSigma). Single cells were resuspended in 100 μL of PBS in preparation for single-cell library creation.
Single cell suspensions were resuspended in PBS containing 0.04% w/v bovine serum albumin and brought to a concentration of 200–700 cells/μL. Appropriate volume of cells was loaded with single cell 5’ gel beads into a single cell chip and run on the Chromium Controller (10x Genomics, Inc; Pleasanton, CA).  Dynabeads MyOne Silane magnetic beads (Thermo Fisher Scientific) were used to clean up the gel bead emulsion reaction mixture.  Full-length, barcoded cDNA was amplified by PCR after cleanup.  All samples were run on Agilent Tapestation 4200 using DNA high sensitivity D5000 tape.  During library preparation, sample index and Illumina adapter sequences (Illumina Inc; San Diego, CA) were added.  After library preparation quality control was performed using DNA D1000 tape on the Agilent Tapestation 4200 and final concentration was measured using the Qubit 4 Fluorometer DNA HS assay (Thermo Fisher Scientific). All samples were loaded at a concentration of 1.5 pM and run on the Illumina NextSeq500 High Output Flowcell.  The run configuration was 26 base pairs (bp) × 98 bp × 8.

value: KRC tumor

value: digested pancreas tumor

tag: mouse strain

value: C57Bl/6 - DBA/2 mixed background


title: normal colon tissue from non-CRC patient [306R]


title: Patient 7 primary


title: normal colon tissue from non-CRC patient [305Y]


title: normal colon tissue from non-CRC patient [304Y]


title: KRC3938


title: Patient 6 primary


title: KRC3851B


title: normal colon tissue from non-CRC patient [303R]


title: normal colon tissue from non-CRC patient [203Y]


title: Patient 5 primary


title: normal colon tissue from non-CRC patient [110Y]


title: Patient 4 primary


title: KRC3851A


title: normal colon tissue from non-CRC patient [988]


title: normal colon tissue from non-CRC patient [985]


title: KRC141


title: Patient 3 primary


title: normal colon tissue from non-CRC patient [979]


title: CtrV_ut__R3 (Sample 3)


title: KRC29


title: Patient 10 primary


title: normal colon tissue from non-CRC patient [978]


title: Patient 2 primary


title: KRC_80b


title: Patient 1 primary


title: normal colon tissue from non-CRC patient [975]


title: normal colon tissue from non-CRC patient [Plate Control 929 rep2]


title: normal colon tissue from non-CRC patient [972]


title: KRC80


title: H1KD_T47D_HiC_1

value: Breast cancer ductal carcinoma

tag: cell line

tag: dox treatment

value: Treated


title: normal colon tissue from non-CRC patient [970]

tag: age

value: F


title: normal colon tissue from non-CRC patient [967]

tag: race


title: KRC_79


title: normal colon tissue from non-CRC patient [966]

tag: disease state


title: normal colon tissue from non-CRC patient [963]

tag: tissue type


title: KRC79

tag: cell type


title: normal colon tissue from non-CRC patient [962]


title: normal colon tissue from non-CRC patient [961]


title: normal colon tissue from non-CRC patient [960]

value: CA


title: normal colon tissue from non-CRC patient [957]


title: Untreated rep 2

city: Parkville

first: Jack

middle: Aatto Laasonen

last: Cooper

state: Victoria

address: 49 College Crescent

country: Australia

institute: University of Melbourne

data_processing:
fastq files were quantified against an Ensembl GRCh38 reference genome using salmon
Salmon quants were aggregated into read counts and imported into R with tximport
Read counts were normalized using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: "normalized_counts.csv" contains the read counts for each of the 12 samples, normalized in DESeq2

source_name: Dermal fibroblasts

growth_protocol: Normal human fibroblasts were obtained from a healthy volunteer skin biopsy and proliferated in 10%FBS DMEM.

extract_protocol:
RNA was extracted using the MagMAX-96 Total RNA Isolation Kit, including DNase treatment (Life Technologies), according to the manufacturer’s instructions.
Samples were sent to the Australian Genome Research Facility (AGRF, Perth and Melbourne, Australia) for whole transcriptome library preparation using the TruSeq Stranded Total RNA Library Prep Kit (Illumina, CA, USA) and ribosomal RNA depletion with the Ribo-Zero-Gold kit (Illumina, CA, USA)
Sequencing as performed using an Illumina HiSeq 2500 (Illumina, CA, USA) to generate 100 base pair single end reads, resulting in an average 25 million reads per sample. Raw sequencing files were quality checked using FastQC (0.11.7), with all files passing

treatment_protocol: 2′ O-methyl phosphorothioate (SMN7D(-10-29) and control sequence) and DNA AOs were transfected into dermal fibroblasts as lipoplexes using 3 μl of Lipofectamine 3000 (Life Technologies, Melbourne, Australia) per 1 ml of OptiMEM, according to the manufacturer’s protocol. The transfection mix was applied to cells seeded at 15,000 cells per well in 24 well plates for RNA extraction and incubated (37°C) for 24 hours prior to RNA extraction.

value: Primary dermal fibroblasts

value: Untreated


title: Untreated rep 3


title: normal colon tissue from non-CRC patient [953]

value: M


title: Pac H9

city: Cambridge

first: Simona

last: Dalin

address: 415 Main Street, 4017b

institute: Broad Institute

data_processing:
Single-end reads were aligned to  the GRCm38 mm10 assembly with gencode M25 annotation using STAR version 2.5.1b
Gene counts from STAR are provided in the countTable.csv file
Genome_build: mm10
Supplementary_files_format_and_content: .csv file containing raw gene counts for every gene and every sample

source_name: Eµ-Myc; p19ARF -/- cell line

growth_protocol: Resistant cells were generated by seeding 10,000 cells into each well of 96-well plates (Falcon), then treated with a dose of paclitaxel (or equivalent DMSO) to kill 85% of cells after three days. After treatment, viability was assessed via PI staining and FACS. Cells were spun out of drug and allowed to recover in drug-free media for four days. During recovery, cells were split as individual wells’ media color started to change. On day four, all wells were split to approximately 10,000 cells per well and the removed cells were frozen at -80C in PCR plates. The cycle was repeated for 12-18 weeks. Cells were cultured in B-cell medium (45% DMEM, 45% IMDM, 10% FBS, supplemented with 2mM L-glutamine and 5uM 2-mercaptoethanol)

extract_protocol:
Total RNA was prepared using the RNeasy Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Paclitaxel


title: normal colon tissue from non-CRC patient [201R]

value: Healthy


title: Parental


title: Untreated rep 1


title: normal colon tissue from non-CRC patient [952]


title: normal colon tissue from non-CRC patient [950]


title: normal colon tissue from non-CRC patient [949]


title: Pac H4


title: Pac H8


title: normal colon tissue from non-CRC patient [973]


title: normal colon tissue from non-CRC patient [944]


title: normal colon tissue from non-CRC patient [946]


title: DNA AO rep 2

value: DNA AO


title: Pac H3


title: DNA AO rep 1


title: normal colon tissue from non-CRC patient [940]


title: normal colon tissue from non-CRC patient [942]


title: Control sequence 2'OMethyl AO rep 3

value: Control sequence 2'OMethyl AO


title: Pac H1


title: normal colon tissue from non-CRC patient [938]


title: normal colon tissue from non-CRC patient [937]


title: normal colon tissue from non-CRC patient [936]


title: WT_T47D_HiC_1

tag: tissue


title: Control sequence 2'OMethyl AO rep 2

tag: treatment


title: Pac F10


title: normal colon tissue from non-CRC patient [935]


title: Pac E2


title: normal colon tissue from non-CRC patient [931]


title: normal colon tissue from non-CRC patient [934]


title: Control sequence 2'OMethyl AO rep 1


title: Pac E1


title: SMN7D(-10-29) 2'OMethyl rep 3

value: SMN7D(-10-29) 2'OMethyl


title: normal colon tissue from non-CRC patient [929]

value: AA


title: normal colon tissue from non-CRC patient [930]


title: Pac D10


title: normal colon tissue from non-CRC patient [928]


title: SMN7D(-10-29) 2'OMethyl rep 1


title: DNA AO rep 3


title: normal colon tissue from non-CRC patient [926]


title: normal colon tissue from non-CRC patient [924]


title: normal colon tissue from non-CRC patient [948]


title: Pac D7


title: normal colon tissue from non-CRC patient [925]


title: normal colon tissue from non-CRC patient [922]


title: Pac D4


title: Pac C11


title: daf2_rep4

city: Bethesda

first: Sijung

last: Yun

state: Maryland

address: 8908 Ewing Drive

institute: NIH/JHU

data_processing:
For data assessment, a quality control with FastQC software (version 0.11.5) was used.
First the raw reads that aligned against the E. coli genome (K12 genome) were removed.
The remaining sequences were aligned against the reference genome of C. elegans WS260 using STAR (version 2.5.4a).
The number of mapped reads to genes was counted using Htseq (version 0.9.1).
Finally, the DEGs were determined using DESeq2 (version 1.20.0) with a cutoff of 0.05 on False Discovery Rate (FDR).
Assembly: WS260
Supplementary files format and content: Text files that contain count information

organism: Caenorhabditis elegans

source_name: Dauers

growth_protocol: daf-2(e1370) and chd-7(gk290);daf-2(e1370) synchronized eggs were kept at 25°C for 10 days and resulting dauers were collected and frozen.

extract_protocol:
Total RNA was extracted with TRIzol (Invitrogen) following the kit´s protocol.
cDNA library was prepared with NEBNext Ultra II RNA library prep kit for Illumina (New England Biolabs)


title: normal colon tissue from non-CRC patient [921]


title: Pac C3


title: daf2_rep3


title: normal colon tissue from non-CRC patient [916]


title: normal colon tissue from non-CRC patient [919]


title: daf2_rep2


title: normal colon tissue from non-CRC patient [911]


title: normal colon tissue from non-CRC patient [915]


title: Pac G9


title: daf2_rep1


title: Pac C1


title: normal colon tissue from non-CRC patient [904]


title: normal colon tissue from non-CRC patient [910]


title: SMN7D(-10-29) 2'OMethyl rep 2


title: Pac B2


title: DMSO 12

value: DMSO


title: normal colon tissue from non-CRC patient [933]


title: daf2chd7_rep3


title: normal colon tissue from non-CRC patient [909]


title: daf2chd7_rep5


title: daf2_rep5


title: Pac A6


title: normal colon tissue from CRC patient [N1018343]

value: Cancer

value: normal colon tissue from CRC patient


title: normal colon tissue from non-CRC patient [902]


title: normal colon tissue from CRC patient [Plate Control N1019702]


title: daf2chd7_rep4


title: normal colon tissue from CRC patient [N1021677]


title: normal colon tissue from CRC patient [N1020871]


title: DMSO 11


title: DMSO 9


title: daf2chd7_rep2


title: normal colon tissue from CRC patient [N1018024]


title: normal colon tissue from CRC patient [N1017724]


title: daf2chd7_rep1


title: normal colon tissue from CRC patient [N1016365]


title: normal colon tissue from CRC patient [N1009706]


title: SIRT5OE TAC rep 4 [99348]

city: Ann Arbor

first: David

middle: B

last: Lombard

state: Michigan

address: 3015 BSRB, 109 Zina Pitcher Place

institute: University of Michigan Ann Arbor

data_processing:
Basecalling was performed by the Illumina HiSeq4000
FastQC was used for FASTQ file quality control
Sequences were aligned to the mm10 transcriptome using Kallisto v0.43.1 with parameters -b 100 --single -l 200 -s 20
Transcripts were counted and converted to genes using Tximport v1.8.0
Assembly: mm10
Supplementary files format and content: Spreadhseet for normalized counts (TPM: transcript per million counts) is included

source_name: Mouse heart

extract_protocol:
Hearts were removed from mice, flash-frozen, pulverized, resuspended in Trizol. RNA was extracted as per the manufacture, and ribodepleted.
RNA libraries were prepared using standard Illumina protocols

tag: surgery

value: TAC

tag: mouse heart

value: Mouse heart


title: normal colon tissue from CRC patient [1019702 Plate-Control-1]


title: normal colon tissue from non-CRC patient [913]


title: normal colon tissue from CRC patient [1019702 Plate-Control-2]


title: normal colon tissue from CRC patient [1020919]


title: SIRT5OE TAC rep 3 [99347]


title: DMSO 7


title: normal colon tissue from CRC patient [1020308]


title: normal colon tissue from CRC patient [1020511]


title: DMSO 6


title: SIRT5OE TAC rep 2 [99346]


title: DMSO 8


title: normal colon tissue from CRC patient [1019808]


title: DMSO 5


title: normal colon tissue from CRC patient [1019702]


title: normal colon tissue from CRC patient [1019666]


title: SIRT5OE TAC rep 1 [99345]


title: SIRT5OE sham rep 3 [99355]

value: sham


title: normal colon tissue from CRC patient [1019619]

value: F


title: normal colon tissue from CRC patient [1019104]

value: CA


title: SIRT5OE sham rep 1 [99353]


title: DMSO 10


title: normal colon tissue from CRC patient [1018746]


title: normal colon tissue from CRC patient [1018361]


title: DMSO 3


title: DMSO 2


title: WT TAC rep 4 [99352]

value: WT


title: normal colon tissue from CRC patient [1018214]


title: normal colon tissue from CRC patient [1018133]


title: normal colon tissue from CRC patient [1016873]


title: normal colon tissue from CRC patient [1017989]


title: DMSO 1


title: WT TAC rep 3 [99351]


title: normal colon tissue from CRC patient [1016324]


title: WT TAC rep 2 [99350]


title: normal colon tissue from CRC patient [1014017]


title: WT sham rep 4 [99359]


title: RRBS_Ocun_fibro_5aza0

organism: Oryctolagus cuniculus

source_name: Primary dermal fibroblasts

growth_protocol: Primary dermal fibroblasts were grown in DMEM-GlutaMax supplemented with 10% fetal bovine serum and 50U/mL penicillin-streptomycin in a humidified atmosphere containing 5% CO2 at 37°C.

treatment_protocol: Fibroblasts were treated with 1 µM final concentration of 5-AzadC (Sigma A3656) for 72 hours and the medium was renewed every day.

value: Female

tag: genome build

value: Control (not treated)

value: Primary dermal fibroblasts


title: RNA-seq_Ocun_fibro_5aza1_3

data_processing:
Reads were aligned to the corresponding genome with HISAT2 v2.0.5 using default parameters and Ensembl transcriptome index.
For data visualization, BigWig files of normalized read counts per base were generated with bamToBed from bedtools and bedGraphToBigWig from UCSC using only reads that map uniquely in the genome.
genome build: hg38, mm10, oryCun2, canFam3, bosTau8, susScr11, galGal6
processed data files format and content: We provide bigWig files for visualization of RNA-seq tracks.

extract_protocol:
RNA samples were prepared using the AllPrep DNA/RNA Mini Kit (Qiagen).
RNA-seq libraries were prepared from 150 to 350 ng of total RNA using the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina), according to the manufacturer's instructions. Briefly, cytoplasmic and mitochondrial ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. The depleted RNA was fragmented using divalent cations at 94°C and cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. cDNA fragments were blunted, adenylated and ligated to adapters using T4 DNA Ligase. The cDNA libraries were generated with 12 cycles of PCR amplification, purified using AMPure XP beads (Beckman-Coulter) and checked for quality and quantified using capillary electrophoresis

value: Treated 5-AzadC 1 microM


title: normal colon tissue from CRC patient [1013970]


title: RNA-seq_Ocun_fibro_5aza1_2


title: normal colon tissue from CRC patient [1013412]

value: M


title: normal colon tissue from CRC patient [1011878]


title: DMSO 4


title: normal colon tissue from CRC patient [1019191]


title: RNA-seq_Ocun_fibro_5aza1_1


title: WT sham rep 2 [99357]


title: normal colon tissue from CRC patient [1009911]


title: WT sham rep 3 [99358]


title: RNA-seq_Ocun_fibro_5aza0_3


title: normal colon tissue from CRC patient [1011109]


title: SIRT5OE sham rep 2 [99354]


title: RNA-seq_Ocun_fibro_5aza0_2


title: normal colon tissue from CRC patient [1008838]


title: normal colon tissue from CRC patient [1008446]