title: M20_Liver_met_W_2


title: AB13001

status: Public on Dec 12 2021

type: SRA

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

library_source: transcriptomic

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Note: Second read contained only cell and molecule barcodes.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: Meta data file associating each single cell with its amplification batch and index sorting readouts

molecule: polyA RNA

organism: Mus musculus

source_name: MARS seq run of mouse MC38 tumor

growth_protocol: Experiments were performed in the Weizmann Institute of Science specific-pathogen free facility, and animals of both sexes were used between the ages of 8-10 weeks. MC38 (2×10^6) cell line were implanted subcutaneously on the right flank of mice and tumor volumes were measured every 2–3 days with an electronic caliper.

extract_protocol:
Isolation of tumor infiltrating leukocytes:  Tumor bearing mice were sacrificed 7 days days after treatment injection inoculation. The tumors underwent mechanical (gentleMACSTM C tube, Miltenyi Biotec Inc., San Diego, CA) and enzymatic digestion (0.1mg/ml DNase type I (Roche), and 1mg/ml Collagenase IV (Worthington) in RPMI-1640) for 15 min at 37°C. Cells then filtered through 100µm cell strainer, washed with ice cold sorting buffer, centrifuged (5 min, 4°C, 300g), and stained with fluorophores conjugated antibodies. LN and spleen were harvested 3 hours after treatment injection.Lymph nodes and spleen were dissected through a 70 µm nylon cell strainer and washed with PBS.
Samples were flow sorted using AriaIII (BD Biosciences, BD Diva Software) cell sorter.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol: When the sum of tumor length and width reached approximately 50 mm3, mice were randomized by tumor size (day 0), and received treatment by intraperitoneal injection as described for each experiment. CD40 mAb or CD40/CD11c bsAb at their respective MTDs (0.175 mg/kg, or 2.5 mg/kg respectively) on days 0, 2, 4, and 6 and/or with 50 ug of both Abs for in-vivo preferential binding. Organs were harvested at day 8 for TME analysis or 3 hours post treatment for in-vivo preferential binding experiment.

tag: strain

tag: organ

value: Tumor

tag: selection marker

tag: treatment

value: PBS

tag: mouse id

tag: timepoint

value: 7 days post injection

tag: mouse age

value: 8 weeks


title: AB13004

value: TCRb


title: M21_Kidney_met_W_3

city: Chicago

first: Navdeep

last: Chandel

state: IL

address: 303 E Superior St, SQ5

department: Pulmonary and Critical Care

country: USA

institute: Northwestern University

data_processing:
Raw BCL read files were demultiplexed and FASTQ files were generated using bcl2fastq and trimmed using Trimmomatic (Bolger et al., 2014).
Next, the reads were aligned to the mouse mm10 reference genome using STAR to generate BAM files (Dobin et al., 2013).
HTSeq was used to count reads in the exons of genes (Anders et al., 2015).
Genome_build: mm10
Supplementary_files_format_and_content: counts_tables.xlsx is an Excel spreadsheet that contains processed counts data for all samples

molecule: total RNA

source_name: Kidney Tissue

growth_protocol: No treatments

extract_protocol:
Whole RNA was extracted using a QIAGEN RNeasy Plus Mini Kit. Tissues were homogenized in RLT Plus Buffer + BME with a QIAGEN TissueRuptor II handheld rotor-stator homogenizer. After tissue homogenization, QIAshredder spin columns were used followed by gDNA elimination columns and an on column DNase digestion with Ambion RNase-free Dnase during the RNeasy RNA preparation manufacturer protocol.
RNA was quantified and QC was checked using an Agilent 4200 TapeStation RNA ScreenTape. mRNA libraries were prepared using NEBNext Ultra Kit with polyA selection (New England BioLabs).

treatment_protocol: mice were either treated with 200mg/kg metformin for 8 hours or were not treated as indicated

tag: genotype

value: WT

tag: age

value: young

value: metformin 200mg per kg 8 hours


title: M18_Kidney_met_H_2

value: NDUFS2 hemizygous


title: AB13003


title: M21_Liver_met_W_3

source_name: Liver Tissue


title: AB12996

value: CD40 bi


title: M20_Kidney_met_W_2


title: AB12995


title: M17_Kidney_met_H_1


title: AB12994

value: CD40 mono


title: AB12993


title: AB12999


title: AB13005


title: M16_Kidney_O_H_4

value: aged


title: AB13000


title: M22_Liver_met_W_4


title: AB12998


title: M17_Liver_met_H_1


title: M16_CD4_O_H_4

source_name: CD4 T cell


title: M16_Liver_O_H_4


title: AB12991


title: AB12997


title: AB12992


title: M18_Liver_met_H_2


title: M15_Liver_O_H_3


title: M15_Kidney_O_H_3


title: M15_CD8_O_H_3

source_name: CD8 T cell


title: AB12990


title: AB12987


title: M14_Liver_O_H_2


title: AB12989


title: M14_CD4_O_H_2


title: M15_CD4_O_H_3


title: AB12986


title: M16_CD8_O_H_4


title: M13_CD8_O_H_1


title: M12_Kidney_O_W_4


title: M13_Liver_O_H_1


title: AB12988


title: AB12917


title: AB12921


title: AB12920


title: M13_CD4_O_H_1


title: AB12923


title: AB12922


title: M14_CD8_O_H_2


title: AB12919


title: M12_Liver_O_W_4


title: AB12918


title: M12_CD4_O_W_4


title: AB12915


title: AB12924


title: M11_Liver_O_W_3


title: M13_Kidney_O_H_1


title: AB12913


title: AB12914


title: M10_Liver_O_W_2


title: M11_CD8_O_W_3


title: M11_Kidney_O_W_3


title: AB12911


title: M11_CD4_O_W_3


title: M10_CD8_O_W_2


title: AB12916


title: AB12907


title: AB12910


title: M12_CD8_O_W_4


title: AB12909


title: M09_CD8_O_W_1


title: AB12905


title: AB12906


title: M09_Kidney_O_W_1


title: AB12903


title: AB12904


title: M09_CD4_O_W_1


title: AB12902


title: M08_Kidney_Y_H_4


title: M08_CD8_Y_H_4


title: AB12912


title: M08_CD4_Y_H_4


title: M10_CD4_O_W_2


title: AB12908


title: AB12900


title: M07_Liver_Y_H_3


title: M07_Kidney_Y_H_3


title: M07_CD8_Y_H_3


title: AB11059


title: AB11058


title: AB11057


title: AB12901


title: AB11056


title: M06_Kidney_Y_H_2


title: AB11055


title: M06_CD8_Y_H_2


title: AB11054


title: M07_CD4_Y_H_3


title: AB11053


title: M06_Liver_Y_H_2


title: AB11052


title: M06_CD4_Y_H_2


title: M08_Liver_Y_H_4


title: M09_Liver_O_W_1


title: M05_Kidney_Y_H_1


title: AB11051


title: AB11050


title: AB11049


title: AB12898


title: M05_CD8_Y_H_1


title: AB11048


title: M04_CD8_Y_W_4


title: M04_Kidney_Y_W_4


title: AB11047


title: M03_Liver_Y_W_3


title: M05_CD4_Y_H_1


title: M05_Liver_Y_H_1


title: AB11043


title: AB11046


title: AB11042


title: AB11040


title: AB11044


title: AB11041


title: AB11045


title: M03_Kidney_Y_W_3


title: M02_Kidney_Y_W_2


title: M02_Liver_Y_W_2


title: M03_CD8_Y_W_3


title: M02_CD4_Y_W_2


title: AB11036


title: M01_Liver_Y_W_1


title: M03_CD4_Y_W_3


title: AB11035


title: AB11034


title: M01_Kidney_Y_W_1


title: M01_CD8_Y_W_1


title: M04_CD4_Y_W_4


title: M01_CD4_Y_W_1


title: AB11033


title: H01_Treg_o_w_1

source_name: Regulatory T cell


title: AB11032


title: AB11031


title: G02_Treg_o_h_4


title: AB11029


title: AB11030


title: G01_Treg_y_h_4


title: M02_CD8_Y_W_2


title: F02_Treg_o_h_3


title: F01_Treg_y_h_3


title: AB10849


title: E02_Treg_o_h_2


title: AB10848


title: D02_Treg_o_h_1


title: AB10850


title: AB10846


title: E01_Treg_y_h_2


title: D01_Treg_y_h_1


title: AB10845


title: C01_Treg_y_w_3


title: AB10844


title: C02_Treg_o_w_4


title: AB10843


title: AB10842


title: Whole-pituitary rep2

city: Bethesda

first: Patrick

middle: Allen

last: Fletcher

state: Maryland

address: 9000 Rockville Pike

institute: NIDDK

description: barcode appendix: -3

data_processing:
Custom extension of 3'UTR annotations for NCBI Rnor6.0 reference transcriptome
CellRanger (v3.1) count for each sample: De-multiplexing, alignment to reference transcriptome and UMI collapsing
CellRanger (v3.1) aggr to merge samples into a common matrix
Genome_build: Rnor6.0 (NCBI annotation)
Supplementary_files_format_and_content: CellRanger generated text file containing merged UMI counts for all four samples (Matrix Market exchange format) with tab-separated list of barcodes and genes

organism: Rattus norvegicus

source_name: Whole pituitary cells

extract_protocol:
Pituitary glands were quickly collected from postpubertal rats and dispersed using a trypsin/EDTA based method. 30 whole pituitaries in one preparation and 30 dissected anterior/posterior pituitaries were collected, pooled, dispersed and counted, and were loaded into the Chromium Single Cell Controller (10X Genomics). The whole pituitary cell preparation was split into two lanes, while anterior and posterior cells were each loaded into separate lanes for a total of four lanes.
Single-cell cDNAs and barcoded sequencing libraries were constructed from the output of the Chromium Single Cell Controller using a Chromium Single Cell 3’ Reagent Kit v3 according to the manufacturer’s protocol (10X Genomics)
Each library received a different sample index; these were multiplexed and sequenced together. Barcodes = cell barcodes. Barcode appendices are used to distinguish samples. The appendix ID for each sample is included in the 'description' field.

value: Sprague Dawley

tag: tissue

value: Whole pituitary

tag: Sex

value: female

value: 75 days

tag: estrus cycle stage

value: Random cycling


title: AB10841

value: Tumor


title: B02_Treg_o_w_3


title: AB10840


title: B01_Treg_y_w_2


title: Whole-pituitary rep1

description: barcode appendix: -2


title: Posterior-pituitary only

description: barcode appendix: -4

source_name: Posterior pituitary cells

value: Posterior pituitary


title: AB10839

value: 7 days post injection


title: ATII09_WT_O_R1_S25

source_name: Alveolar type II cell


title: AB10838

value: 8 weeks


title: ATII08_WT_Y_R4_S16


title: AB10847

value: TCRb

value: PBS


title: Anterior-pituitary only

description: barcode appendix: -1

source_name: Anterior pituitary cells

value: Anterior pituitary


title: tissue_WaterNeg_tissue

city: Ann Arbor

first: Yatrik

last: Shah

state: Michigan

address: 500 S State Street

institute: University of Michigan

library_source: genomic

data_processing:
The V4 region of the 16S rRNA was amplified from freshly collected mouse feces using the Dual-indexing sequencing strategy. For tissue, colonic tissue was collected following dissection.
Sequencing was done on the Illumina MiSeq platform, using a MiSeq reagent kit V2 500 cycles, according to the manufacturer’s instructions.
Bacterial community analysis was performed using Mothur (v1.42.3) aligning to the full SILVA reference alignment (release 132) provided by Mothur
Genome_build: Mothur's Silva release 132
Supplementary_files_format_and_content: fecal_taxonomy_reads.txt and tissue_taxonomy_reads.txt representing annotated read counts

molecule: other

organism: synthetic construct

source_name: control

extract_protocol:
Feces were collected from the terminal colon at sacking. rRNA was extracted using the Qiagen MagAttract PowerMicrobiome kit.
Libraries were cleaned, normalized and underwent quality control before sequencing on Illumina MiSeq platform.

treatment_protocol: Mice were genotyped and DoubleMut, TripleMut and CRE-negative litter mate controls were induced with 1 dose of 100 mg/kg tamoxifen. Bedding was mixed daily throughout the experiment. Mice were euthanized on day 10. Feces were collected from the terminal colon at sacking.

tag: cell type

value: control

tag: sample type


title: AB10837


title: fecal_WaterNeg_feces


title: ATII06_WT_Y_R3_S14

value: WT

value: young


title: Ubn2_KD rep2

city: Tianjin

first: Xiao

last: Feng

address: No.38 Tongyan Road, Haihe Education Park, Jinnan District

department: State Key Laboratory of Medicinal Chemical Biology

country: China

institute: College of Pharmacy, Nankai University

data_processing:
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by Trimgalore, then sequence reads were mapped to Grcm38 genome using STAR.
Raw count were generated by featureCounts.
Genome_build: Grcm38
Supplementary_files_format_and_content: tab-delimited text file include raw count values for each Sample.

source_name: Embryonic stem cell

growth_protocol: Mouse E14 embryonic stem cells (ESCs) were cultured under 5% CO2 at 37℃ on well plate coated with 0.2% gelatin(Sigma),in medium(Hyclone) that supplement with 15% FBS（Hyclone）,10ng/ml mLIF (GeneScript)，1% Penicillin-Streptomycin (Solarbio)，1% GlutaMAX(Solarbio), 1% nonessential amino acids(Gibco), 0.1 mM β-mercaptoethanol (Sigma).

extract_protocol:
Total RNA was extracted with RNAiso Plus (Takara) and was subjected to Dnase I (Thermo Scientific) for 30min
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (VAHTS mRNA-seq V2 Library Prep Kit for Illumina). The mRNA fragmentation and priming was performed using VAHTSFirst Strand Synthesis Reaction Buffer and VAHTS Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA（byAxyPrep Mag PCR Clean-up (Axygen)was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

value: Ubn2 knowdown


title: Ubn2_KD rep1


title: E016

city: Beijing

first: Mengliang

last: Hu

address: 8 Xishiku St, Xicheng District

department: Department of Geriatrics

institute: Peking University First Hospital

description:
gene_expression.xlsx
miRNA_expression.xlsx
lncRNA_expression.xlsx
circRNA_expression.xlsx
diff_mRNA_lncRNA_miRNA_interaction.xlsx

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: peripheral blood

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

tag: disease

value: multi-vessel coronary artery disease


title: ATII05_NDUFS2_Y_R3_S13

value: NDUFS2 hemizygous


title: fecal_DNA-ExtractionCtrl_feces


title: E019


title: E014


title: E013


title: ATII03_WT_Y_R2_S11


title: ATII02_NDUFS2_Y_R1_S10


title: Ubn1_KD rep1

value: Ubn1 knowdown


title: ATII04_NDUFS2_Y_R2_S12


title: Ubn1_KD rep2


title: Hira_KD rep2

value: Hira knowdown


title: ATII07_NDUFS2_Y_R4_S15


title: E012


title: Control rep2

value: wild type


title: Hira_KD rep1


title: ATII016_NDUFS2_O_R4_S32

value: aged


title: ATII015_NDUFS2_O_R3_S31


title: E010


title: Control rep1


title: ATII014_NDUFS2_O_R2_S30


title: E007


title: LTHSC-RUNX1_rep2

first: Chen

last: Li

state: Beijing

address: Yihe Yuan Road No.5

department: Institute of Molecular Medicine

institute: Peking University

data_processing:
The quality of sequencing was analyzed with fastqc (v.0.11.8).
Raw reads were trimmed and removed for adaptor sequences with cutadapt (v.2.6)
The trimmed reads were mapped to mm10 mouse genome by Bowtie2 (v.2.3.5) with the parameter “-N 1”.
Mapped sam files were transferred to bam files with samtools (v.1.9) and selected for uniquely mapped reads with samtools (v.1.9) by MAPQ >= 30.
Duplicates were removed with picard MarkDuplicates (v.2.2.4). Only non-duplicated reads were used for the further analysis.
Reads of replicates were sampled by samtools (v.1.9) to the same level for comparison.
Peaks were called with non-duplicated bam files by MACS2 callpeak (v.2.2.5).
Bigwig files were generated with bamCoverage (v.3.3.1), normalized to 1 M or 10 M reads.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were bigwig files.

molecule: genomic DNA

source_name: E14.5 fetal liver

extract_protocol:
The different cell populations of WT mouse embryo were sorted by FACS and fixed, then used for ChIP-seq.
After PCR enrichment with NEBNext Q5 polymerase, products were purified and selected by AMPure XP beads for 200-1000 bp.

tag: cell statement

value: E14.5 fetal liver LT-HSCs

tag: chip anitbody


title: ATII013_NDUFS2_O_R1_S29


title: E002


title: C0019


title: ATII012_WT_O_R4_S28


title: LTHSC-RUNX1_rep1

tag: strain


title: C0016


title: ATII011_WT_O_R3_S27


title: LTHSC-H3K4me3_rep3


title: C0015


title: C0005


title: ATII010_WT_O_R2_S26


title: E018

value: single-vessel coronary artery disease


title: ATII01_WT_Y_R1_S9


title: LTHSC-H3K4me3_rep1


title: E015


title: C0002


title: LTHSC-H3K4me1_rep1


title: LTHSC-H3K4me1_rep2


title: LTHSC-H3K27me3_rep2


title: E003


title: AM08_WT_Y_R4

source_name: Alveolar macrophage


title: LTHSC-H3K27me3_rep1


title: C0017


title: LTHSC-H3K4me3_rep2


title: LTHSC-H3K27ac_rep3


title: AM05_NDUFS2_Y_R3


title: C0009


title: LTHSC-H3K27ac_rep2


title: AM09_WT_O_R1


title: AM07_NDUFS2_Y_R4


title: AM04_NDUFS2_Y_R2


title: C0006


title: AM03_WT_Y_R2


title: LTHSC-H3K27ac_rep1


title: AM06_WT_Y_R3


title: preHSC-RUNX1_rep2

source_name: E11.0 AGM

value: E11.0 AGM pre-HSCs


title: AM016_NDUFS2_O_R4


title: tissue_TripleMut_10

description:
t_519.5
tissue_taxonomy_reads.txt

organism: mouse gut metagenome

source_name: mouse colonic tissue

value: colonic tissue bacteria

value: TripleMut

tag: cage


title: Affected patient lens

city: Sewickley

first: Bharesh

middle: Kumar

last: Chauhan

state: PA

address: 400 45th St., Faculty Pavilion, Suite 5111

department: Ophthalmology

institute: University of Pittsburgh

data_processing:
Illumina CASSAVA 1.8.2 program used for converting primary sequencing output .bcl basecall files into .fastq
Sequenced reads were trimmed for adaptor sequence, and then mapped to hg38 human genome using CLC Genomics Workbench Version 9.5 with parameters: mismatches 2, maximum number of hits for a read 10.
Transcripts per million reads (TPM) were calculated using methodology and calculations from Wagner et al., Theory in Biosciences, 2012. To calculate the TPM, divide the read counts by the length of each gene in kilobases (gives reads per kilobase (RPK)). Then divide the RPK values by 1,000,000 to give TPM.
Expression values were transformed (logarithm 2) and normalized by the mean. Differential expression was then identified through Kal's test [Kal et al., Molecular Biology of the Cell, 1999] and two kinds of corrected p-values were added to the analysis (in addition to the standard p-value produced for the test statistic): Bonferroni corrected and FDR corrected, with p < 0.05 in both cases.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM and RPKM values for each donor lens (L_ATCACG_L002_R1_001.txt) and age-related affected lens (ML_GGCTAC_L001_R1_001.txt)

source_name: Affected patient lens

extract_protocol:
Lens tissue was placed in RLT lysis buffer (Qiagen RNeasy) and efficiently disrupted using MagNA lyser green beads and instrument (Roche). The resulting lysate was then homogenized using QIAshredder and the homogenate supernatant run through a RNeasy mini spin column according to instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lens

value: 4 yrs


title: preHSC-RUNX1_rep1


title: preHSC-H3K4me3_rep2


title: AM015_NDUFS2_O_R3


title: Smad4 3

type: RNA

city: Heidelberg

first: Matthias

last: Bozza

address: Im Neuenheimer Feld 242

country: Germany

institute: DKFZ Heidelberg

description: Capan-1 cells established with pS/MAR-Smad4-Luciferase

hyb_protocol: cRNA was hybridized to human whole-genome Illumina HumanHT-12 V4.0 expression beadchip (Illumina, Inc.)

scan_protocol: BeadChips were scanned with an Illumina iScan system (Illumina Inc.) Scanning and feature extraction was performed using BeadScan and BeadStudio sofware (Illumina) with standard settings for the chips used.

data_processing: The analysis was done on the bead-level data using R following outlier removal (by taking only beads with an expression value > 20 before using the 2.5 MADs rule). The ProbeIDs expression values are the mean of the remaining beads. Finaly, quantile normalization was performed.

label: biotin

source_name: cell line

label_protocol: RNA (500 ng per sample) were labelled using the Illumina® TotalPrep™ RNA Amplification Kit according to the manufacturers' instructions.

growth_protocol: Capan-1 were growth in IMDM supplemented with 20% FBS. 2e5 cells were injected orthotopically in the pancreas of Nod/SCID mice and upon tumour resection cells were isolated

extract_protocol: Total RNA was extracted using teh Qiagen RnEasy Mini Kit according to manufacturer's instructions.

treatment_protocol: Capan-1 luciferase and Smad4 luciferase were transfected with pS/MAR and selected with G418 until stable clones were generated

value: Pancreas


title: Luciferase 2

description: Capan-1 cells established with pS/MAR-Luciferase


title: Normal donor lens

source_name: Normal donor lens


title: tissue_TripleMut_9

description:
t_519.4
tissue_taxonomy_reads.txt


title: AM013_NDUFS2_O_R1


title: Smad4 1


title: AM014_NDUFS2_O_R2


title: AM02_NDUFS2_Y_R1


title: preHSC-H3K4me3_rep1


title: preHSC-H3K4me1_rep2


title: Luciferase 3


title: tissue_TripleMut_8

description:
t_519.3
tissue_taxonomy_reads.txt


title: tissue_CRE NEG_8

description:
t_519.2
tissue_taxonomy_reads.txt

value: CRE NEG


title: AB11037

source_name: MARS seq run of mouse MC38 tumor

tag: organ

value: Tumor

tag: selection marker

value: TCRb

value: CD40 bi

value: 7 days post injection

value: 8 weeks


title: AM012_WT_O_R4

value: WT

tag: treatment


title: AM011_WT_O_R3


title: tissue_CRE NEG_7

description:
t_518.4
tissue_taxonomy_reads.txt


title: Smad4 2


title: tissue_DoubleMut_7

description:
t_519.1
tissue_taxonomy_reads.txt

value: DoubleMut


title: AM010_WT_O_R2

value: aged


title: Wild type 1

description: Capan-1 cells unmodified


title: preHSC-H3K27me3_rep1


title: preHSC-H3K27me3_rep2


title: Wild type 3

description: Capan-1 cells unmodified


title: preHSC-H3K27ac_rep2


title: tissue_DoubleMut_6

description:
t_518.3
tissue_taxonomy_reads.txt


title: Luciferase 1


title: tissue_DoubleMut_5

description:
t_518.2
tissue_taxonomy_reads.txt


title: preHSC-H3K27ac_rep1


title: AM01_WT_Y_R1

value: young


title: tissue_TripleMut_7

description:
t_517.1
tissue_taxonomy_reads.txt


title: preHSC-H3K4me1_rep1


title: HEC-RUNX1_rep2

source_name: E10.0 AGM

value: E10.0 AGM HECs


title: A01_Treg_y_w_1

source_name: Regulatory T cell


title: Wild type 2

description: Capan-1 cells unmodified


title: PacoSMAD4 2

description: Paco2 cells established with nS/MAR SMAD4-GFP

source_name: PDX

growth_protocol: PACO2 were growth in medium in absence of TGFB.

treatment_protocol: Paco-2 GFP and Smad4 GFP were transfected with nS/MAR and selected with Puromycin until stable clones were generated


title: tissue_TripleMut_6

description:
t_516.3
tissue_taxonomy_reads.txt


title: HEC-RUNX1_rep1


title: PacoSMAD4 4


title: tissue_TripleMut_5

description:
t_516.2
tissue_taxonomy_reads.txt


title: tissue_DoubleMut_4

description:
t_516.1
tissue_taxonomy_reads.txt


title: PacoSMAD4 1


title: HEC-H3K4me3_rep1


title: A02_Treg_o_w_2


title: Gar15-13 Vehicle 4 FOXA1

city: Adelaide

first: Joanna

last: Achinger-Kawecka

state: SA

address: AHMS Building, North Terrace

country: Australia

institute: South Australian Immunogenomics Cancer Institute

data_processing:
ChIP-seq reads were aligned against human genome (hg38/GRCh38) using bowtie2 with default parameters.
Peak calling of individual ChIP–seq experiments was performed with MACS2 with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: narrowpeak files contain peaks generated using Macs2 (FDR < 55).

source_name: Gar15-13 Vehicle tumour

growth_protocol: A single patient-derived tumor tissue was divided and implanted into the 4th inguinal mammary gland of 6-week-old female NOD-SCID-IL2γR-/- (NSG) mice. Where relevant (PDX model HCI-005), mice were also subcutaneously implanted with an E2 pellet.

extract_protocol:
Samples snap-frozen in Optimal Cutting Temperature compound (Tissue-Tek) were used for ER and FOXA1 ChIP-seq experiments. Using a cryostat (Leica, #CM3050-S), 15x 30 µm sections were cut from each tumour at  -20 ̊C and these samples were subjected to double fixation with DSG and formaldehyde as previously described (Singh et al., 2019).
Library preparation for ChIP-Seq was performed using the QIAseq Ultralow Input Library Kit (Qiagen, #180495).

treatment_protocol: Mice were randomly assigned to treatment groups and treated  with either a vehicle (0.5mg/kg PBS) or Decitabine (0.5mg/kg DAC).

value: Breast cancer PDX model Gar15-13

value: Vehicle

tag: replicate

tag: chip antibody


title: Gar15-13 Input FOXA1

value: Input


title: Gar15-13 Vehicle 3 FOXA1


title: tissue_CRE NEG_6

description:
t_515.4
tissue_taxonomy_reads.txt

value: colonic tissue bacteria

tag: genotype


title: HEC-H3K4me1_rep2


title: Gar15-13 Vehicle 2 FOXA1


title: PacoGFP 2

description: Paco2 cells established with nS/MAR GFP


title: HEC-H3K4me1_rep1


title: HEC-H3K4me3_rep2


title: PacoGFP 1

description: Paco2 cells established with nS/MAR GFP


title: Gar15-13 Vehicle 1 FOXA1


title: tissue_TripleMut_4

description:
t_515.2
tissue_taxonomy_reads.txt

value: TripleMut


title: HEC-H3K27me3_rep2


title: HCI-005 Decitabine 1_methylation

type: genomic

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

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

data_processing: Raw intensity data (IDAT) files were imported and quality controlled using minfi package (v.1.34.0) (Aryee et al., 2014). Data was then normalised with background correction. To reduce the risk of false discoveries, we removed probes affected for cross-hybridization to multiple locations on the genome or overlapped SNPs, as previously described (Pidsley et al., 2016). Beta (β) values were calculated from unmethylated (U) and methylated (M) signal [M/(U + M + 100)] and ranged from 0 to 1 (0 to 100% methylation). β values of loci whose detection P values were > 0.01 were assigned NA in the output file. To map EPIC arrays to hg38/GRCh38 assembly, all probes were annotated with the EPIC.hg38.manifest.tsv.gz files as described in (Zhou et al., 2017).

label: Cy5 and Cy3

source_name: HCI-005 Decitabine tumour

label_protocol: Standard Illumina Protocol

extract_protocol: Gernomic DNA from Decitabine-treated and Vehicle tumours from two PDX models (GAR15-13D and HCI-005) was isolated from snap-frozen tumour samples using the  QIAamp DNA Mini Kit (Qiagen).

treatment_protocol: Mice were randomly assigned to treatment groups and treated for 5 days with either a vehicle or Decitabine.

value: Breast cancer PDX model HCI-005

value: Decitabine


title: tissue_DoubleMut_3

description:
t_515.3
tissue_taxonomy_reads.txt


title: HIC005 Decitabine Input ER

source_name: HCI005 Decitabine tumour

value: Breast cancer PDX model HCI005


title: PacoSMAD4 3

value: Pancreas


title: Gar15-13 Vehicle 2_methylation

extract_protocol: Gernomic DNA from Decitabine-treated and Vehicle tumours from two PDX models (GAR15-13d and HCI-005) was isolated from snap-frozen tumour samples using the  QIAamp DNA Mini Kit (Qiagen).


title: tissue_TripleMut_3

description:
t_515.1
tissue_taxonomy_reads.txt


title: tissue_CRE NEG_5

description:
t_514.4
tissue_taxonomy_reads.txt

value: CRE NEG


title: HEC-H3K27me3_rep1


title: HEC-H3K27ac_rep2


title: Gar15-13 Vehicle 1_methylation


title: PacoGFP 3

description: Paco2 cells established with nS/MAR GFP


title: HCI-005 Vehicle 2_methylation

source_name: HCI-005 Vehicle tumour


title: Gar15-13 Decitabine 9_methylation

source_name: Gar15-13 Decitabine tumour


title: PacoGFP 4

description: Paco2 cells established with nS/MAR GFP


title: Gar15-13 Decitabine 10_methylation


title: HCI005 Decitabine 3 ER

value: ER (Millipore SC-543X)


title: Paco WT 4

description: Paco2 cells unmodified


title: normal3

city: Nanjing

first: Jiaheng

last: Xie

address: 300 Guangzhou Rd

department: Burn and Plastic Surgery

institute: Jiangsu Province Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: normal

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

tag: age

tag: gender

value: female

tag: country

value: China


title: Paco WT 3

description: Paco2 cells unmodified

tag: tissue


title: HEC-H3K27ac_rep1


title: Paco WT 2

description: Paco2 cells unmodified


title: Paco WT 1

description: Paco2 cells unmodified


title: HCI005 Decitabine 1 ER


title: HCI-005 Decitabine 3_methylation


title: HCI-005 Vehicle 1_methylation


title: HCI005 Decitabine 2 ER


title: tissue_CRE NEG_2

description:
t_514.1
tissue_taxonomy_reads.txt

tag: cell type


title: HCI005 Vehicle Input ER

source_name: HCI005 Vehicle tumour


title: HCI005 Vehicle 4 ER


title: AEC-RUNX1_rep3

value: E10.0 AGM early AECs


title: AEC-RUNX1_rep2


title: normal1


title: tissue_DoubleMut_2

description:
t_513.4
tissue_taxonomy_reads.txt

value: DoubleMut


title: tissue_TripleMut_2

description:
t_513.5
tissue_taxonomy_reads.txt


title: AEC-RUNX1_rep1


title: keloid2

source_name: keloid

value: male


title: HCI005 Vehicle 2 ER


title: AEC-H3K4me3_rep2


title: HCI005 Vehicle 3 ER

value: Breast cancer PDX model HCI006


title: tissue_DoubleMut_1

description:
t_513.3
tissue_taxonomy_reads.txt


title: HCI005 Vehicle 1 ER


title: AEC-H3K4me3_rep1


title: tissue_CRE NEG_3

description:
t_514.2
tissue_taxonomy_reads.txt


title: tissue_CRE NEG_4

description:
t_514.3
tissue_taxonomy_reads.txt


title: normal2


title: Gar15-13 Input ER

value: Breast cancer PDX model Gar15-13


title: tissue_CRE NEG_1

description:
t_513.2
tissue_taxonomy_reads.txt


title: MCF-10A LA treated replicate 2

first: Susan

middle: Elizabeth

last: Clare

address: 303 E Superior, LURIE  4-105

department: Department of Surgery

institute: FEINBERG SCHOOL OF MEDICINE, Northwestern University

description:
F2
paired end RNA-seq

data_processing:
Illumina adapter sequences and low-quality base calls were trimmed off the paired end reads with Trim Galore v0.4.3.
Sequence reads were aligned to human reference genome hg38 using bowtie2. Duplicate reads were discarded with Picard. Reads mapped to mitochondrial DNA together with low mapping quality reads were excluded from further analysis.
Peak regions were identified using MACS2. Peaks for samples in the same condition were merged using the function ‘merge’ of bedtools and peaks for samples in different conditions were intersected using the function of ‘intersect’ of bedtools.
Genome_build: human reference genome hg38 (GRCh38)
Supplementary_files_format_and_content: bigWig files

source_name: MCF-10A cell line

growth_protocol: MCF-10A were cultured in complete mammary epithelial cell growth basal medium (Lonza).

extract_protocol:
Cells were pelleted and lysed in ATAC resuspension buffer.
Libraries were prepared using the Illumina atac kit # 20034197.

treatment_protocol: Cells treated with LA or vehicle.

tag: cell line

value: LA Treated


title: AEC-H3K4me1_rep2


title: MCF-10A LA treated replicate 1

description:
F1
paired end RNA-seq


title: Gar15-13 Decitabine 10 ER


title: AEC-H3K27me3_rep2


title: keloid1


title: Gar15-13 Decitabine 4 ER


title: AEC-H3K27ac_rep2


title: MCF-10A vehicle treated replicate 2

description:
V2
paired end RNA-seq

value: Vehicle


title: AEC-H3K27me3_rep1


title: Bone marrow macrophage, Day 18 Rep 2

city: Duarte

first: Xu

last: Cao

state: CA

address: 1500 E Duarte Rd

institute: City of Hope Comprehensive Cancer Center

data_processing:
Reads containing adapter or poly-N and those of low quality were trimmed, after which gene counts were obtained though mapping the clean reads to reference genome mm10 using STAR 2.5.3a.
The bulk RNAseq data was aligned to mm10 mouse genome (GENCODE vM23/Ensembl 98)) with STAR(v.2.5.3a) on the PartekFlow platform
Supplementary_files_format_and_content: Raw_Gene_counts_matrix.xlsx

source_name: Bone marrow macrophage

extract_protocol:
RNA of sorted femur macrophages (CD11b+F4/80+) were extracted with an RNA extraction kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BALB/c

value: Bone marrow

value: Macrophages

value: 18 days after Raji i.v. engraftment


title: Bone marrow macrophage, Day 4 Rep 2

value: 4 days after Raji i.v. engraftment


title: MCF-12A control replicate 2

description:
12A-OVE-2
mRNA
paired end RNA-seq

data_processing:
The sequence reads were mapped to the hg38 reference genome using STAR (version 2.5; Dobin et al. 2012). To evaluate the quality of the RNA-seq data, number of reads that fall into different annotated regions (exonic, intronic, splicing junction, intergenic, promoter, UTR, etc.) of the reference genes were determined with bamUtils (version 0.5.9; Breese and Liu 2013). Differential gene expression analysis was performed with edgeR (version 3.30.3; Robinson, Mccarthy, and Smyth 2010). In this workflow, the statistical methodology applied uses negative binomial generalized linear models with likelihood ratio tests.
Sequencing quality using FastQC/MultiQC version 0.11.5
Read counting using subread/featureCounts version 1.5.1 (Liao, Smyth, and Shi 2013).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: MCF-12A_veh_vs_OA_counts.xlsx: Excel file

source_name: MCF-12A cell line

growth_protocol: MCF-12A were cultured in complete mammary epithelial cell growth basal medium (Lonza).

extract_protocol:
RNA was isolated with Qiagen RNeasy plus mini Kit.
Total RNA was first evaluated for its quantity, and quality, using Agilent Bioanalyzer 2100. A RIN (RNA Integrity Number) of eight or higher was required to pass the quality control. One hundred to 250 nanograms of total RNA per sample were used for library preparation using KAPA RNA HyperPrep Kit (Roche) for Illumina NGS platform. Each indexed library was quantified and its quality accessed by Qubit and Agilent Bioanalyzer, and 6 libraries were pooled in equal molarity. 5µL of 4nM pooled libraries were denatured, neutralized and a final concentration of 1.5 pM of pooled libraries was loaded to Illumina NovatSeq 6000 for 75bp single-read sequencing.

treatment_protocol: Cells treated with OA or vehicle.


title: Bone marrow macrophage, Day 18 Rep 1


title: Bone marrow macrophage, Day 0 Rep 2

value: non-engrafted


title: keloid3


title: Bone marrow macrophage, Day 4 Rep 1


title: MCF-10A vehicle treated replicate 1

description:
V1
paired end RNA-seq


title: MCF-12A control replicate 1

description:
12A-OVE-1
mRNA
paired end RNA-seq


title: Gar15-13 Vehicle 4 ER


title: AEC-H3K27ac_rep1


title: LTHSC-hic-rep4

data_processing:
HiCExplorer (v.3.4.2) was used for the processing of Hi-C data. Only uniquely mapped read pairs (MAPQ >= 10) were saved for further trimming of dangling end reads, same fragment reads, self-circled reads, self-ligated reads and other invalid Hi-C reads.
Non-duplicated reads were used to generate Hi-C matrix at 5kb,10 kb and 40 kb resolution with cooler (v.0.8.5).
After filtering bins with low counts, the matrices were balanced by Knight-Ruiz (KR) with hicCorrectMatrix in HiCExplorer.
Total read count of Hi-C matrices were normalized to the smallest level by hicNormalize in HiCExplorer with “--normalize smallest” parameter.
Compartments were calculated with matrices of 100 kb resolution and regarded as A or B according to the gene density.
TADs were identified with hicFindTADs at 40 kb resolution, while loops were identified with hicDetectLoops at 10 kb resolution.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were cool matrix files.

source_name: E14.5 fetal liver

extract_protocol:
Different cell populations sorted by FACS and fixed with 1% formaldehyde solution at room temperature for 10 min. MboI enzyme (NEB, R0147M) was used to digest chromatin. After biotinylation, ligation and proteinase K treatment, DNA was purified and sheared to 300-500 bp with Covaris M220, followed by Dynabeads Myone Streptavidin C1 bead pulling down.
The Hi-C library were amplified 12-15 cycles with Extaq (Takara). Size selection was performed by adding 0.48X volume beads for the first time and 1X volume beads for the second time to get 200-1000 bp DNA fragment.

value: E14.5 fetal liver LT-HSCs

tag: restriction enzyme

value: MboI


title: Gar15-13 Vehicle 3 ER

value: ER (Millipore SC-543X)


title: tissue_TripleMut_1

description:
t_513.1
tissue_taxonomy_reads.txt

source_name: mouse colonic tissue

value: colonic tissue bacteria

value: TripleMut


title: MCF-12A treated replicate 2

description:
12A-OCT-2
mRNA
paired end RNA-seq

value: OA Treated


title: Gar15-13 Vehicle 2 ER


title: Bone marrow macrophage, Day 0 Rep 1


title: AEC-H3K4me1_rep1

tag: cell statement

value: E10.0 AGM early AECs


title: Gar15-13 Decitabine 9 ER

value: Decitabine


title: MCF-12A control replicate 3

description:
12A-OVE-3
mRNA
paired end RNA-seq


title: Gar15-13 Decitabine 5 ER

value: Breast cancer PDX model Gar15-13


title: LTHSC-hic-rep2


title: LTHSC-hic-rep3


title: MCF-12A treated replicate 1

description:
12A-OCT-1
mRNA
paired end RNA-seq


title: LTHSC-hic-rep1


title: HCI005 Decitabine 4_RNA-seq

description:
Veh.vs.Dec_HCI005.cntTable
HCI005_Decitabine_4

data_processing:
Sequence adaptors were trimmed using Trim Galore (v.0.11.2), reads were processed with Xenome v.10.1. (Conway et al., 2012) to remove mouse sequences and remaining reads were mapped with STAR (v.2.7.7a) (Dobin et al., 2013) to the hg38/GRCh38 human genome build with GENCODE v33 used as a reference transcriptome (parameter settings: –quantMode TranscriptomeSAM–outFilterMatchNmin 101 –outFilterMultimapNmax 20).
TPM counts for each sample were obtained from DESeq2.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: normalized transcript abundance measurment

extract_protocol:
RNA was extracted from snap-frozen tumour PDX tissue samples using the RNeasy Mini Kit (QIAGEN)
RNA was prepared for sequencing using the TruSeq Stranded mRNA Library Prep kit (Illumina) and libraries were sequenced on Illumina NovaSeq S4 in paired-end mode.

value: Breast cancer PDX model HCI005


title: ALKBH1 si rep2

city: Chengdu

first: yuting

last: Liu

address: people's south road 14

institute: Sichuan University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index ofthe reference genome was builtusing Hisat2 v2.0.5 andpaired-endcleanreadswerealignedtothereferencegenomeusingHisat2v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Homo_sapiens_Ensemble_94.fa
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: bone marrow mesenchymal stem cells

growth_protocol: high-glucose DMEM

extract_protocol:
human bone marrow were extracted, cultured in high-glucose DMEM and RNA was harvested using Trizol reagent.
Libraries were prepared according to Illumina's instructions of RNA sample. Paired-end method was adopted for further processes.

value: bone marrow

value: mesenchymal stem cells

value: treated with ALKBH1 siRNA


title: HCI005 Decitabine 3_RNA-seq

description:
Veh.vs.Dec_HCI005.cntTable
HCI005_Decitabine_3


title: fecal_MockZymoPos_feces

organism: Bacteria

source_name: control

value: bacteria

tag: sample type


title: preHSC-hic-rep5

source_name: E11.0 AGM

tag: strain

value: E11.0 AGM pre-HSCs


title: ALKBH1 si rep1


title: WT rep1

value: treated with control siRNA


title: HCI005 Decitabine 2_RNA-seq

description:
Veh.vs.Dec_HCI005.cntTable
HCI005_Decitabine_2


title: preHSC-hic-rep2


title: HCI005 Decitabine 1_RNA-seq

description:
Veh.vs.Dec_HCI005.cntTable
HCI005_Decitabine_1


title: MCF-12A treated replicate 3

description:
12A-OCT-3
mRNA
paired end RNA-seq


title: preHSC-hic-rep3


title: WT rep2


title: HCI005 Vehicle 4_RNA-seq

description:
Veh.vs.Dec_HCI005.cntTable
HCI005_Veh_4

value: Vehicle


title: HCI005 Vehicle 3_RNA-seq

description:
Veh.vs.Dec_HCI005.cntTable
HCI005_Veh_3


title: Gar15-13 Decitabine 5_PCHiC

data_processing:
Library strategy: PCHi-C
PCHi-C sequenced reads were mapped and filtered using HiCUP (v.0.7.4) (Wingett et al., 2015) with hg38/GRCh38 genome digested with –arima flag and minimum di-tag length set to 20.
Unique, valid mapped reads from HiCUP were converted into .chinput files using bam2chicago.sh utility and obtained chinput files were further filtered and processed with CHiCAGO (v.1.14.0)
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: chinput files containing unique, valid mapped reads.

extract_protocol:
Hi-C experiments were performed on fresh-frozen tumour samples using the Arima Hi-C+ kit (Arima Genomics, Inc.) with minor modifications. Hi-C libraries were then used for Promoter Capture enrichment.
PCHi-C libraries were prepared using the SureSelect target enrichment system (SureSelect XT HS2 DNA kit, Agilent Technologies) using custom-design RNA bait library.


title: Gar15-13 Decitabine 4_PCHiC


title: Physical exercise combine neural progenitor transplantation group_rep4

city: Guangzhou

first: Rui

last: Wu

state: GuangDong

address: NO.600 Tianhe Road, Tianhe District

department: Department of Rehabilitation Medicine

institute: The Third Affiliated Hospital, Sun Yat-sen University,

data_processing:
Illumina Casava software used for basecalling
1. Remove adapter polluted reads (remove reads contain adapter more than 5bp. For paired-end sequencing, both reads will be filtered if either end is polluted ). 2. Remove low-quality reads (low-quality reads refer to reads in which more than 15% bases with base calling quality Q≤19. For paired-end sequencing, both reads will be filtered if either end is low-quality). 3. Remove reads which contain N higher than 5% (For paired-end sequencing, both reads will be filtered if either end has N beyond the offset 5%).
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DESeq2 was designed for differential gene expression analysis between two samples with biological replicates. Genes with q≤0.05 and |log2_ratio|≥1 are identified as differentially expressed genes.
Genome_build: The reference genomes and the annotation file were downloaded from ENSEMBL databas (http://www.ensembl.org/index.html)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample …
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Ischemic striatum  form NPCs+PE-4

extract_protocol:
The ischemic striatum were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Stroke-damaged rats were then randomly divided into 4 groups: sham injection (Vehicle alone), physical exercise after sham injection (Vehicle plus PE), NPC transplantation alone (NPCs alone) and NPC transplantation combined with physical exercise (NPCs plus PE). hNPCs were derived from human embryonic stem cell (ESCs) in which CAG promoter-driven DsRed gene was targeted to AAVS1 locus via CRISPR-Cas9 gene editing, and intracerebrally transplanted into the ischemia striatum on Day 3 after tMCAO (2.4 × 105 cells suspended in 3μl DMEM/F12). Rats in vehicle groups were injected with DMEM/F12 of equal volume. For physical exercise training, an enforced wheel running program with a moderate-intensity started from Day 7 after tMCAO until sacrifice.

value: Brain

value: Sprague-Dawley


title: Physical exercise combine neural progenitor transplantation group_rep3

source_name: Ischemic striatum  form NPCs+PE-3


title: Gar15-13 Vehicle 1 ER

source_name: Gar15-13 Vehicle tumour

value: ER (Millipore SC-543X)


title: HEC-hic-rep2

source_name: E10.0 AGM

value: E10.0 AGM HECs

value: MboI


title: tissue_MockZymoPos_tissue

data_processing:
The V4 region of the 16S rRNA was amplified from freshly collected mouse feces using the Dual-indexing sequencing strategy. For tissue, colonic tissue was collected following dissection.
Sequencing was done on the Illumina MiSeq platform, using a MiSeq reagent kit V2 500 cycles, according to the manufacturer’s instructions.
Bacterial community analysis was performed using Mothur (v1.42.3) aligning to the full SILVA reference alignment (release 132) provided by Mothur
Genome_build: Mothur's Silva release 132
Supplementary_files_format_and_content: fecal_taxonomy_reads.txt and tissue_taxonomy_reads.txt representing annotated read counts

extract_protocol:
Feces were collected from the terminal colon at sacking. rRNA was extracted using the Qiagen MagAttract PowerMicrobiome kit.
Libraries were cleaned, normalized and underwent quality control before sequencing on Illumina MiSeq platform.


title: HCI005 Vehicle 2_RNA-seq

description:
Veh.vs.Dec_HCI005.cntTable
HCI005_Veh_2


title: preHSC-hic-rep1


title: preHSC-hic-rep4


title: HEC-hic-rep1_part2


title: Gar15-13 Vehicle 4_PCHiC


title: Gar15-13 Decitabine 10_RNA-seq

description:
Veh.vs.Dec_GAR15-13D.cntTable
Gar15-13_Decitabine_4


title: Neural progenitor transplantation group_rep3

source_name: Ischemic striatum form NPCs-3

value: Neural progenitor transplantation group


title: Gar15-13 Decitabine 9_PCHiC

source_name: Gar15-13 Decitabine tumour


title: HCI005 Vehicle 1_RNA-seq

description:
Veh.vs.Dec_HCI005.cntTable
HCI005_Veh_1


title: Neural progenitor transplantation group_rep1

source_name: Ischemic striatum form NPCs-1


title: HEC-hic-rep1_part1


title: Gar15-13 Vehicle 2_PCHiC


title: AEC-hic-rep3_part2

value: E10.0 AGM early AECs


title: Gar15-13 Decitabine 9_RNA-seq

description:
Veh.vs.Dec_GAR15-13D.cntTable
Gar15-13_Decitabine_3

value: Decitabine


title: Gar15-13 Vehicle 1_PCHiC

value: Breast cancer PDX model Gar15-13


title: Culture medium injection group_rep3

source_name: Ischemic striatum form Vehicle-3

value: Culture medium injection


title: Physical exercise combine neural progenitor transplantation group_rep2

source_name: Ischemic striatum  form NPCs+PE-2


title: Gar15-13 Decitabine 9_HiC

data_processing:
Reads were aligned to the human genome (hg38/GRCh38), filtered and interactions normalised using HiC-Pro (v.2.11.4).
Juicebox hic files were prepared using hicpro2juicebox script (Servant et al., 2015).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: allValidPairs files contain all valid interactions identified at multiple resolutions (10kb, 20kb, 40kb, 150kb, 500kb and 1Mb) using HiC-Pro pipeline. The validPairs are stored using a tab-delimited text format as described in (Servant et al., 2015). hic files contain compressed contact matrices at all resolutions. hic format can also be used to visualise Hi-C data in Juicebox (Durand et al., 2016; Robinson et al., 2018) or WashU Epigenome Browser (Zhou et al., 2013).

extract_protocol:
Hi-C experiments were performed on fresh-frozen tumour samples using the Arima Hi-C+ kit (Arima Genomics, Inc.) with minor modifications.
Hi-C libraries were prepared using the Swift Biosciences Accel-NGS 2S Plus DNA Library Kit with a modified protocol provided by Arima.


title: Physical exercise combine neural progenitor transplantation group_rep1

source_name: Ischemic striatum form NPCs+PE-1


title: Culture medium injection group_rep2

source_name: Ischemic striatum form Vehicle-2


title: AEC-hic-rep2_part2


title: Gar15-13 Decitabine 5_HiC


title: Gar15-13 Decitabine 4_RNA-seq

description:
Veh.vs.Dec_GAR15-13D.cntTable
Gar15-13_Decitabine_1


title: Gar15-13 Decitabine 5_RNA-seq

description:
Veh.vs.Dec_GAR15-13D.cntTable
Gar15-13_Decitabine_2


title: Culture medium injection group rep1

source_name: Ischemic striatum form Vehicle-1


title: Gar15-13 Vehicle 4_RNA-seq

description:
Veh.vs.Dec_GAR15-13D.cntTable
Gar15-13_Veh_4


title: Gar15-13 Decitabine 4_HiC


title: AEC-hic-rep1_part2


title: Neural progenitor transplantation group_rep2

source_name: Ischemic striatum form NPCs-2


title: AEC-hic-rep2_part1


title: Gar15-13 Vehicle 3_RNA-seq

description:
Veh.vs.Dec_GAR15-13D.cntTable
Gar15-13_Veh_3


title: Gar15-13 Vehicle 4_HiC


title: Physical exercise group_rep3

source_name: Ischemic striatum from PE+Vehicle-3

value: Physical exercise


title: Physical exercise group_rep4

source_name: Ischemic striatum from PE+Vehicle-2


title: Gar15-13 Vehicle 2_HiC


title: AEC-hic-rep1_part1


title: AEC-hic-rep3_part1


title: Gar15-13 Vehicle 2_RNA-seq

description:
Veh.vs.Dec_GAR15-13D.cntTable
Gar15-13_Veh_2


title: Physical exercise group_rep2


title: Gar15-13 Vehicle 1_RNA-seq

description:
Veh.vs.Dec_GAR15-13D.cntTable
Gar15-13_Veh_1


title: Gar15-13 Vehicle 1_HiC


title: Physical exercise group_rep1

source_name: Ischemic striatum from PE+Vehicle-1


title: LGG_24h

city: Seoul

first: Sangdon

last: Ryu

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science

description: miRNA expression data by microbial exposure

hyb_protocol: Bitin-laboeled samples were hybridized using GeneChip® Hybridization Oven to the Affymetrix miRNA microarray

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 Dx v.2

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

label: Biotin

organism: Caenorhabditis elegans

source_name: Exposure of LGG to C. elegans for 24 hours

label_protocol: From each sample, 1 μg total RNA was labeled using the FlashTag™ Biotin HSR RNA Labeling Kit

growth_protocol: L4/young adult worms were placed on plates exposed to LGG or OP50 for 24 h at 25°C.

extract_protocol: miRNA was isolated using QlAGEN™ miRNeasy Mini Kit

treatment_protocol: Nematodes were collected through M9 buffer after 24 h exposure to LGG or OP50, washed three times, and pelleted by centrifugation for RNA isolation.

tag: developmental stage

value: L4/young adult

value: whole animal


title: Vehicle (0.2% DMSO-treated monocyte) [Veh-1-2]

status: Public on Dec 11 2021

first: Hailian

last: Quan

address: 103 Daehak-ro, Jongno-gu,

department: Department of Microbiology and Immunology, and Institute of Endemic Disease

institute: Seoul, South Korea

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence (using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2.
Read count extraction using bedtools.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include read count values for each Sample.

source_name: THP-1 cells

growth_protocol: The human acute monocytic leukemia THP-1 (ATCC TIB-202) cell line was obtained from the ATCC and maintained in RPMI media containing 10% FBS (Gibco) and 1% penicillin-streptomycin (PS; Gibco) at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: THP-1 cells were seeded in 24-well plates at a concentration of 5 × 10^5 cells/ml (500 μl total volume/well). After 2 h of incubation, added fresh medium with test substances to 1× CV90 concentration or 0.1% DMSO as vehicle control. After 12h of exposure, cells were collected for RNA-Seq.

value: Monocytes

tag: passages


title: Control (w/o chemical treated monocytes) [Basal-2-3]


title: Vehicle (0.3% DMSO-treated monocyte) [Veh-1-3]


title: Vehicle (0.1% DMSO-treated monocyte) [Veh-1-1]


title: Vehicle (0.4% DMSO-treated monocyte) [Veh-2-1]


title: Control (w/o chemical treated monocytes) [Basal-1-2]


title: Vehicle (0.5% DMSO-treated monocyte) [Veh-2-2]


title: Control (w/o chemical treated monocytes) [Basal-2-2]


title: Control (w/o chemical treated monocytes) [Basal-1-1]


title: AB5075_arcA_tn

city: Tampa

first: Lindsey

middle: N

last: Shaw

state: FL

address: 4202 E Fowler Avenue

department: CMMB

institute: University of South Florida

data_processing:
Raw data files (.fastq) were exported from the Illumina BaseSpace Server
Raw data files (.fastq) were imported into Qiagen Bioinformatics software platform (version 11) as paired-end reads for analysis and adapter indices trimmed.
Reads corresponding to ribosomal RNA were filtered out and removed
Expression values and fold change for filtered reads were caculated using RNA-Seq Analysis function with experimental fold change feature in Qiagen Bioinformatics software
Expression values and fold change were normalized by quantile normalization
Normalized expression values and fold change comparisons were exported in excel format
Genome_build: The accession number for the Genbank genome file used as references was NZ_CP008706.1
Supplementary_files_format_and_content: Expression values calculated for each gene are presented as normalized RPKM values in excel format

organism: Acinetobacter baumannii

source_name: bacterial cells, pelleted

growth_protocol: Overnight A. baumannii cultures were used to inoculate fresh LB broth and grown for 3 hours. These exponentially growing cultures were subsequently used to seed fresh LB medium at OD600 0.05. After 1 hour of growth, CCCP was added to a final sub-inhibitory concentration of 6.25 μg /mL. Test cultures were grown for 2 additional hours and 5 mL of cells were harvested for RNA isolation.

extract_protocol:
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit and contaminating DNA was removed by treatment with Ambion DNA-free kit. Total RNA was enriched for mRNA using MicrobExpress kit and Illumina RiboZero rRNA removal kit for Gram-negative bacteria.
Library construction was performed using the TruSeq Stranded mRNA Kit from Illumina omitting mRNA enrichment steps.

treatment_protocol: Samples were pelleted and stored at -80°C prior to RNA extraction.

value: arcA transposon mutant strain

tag: growth medium

value: LB

tag: growth conditions

value: 2h/37°C with 6.25 μg /mL CCCP


title: AB5075_WT

value: Wildtype parental strain


title: Control (w/o chemical treated monocytes) [Basal-2-1]

tag: treatment


title: Vehicle (0.6% DMSO-treated monocyte) [Veh-2-3]

value: Vehicle


title: Cyclosporine-treated monocytes [Cyclosporine-1]

value: Cyclosporine


title: Mercuric chloride-treated monocytes [Mercuric chloride-3]

description: Mercuric chloride-3

value: Mercuric chloride


title: Cyclosporine-treated monocytes [Cyclosporine-3]


title: Ribavirin-treated monocytes [Ribavirin-2]

value: Ribavirin


title: Ribavirin-treated monocytes [Ribavirin-3]


title: Cyclosporine-treated monocytes [Cyclosporine-2]


title: Mercuric chloride-treated monocytes [Mercuric chloride-2]

description: Mercuric chloride-2


title: Genistein-treated monocytes [Genistein-3]

value: Genistein


title: Genistein-treated monocytes [Genistein-2]


title: Genistein-treated monocytes [Genistein-1]


title: OP50_24h

source_name: Exposure of OP50 to C. elegans for 24 hours


title: LPS-treated monocytes [LPS-2]

value: LPS


title: Control (w/o chemical treated monocytes) [Basal-1-3]


title: Mercuric chloride-treated monocytes [Mercuric chloride-1]

description: Mercuric chloride-1


title: Benzoic acid-treated monocytes [Benzoic acid-1]

description: Benzoic acid-1

value: Benzoic acid


title: Benzoic acid-treated monocytes [Benzoic acid-3]

description: Benzoic acid-3


title: TE7cells_CDH26_transduced_rep3

city: Cincinnati

first: Marc

middle: E

last: Rothenberg

state: OH

address: 3333 Burnet Ave. MLC-7028

department: Allergy

institute: Cincinnati Children's Hospital Medical Center

description: TE7 CDH26 3

hyb_protocol: 3.85 ug of fragmented cDNA were hybridized to a Human Gene 2.0 ST arrays (Affymetrix). Probe arrays were incubated at 45°C for 17 hrs in the Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Probe arrays were washed and stained using the Fluidics Station 450 (Affymetrix), utilizing the fluidics protocol FS450-0002. The Stain and Antibody solutions are produced by Affymetrix and contained in the Genechip Hybridization Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The .cel were created by Command Console (Affymetrix). The .cel files were analyzed by Expression Console (Affymetrix) to create the .chp files.  GeneSpring was used to analyze data.  Summarization algorithm: ExonRMA16; Confidence level: all; Normalization: quantile; Baseline transformation: median of control samples

source_name: TE7 cells transduced with pMIRNA1-puro-CDH26, clone 3

label_protocol: The Ambion® WT Expression Kit (Life Technologies) combined with the GeneChip® WT Terminal Labeling Kit (Affymetrix), was used to create biotin–labeled sens -strand cDNA targets for hybridization to the Gene 2.0 ST Arrays.

extract_protocol: Total RNA was extracted using the miRNeasy kit (Qiagen, Valencia, CA) per the manufacturer's instructions.  Quality control steps:  The quality of the Total RNA was checked by the Agilent 2100 Bioanalyzer using the RNA 6000 Nano Assay.

treatment_protocol: TE7 cells were transduced with either pMIRNA1-puro-control or pMIRNA1-puro-CDH26, and clones derived from single cells were grown to confluency. Cells were then cultured in RPMI + 1.8 mM Ca2+ for 24 h.

tag: expression construct


title: LPS-treated monocytes [LPS-3]


title: TE7cells_CDH26_transduced_rep1

description: TE7 CDH26 1

source_name: TE7 cells transduced with pMIRNA1-puro-CDH26, clone 1


title: Aciclovir-treated monocytes [Aciclovir-1]

value: Aciclovir


title: TE7cells_CDH26_transduced_rep2

description: TE7 CDH26 2

source_name: TE7 cells transduced with pMIRNA1-puro-CDH26, clone 2


title: LPS-treated monocytes [LPS-1]


title: TE7cells_Control_transduced_rep1

description: TE7 control 1

source_name: TE7 cells transduced with pMIRNA1-puro-control, clone 1

value: control


title: TE7cells_Control_transduced_rep2

description: TE7 control 2

source_name: TE7 cells transduced with pMIRNA1-puro-control, clone 2


title: Benzoic acid-treated monocytes [Benzoic acid-2]

description: Benzoic acid-2


title: Ribavirin-treated monocytes [Ribavirin-1]


title: Aciclovir-treated monocytes [Aciclovir-3]


title: Aciclovir-treated monocytes [Aciclovir-2]


title: SLS-treated monocytes [SLS-1]

value: Sodium lauryl sulfate


title: Prednisolone-treated monocytes [Prednisolone-2]

value: Prednisolone


title: Tacrolimus-treated monocytes [Tacrolimus-3]

value: Tacrolimus


title: SLS-treated monocytes [SLS-3]

value: Monocytes


title: Prednisolone-treated monocytes [Prednisolone-3]


title: Tacrolimus-treated monocytes [Tacrolimus-2]


title: Tacrolimus-treated monocytes [Tacrolimus-1]


title: Tofacitinib-treated monocytes [Tofacitinib-3]

value: Tofacitinib


title: Tofacitinib-treated monocytes [Tofacitinib-2]


title: Dexamethasone-treated monocytes [Dexamethasone-2]

value: Dexamethasone


title: Dexamethasone-treated monocytes [Dexamethasone-3]


title: SLS-treated monocytes [SLS-2]


title: Dexamethasone-treated monocytes [Dexamethasone-1]


title: Tofacitinib-treated monocytes [Tofacitinib-1]


title: Prednisolone-treated monocytes [Prednisolone-1]


title: E135_EpCAM_Dist_2

city: Copenhagen N

first: Marianne

middle: Terndrup

last: Pedersen

address: Ole Maaloes Vej 5

department: University of Copenhagen

country: Denmark

institute: BRIC

data_processing:
Mapping and quantification of fastq files were done via the Rsubread package.
Reads were mapped to the mm10/GRch38 genome assembly using the align-function with default settings, except nBestLocations=16 and nTrim5=6.
Mapped reads were quantified across RefSeq gene models using the featureCounts-function with default settings, except strandSpecific=2. This approach retains multi-mapping reads for gene-level quantification, as long as only one of the multiple locations maps to an annotated gene.
DE analysis was carried out using edgeR and limma with default settings unless otherwise noted.
RPKM-values were extracted using the rpkm and rpkmByGroup functions from the edgeR package.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

source_name: EpCAM+/DAPI-/CD31-/CD45- cells isolated from the distal region of E13.5 intestine

growth_protocol: Intestines were isolated from E16.5 or E13.5 mouse fetuses. Where indicated, the pregnant dams had been treated twice daily from E12.5 to E16.5 with vehicle or LGK-974, a PORCN inhibitor preventing secretion of Wnt ligands.

extract_protocol:
Cells were sorted into RLT buffer and RNA extracted using the RNeasy micro kit (Qiagen).
RNA-seq libraries were prepared using the SMARTer Stranded Total RNA-Seq v2 Pico Input Mammalian kit (Takara).

treatment_protocol: Intestines dissected from E16.5 mouse fetuses were divided into five sections of equal size of which the most proximal, the mid and the most distal segments were processed. Intestines isolated from E13.5 mouse fetuses were divided into three regions and the proximal and distal regions selected. Intestinal regions were incubated with collagenase to obtain single cells. After antibody staining, the indicated cell populations were isolated using a FACSAria III.

tag: intestinal region

value: Distal E13.5 intestine


title: E135_EpCAM_Prox_3

source_name: EpCAM+/DAPI-/CD31-/CD45- cells isolated from the proximal region of E13.5 intestine

value: Proximal E13.5 intestine


title: LGK974_EpCAM_Prox_1

source_name: EpCAM+/DAPI-/CD31-/CD45- cells isolated from the proximal region of E16.5 intestine

value: Proximal E16.5 intestine


title: Vehicle_EpCAM_Dist_1

source_name: EpCAM+/DAPI-/CD31-/CD45- cells isolated from the distal region of E16.5 intestine

value: Distal E16.5 intestine

value: Vehicle


title: Vehicle_EpCAM_Mid_1

source_name: EpCAM+/DAPI-/CD31-/CD45- cells isolated from the mid region of E16.5 intestine

value: Mid E16.5 intestine


title: LGK974_EpCAM_Dist_2


title: LGK974_EpCAM_Dist_1


title: E135_EpCAM_Dist_1


title: LGK974_EpCAM_Mid_3


title: LGK974_EpCAM_Prox_3


title: E135_EpCAM_Dist_3


title: LGK974_EpCAM_Dist_3


title: LGK974_EpCAM_Mid_1


title: Vehicle_EpCAM_Prox_1


title: CD29-HIGH_Prox_3

source_name: PDGFRamed/CD29high/EpCAM-/DAPI-/CD31-/CD45- isolated from the proximal region of E16.5 intestine


title: CD29-HIGH_Dist_3

source_name: PDGFRamed/CD29high/EpCAM-/DAPI-/CD31-/CD45- isolated from the distal region of E16.5 intestine


title: CD29-HIGH_Mid_3

source_name: PDGFRamed/CD29high/EpCAM-/DAPI-/CD31-/CD45- isolated from the mid region of E16.5 intestine


title: E135_EpCAM_Prox_1


title: CD29-HIGH_Dist_2


title: CD29-HIGH_Prox_2


title: LGK974_EpCAM_Mid_2


title: CD29-HIGH_Mid_1


title: CD29-HIGH_Dist_1


title: LGK974_EpCAM_Prox_2


title: CD29-HIGH_Prox_1


title: E135_EpCAM_Prox_2


title: MUT IP 93

city: New Brunswick

first: Lauren

last: Chukrallah

state: New Jersey

address: 59 Dudley Road, Foran 328

department: Animal science

institute: Rutgers University

data_processing:
Ends of sequenced reads were trimmed for quality and reads mapping to rRNA were subtracted
Reads were mapped (via RSEM v1.3.3) to an expanded mouse testis transcriptome generated by appending appending novel testis-specific genes and isoforms (Gamble et al., 2020) to the current Ensembl version Mus_musculus.GRCm38.90, mm10
For input samples, differential expression was calculated by EBSeq (release 3.12) (Seirup et al., 2020) with a cutoff of PPDE  0.95 and a directional fold change greater than one
Ribosomal association (RA) was determined by calculating the ratio of IP TPM over input TPM. Any transcripts with any input values equaling zero were removed. A Welch t-test was conducted using R (matrixTests) to identify differential ribosome association (DRA, p < 0.05)
Genome_build: mm10
Supplementary_files_format_and_content: Text table with ENSMUSG IDs of signifcant genes and the tpms for every sample

source_name: Whole testis lysate

extract_protocol:
Testes were removed, flash frozen, and ground on dry ice. RNA was harvested using miRNEasy mini kit (Qiagen  217004).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: Adad2 Mutant

tag: fraction

value: IP


title: MUT IP 69


title: MUT IP 94


title: PDGFRA-MED_Mid_3

source_name: PDGFRamed/CD29med/EpCAM-/DAPI-/CD31-/CD45- isolated from the mid region of E16.5 intestine


title: MUT IP 12


title: PDGFRA-HIGH_Dist_3

source_name: PDGFRahigh/CD29med/EpCAM-/DAPI-/CD31-/CD45- cells isolated from the distal region of E16.5 intestine


title: PDGFRA-MED_Dist_3

source_name: PDGFRamed/CD29med/EpCAM-/DAPI-/CD31-/CD45- isolated from the distal region of E16.5 intestine


title: PDGFRA-HIGH_Mid_3

source_name: PDGFRahigh/CD29med/EpCAM-/DAPI-/CD31-/CD45- cells isolated from the mid region of E16.5 intestine


title: CD29-HIGH_Mid_2


title: EpCAM_Mid_3


title: MUT Input 12

value: Input


title: WT IP 140

value: Wildtype


title: PDGFRA-MED_Prox_3

source_name: PDGFRamed/CD29med/EpCAM-/DAPI-/CD31-/CD45- isolated from the proximal region of E16.5 intestine


title: MUT Input 94


title: WT IP 17


title: WT IP 121


title: EpCAM_Dist_2


title: MUT Input 93


title: WT Input 121


title: PDGFRA-HIGH_Prox_3

source_name: PDGFRahigh/CD29med/EpCAM-/DAPI-/CD31-/CD45- cells isolated from the proximal region of E16.5 intestine


title: WT Input 17


title: WT Input 140


title: PDGFRA-MED_Mid_2


title: PDGFRA-HIGH_Dist_2


title: PDGFRA-MED_Prox_2


title: PDGFRA-HIGH_Prox_2


title: PDGFRA-HIGH_Mid_2


title: PDGFRA-MED_Dist_1


title: EpCAM_Dist_3


title: Endothelial-enriched population isolated from breast tissue based on the cell surface expression of CD36 and or CD31

city: San Francisco

first: Thea

last: Tlsty

address: 513 Parnassus Avenue

department: Pathology

institute: University of California, San Francisco

data_processing:
The library concentration was quantified using a DNA Bioanalyzer chip (Agilent) and the Illumina Library Quantification Kit (Kapa Biosystems) and sequenced on one lane of an Illumina HiSeq4000 sequencer with an average depth of 21,805 reads/cell. The Cell Ranger software (version 1.31) was utilized for sample pre-processing, including cell barcode classification, quality control, sequence alignment (human reference genome GRCh37) and counting of unique molecular identifiers (UMIs). The deMULTIplex package (version 1.0.2) in R (version 3.6.1) was utilized for sample barcode classification.
The matrix.mtx files contains read counts for all cells. The barcode.tsv file contains the 10X barcodes used to identify cells. The features.tsv.gz contains the corresponding gene symbols. The matrix.mtx can be read into R with the  features.tsv and barcode.tsv files using the Read10X function of the Seurat software package.  RM.CD31.CD36.robj is a Seurat object containing processed data.
Supplementary_files_format_and_content: RM.CD31.CD36.robj
Supplementary_files_format_and_content: mtx

source_name: Disease-free Human Breast from reduction mammoplasty (RM)

extract_protocol:
Human breast tissue was minced and enzymatically dissociated in Roswell Park Memorial Institute medium (RPMI)-1640 with 2.1 mM L-glutamine and 25 mM HEPES supplemented with 10% (v/v) fetal bovine serum (FBS), 100 U·ml-1 penicillin, 100 mg·ml-1 streptomycin, 0.25 mg·ml-1 fungizone, 50 μg·ml-1 gentamycin, 200 U·ml-1 Collagenase Type-2 and 100 U·ml-1 hyaluronidase at 37°C for 12-16 h. The digest was centrifuged at 300 x g for 10 min and washed with RPMI 1640 + 10% FBS. Large epithelial-enriched structures (referred to as tissue organoids) were recovered by filtration through a 150 μm nylon mesh filter. Tissue organoids were dissociated to single cells using first 5 U·ml-1 Dispase containing 1 μg·ml-1 DNAse I for 5-10 minutes and then 0.05% trypsin-EDTA for 5-10 minutes . The cells were washed with PBS + 1% BSA. Unique lipid-modified oligonucleotides (LMOs) barcodes were stably incorporated into the plasma membrane of dissociated human breast cells from 14 donors by first incubating cells with 10X Anchor-Barcode for 5 minutes and then Co-Anchor for 5 minutes in basal media. Cells were pooled, filtered through a 40-μm cell strainer, resuspended at a concentration of 1x106 cells in 100 uL of PBS + 1% BSA and stained for 30 minutes at 4oC with fluorophore (CD36 and CD31) and/or biotin conjugated (CD4, CD3, CD16, CD64, CD45 and CD8) antibodies. The cells were again washed with PBS + 1% BSA and stained for 15 minutes at 4oC with BV785-streptavidin and 0.5 μg·ml-1 DAPI. The cells were again washed, resuspended at 1x106 in 100 μL PBS + 1% BSA, filtered through a 40-μm cell strainer and loaded onto a FACS Aria II Cell Sorter (Becton Dickinson) fitted with a 100 μm nozzle. After gating out debris, doublets, dead (DAPI+) and immune cell types, the cells expressing CD36 and/or CD31 were collected into a 1.5 mL tube containing PBS + 1% BSA.
Single cell cDNA libraries were prepared using the 10X Genomics Single Cell V2 platform as described by the manufacturer except for the addition of 1 μL 2.5μM MULTI-seq primer to the cDNA amplification master-mix.

value: Disease-free breast

value: Endothelial-enriched cell population isolated from  based on the cell surface expression of CD36 and or CD31

tag: multiplexed samples

value: Cells from 14 tissues donors were pooled sing LMO barcodes


title: MUT Input 69


title: EpCAM_Dist_1


title: PDGFRA-HIGH_Dist_1


title: PDGFRA-MED_Dist_2


title: PDGFRA-HIGH_Mid_1


title: EpCAM_Mid_1


title: EpCAM_Mid_2


title: PDGFRA-MED_Prox_1


title: PDGFRA-MED_Mid_1


title: PDGFRA-HIGH_Prox_1


title: E16.5 intestinal epithelial cells, TCF7L2/TCF4

data_processing:
Concatenated reads were trimmed using Trim Galore! (Galaxy version 0.4.2) with trimming of “Illumina Universal” adaptor sequences and standard settings except N=2 (remove 2 bp from the 3’ end), and N=25 (Discard reads that became shorter than length 25).
Trimmed reads were mapped to mm10 canonical (April 2020) using Map with Bowtie for Illumina (Galaxy version 1.2.0) with standard settings except m=1 (supress all alignments if >1 exist).
After SAM-to-BAM conversion, duplicate reads were removed using the RmDup function (Galaxy Version 2.0.1).
Peak calling was performed using MACS2 callpeak (Galaxy Version 2.1.1.20160309.6) using the IgG ChIP sample as negative control and standard settings except effective genome size=M. musculus (1.87e9).
BAM files (without duplicate reads) were converted to wig files in Easeq with 1 bp bin size and normalization to reads per 10 million.
Peak tabular files were generated using MACS2 callpeak (Galaxy Version 2.1.1.20160309.6) using the IgG ChIP sample as negative control and standard settings except effective genome size=M. musculus (1.87e9).
Genome_build: mm10
Supplementary_files_format_and_content: wigs, peak tabular file

source_name: E16.5 intestinal epithelial cells (EpCAM+/DAPI-/CD31-/CD45-)

extract_protocol:
Cells were fixed in 1% formaldehyde for 10 min and subjected to chromatin immunoprecipitation.
Adaptor-ligated libraries were generated using the Accel-NGS 2S Plus DNA Library kit for Illumina (Swift Bioscience) in combination with the 2S Indexing Kit for Illumina (Swift Bioscience) according to manufacturer’s instructions.

treatment_protocol: The intestine was dissected from E16.5 mouse fetuses and incubated with collagenase to obtain single cells. After antibody staining, EpCAM+/DAPI-/CD31-/CD45- cells were isolated using a FACSAria III.

tag: age

value: EpCAM+/DAPI-/CD31-/CD45- isolated from E16.5 intestinal tissue

tag: chip antibody

value: anti-TCF7L2/TCF4 (clone C48H11, #2569, Cell Signaling)


title: E16.5 intestinal epithelial cells, IgG

tag: cell type

value: rabbit IgG (Abcam)


title: AGS _Control-2, Biological Replicate 2

city: Madurai

first: Kumaresan

last: Ganesan

state: Tamil Nadu

address: School of Biological Sciences,

department: Genetics

country: India

institute: Madurai Kamaraj University

description: Gene expression data of AGS gastric cancer cell line treated with DMSO - Replicate 2

hyb_protocol: The fragmented and labelled cDNA were hybridized for 16 hr at 45°C with Affymetrix Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000.

data_processing: Gene level normalized expression signals were calculated from Affymetrix CEL files by RMA,in Affymetrix Expression Console (v1.4.1.46).

source_name: DMSO treated AGS, gastric cancer cells - Replicate 2

label_protocol: 500 ng of total RNA was used to generate fragmented and biotin labelled sense cDNA using Ambion WT Expression kit (Affymetrix).

growth_protocol: AGS gastric cancer cells were seeded in 6 well culture dishes and maintained in DMEM-F12 media with 10% FBS in a humidified incubator at 37˚C and 5% CO2.

extract_protocol: 48 Hrs after treatment, the total RNA was isolated from the cells using Trizol (Invitrogen).

treatment_protocol: Upon reaching 80-90% confluency, the cells were treated with 5µM of PD98059 or with DMSO as control.

tag: tissue

value: Gastric adenocarcinoma cell line


title: AGS _Control-3, Biological Replicate 3

description: Gene expression data of AGS gastric cancer cell line treated with DMSO - Replicate 3

source_name: DMSO treated AGS, gastric cancer cells - Replicate 3


title: AGS _Control-1, Biological Replicate 1

description: Gene expression data of AGS gastric cancer cell line treated with DMSO - Replicate 1

source_name: DMSO treated AGS, gastric cancer cells - Replicate 1


title: AGS _PD98059-2, Biological Replicate 2

description: Gene expression data of AGS gastric cancer cell line treated with PD98059 - Replicate 2

source_name: PD98059 treated AGS, gastric cancer cells - Replicate 2


title: AGS _PD98059-1, Biological Replicate 1

description: Gene expression data of AGS gastric cancer cell line treated with PD98059 - Replicate 1

source_name: PD98059 treated AGS, gastric cancer cells - Replicate 1


title: AGS _PD98059-3, Biological Replicate 3

description: Gene expression data of AGS gastric cancer cell line treated with PD98059 - Replicate 3

source_name: PD98059 treated AGS, gastric cancer cells - Replicate 3


title: Peripheral_blood_cells_AIA_H_BHGZD_rep5

first: Weijie

last: LI

address: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, China

description:
Peripheral_blood_cells_AIA_H_BHGZD_rep5
AIA_H_B58

data_processing:
Sequencing: RNA-seq reads
Read alignment: HISAT2
Transcript compilation: StringTie
Expression estimation: StringTie
Differential expression: Ballgown
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads.
Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA).
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: gene_count_matrix.csv with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: transcript_count_matrix.csv with raw transcrip counts for every transcript and every sample
Supplementary_files_format_and_content: gene_fpkm_all_samples
Supplementary_files_format_and_content: transcript_fpkm_all_samples

source_name: Peripheral blood cells

extract_protocol:
Peripheral blood mononuclear cells were collected after 8 hours stored in liquid nitrogen for microarray detection. Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads.

treatment_protocol: Briefly, male Lewis rats were injected intradermally at the base of tail with 10mg/mL M tuberculosis H37 Ra (Difco, BD company, New Jersey, US) suspended in liquid paraffin (Freund's complete adjuvant, CFA). From the day of primary immunization, male Lewis rats were kept in the artificial climate box (production license no. RXZ-380A-LED) for 2 hours daily with certain wind velocity (6m/s), temperature (37℃) and humidity (90%) for a period of 15 days.  In AIA_H_BHGZD treatment group, the dosage selection for BHGZD was 21.4 g/kg, nearly equivalent two times of the daily dosage of RA patients in clinics.

value: Lewis

value: Peripheral blood cells

tag: group

value: BHGZD treatment group


title: Peripheral_blood_cells_AIA_H_BHGZD_rep4

institute: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

description:
Peripheral_blood_cells_AIA_H_BHGZD_rep4
AIA_H_B57

growth_protocol: Peripheral blood mononuclear cells were collected after 8 hours stored in liquid nitrogen for microarray detection.


title: Peripheral_blood_cells_AIA_H_BHGZD_rep3

description:
Peripheral_blood_cells_AIA_H_BHGZD_rep3
AIA_H_B55


title: metaphyseal mesenchymal stromal cells Rep1

city: Muenster

first: Kishor Kumar

last: Sivaraj

address: Roentgenstrasse 20

department: Department of Tissue Morphogenesis

institute: Max Planck Institute for Molecular Biomedicine

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina ‘s bcl2fastq software. Raw reads were pre-processed using fastp (Chen et al, Bioinformatics 2018) (version 0.20)  excluding reads with an average phred score of less than 20, trimming the ends of reads base by base with a quality score less than 20 and requiring all reads to be their minimum expected length, based on the number of cycles during sequencing for the first read, containing the cellular barcode and UMI.
Preprocessed read data was aligned to the mouse reference genome (mm10, Gencode M23 with H2B-GFP added) with STAR (Dobin et al., 2013) (version 2.7.3a) through its single-cell functionality STARsolo, using parameters to mirror unfiltered 10x Genomics CellRanger 3 output for sample demultiplexing, barcode processing and transcript counting.  The official 10x Genomics whitelist for the respective Chromium version was used.
Genome_build: mm10
Supplementary_files_format_and_content: Feature count matrices were generated using STARsolo and are present in mtx format with annotations present in tsv format

source_name: mouse long bone

extract_protocol: 10x genomics Chromium V2/V3

value: metaphyseal mesenchymal stromal cells

value: post natal week 3

value: untreated

value: bone


title: Pdgfra-GFP+ mouse long bone stromal cells


title: Peripheral_blood_cells_AIA_H_BHGZD_rep2

description:
Peripheral_blood_cells_AIA_H_BHGZD_rep2
AIA_H_B54


title: metaphyseal mesenchymal stromal cells Rep2


title: Peripheral_blood_cells_AIA_H_BHGZD_rep1

description:
Peripheral_blood_cells_AIA_H_BHGZD_rep1
AIA_H_B52


title: Peripheral_blood_cells_AIA_H_rep5

description:
Peripheral_blood_cells_AIA_H_rep5
AIA_H_46

value: AIA-H model  group (AIA_H)


title: MDA-MB-231 shDAXX-2

city: Gainesville

first: Daiqing

last: Liao

address: 2033 Mowry Rd

department: Anatomy and Cell Biology

institute: University of Florida

description: Gene expression data from MDA-MB-231 cells with shDAXX

hyb_protocol: Sense strand DNA was fragmented, biotinylated, and hybridized with rotation at 45Â°C for 16 hr to the GeneChipÂ® Human Transcriptome Array 2.0.

scan_protocol: The arrays were washed and stained with streptavidin-phycoerythrin (SAPE) on an Affymetrix Fluidics Station 450, and scanned on a GeneChipÂ® 7G Scanner (Affymetrix, Inc).

data_processing: We used the AffymetrixÂ® Expression Consoleâ„¢ Software  (Version 1.3) to generate .txt files for each RNA hybridization.

source_name: Stable DAXX knockdown

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA

growth_protocol: MDA-MB-231 cells were seeded in a well in a 6-well plate and cultured in complete DMEM medium for 24 hours

extract_protocol: Extraction of total RNA with the RNeasy mini kit was performed according to the manufacturer's instructions.

tag: cell line


title: MDA-MB-231 shDAXX-3


title: Peripheral_blood_cells_AIA_H_rep4

city: Beijing

description:
Peripheral_blood_cells_AIA_H_rep4
AIA_H_43

tag: strain


title: MDA-MB-231 shDAXX-1


title: Peripheral_blood_cells_AIA_H_rep3

description:
Peripheral_blood_cells_AIA_H_rep3
AIA_H_42


title: Genomic DNA of MDS03 MCSs

city: Tours

first: Benjamin

last: Roux

address: 2 boulevard Tonnelle

country: France

institute: CHRU Tours

description: MDS MSCs

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: ChAMP 2.10.2 was used to compute beta-values after BMIQ normalization

label: Cy3 and Cy5

label_protocol: standard Illumina protocol

growth_protocol: In vitro amplification of MSCs for two passages after isolation from bone marrow. Medium: alpha-MEM, 10% FBS, 1% L-glutamine, 10ng/mL rh-FGF2

extract_protocol: Genomic DNA was extracted from MSCs samples using Qiagen  Kit according to standard instructions

treatment_protocol: No treatment applied

tag: gender

value: F


title: Genomic DNA of AML07 MCSs

description: AML MSCs

value: M


title: Genomic DNA of AML01 MCSs

description: AML MSCs


title: Genomic DNA of MDS07 MCSs

description: MDS MSCs


title: Genomic DNA of AML06 MCSs

description: AML MSCs


title: MDA-MB-231 shControl-3

description: Gene expression data from MDA-MB-231 cells with scrambled control

source_name: Scrambled control


title: Genomic DNA of MDS06 MCSs

description: MDS MSCs


title: Genomic DNA of MDS11 MCSs (did not pass QC)

description: MDS MSCs


title: Genomic DNA of AML03 MCSs

description: AML MSCs


title: Peripheral_blood_cells_AIA_H_rep2

description:
Peripheral_blood_cells_AIA_H_rep2
AIA_H_39


title: Genomic DNA of AML02 MCSs

description: AML MSCs


title: Genomic DNA of MDS02 MCSs

description: MDS MSCs


title: Genomic DNA of AML09 MCSs (did not pass QC)

description: AML MSCs


title: Genomic DNA of AML10 MCSs

description: AML MSCs


title: Peripheral_blood_cells_AIA_H_rep1

description:
Peripheral_blood_cells_AIA_H_rep1
AIA_H_37


title: Genomic DNA of MDS08 MCSs

description: MDS MSCs


title: Genomic DNA of AML08 MCSs

description: AML MSCs


title: 231-JQ-2-IP

city: GuangZhou

first: YOU

address: Xiaoguwei

institute: SUN YAT-SEN UNIVERSITY

data_processing:
Library strategy: MeRIP-seq
RNA libraries were run on Illumina NovaSeq6000, basecalling was performed using Real-Time Analysis (RTA) v3.3.3
FastQC V0.11.7 was used for quality contriol
For MeRIP-seq, trimmed raw data performed by Trimmomatic V0.32 software, and mapped to the reference genome by using hisat2 (v2.1.0). The m6A peaks were identified using exomePeak R package (v2.13.2).
Genome_build: hg19

source_name: MDA-MB-231 cancer cells

growth_protocol: MDA-MB-231 cancer cells cultrued in RPMI-1640 medium with 10% FBS

extract_protocol:
The purity and concentration of total RNA samples were determoned withNanoDrop ND-1000. Intact mRNA was isolated from total RNA samples using Arraystar Seq-Star ploy(A) mRNAIsolation Kit according to the manufacturer's protocol.Isolated mRNA was chemcally fragmented into 100-nucleotide-long fragments by incubation in fragmentation buffer.Then using m6A antibody enrich modified RNA.
Constructed m6A and input RNA library using KAPA Stranded RNA-Seq Library Prep Kit (Illumina).

treatment_protocol: 231-con treated with DMSO for 24h，231-JQ treated with 1μM JQ1 for 24 hours

value: breast cancer

value: treated with 1uM JQ1 for 24 hours


title: 231-JQ-2-input


title: Genomic DNA of MDS09 MCSs

description: MDS MSCs


title: Genomic DNA of MDS05 MCSs

description: MDS MSCs


title: Genomic DNA of AML05 MCSs

description: AML MSCs


title: IMR90 ER:RAS siCASP4 d8 rep3

city: Santander

first: Juan Carlos

last: Acosta

state: Cantabria

address: C. Albert Einstein, 22

department: Institute of Biology and Biotechnology of Cantabria (IBBTEC)

country: Spain

institute: Consejo Superior de Investigaciones Cientificas (CSIC)

data_processing:
Ampliseq processing: the torrent suite software version for BAM File generation was Torrent Suite v 5.2.0 Depth of reads= 10 million/sample
two-step alignment approach for RNA-seq alignment. First, TopHat (v.2.0.3)  was used to map  RNA data onto a reference genome. Second, unmapped reads from step one were realigned using Bowtie2.
HTseq(v0.6) was used for calculating raw read counts of Proton RNA-seq
raw read counts for AmpliSeq was produced by the ampliSeqRNA plugin v5.2.0.3 available for Ion TorrentTM sequencing platforms
Genome_build: UCSC hg19
Supplementary_files_format_and_content: FernandezDuran et al 2021 ampliseq  RNAseq reads matrix.txt

source_name: IMR90 ER:RAS human primary fibroblast cells

growth_protocol: Cells were maintained in DMEM + 10% FBS, 1% Antibiotic-Antimycotic, 200 μg/ml geneticin

extract_protocol:
RNA was extracted using the Qiagen Rneasy plus kit following manufacturer's protocol
Libraries were prepared using the  Ion AmpliSeq™ Transcriptome Human Gene Expression Kit (#A26325) ,Ion Xpress™ Barcode Adapters 1-96 Kit (#4474517) and Ion Library TaqMan™ Quantitation Kit (#4468802)
RNA-seq (ampli-seq)

treatment_protocol: Cells were induced to senescence by addition of 100 nM 4-hydroxytamoxifen (4OHT)

value: Oncogene-induced senescence day 8 4OHT siCASP4


title: Genomic DNA of MDS10 MCSs  (did not pass QC)

description: MDS MSCs


title: 231-JQ-1-IP


title: IMR90 ER:RAS siCASP4 d8 rep2

value: IMR90 ER:RAS human primary fibroblast cells


title: Genomic DNA of MDS01 MCSs

description: MDS MSCs


title: Peripheral_blood_cells_Con_rep5

description:
Peripheral_blood_cells_Con_rep5
C13

value: Normal control


title: Peripheral_blood_cells_Con_rep4

description:
Peripheral_blood_cells_Con_rep4
C12


title: Genomic DNA of MDS04 MCSs

description: MDS MSCs


title: 231-JQ-1-input


title: Genomic DNA of AML04 MCSs

description: AML MSCs


title: MDA-MB-231 shControl-2


title: Genomic DNA of HD08 MCSs

description: Normal MSCs


title: Genomic DNA of HD11 MCSs (did not pass QC)

description: Normal MSCs


title: Genomic DNA of HD10 MCSs

description: Normal MSCs


title: IMR90 ER:RAS siCASP4 d8 rep1


title: 231-con-1-IP

value: treated with DMSO for 24 hours


title: 231-con-2-IP


title: 231-con-1-input


title: IMR90 ER:RAS siCASP4 d5 rep3

value: Oncogene-induced senescence day 5 4OHT siCASP4


title: IMR90 ER:RAS d8 rep3

value: Oncogene-induced senescence day 8 4OHT siNTP


title: 231-con-2-input


title: IMR90 ER:RAS siCASP4 d5 rep2


title: Peripheral_blood_cells_Con_rep3

description:
Peripheral_blood_cells_Con_rep3
C11

value: Lewis

value: Peripheral blood cells


title: Peripheral_blood_cells_Con_rep2

description:
Peripheral_blood_cells_Con_rep2
C8


title: DLD1 p85β K477A/R478A mutant cells, H3K27me3 IP ChIPSeq

city: Shanghai

first: Baoyu

last: He

address: No. 25, Lane 2200, Xietu Road

institute: Renji Hospital

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Raw reads were treated with Trimmomatic tools(V0.36) to remove adapters. Following reads quality control:Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15, drop reads which are less than 35% of initiation read length. Then reads quality was inspected using the FastQC software then output statistical result.
The reads that passed the prefiltering step were aligned with the Bowtie2 v2.4.2 software to the human genome (hg19). Peak calling was performed with MACS2. Homer software was used to annotate ChIP-seq peaks, and getDifferentialPeaks was used to find differential peaks between DLD1 parental cells and DLD1 p85β K477A/R478A mutant cells.
Genome_build: hg19
Supplementary_files_format_and_content: peak bigwig files

source_name: DLD1 p85β K477A/R478A mutant cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with anti-H3K27me3 antibody.
ChIP was performed using the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology, 9003) following the manufacturer’s instructions. Chromatin was sonicated and immunoprecipitated with anti-H3K27me3 antibody. Purified ChIP DNA was verified on agarose gel to ensure proper fragmentation and then sent to the Sequencing. Sequencing was performed at RiboBio Inc，Guangzhou on an lllumina nova machine. Raw reads (Paired-end, 150bp) were aligned to human reference genome hg19 using bowtie2 (v2.4.2), allowing up to one mismatch. Peak calling was performed using model-based analysis of ChIP–seq (MACS, v2.2.7) with a cutoff of P ≤ 1 × 10-8.

value: colon

value: p85{beta} K477A/R478A mutant

tag: chip antibdy

value: H3K27me3 (Cell Signaling Technology, Cat# 9733, RRID:AB_2616029)


title: IMR90 ER:RAS siCASP4 d5 rep1


title: IMR90 ER:RAS d8 rep2


title: C4-2_shßArr1_rep3

first: HAMSA

last: THAYELE PURAYIL

state: Florida

address: 2033 Mowry Road

department: ANATOMY AND CELL BIOLOGY

institute: UNIVERSITY OF FLORIDA

description: Sample 6

data_processing:
Reads were quality filtered at Q20 and trimmed to remove remaining adaptors using Trimmomatic version 0.36
Reads were aligned to Illumina iGenome Homo sapiens hg19 reference genome using Tophat version 2.1.1 utilizing Bowtie2 version 2.3
Alignments were processed using Cufflinks version 2.2.1 along with Illumina iGenome Homo sapiens hg19 Gene transfer format file
We used cuffquant to perform transcript quantification and exported the raw counts (un-normalized counts) to text files
Raw counts were imported to edgeR version 3.16.5 for detecting differentially expressed (DE) genes
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Prostate cancer cells

growth_protocol: Both control and ßArr1 knockdown cells were grown in RPMI-1640 supplemented with 10% (v/v) fetal bovine serum (FBS) and 100U pencillin/ml and 100ug streptmycin/ml at 37C in a humidified (95% air, 5% Co2) atmosphere.

extract_protocol:
Total RNA was isolated using High Pure RNA Isolation Kit  ((Roche, Pleasanton, CA, USA) with DNase
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Castration resistant prostate cancer cells

tag: knockdown


title: C4-2_shßArr1_rep2

description: Sample 5


title: Genomic DNA of HD06 MCSs

description: Normal MSCs


title: IMR90 ER:RAS d5 rep2

value: Oncogene-induced senescence day 5 4OHT siNTP


title: IMR90 ER:RAS d5 rep1


title: IMR90 ER:RAS d8 rep1


title: C4-2_shControl_rep2

description: Sample 2

value: control


title: C4-2_shßArr1_rep1

description: Sample 4


title: C4-2_shControl_rep3

description: Sample 3


title: IMR90 ER:STOP d5 rep3

source_name: IMR90 ER:STOP human primary fibroblast cells

value: Control day 5 4OHT siNTP


title: HG001-rep3

city: Singapore

first: Kelvin

last: Chong

address: 60 Nanyang Drive

department: SCELSE

country: Singapore

institute: Nanyang Technological University

data_processing:
Illumina Casava1.7 software used for basecalling.
Demultiplexed sequencing reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to respective bacterial genome using BWA (version 0.7.15-r1140) with default parameters.
Reads were counted with predicted open reading frames to each reference genome using HTSeq (version 0.6.1)  and subjected to differential analysis using EdgeR (3.36.0)
Genome_build: HG001 (GCA_000013425.1) and UTI89 (GCA_000013265.1)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

organism: Staphylococcus aureus

extract_protocol:
Macrocolonies were excised and subjected to RNA extraction in Trizol and mechanical lysis. Dnase treatment was performed and remaining RNA was depleted of ribosomal RNA before subjected to first and second strand synthesis.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Wild type

tag: background

value: Single species


title: IMR90 ER:STOP d5 rep2

value: IMR90 ER:STOP human primary fibroblast cells

tag: treatment


title: IMR90 ER:RAS d5 rep3

value: IMR90 ER:RAS human primary fibroblast cells


title: IMR90 ER:STOP d5 rep1


title: C4-2_shControl_rep1

description: Sample 1


title: Genomic DNA of HD05 MCSs

description: Normal MSCs

value: unknown

value: M


title: MDA-MB-231 shControl-1