title: Patient #06, d0, technical replicate 1

description:
06_d0-1
gene expression data from AML patients at day 0 of DAC treatment

tag: tissue


title: HAP1_1_58

status: Public on Mar 09 2021

type: SRA

city: Shenzhen

first: Guipeng

last: Li

address: 1088 Xueyuan Avenue

country: China

institute: Southern University of Science and Technology

library_source: genomic

data_processing:
peaks were called by macs2
peak-cell matrices were determined using featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: txt file, peak-by-cell count matrix

molecule: genomic DNA

organism: Homo sapiens

source_name: HAP1 cells

extract_protocol:
Plate-based snATAC-seq
1)One day before the experiment, prepare the 96-well plates by adding 1µL 2X Lysis Buffer (100 mM NaCl pH 7.4, 100 mM Tris-HCl pH 8.0, 40 µg/mL proteinase K, 0.4 % SDS) to each well. Then add 1µL of 10 µM S5xx/N7xx Nextera Index Primer Mix (5 µM each) (TD202, Vazyme) to each well. Seal the plate and store in -80 ºC. Thaw plates at room-temperature before use.
2)Pre-coat 1.5 mL Eppendorf tubes with 500 µL 0.5% BSA/DPBS. Collect 5×105 cells in DPBS into 1.5 mL Eppendorf tube. Centrifuge at 300 g for 5 min at room-temperature. Wash the cells once with 200µL DPBS, then with 200 µL ATAC resuspension buffer (10 mM NaCl, 10 mM Tris-HCl pH 7.4, 3 mM MgCl2). Centrifuge condition is 600 g, 5 min at 4 ˚C.
3)After two steps wash, resuspend cells in 100 µL ATAC cell lysis buffer (10 mM NaCl, 10 mM Tris-HCl pH 7.4, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP40, 0.01% Digitonin), then add 2.5 µL assembled CASB complex (control group was only resuspended in ATAC cell lysis buffer). Mix thorough by pipette. Incubate on ice for 5 min, then add 950 µL ATAC wash buffer (10 mM NaCl, 10 mM Tris-HCl pH 7.4, 3 mM MgCl2, 0.1% Tween-20) to quench reaction.
4)Centrifuge nuclei at 1000 g for 5 min at 4 ˚C, discard the supernatant by pipette carefully. Resuspend nuclei in 1 mL ATAC wash buffer. Centrifuge again.
5)Resuspend nuclei in 50 µL tagmentation reaction (TD501, Vazyme). Incubate at 37 ˚C on a thermomixer (600 rpm) for 30 min. Then, stop the reaction by adding 50 µL tagmentation stop buffer (20 mM EDTA, 10 mM Tris-HCl pH 8.0). Incubate on ice for 10 min.
6)Add 300 µL 0.5% BSA/DPBS into nuclei. Then add DAPI according to manufacturer’s instruction. Use FACS (MA900, Sony) to sort single nucleus into each well of prepared 96-well plates.
7)Set lip temperature of PCR machine to 100 ˚C, then incubate plates at 65 ºC for 15 min.
8)Add 2 µL 10% Tween-20 into each well to quench SDS. Then add 6 µL PCR mix (from TD501, Vazyme). PCR reaction as follow: 72 ˚C 10 min, 98 ˚C 1 min, (98 ˚C 30 s, 63 ˚C 30 s, 72 ˚C 30 s) ×25, 72 ˚C 5 min, 10 ˚C hold.
9)Collect all products into a 15 mL conical centrifuge tube. Purify the product using ZYMO DNA clean & concentrator kit.
10)Perform size

tag: cell line


title: Experimental cell RNA, rep 2

city: Orlando

first: Ratna

last: Chakrabarti

address: 12722 Research Parkway

country: USA

institute: University of Central Florida

description:
E2
polyA+ mRNA
Expression_Gene.xlsx
Expression_Transcript.xlsx

library_source: transcriptomic

data_processing:
Sequence quality was examined using the FastQC.
The raw sequences were trimmed off 5’, 3’-adaptor bases using cutadapt.
The trimmed sequences were aligned to reference genome using Hisat2 software.
The aligned reads were assembled to transcripts by StringTie and FPKMs were computed.
The differentially expression of the genes and transcripts were analyzed using Ballgown R package.
rMATS was used to analyze alternative splicing events.
Genome_build: GENCODE mouse GRCm38
Supplementary_files_format_and_content: Gene/transcript expression levels in FPKM.

molecule: total RNA

source_name: Stably transfected C4-2B prostate cancer cells

growth_protocol: Stable sublines of C4-2B prostate cancer cells constitutively expressing LINC00888 or the empty vector were maintained in RPMI1640 with 10% FBS.

extract_protocol:
Total RNA was extracted using Zymo RNA extraction kit and used for RNA-seq analysis.
Libraries were prepared according to Roche KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Briefly, polyA+ mRNAs were enriched by oligo (dT) magnetic beads from the total RNA samples; RNA-seq library preparation using KAPA Stranded RNA-Seq Library Prep Kit (Illumina), which incorporates dUTP into the second cDNA strand and renders the RNA-seq library strand-specific; The completed libraries were qualified with Agilent 2100 Bioanalyzer and quantified by absolute quantification qPCR method; The barcoded libraries were mixed, denatured to single strands in NaOH, captured on Illumina flow cell, amplified in situ, and sequenced for 150 cycles for paired-ends on an Illumina HiSeq 4000 system.

treatment_protocol: Overexpression of LINC00888 with a fold change in expression 15.27±2.4 (Mean±SD) was determined by qRT-PCR in the extracted total RNA used for RNA-seq analysis.

tag: cell type

value: Prostate cancer cell line

tag: vector

value: pcDNA 3.1+LINC00888


title: HAP1_1_56


title: HAP1_1_57


title: HAP1_1_55


title: Experimental cell RNA, rep 1

description:
E1
polyA+ mRNA
Expression_Gene.xlsx
Expression_Transcript.xlsx


title: Control RNA, rep 3

description:
C3
polyA+ mRNA
Expression_Gene.xlsx
Expression_Transcript.xlsx

value: pcDNA 3.1 vector only


title: HAP1_1_60


title: HAP1_1_54


title: HAP1_1_53


title: HAP1_1_52


title: HAP1_1_51


title: Control RNA, rep 2

description:
C2
polyA+ mRNA
Expression_Gene.xlsx
Expression_Transcript.xlsx


title: HAP1_1_50


title: Patient #06, d8, technical replicate 1

type: RNA

city: Freiburg

first: Gabriele

last: Greve

address: Hugstetter Str 55

department: Department of Internal Medicine 1

country: Germany

institute: University of Freiburg Medical Center

description:
06_d8-1
gene expression data from AML patients at day 8 of DAC treatment

hyb_protocol: Samples were hybridized according to manufacturer's protocol (Affymetrix).

scan_protocol: Samples were scanned according to manufacturer's protocol (Affymetrix).

data_processing: Raw data was analyzed with the Partek Genomics Suite.

label: Biotin

source_name: isolated blasts from peripheral blood

label_protocol: Samples were labeled with Biotin according to manufacturer's protocol (Affymetrix).

growth_protocol: Mononuclear cells were isolated out of AML patients' whole blood samples by Pancoll density centrifugation. AML blasts were enriched by automated magnetic sorting using anti-CD34 and -CD117 beads.

extract_protocol: Total RNA was extracted with Trizol Reagent (ThermoScientific)/Chloroform followed by DNase I digestion and column clean-up with the Qiagen RNeasy MinElute Cleanup Kit according to manufacturers' protocols. The subsequent steps were performed in technical triplicates (data only available in duplicates for samples 02_d8, 04_d0, 17_d0 and 17_d8 due to array QC failure)

treatment_protocol: AML patients were treated within the DECIDER trial (NCT00867672) with decitabine (DAC; 0 mg/m2 intravenously over 1 hour for 5 days).

tag: disease state

value: AML

tag: individual

value: Patient #06

tag: treatment

value: decitabine (DAC)

tag: time

value: day 8

value: peripheral blood


title: HAP1_1_4


title: MC-RR at 1000 μg/L [ES150]

city: Durham

first: Weichun

last: Huang

state: NC

address: 109 TW Alexander Dr

department: ORD

institute: US EPA

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.19.1
read quality was checked for each sample using FastQC
raw reads were mapped to the transcript sequences of the human reference genome from NCBI using BWA default single-end read mapping protocol
Read count data were normalized and filtered out batch effects
Genome_build: GRCh38
Supplementary_files_format_and_content: Normalized and batch-adjusted read count in the tab-delimited text format

source_name: The human hepatocyte cell line HepaRG

growth_protocol: HepaRG cells were seeded at 5 X 105 cells/well onto a pre-wetted sterile flat-bottom collagen coated 24-well plate (Life Technologies, Carlsbad, CA, USA) and incubated overnight. WM was replaced with pre-warmed HepaRG Toxicity Working Medium (TM; Williams’ medium E supplemented with glutamine and HepaRG toxicity medium supplement) and re-incubated until MC exposure on day 7

extract_protocol:
Cells were thawed in Qiazol lysis buffer (Qiagen, Hilden, DE) further homogenized (Bullet Blender Storm 24 mixer mill, Next Advance, Averill Park, NY) using the manufacturer’s recommended settings.  Approximately 250 µl of chloroform:isoamyl alcohol (24:1; Sigma-Aldrich Chemical Co., St. Louis, MO) was added to each tube, mixed by inversion, and vortexed and incubated at room temperature for 3 min and transferred to a 1.5 ml Heavy Phase Lock Gel microfuge tube (5Prime, Inc., Gaithersburg, MD), incubated on ice (10 min) and centrifuged at 14,200 g (5 min, room temperature (RT)). The supernatant was transferred to a microcentrifuge tube (Eppendorf North America, Hauppauge, NY) and mixed with an equal volume of 70% ethanol and put on a RNeasy® MinElute Clean Up kit 2.0 ml column (Qiagen) and processed according to the manufacturer’s protocol with DNase treatment (RNase-free DNase kit, Qiagen) prior to final cleanup and elution. RNA was quantified and quality was confirmed using an Agilent RNA 6000 Nano kit with a 2100 Bioanalyzer (Agilent Technologies, Inc., Wilmington, DE). Typical RIN scores were above 9.  RNA eluates were stored at -80 °C
Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep for NeoPrep kit (Illumina), following the manufacturer’s protocol. An input of 100 ng total RNA was used for each sample. Additional resuspension buffer was added to each library to obtain a final total volume of about 24 µL. The concentration of each library was determined using either the KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems) or the Qubit dsDNA HS Assay kit (Thermo Fisher Scientific).  Libraries were normalized to 10 nM and combined into pools of 8-16 samples. Dilutions of libraries for quantitation and pooling was done using 10 mM Tris-HCl, pH 8.5.

treatment_protocol: MCs (MC-RR or -LR; Calbiochem, La Jolla, CA) were diluted in TM and used on the same day. Cells were exposed with 10, 100 and 1000 ng mL-1 of MC-LR or MC-RR, or to solvent (methanol) in replicates for 2 hr in a humidified 5% CO2, 37oC incubator. Cells were harvested and washed with 1 mL Hank’s Balanced Salt Solution (HBSS; Thermo Fisher Scientific, Waltham, MA, USA), lysed in QIAzol TM Lysis Reagent (Qiagen, Germantown, MD), and stored at -80°C until RNA isolation

tag: group

value: RR1000 exposure group

value: HepaRG

tag: agent

value: 1000 microg/L MC-RR

tag: time point

value: 2 hours


title: Patient #05, d8, technical replicate 2

description:
05_d8-2
gene expression data from AML patients at day 8 of DAC treatment

value: Patient #05


title: Patient #05, d8, technical replicate 3

description:
05_d8-3
gene expression data from AML patients at day 8 of DAC treatment


title: Patient #05, d0, technical replicate 3

description:
05_d0-3
gene expression data from AML patients at day 0 of DAC treatment

value: control

value: day 0


title: Control RNA, rep 1

description:
C1
polyA+ mRNA
Expression_Gene.xlsx
Expression_Transcript.xlsx


title: HAP1_1_49


title: Patient #05, d8, technical replicate 1

description:
05_d8-1
gene expression data from AML patients at day 8 of DAC treatment


title: HAP1_1_48


title: HAP1_1_44


title: HAP1_1_45


title: HAP1_1_42


title: HAP1_1_41


title: MC-RR at 1000 μg/L [ES149]


title: HAP1_1_43


title: MC-RR at 1000 μg/L [ES147]


title: MC-RR at 1000 μg/L [ES146]


title: MC-RR at 1000 μg/L [ES148]


title: HAP1_1_46


title: HAP1_1_3


title: HAP1_1_39


title: HAP1_1_38


title: MC-RR at 1000 μg/L [ES145]


title: HAP1_1_37


title: Patient #04, d8, technical replicate 2

description:
04_d8-2
gene expression data from AML patients at day 8 of DAC treatment

value: Patient #04


title: Patient #04, d8, technical replicate 3

description:
04_d8-3
gene expression data from AML patients at day 8 of DAC treatment


title: Patient #04, d0, technical replicate 1

description:
04_d0-1
gene expression data from AML patients at day 0 of DAC treatment


title: Patient #05, d0, technical replicate 1

description:
05_d0-1
gene expression data from AML patients at day 0 of DAC treatment


title: Patient #04, d8, technical replicate 1

description:
04_d8-1
gene expression data from AML patients at day 8 of DAC treatment


title: Patient #05, d0, technical replicate 2

description:
05_d0-2
gene expression data from AML patients at day 0 of DAC treatment


title: MC-RR at 1000 μg/L [ES99]


title: MC-RR at 1000 μg/L [ES100]


title: Patient #03, d8, technical replicate 3

description:
03_d8-3
gene expression data from AML patients at day 8 of DAC treatment

value: Patient #03


title: Patient #04, d0, technical replicate 2

description:
04_d0-2
gene expression data from AML patients at day 0 of DAC treatment


title: HAP1_1_40


title: HAP1_1_36


title: HAP1_1_35


title: HAP1_1_34


title: MC-RR at 1000 μg/L [ES98]


title: HAP1_1_32


title: Patient #03, d8, technical replicate 2

description:
03_d8-2
gene expression data from AML patients at day 8 of DAC treatment


title: MC-RR at 1000 μg/L [ES97]


title: Patient #03, d8, technical replicate 1

description:
03_d8-1
gene expression data from AML patients at day 8 of DAC treatment


title: HAP1_1_33


title: MC-RR at 1000 μg/L [ES96]


title: HAP1_1_30


title: HAP1_1_31


title: HAP1_1_47


title: HAP1_1_29


title: HAP1_1_2


title: HAP1_1_28


title: MC-RR at 1000 μg/L [ES95]


title: iPSC-derived astrocytes, CP2A2_1

city: Bergen

first: Kristina Xiao

last: Liang

state: Hordaland

address: Jonas Lies vei 87, P. O. Box 7804

country: Norway

institute: University of Bergen

data_processing:
The sequencing was performed at BGI-Shenzhen using BGISEQ-500. The sequencing data was filtered using SOAPnuke (v1.5.2) software.
The processed FASTQ files were mapped to the human transcriptome and genome using HISAT2 (v2.0.4).
The genome version was GRCh38, with annotations from Bowtie2 (v2.2.5).
Expression level of the gene was calculated by RSEM (v1.2.12) software.
The set of differentially expressed genes identified from pairwise comparisons was identified using DEseq2 (v1.4.5) package (BGI, Wuhan, China). The number of reads per kilobase per million reads (RPKM) method was used to calculate the modification levels of unique genes. Significantly differentially expressed genes were defined as ones with at least 0.3 FPKM level of expression in at least one of the conditions and a q-value less than 0.05 by Bonferroni test. KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expressed genes was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test.
Genome_build: NCBI: GCF_000001405.38_GRCh38.p12
Supplementary_files_format_and_content: Matrix table with raw read counts for every gene and every sample

source_name: Astrocytes

growth_protocol: The cells were cultured in maturation medium AGMTM Astrocyte Growth Medium BulletKitTM (Lonza, CC-3186) and kept in a 37°C incubator with a humidified.

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy Kit (QIAGEN, 74104) following manufacturer’s instructions. Samples were sent to BGI, Wu Han, for library preparation. Libraries were constructed following a custom protocol from samples that passed quality controls (mass > 2µg, concentration>80ng/microl, OD260/280 ~= 2.00, OD260/230 ~= 2.20, RIN>6.5, 28S/18S<1.0, baseline smooth). After mRNA enrichment, RNA was fragmented and reverse transcribed to double-strand cDNA (dscDNA) by N6 random primer. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments. The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer, splint oligo and DNA ligase, followed by sequencing on BGISEQ-500 platform, generating an average 24M reads of 50bp per sample
Library preparation was conducted at BGI, Shenzhen, China, following the guide of the standard protocol.
Library preparation (BGISEQ-500RS High-throughput sequencing kit, PE50, V3.0, MGI Tech Co, Ltd, Shenzhen, China), hybridization and sequencing were performed according to the manufacturer's standard procedure provided by BGI (BGI-Shenzhen).

value: iPSC-derived astrocytes

tag: genotype

value: POLG mutated (heterozygous c.1399G>A/c.2243G>C; p.A467T/W748S)


title: iPSC-derived astrocytes, CP2A2_2


title: Patient #03, d0, technical replicate 2

description:
03_d0-2
gene expression data from AML patients at day 0 of DAC treatment


title: Patient #03, d0, technical replicate 3

description:
03_d0-3
gene expression data from AML patients at day 0 of DAC treatment


title: Patient #02, d8, technical replicate 2

description:
02_d8-2
gene expression data from AML patients at day 8 of DAC treatment

value: Patient #02


title: MC-RR at 1000 μg/L [ES45]


title: Patient #03, d0, technical replicate 1

description:
03_d0-1
gene expression data from AML patients at day 0 of DAC treatment

value: AML


title: iPSC-derived astrocytes, CP2A1_3


title: MC-RR at 1000 μg/L [ES44]


title: Patient #02, d0, technical replicate 3

description:
02_d0-3
gene expression data from AML patients at day 0 of DAC treatment


title: iPSC-derived astrocytes, CP2A1_2


title: HAP1_1_27


title: iPSC-derived astrocytes, CP2A2_3


title: iPSC-derived astrocytes, CP2A1_1


title: HAP1_1_25


title: HAP1_1_26


title: MC-RR at 1000 μg/L [ES42]


title: MC-RR at 1000 μg/L [ES43]


title: MC-RR at 1000 μg/L [ES46]


title: T_3

city: shanghai

first: Yongli

last: Zhang

address: No.2699 Gaokexi Road, Shanghai

department: Obstetrics and Gynecology

institute: Shanghai First Maternity and Infant Hospital

description:
sample_cir_count_with_gene_symbol_cirbase.xls
transcript_sample_FPKM.xls

data_processing:
Paired-end 150 bp reads was sequenced by Illumina Hiseq sequencer. Trim Galore software (v0.4.2) was used to remove adaptor and low quality reads. FastQC software (v0.11.5) was used for quality control.  High quality reads was mapped to human hg38 reference sequence by STAR software (v2.5.3a).
For mRNA and lncRNA transcripts, FPKMs (Fragments Per Kilobase of transcript per Million fragments mapped) were calculated as the expression of transcript.
For circRNA, BackSplice reads were counted and  BSRP (Back Spliced Reads Per million mapped reads) were calculated as the expression of circRNAs.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM & COUNTS

growth_protocol: 10% Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum

extract_protocol:
Total RNA was extracted from cells using TRIzolTM Reagent (#15596026, Invitrogen, Carlsbad, CA, USA) per the manufacturer’s protocol, and ribosomal RNA was removed using the Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA).
Fragmented RNA (average length of ~200 bp) were subjected to first-strand and second-strand cDNA synthesis followed by adaptor ligation and enrichment with a low cycle per the instructions of the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA). The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit 2.0 (Life Technologies, USA).

tag: tag

value: tumor tissue from the third patient

value: uterine leiomyoma


title: HAP1_1_24


title: Patient #02, d8, technical replicate 1

description:
02_d8-1
gene expression data from AML patients at day 8 of DAC treatment

value: decitabine (DAC)

value: day 8


title: MC-RR at 1000 μg/L [ES41]

value: RR1000 exposure group


title: HAP1_1_23


title: Patient #02, d0, technical replicate 1

description:
02_d0-1
gene expression data from AML patients at day 0 of DAC treatment

value: peripheral blood


title: iPSC-derived astrocytes, WS5A3_1

value: POLG mutated (homozygous for c.2243G>C; p.W748S)


title: Patient #02, d0, technical replicate 2

description:
02_d0-2
gene expression data from AML patients at day 0 of DAC treatment


title: HAP1_1_22


title: Patient #01, d8, technical replicate 3

description:
01_d8-3
gene expression data from AML patients at day 8 of DAC treatment

value: Patient #01


title: iPSC-derived astrocytes, WS5A2_3


title: MC-RR at 100 μg/L [ES143]

value: RR100 exposure group

value: HepaRG

value: 100 microg/L MC-RR

value: 2 hours


title: MC-RR at 100 μg/L [ES142]


title: iPSC-derived astrocytes, WS5A3_3


title: Patient #01, d8, technical replicate 1

description:
01_d8-1
gene expression data from AML patients at day 8 of DAC treatment


title: Patient #01, d8, technical replicate 2

description:
01_d8-2
gene expression data from AML patients at day 8 of DAC treatment


title: iPSC-derived astrocytes, WS5A2_1


title: iPSC-derived astrocytes, WS5A3_2


title: HAP1_1_21


title: MC-RR at 100 μg/L [ES140]


title: iPSC-derived astrocytes, WS5A2_2


title: Su_DHL_4_dCas9_KRAB_ChiPSeq_H3K27ac

city: Lausanne

first: Yuanlong

last: Liu

address: Quartier UNIL-Sorge

department: Department of Computational Biology

country: Switzerland

institute: University of Lausanne

data_processing:
Fastq files were mapped to a meta reference genome consisting of hg19 and Drosophila dm6 using Bowtie2. The output bam files were sorted and removed for PCR duplicates using samtools, and converted to reference-adjusted reads per million (RRPM) tracks using bamCoverage 3.4.3 with parameter binsize=100bp and scaleFactor=Normalization factor (computed as described in the ChiP-RX paper DOI: 10.1016/j.celrep.2014.10.018)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig (.bw) format represent reference-adjusted reads per million binned at 100bp

source_name: Su_DHL_4 cells

growth_protocol: standard grwoth condition as described in Sungalee et al. 2021

extract_protocol:
standard protocol for ChIPseq sample preparation as described in Sungalee at al. 2021
standard Illumina sequencing protocol for library prepraration

treatment_protocol: as described in Sungalee et al. 2021

value: lymphoma cells

tag: tissue type

value: lymphonode

value: expressing dCas9-KRAB

tag: chip antibody


title: MC-RR at 100 μg/L [ES141]


title: HAP1_1_20


title: iPSC-derived astrocytes, WS5A1_2

value: iPSC-derived astrocytes


title: MC-RR at 100 μg/L [ES144]


title: Patient_7_ChiPSeq_H3K27ac

description: no control access needed

source_name: Patient sample 7 cells

value: ABC-DLBCL tumor suntype

value: lymphonode biopsy

value: untreated


title: HAP1_1_1


title: MC-RR at 100 μg/L [ES139]


title: Su_DHL_4_dCas9_KRAB_sgRNA2_ChiPSeq_H3K27ac

value: expressing dCas9-sgRNA2 targeting BCL11A enhancer


title: iPSC-derived astrocytes, WS5A1_3


title: Patient #01, d0, technical replicate 3

description:
01_d0-3
gene expression data from AML patients at day 0 of DAC treatment

value: AML

value: control

value: day 0


title: HAP1_1_18


title: HAP1_1_19


title: Patient_1_ChiPSeq_H3K27ac

description: no control access needed

source_name: Patient sample 1 cells

value: DLBCL double hit


title: Patient #01, d0, technical replicate 2

description:
01_d0-2
gene expression data from AML patients at day 0 of DAC treatment

value: Patient #01

value: peripheral blood


title: WSU-DLCL2_ChiPSeq_H3K27ac

source_name: WSU-DLCL2 cells


title: HAP1_1_17


title: MC-RR at 100 μg/L [ES92]

value: RR100 exposure group

value: HepaRG


title: Human astocyte cell line, HNA_3

value: Human astocyte cell line

value: wild type


title: Patient #01, d0, technical replicate 1

description:
01_d0-1
gene expression data from AML patients at day 0 of DAC treatment


title: HAP1_1_16


title: iPSC-derived astrocytes, WS5A1_1

value: POLG mutated (homozygous for c.2243G>C; p.W748S)


title: MC-RR at 100 μg/L [ES91]

value: 100 microg/L MC-RR

value: 2 hours


title: MC-RR at 100 μg/L [ES94]


title: MC-RR at 100 μg/L [ES93]


title: MC-RR at 100 μg/L [ES90]


title: ESC-derived astrocytes, ESC_3

value: ESC-derived astrocytes


title: Human astocyte cell line, HNA_2


title: ESC-derived astrocytes, ESC_2


title: WSU-DLCL2_A485_treated_ChiPSeq_H3K27ac

value: lymphoma cells

value: lymphonode

value: treated with A-485 for 48 hours


title: ESC-derived astrocytes, ESC_1


title: HAP1_1_13


title: iPSC-derived astrocytes, CTRL4_3

value: iPSC-derived astrocytes


title: HAP1_1_14


title: HAP1_1_11


title: MC-RR at 100 μg/L [ES89]


title: HAP1_1_10


title: MC-RR at 100 μg/L [ES39]


title: HAP1_1_15


title: iPSC-derived astrocytes, CTRL4_2


title: MC-RR at 100 μg/L [ES37]


title: MC-RR at 100 μg/L [ES36]


title: iPSC-derived astrocytes, CTRL3_3


title: G047_Gale105_I_5_I_48_2

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

description: iPSC-WTC 5 infected

data_processing:
Read quality for each sample was first assessed with FASTQC
Globin and rRNA reads were filtered out using bowtie2v2.1.0
Remaining reads were alligned to the hg19 genome using STARv2.7.5a
Gene counts were calculated with HTSeqv0.12.4
Genome_build: hg19

source_name: iPSC differentiated male cardiomyocytes, subtype WTC

growth_protocol: Cardiomyocytes from RUES2 and WTC11c were differentiated as previously described by A. Bertero et al., Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory. Nat Commun 10, 1538 (2019)

extract_protocol:
Cardiomyocytes RNAs were extracted using Direct-zol RNA MIniprep Plus kit from Zymo Research following manufacturer's manual and eluted in nuclease free water.
Bulk mRNA-seq data from cardiomyocytes were generated by constructing mRNA-seq libraries using the KAPA mRNA HyperPrep Kit (Kapa Biosystems) and 100 ng of RNA. Both the RNA and resulting libraries were quality controlled and quantified using a 4200 TapeStation System (Agilent Technologies, Inc.) and a Qubit Fluorometer (Invitrogen).
Libraries were sequenced on an Illumina NovaSeq using S2 200 cycle flow cell which generates paired-end reads of 100 nucleotides. Each sample was sequenced to a minimum of 20 million mapped reads

treatment_protocol: SARS-CoV-2 was diluted to the desired MOI in DMEM and incubated on hPSC-CMs for 1 h at 37 °C (non-infected [mock] controls were incubated with DMEM only). Cells were then washed with DPBS and cultured in RPMI-1640 supplemented with B-27.

value: 48 hours

tag: replicate

value: WTC11c hiPSCs


title: G048_Gale105_I_5_I_48_3

description: iPSC-WTC 5 infected


title: iPSC-derived astrocytes, CTRL3_2


title: iPSC-derived astrocytes, CTRL3_1


title: G046_Gale105_I_5_I_48_1

description: iPSC-WTC 5 infected


title: MC-RR at 100 μg/L [ES34]


title: G045_Gale105_I_5_M_48_3

description: iPSC-WTC 5 mock

value: mock


title: HAP1_1_12


title: MC-RR at 100 μg/L [ES35]


title: MC-RR at 100 μg/L [ES38]


title: iPSC-derived astrocytes, CTRL2_1


title: MC-RR at 100 μg/L [ES32]


title: iPSC-derived astrocytes, CTRL2_3


title: MC-RR at 10 μg/L [ES88]

value: RR10 exposure group

value: 10 microg/L MC-RR


title: Human astocyte cell line, HNA_1


title: G044_Gale105_I_5_M_48_2

description: iPSC-WTC 5 mock


title: MC-RR at 100 μg/L [ES33]

value: RR100 exposure group


title: iPSC-derived astrocytes, CTRL1_3


title: MC-RR at 10 μg/L [ES87]

value: HepaRG


title: G042_Gale105_E_5_I_48_3

description: ESC-H7 5 infected

source_name: ESC differentiated female cardiomyocytes, subtype H7

value: Undifferentiated RUES2 hESCs (RUESe002-A; WiCell)


title: G041_Gale105_E_5_I_48_2

description: ESC-H7 5 infected


title: G043_Gale105_I_5_M_48_1

description: iPSC-WTC 5 mock


title: G040_Gale105_E_5_I_48_1

description: ESC-H7 5 infected


title: iPSC-derived astrocytes, CTRL1_2

value: wild type


title: MC-RR at 10 μg/L [ES86]


title: G039_Gale105_E_5_M_48_3

description: ESC-H7 5 mock


title: iPSC-derived astrocytes, CTRL2_2


title: MC-RR at 100 μg/L [ES31]


title: G038_Gale105_E_5_M_48_2

description: ESC-H7 5 mock


title: AML1_EKO_UM171_800nM_D14

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

data_processing:
Library strategy: CRISPR screen
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20.
Reads trimmed using Trim Galore 0.5.0
Reads mapped using Bowtie2 2.3.3.1
Counts obtained using MAGeCK 0.5.7
Genome_build: GRCh38; the file sgRNA sequences.txt (available on the series record) contains the sgRNA sequence for our CRISPR experiment with columns: A) sgRNA identifier, B) sequence, C) gene or chromosome location.
Supplementary_files_format_and_content: Counts per gene

source_name: AML cell line

growth_protocol: OCI-AML1-Cas9 EKO library cells were treated with Doxycyclin (2 ug/mL) for 7 days for Cas9 activation and gene KO. Cells were then split in 6 conditions: DMSO, Um171 250nM, UM171 800nM. Cells were collected every 2 dyas for gDNA extraction and split with fresh media up to 14 days

extract_protocol:
Proteinase-K/ammonium acetate/ethanol extraction - in-house protocol
Illumina index sequencies were added to each sample by PCR (PCR2)

treatment_protocol: Fresh media (DMEM, 10% FBS, 10ng/ml GM-CSF)was prepared every 2 days and compounds were added to the right concentration and 0,01% DMSO

value: AML

tag: day

tag: sequenced molecule

value: sgRNA ID sequence


title: AML1_EKO_UM171_800nM_D8

tag: cell line


title: MC-RR at 10 μg/L [ES85]

value: 2 hours


title: MC-RR at 10 μg/L [ES84]


title: PNT-Prdm1KO-D8

city: GuangZhou

first: Jiangping

last: He

address: Kai yuan avenue 190

institute: Guangzhou Institutes of Biomedicine and Health (GIBH), CAS

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (mm10 vM21) transcriptome using STAR (version 2.7)
The gene expression level was calculated by using  STAR
Fastq reads were aligned to the genome using STARsolo with the setting ‘--outSAMattributes NH HI AS nM CR CY UR UY --readFilesCommand zcat --outFilterMultimapNmax 100 --winAnchorMultimapNmax 100 --outMultimapperOrder Random --runRNGseed 777 --outSAMmultNmax 1’.
Genome_build: mm10
Supplementary_files_format_and_content: expression matrix; genes.tsv, barcodes.tsv, matrix.mtx etc.

molecule: polyA RNA

organism: Mus musculus

source_name: PNT reprogramming cell Day8

growth_protocol: For reprogramming of EpiSCs into naïve state, EpiSCs were passaged with Accutase into singular cell and seeded at a density of 5,000 cells per well of 24-well plate coated with FBS in N2B27+XAV939+FA medium with the addition of 5 μM Y-27632. The medium was replaced with Stage 1 medium and changed daily for the first 3 days. The Stage 2 medium was refreshed daily for the last 5 days.

extract_protocol:
Cells at different induction time points of PNT were collected ad resuspended in DPBS with 0.04% BSA. Then, cells suspensions (500-1000 cells per microliter) were loaded on a Chromium Single Cell Controller (10x Genomics) to obtain single-cell gel beads in emulsion (GEMs) by using Single Cell 3’ Library and Gel Bead Kit V2 (10x genomics, 120237). Captured cDNAs were lysed and the released RNA were barcoded through reverse transcription in singular GEMs (Zheng et al., 2017). Barcoded cDNAs were pooled and cleaned by DynaBeads® MyOne Silane Beads (Invitrogen, 37002D).
Single-cell RNA-seq libraries were prepared by Single Cell 3’ Library Gel Bead Kit V2 (10x Genomics, 120237) following the manufacturer’s instruction. Sequencing was operated on an Illumina HiSeq X Ten

tag: genotype/variation

tag: cell type

value: PNT reprogramming cell


title: G035_Gale105_I_5_I_24_2

description: iPSC-WTC 5 infected

value: 24 hours


title: G037_Gale105_E_5_M_48_1

description: ESC-H7 5 mock


title: G036_Gale105_I_5_I_24_3

description: iPSC-WTC 5 infected


title: PNT-Prdm1KO-D2

source_name: PNT reprogramming cell Day2


title: PNT-Prdm1KO-D3

source_name: PNT reprogramming cell Day3


title: MC-RR at 10 μg/L [ES83]


title: MC-RR at 10 μg/L [ES29]


title: iPSC-derived astrocytes, CTRL4_1


title: PNT-Prdm1KO-D5

source_name: PNT reprogramming cell Day5


title: MC-RR at 10 μg/L [ES28]


title: PNT-Prdm1KO-D1

source_name: PNT reprogramming cell Day1


title: AML1_EKO_UM171_250nM_D8


title: MC-RR at 10 μg/L [ES30]


title: AML1_EKO_DMSO_D8

value: DMSO


title: G033_Gale105_I_5_M_24_3

description: iPSC-WTC 5 mock


title: PNT-Prdm1KO-D0

source_name: mouse epiblast stem cell

value: mouse epiblast stem cell (EpiSCs)


title: iPSC-derived astrocytes, CTRL1_1

value: iPSC-derived astrocytes


title: AML1_EKO_DMSO_D2


title: MC-RR at 10 μg/L [ES27]


title: G032_Gale105_I_5_M_24_2

description: iPSC-WTC 5 mock


title: AML1_EKO_DMSO_D14


title: MC-RR at 100 μg/L [ES40]

value: 100 microg/L MC-RR


title: AML1_EKO_UM171_250nM_D14


title: PNT-D8


title: MC-RR at 10 μg/L [ES26]


title: G034_Gale105_I_5_I_24_1

description: iPSC-WTC 5 infected

value: WTC11c hiPSCs


title: AML5_EKO_UM171_800nM_D8

growth_protocol: OCI-AML5-Cas9 EKO library cells were treated with Doxycyclin (2 ug/mL) for 7 days for Cas9 activation and gene KO. Cells were then split in 6 conditions: DMSO, Um171 250nM, UM171 800nM. Cells were collected every 2 days for gDNA extraction and split with fresh media up to 14 days

value: UM171 800nM and Dexamethasone


title: G031_Gale105_I_5_M_24_1

description: iPSC-WTC 5 mock

value: mock


title: AML5_EKO_UM171_250nM_D8

value: UM171 250nM and Dexamethasone


title: MC-RR at 10 μg/L [ES24]

value: RR10 exposure group

value: 10 microg/L MC-RR


title: G029_Gale105_E_5_I_24_2

description: ESC-H7 5 infected

value: Undifferentiated RUES2 hESCs (RUESe002-A; WiCell)


title: AML5_EKO_UM171_250nM_D14


title: MC-LR at 1000 μg/L [ES138]

value: LR1000 exposure group

value: HepaRG

value: 1000 microg/L MC-LR


title: PNT-D5


title: G030_Gale105_E_5_I_24_3

description: ESC-H7 5 infected


title: AML5_EKO_DMSO_D8

value: AML

value: sgRNA ID sequence


title: MC-LR at 1000 μg/L [ES137]

value: 2 hours


title: PNT-D2

value: PNT reprogramming cell


title: G027_Gale105_E_5_M_24_3

description: ESC-H7 5 mock

value: 24 hours


title: AML5_EKO_DMSO_D2

value: DMSO


title: MC-LR at 1000 μg/L [ES136]


title: PNT-D0

value: mouse epiblast stem cell (EpiSCs)


title: G026_Gale105_E_5_M_24_2

description: ESC-H7 5 mock


title: AML5_EKO_DMSO_D14


title: SKO-L80A+Ga_ATAC-seq

city: Guangzhou

first: Keshi

last: Chen

address: 190 Kai Yuan Avenue

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Science

data_processing:
The sequencing reads were filtered by Trimmomatic(0.35) and Cutadapt(1.13), and then mapped to mouse reference sequence for mm10 using Bowtie2(2.2.5) with parameters "-X2000 --local".
Mapped reads were then sorted and deduplicated using Samtools (1.3.1) with parameters "-F 1804 -f 2 -q 30", and Picard tools MarkDuplicates(1.90).
We performed peak calling using the MACS2(2.1.0) callpeak module with parameters "-p 0.01 --nomodel --extsize 150 -B --SPMR --keep-dup all --call-summits" on pooled replicates, and then only peaks with qvalue less than 1e-05 were keeped.
Signal density was computed using computeMatrix and Bedtools(2.25.0). ChIPpeakAnno(3.16.1) was used for identifying nearby genes from the peaks obtained from MACS. Differential binding genes were computed according to signal density using DESeq2(1.22.2).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized signal density for each Sample ...

source_name: mouse embryonic fibroblast

growth_protocol: MEFs were derived from E13.5 embryos that carry a transgenic Oct4 promoter driving GFP expression and used for reprogramming within two passages. MEFs and plat-E cells were maintained in DMEM/high glucose supplemented with 10% fetal bovine serum (FBS) (Hyclone). Mouse ESCs and iPSCs were maintained in a media containing DMEM/high glucose, 15% FBS (Gibco), NEAA (Gibco), GlutaMax (Gibco), and lif

extract_protocol:
Around 50000 living cells were taken for each library preparation. The cells were lysed in 1* Lysis Buffer to get the nuclei.
The cells were lysed in 1* Lysis Buffer to get the nuclei, and TruePrepTM DNA Library Prep Kit V2 for Illumina (Vazyme Biotech, Nanjing, China) was used to construct the transposase-treated libraries

treatment_protocol: Retroviral vectors (pMXs) carrying the factors were transfected into plat-E cells using PEI (Polyscience) transfection. The viral supernatants were collected and filtered prior to infecting MEFs with polybrene (Sigma). Viruses containing Oct4, Sox2, Klf4 and other factors were infected OG2-MEFs to generated iPSCs.

value: mouse embryonic fibroblast

tag: strain

value: ICR

value: mESC medium

value: infected with virus expressing Sox2, Klf4, Oct4 L80A and Gadd45a


title: MC-LR at 1000 μg/L [ES135]


title: MC-RR at 10 μg/L [ES25]

value: RR10 exposure group


title: SKO-L80A+Vc_ATAC-seq

value: mESC medium with vitamin C (50ug/ml)

value: infected with virus expressing Sox2, Klf4, and Oct4 L80A mutant


title: G025_Gale105_E_5_M_24_1

description: ESC-H7 5 mock

value: mock

value: Undifferentiated RUES2 hESCs (RUESe002-A; WiCell)


title: G024_Gale105_I_1e-1_I_72_3

description: iPSC-WTC 0.1 infected

value: 72 hours

value: WTC11c hiPSCs


title: MEF KO Heat Shock (B4) rep2

city: Rome

first: Mauro

last: Piacentini

address: via della ricerca scientifica 1

department: Department of Biology

country: Italy

institute: University of Rome Tor Vergata

data_processing:
Indexed libraries were prepared from 500 ng/ea purified RNA with TruSeq Stranded mRNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions. Libraries were quantified using the TapeStation 4200 (Agilent Technologies) and Qubit fluorometer (Invitrogen Co.), then pooled such that each index-tagged sample was present in equimolar amounts, with final concentration of the pooled samples of 2nM. The pooled samples were subject to cluster generation and sequencing using an Illumina NextSeq 500 System (Illumina) in a 2x75 paired-end format at a final concentration of 1.8 pmol
The raw sequence files generated (.fastq files) underwent quality control analysis using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and the quality checked reads were trimmed with cutadapt v.1.10 and then aligned to the mouse genome (mm9 assembly) using STAR v.2.5.2.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: MEF KO Heat Shock (B4) rep2

growth_protocol: MEF cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum, 100 μg/ml streptomycin and 100 units/ml penicillin, at 37°C and 5% CO2 in a humidified atmosphere.

extract_protocol:
Cells were lysed in Trizol reagent and total RNA was extracted using Direct-Zol™ RNA MiniPrep Plus according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To induce Heat shock cells were placed in a water bath at 42°C for 20 minutes

value: Mouse embryonic fibroblasts


title: SKO+shBrg1_ATAC-seq

value: infected with virus expressing Sox2, Klf4, Oct4 and shBrg1


title: PNT-D1

value: PNT reprogramming cell


title: MC-LR at 1000 μg/L [ES134]

source_name: The human hepatocyte cell line HepaRG

value: LR1000 exposure group

value: HepaRG

value: 1000 microg/L MC-LR

value: 2 hours


title: MEF KO Heat Shock (C4) rep3

source_name: MEF KO Heat Shock (C4) rep3


title: MEF KO Heat Shock (A4) rep1

source_name: MEF KO Heat Shock (A4) rep1


title: PNT-D3


title: MC-LR at 1000 μg/L [ES82]


title: SKO-L80A_ATAC-seq

value: mouse embryonic fibroblast

value: ICR

value: infected with virus expressing Sox2, Klf4 and Oct4 L80A mutant


title: G028_Gale105_E_5_I_24_1

description: ESC-H7 5 infected

value: 24 hours


title: G023_Gale105_I_1e-1_I_72_2

description: iPSC-WTC 0.1 infected


title: MC-LR at 1000 μg/L [ES81]


title: MEF KO CTRL (B3) rep2

source_name: MEF KO CTRL (B3) rep2


title: G021_Gale105_I_1e-1_M_72_3

description: iPSC-WTC 0.1 mock


title: MEF KO CTRL (C3) rep3

source_name: MEF KO CTRL (C3) rep3


title: MC-LR at 1000 μg/L [ES80]


title: Oct4_ATAC-seq

value: mESC medium

value: infected with virus expressing Oct4


title: G022_Gale105_I_1e-1_I_72_1

description: iPSC-WTC 0.1 infected


title: G020_Gale105_I_1e-1_M_72_2

description: iPSC-WTC 0.1 mock

value: mock


title: MEF KO CTRL (A3) rep1

source_name: MEF KO CTRL (A3) rep1


title: Klf4_ATAC-seq

value: infected with virus expressing Klf4


title: G019_Gale105_I_1e-1_M_72_1

description: iPSC-WTC 0.1 mock

source_name: iPSC differentiated male cardiomyocytes, subtype WTC

value: 72 hours


title: MEF WT Heat Shock (C2) rep3

source_name: MEF WT Heat Shock (C2) rep3

value: wild type


title: MC-LR at 1000 μg/L [ES133]


title: Sox2_ATAC-seq

value: infected with virus expressing Sox2


title: Oct4-L80A_ATAC-seq

value: infected with virus expressing Oct4 L80A mutant


title: G018_Gale105_E_1e-1_I_72_3

description: ESC-H7 0.1 infected

source_name: ESC differentiated female cardiomyocytes, subtype H7

value: Undifferentiated RUES2 hESCs (RUESe002-A; WiCell)


title: SKO_ATAC-seq

value: infected with virus expressing Sox2, Klf4 and Oct4


title: MC-LR at 1000 μg/L [ES78]

value: LR1000 exposure group

value: HepaRG


title: MEF WT Heat Shock (B2) rep2

source_name: MEF WT Heat Shock (B2) rep2

value: Mouse embryonic fibroblasts


title: Flag_ATAC-seq

value: mouse embryonic fibroblast

value: infected with virus expressing Flag control


title: MEF WT Heat Shock (A2) rep1

source_name: MEF WT Heat Shock (A2) rep1


title: G017_Gale105_E_1e-1_I_72_2

description: ESC-H7 0.1 infected


title: MC-LR at 1000 μg/L [ES22]

value: 1000 microg/L MC-LR

value: 2 hours


title: MC-LR at 1000 μg/L [ES23]


title: MEF WT CTRL (B1) rep2

source_name: MEF WT CTRL (B1) rep2


title: MEF WT CTRL (C1) rep3

source_name: MEF WT CTRL (C1) rep3


title: G016_Gale105_E_1e-1_I_72_1

description: ESC-H7 0.1 infected


title: G014_Gale105_E_1e-1_M_72_2

description: ESC-H7 0.1 mock


title: G015_Gale105_E_1e-1_M_72_3

description: ESC-H7 0.1 mock


title: MC-LR at 1000 μg/L [ES21]


title: G013_Gale105_E_1e-1_M_72_1

description: ESC-H7 0.1 mock


title: MC-LR at 1000 μg/L [ES20]


title: mPylorus WT rep3

city: Vienna

first: Georg

last: Busslinger

address: Lazarettgasse 14

country: Austria

institute: Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
Library was demultiplexed and reads were mapped to transcriptome reference fastq file.
Dupicated reads were then eliminated based on unique molecule identifiers (UMI)
There counts were then used for further data analyses.
Genome_build: mm9
Supplementary_files_format_and_content: UMI normalized read counts

source_name: gastric Pylorus region

growth_protocol: not applicable

extract_protocol:
Freshly isolated gastric epithelium was isolated according to Bartfeld et al. 2015. In short, gastric human biopsies or mouse tissue regions were cut into pieces and incubated rotating in chelating solution at 4 °C for 30 min. Thereafter, gastric glands were squeezed out of the tissue pieces by applying pressure on a glass slide, which was placed on top, and collected for single cell digestion for 5 min in TrypLE solution. The resulting single cell suspension was then used for FACS. Living single cells (DAPI negative) were sorted in 384 well plates.
The RNA of single cells was processed according the CEL-seq2 protocol (Muraro et al., 2016). In short, total RNA of single cells was reverse transcribed into cDNA in the 384 well plate, thereafter pooled and in vitro transcribed by T7 polymerase overnight. After fragmentation of the amplified RNA, it was once more reverse transcribed before library preparation for next generation sequencing was performed. The quality of the fragmented RNA and cDNA library was check by PICO RNA or DNA hypersensitivity chip (Agilent), respectively. The samples were then paired-end sequenced on NextSeq500 (2x 75bp) by the Utrecht Sequencing Facilities (www.useq.nl).

treatment_protocol: not applicable

tag: tissue

value: gastric Pylorus region

tag: method

value: SORT-seq


title: MC-LR at 1000 μg/L [ES79]


title: MC-LR at 1000 μg/L [ES19]


title: G012_Gale105_I_1e-1_I_48_3

description: iPSC-WTC 0.1 infected

tag: time

value: 48 hours

tag: treatment

value: WTC11c hiPSCs


title: MC-LR at 1000 μg/L [ES18]

tag: group

tag: agent


title: mPylorus WT rep1


title: MC-LR at 1000 μg/L [ES77]

tag: time point


title: mPylorus WT rep2


title: mCorpus WT rep4

source_name: gastric Corpus region

value: gastric Corpus region


title: MEF WT CTRL (A1) rep1

source_name: MEF WT CTRL (A1) rep1

tag: genotype

value: wild type


title: mCorpus WT rep3


title: G010_Gale105_I_1e-1_I_48_1

description: iPSC-WTC 0.1 infected


title: G008_Gale105_I_1e-1_M_48_2

description: iPSC-WTC 0.1 mock

value: mock


title: G011_Gale105_I_1e-1_I_48_2

description: iPSC-WTC 0.1 infected


title: G009_Gale105_I_1e-1_M_48_3

description: iPSC-WTC 0.1 mock


title: MC-LR at 100 μg/L [ES131]

value: LR100 exposure group

value: 100 microg/L MC-LR


title: MC-LR at 100 μg/L [ES132]


title: MC-LR at 100 μg/L [ES129]


title: MC-LR at 100 μg/L [ES130]


title: MC-LR at 100 μg/L [ES128]


title: mCorpus WT rep2


title: G006_Gale105_E_1e-1_I_48_3

description: ESC-H7 0.1 infected

value: Undifferentiated RUES2 hESCs (RUESe002-A; WiCell)


title: mCorpus WT rep1


title: Granulocytes_PrePMF_35

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

institute: Centre for Regenerative Medicine

description: Gene expression of granulocytes from PrePMF peripheral blood

hyb_protocol: Microarray hybridization and staining was performed by means of GeneAtlas™ Hybridization, Wash, and Stain Kit (Affymetrix) using the GeneAtlas System (Affymetrix) following the manufacturer’s recommendations.

scan_protocol: Microarray scanning was performed by means of GeneAtlas™ Hybridization, Wash, and Stain Kit (Affymetrix) using the GeneAtlas System (Affymetrix) following the manufacturer’s recommendations.

data_processing: Partek® Genomics Suite® software, version 7.0 (Partek Inc., St. Louis, MO, USA) was used to normalize the probe level data and convert them into expression values by means of robust multiarray average (RMA). An exploratory principal component analysis (PCA) was performed and existing batch effect was removed by means of the specific tool implemented in Partek® GS®.

label: biotin

source_name: Granulocytes from PrePMF peripheral blood

label_protocol: Biotin-labeled complementary RNA was synthesized starting from 100 ng total RNA by means of GeneChip™ HT 3' IVT PLUS Reagent Kit (Applied Biosystems) according to the standard protocol supplied.

extract_protocol: Total cellular RNA was isolated from stored frozen granulocyte pellets by means of TrizolTM Reagent (InvitrogenTM, ThermoFisher Scientific) following manufacturer’s instructions. RNA sample concentration was evaluated using NanoDrop ND-1000 spectrophotometer (ThermoFisher Scientific) and purity was assessed by means of 260/280 nm and 260/230 ratios. Agilent 2100 Bioanalyzer (Agilent Technologies) was used to determine the integrity of total RNA.

tag: disease

value: Pre-PMF

tag: driver mutation


title: Granulocytes_PrePMF_34


title: Granulocytes_PrePMF_33


title: Rif1-DP3

city: Basel

first: Ilya

middle: M.

last: Flyamer

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research

description:
DP_F8
Rif1-DP.mm10.mapq_30.1000.mcool

data_processing:
FASTQ files were processed with the distiller pipeline (https://github.com/mirnylab/distiller-nf, DOI:10.5281/zenodo.2630563) to obtain .mcool files used in downstream analyses.
Briefly, reads were mapped to the mm19 genome assembly, Hi-C valid pairs were identified using pairtools, and they were used for construction of .cool files a1000 bp resolution.They were then zoomified to obtain .mcool failes with multiple resolutions, and each resolution was balanced.
Genome_build: mm10
Supplementary_files_format_and_content: .mcool files with binned Hi-C data (https://cooler.readthedocs.io/en/latest/)

source_name: mESCs

growth_protocol: Mouse embryonic stem cell (ESC) cells were derived as described in (Foti, Gnan et al. 2016), with the addition of 1 μM MEK inhibitor PD0325901 and 3 μM GSK3 inhibitor CHIR99021 (MRC PPU Reagents and Services, School of Life Sciences, The University of Dundee) in the culture media, from the start of the protocol.  ESCs were grown at 37°C in 7.5 % CO2 in Knockout DMEM (Gibco 10829-018), containing 12.5% heat-inactivated fetal bovine serum (Pan-Biotech), 1 % non-essential amino acids (Gibco 11140-035), 1% Penicillin/Streptomycin (Gibco 15070063), 0.1 mM 2-Mercaptoethanol (Gibco 31350-010), 1% L-Glutamine (Gibco 25030024)), supplemented with 1 μM PD0325901 and 3 μM CHIR99021 and 20 ng/ml leukemia inhibitory factor (LIF, EMBL Protein Expression and Purification core facility).

extract_protocol:
After four days of OHT treatment, cells were collected and counted. Cells were washed twice in cold DPBS and resuspended in full media. Samples were crosslinked for 10 minutes rotating at room temperature in 1% formaldehyde (106 cells/ml). Crosslinking was stopped by adding glycine at the final concentration of 0.2 M for 5 minutes at RT. Samples were washed twice in cold DPBS and pellets were snap frozen. 2-5 × 106 cells per sample were lysed in 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% IGEPAL (Sigma, I3021) supplemented with protease inhibitor (Thermo Scientific, 78430) for 15 minutes on ice. Nuclei were washed twice in cold lysis buffer, resuspended in 50 μl of NEBuffer 3.1 (NEB, B7003S) supplemented with 0.3% SDS and incubated at 62°C for 10 minutes. After diluting and quenching the SDS by adding 57.5 μl of NEBuffer 3 and 12.5 μl of 20% Triton X-100 (Sigma, 93443), samples were incubated at 37°C for 60 minutes. Nuclei were spun and incubated in 250 μl of 1× DpnII buffer with 600 U of DpnII restriction enzyme (NEB, R0543L) overnight at 37°C. An additional 200 U of DpnII were added to each sample the following day and incubated for a further 2 hours.  After heat inactivation of DpnII for 20 min at 65°C, restriction fragments ends were filled by DNA polymerase I, Large (Klenow) Fragment (NEB, M0210), 0.8 U/μl of DNA, in 50 μl of 0.3 mM biotin-14-dATP (Thermo Fisher, 19524016), 0.3 mM dCTP/ dGTP/ dTTP for 1.5 hours at 37°C.  900 μl of ligation master mix were then add to the samples: 1.33x NEB T4 DNA ligase buffer (NEB, B0202), 1.1% Triton X-100, 1.33 mg of Bovine Serum Albumin and 2000 U of T4 DNA Ligase (NEB, M0202). Samples were incubated for 4 hours rotating. Nuclei were spun and resuspended in water and digested with proteinase K (Sigma, P6556) 1.2 mg/ml and 0.8% SDS at 55°C for 30 minutes. 130 μl of 5 M NaCl were added and samples were incubated at 65°C overnight.
After ethanol precipitation, DNA was resuspended in 500 μl of 10 mM Tris-HCl pH8.0 and washed trice using the same buffer using Amicon filters (Millipore, UFC503096). Samples were diluted in 50 mM Tris pH 8.0, 0.1% SDS, 10 mM EDTA and sonicated to about 500 bp using a probe-based sonicator. Washes were then repeated as in the previous step. Biotinylated DNA was pulled down using 30 ul of 10 mg/ml Dynabeads MyOne Streptavidin T1 beads (Life technologies, 65602) in 10 mM Tris-HCl (pH 7.5); 1 mM EDTA; 2 M NaCl for 15 minutes at room temperature rotating. Beads were washed in TWB: 5 mM Tris-HCl (pH 7.5); 0.5 mM EDTA; 1 M NaCl; 0.05% Tween 20 for 2 minutes at 55° C twice, resuspended in 20 ul 1× NEB T4 DNA ligase buffer, transferred to a new tube and incubated for 30 minutes at room temperature with 100 μl of: 1x NEB T4 DNA ligase buffer, 0.5 mM dNTPs, 50 U T4 PNK (NEB, M0201), 12 U T4 DNA polymerase I (NEB, M0203), 5 U DNA polymerase I, Large (Klenow) Fragment. After two washes in TWB at 55°C for 2 minutes, beads were transferred to 1× NEBuffer 2 (NEB, B7002S) and moved to a new tube. Beads were then incubated at 37°C for 30 minutes in 100 ul of 0.9X NEBuffer 2, 0.5 mM dATP and 25 U Klenow exo minus (NEB, M0212). Beads were washed again as before and transferred to T4 ligation buffer. DNA was ligated for 2.5 hours with Illumina adaptors in 50 μl of the following reaction mix: 1X T4 ligation buffer, 1.2 µM Illumina adaptors, 1U T4 DNA ligase. Beads were washed once again with TWB as before, to be then resuspended and stored in 50 μl of 10 mM Tris-HCl (pH8.0).  Libraries were amplified in six parallel 50 µl PCR reactions using Illumina primers and 4 μl of beads (or DNA removed off the beads by heating at 95°C for 20 min) per reaction after testing optimal amplification cycles. Size selection was performed on an agarose gel, isolating fragments between 300-700 base pairs, followed by purification with QIAquick Gel Extraction Kit (Qiagen 28704).
Each library was test sequenced at low depth to test its quality, and then selected libraries were sequenced on the equivalent of approximately one mid-output lane of Illumina NextSeq 500/550 (75 bp  paired end reads). All data were used in the final analyses.

treatment_protocol: Experiments were carried out each time from a frozen vial of cells, at least two passages after thawing. 5.2x10e6 cells for Rif1-WT and 6.5x10e6 Rif1-KO lines, per 15 cm plate (or the equivalent for different sized plates) were plated at day zero, when treatment with 200 nM 4-hydroxytamoxifen (OHT, Sigma H7904) started. Fresh medium with OHT was added after 48 hours. Cells were collected about 96 hours after starting OHT treatment.

value: ESCs

tag: molecule subtype

value: Proximity ligated genomic DNA


title: Granulocytes_PMF_35

description: Gene expression of granulocytes from PMF peripheral blood

source_name: Granulocytes from PMF peripheral blood

value: Overt-PMF

value: TN


title: MC-LR at 100 μg/L [ES127]

source_name: The human hepatocyte cell line HepaRG

value: HepaRG


title: G005_Gale105_E_1e-1_I_48_2

description: ESC-H7 0.1 infected

tag: replicate


title: Rif1-DP2

description:
DP_14H2
Rif1-DP.mm10.mapq_30.1000.mcool


title: G007_Gale105_I_1e-1_M_48_1

description: iPSC-WTC 0.1 mock


title: Granulocytes_PrePMF_32


title: Granulocytes_PMF_34

value: MPL


title: G004_Gale105_E_1e-1_I_48_1

description: ESC-H7 0.1 infected


title: Rif1-DP1

description:
DP_14H1
Rif1-DP.mm10.mapq_30.1000.mcool


title: Granulocytes_PMF_37


title: G003_Gale105_E_1e-1_M_48_3

description: ESC-H7 0.1 mock


title: Granulocytes_PMF_36


title: MC-LR at 100 μg/L [ES75]

value: 2 hours


title: Rif1-tgWT3

description:
tgWT_G10
Rif1-tgWT.mm10.mapq_30.1000.mcool


title: MC-LR at 100 μg/L [ES74]


title: Granulocytes_PrePMF_30


title: Granulocytes_PMF_33


title: G002_Gale105_E_1e-1_M_48_2

description: ESC-H7 0.1 mock


title: Granulocytes_PrePMF_31


title: MC-LR at 100 μg/L [ES73]


title: MC-LR at 100 μg/L [ES76]


title: G001_Gale105_E_1e-1_M_48_1

description: ESC-H7 0.1 mock


title: ChIP-seq: GSC11 NS H3K27me3

city: Clermont-Ferrand

first: franck

last: court

address: 28 Place Henri Dunant

country: France

institute: GReD CNRS

data_processing:
ChIP-seq R1 reads were mapped to the human genome (hg19) using Bowtie2 (v 2.3.4.3).
Alignments were filtered according to their quality (Mapq>30) using SamTools (v 1.9) .
ChIP-seq signals coverage were generated with Bamcoverage (v 3.1.3)  (options: normalizeUsing RPKM, extendReads 200, ignoreDuplicates, binSize 20)
Peak detection was carried out with MACS (v 1.4.2)  using Input as a control (options: nomodel shiftsize 73, for H3K27ac and H3K4me3 pvalue= 1e-5 , for H3K27me3 pvalue= 1e-3).
Genome_build: hg19
Supplementary_files_format_and_content: coverage signal; bigwig

source_name: glioblastoma stem cell

growth_protocol: Glioblastoma stem cells were cultured in Neurobasal Medium supplemented with B27 1%; N2 0.5%; bFGF 0.05% and EGF 0.005% at 37°C in 5% CO2 humidified incubator. Culture medium was replaced twice a week and when spheres became large and numerous, they were enzymatically dissociated with accutase. Glioblastoma stem cell cultures were characterized by assessing self renewal, differentiation and tumorigenic ability as well as their expression of stemness markers (CD133, SOX2). Finally, all cultures were also classified according to Verhaak's classification of glioblastomas using the method of classification to nearest centroids (ClaNC) with a 840 gene signature.

extract_protocol:
ChIP-seq were performed on native chromatin isolated from frozen GSC pellets
Library preparation and sequencing on NovaSeq 6000 (Illumina) were performed by IntegraGen SA, according to the manufacturer’s recommendations

treatment_protocol: SMART vector non targeting PGK-TurboGFP (VSC11713) was purchased from GE Healthcare (Little Chalfont, UK). Viral particles were produced and concentrated by the Vectorology platform of Montpellier (Biocampus, Montpellier, France). GSCs were infected using a multiplicity of infection of 10 and processed 120 h later for ChIP-seq analysis

tag: glioblastoma stem cell culture

value: Glioblastoma stem cells

tag: chip antibody

value: H3K27me3 (Millipore 07-449)

value: non targeting shRNA


title: Granulocytes_PMF_32


title: Granulocytes_PMF_31


title: Rif1-WT1

description:
WT_B
Rif1-WT.mm10.mapq_30.1000.mcool


title: Rif1-het


title: MC-LR at 100 μg/L [ES71]

tag: cell line


title: ChIP-seq: GSC11 NS H3K4me3

tag: cell type

value: H3K4me3 (Diagenode 03-050)


title: Granulocytes_PrePMF_29


title: ChIP-seq: GSC11 NS H3K27c

value: H3K27ac (Abcam Ab4729)


title: Rif1-tgWT2

description:
tgWT_14H4
Rif1-tgWT.mm10.mapq_30.1000.mcool


title: WT

city: Palo Alto

first: Christoph

last: Thaiss

state: CA

address: 3181 Porter Dr.

department: Immunology and Pathology

institute: Arc Institute

data_processing:
Cell Ranger 2.1.1 pipeline used for data processing
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: Endothelial Cells

extract_protocol:
Tumor were harvested from 4 individual mice and pulled together to digest and process for signle cell suspension with a cocktail of Collagenase-II, Dispase-II, and Deoxyribonuclease 1. Samples were stained with PE-Cy7 CD31 and APC CD45 antibodies. CD45-CD31+ endothelial cells were FACS sorted using BD FACSAria II.
Single-cell RNA-seq libraries were prepared using version 1 Chromium Single-cell 3′ Library, Gel Bead & Mutiplex Kit (10X Genomics).
single-cell RNA-seq

tag: strain

value: Tumor

value: WT


title: MC-LR at 100 μg/L [ES17]

value: LR100 exposure group

value: 100 microg/L MC-LR


title: MC-LR at 100 μg/L [ES16]


title: ChIP-seq: GSC11 NS Input


title: Granulocytes_PrePMF_27

value: Pre-PMF

value: CALR Type 2


title: Granulocytes_PrePMF_28


title: MC-LR at 100 μg/L [ES72]


title: ChIP-seq: GSC6  NS H3K27me3


title: Rif1-tgWT1

description:
tgWT_14A7
Rif1-tgWT.mm10.mapq_30.1000.mcool

value: ESCs

value: Proximity ligated genomic DNA


title: Granulocytes_PMF_30

value: Overt-PMF


title: MC-LR at 100 μg/L [ES15]

value: HepaRG


title: ChIP-seq: GSC6  NS H3K4me3


title: Granulocytes_PrePMF_26


title: ChIP-seq: GSC6  NS H3K27ac


title: MC-LR at 100 μg/L [ES13]


title: Granulocytes_PrePMF_25


title: Granulocytes_PrePMF_24


title: MC-LR at 100 μg/L [ES12]


title: ChIP-seq: GSC6  NS Input


title: KR_UM171_72h_3

data_processing:
Basecalls performed using Illumina RTA.
Samples demultiplexed using bcl2fastq 2.20.
Sequenced reads were trimmed for sequencing adapters and low quality extrimities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on annotations from Gencode version 32, based on Ensembl version 92.
Expression values were also computed using RSEM version 1.2.28 based on Gencode version 32 transcript annotations
Reported expression values take into account a reverse strand orientation.
Genome_build: GRCh38
Supplementary_files_format_and_content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary_files_format_and_content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column)

growth_protocol: AML1 cell lines with sgRNA or shRNA of interest were cultured in DMEM/10% FBS and exposed to UM171, UM134, TCP1 (LSD1 inhibitor) or DMSO for 0, 24, 48 or 72h as indicated.

extract_protocol:
Trizol extraction + QIAGEN RNAeasy Clean-up
NEB mRNA stranded library preparation

treatment_protocol: UM171 and UM134  were used at 500nM, TCP1 was used at 10uM

tag: guide rna

value: sgKBTBD4 tagged with tRFP647

tag: knockdown

value: shRCOR1 tagged with GFP


title: MC-LR at 100 μg/L [ES14]

value: 2 hours


title: Granulocytes_PPV_16

description: Gene expression of granulocytes from PPV peripheral blood

source_name: Granulocytes from PPV peripheral blood

value: PPV


title: MC-LR at 100 μg/L [ES11]


title: Granulocytes_PET_26

description: Gene expression of granulocytes from PET peripheral blood

source_name: Granulocytes from PET peripheral blood

value: PET

value: TN


title: Granulocytes_PET_25


title: MC-LR at 100 μg/L [ES9]


title: KR_UM171_72h_2

tag: time


title: MC-LR at 100 μg/L [ES8]


title: Granulocytes_PET_24


title: KR_UM171_72h_1

tag: treatment


title: mBL_9_hybridized to 250K_Nsp

type: genomic

city: Omaha

first: Javeed

last: Iqbal

state: NE

address: 601 S 42nd St

institute: UNMC

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing: Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Affymetrix Genotyping console software. Log2 intensities were generated from genotyping console were exported for further processing using the DNAcopy package for R. For gene expression data profiled by Affymetrix U133 plus 2.0 array, the raw signal intensities were imported into BRB-ArrayTools (v 4.5.0)  and normalized by MAS 5.0 with default settings.

source_name: tumor biopsy

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA and total RNA was extracted from cryopreserved lymphoma tissue using the Qiagen AllPrep DNA/RNA kit. DNA and RNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

tag: tumor type

value: lymphoma

tag: age group

value: Adult


title: KR_UM171_48h_3


title: MC-LR at 10 μg/L [ES126]

tag: group

value: LR10 exposure group

tag: agent

value: 10 microg/L MC-LR

tag: time point


title: MC-LR at 100 μg/L [ES10]

value: LR100 exposure group

value: 100 microg/L MC-LR


title: KR_UM171_48h_2


title: MC-LR at 10 μg/L [ES125]


title: Granulocytes_PrePMF_23

tag: disease

value: Pre-PMF

tag: driver mutation


title: KR_UM171_48h_1


title: Granulocytes_PET_23


title: Granulocytes_PMF_29


title: mBL_69_hybridized to 250K_Nsp

value: Pediatric


title: mBL_67_hybridized to 250K_Nsp


title: mBL_66_hybridized to 250K_Nsp


title: Granulocytes_PrePMF_22

value: CALR Type 2


title: MC-LR at 10 μg/L [ES124]


title: Granulocytes_PET_22


title: KR_UM171_24h_3


title: KR_UM171_24h_2


title: MC-LR at 10 μg/L [ES123]


title: MC-LR at 10 μg/L [ES122]


title: mBL_64_hybridized to 250K_Nsp


title: Granulocytes_PPV_15

value: JAK2 ex12


title: KR_UM171_24h_1


title: mBL_62_hybridized to 250K_Nsp


title: KR_DMSO_3

value: DMSO


title: KR_DMSO_2

value: sgKBTBD4 tagged with tRFP647


title: MC-LR at 10 μg/L [ES70]

value: HepaRG


title: MC-LR at 10 μg/L [ES121]

value: 2 hours


title: MC-LR at 10 μg/L [ES69]


title: KR_DMSO_1

value: shRCOR1 tagged with GFP


title: mBL_61_hybridized to 250K_Nsp


title: mBL_63_hybridized to 250K_Nsp


title: KL_TCP_24h_3

value: shLuciferase tagged with GFP

value: TCP


title: Granulocytes_PrePMF_20

value: TN


title: Granulocytes_PET_21

value: PET


title: MC-LR at 10 μg/L [ES67]

value: LR10 exposure group


title: Granulocytes_PrePMF_18


title: KL_TCP_24h_2


title: Granulocytes_PrePMF_21


title: mBL_58_hybridized to 250K_Nsp

value: lymphoma

value: Adult


title: Granulocytes_PMF_28

value: Overt-PMF


title: Granulocytes_PrePMF_19

value: Pre-PMF


title: mBL_60_hybridized to 250K_Nsp


title: mBL_56_hybridized to 250K_Nsp

value: Pediatric


title: MC-LR at 10 μg/L [ES68]

value: 10 microg/L MC-LR


title: MC-LR at 10 μg/L [ES65]


title: KL_TCP_24h_1


title: Granulocytes_PET_20

value: CALR Type 1


title: MC-LR at 10 μg/L [ES66]


title: MC-LR at 10 μg/L [ES7]


title: mBL_57_hybridized to 250K_Nsp


title: mBL_54_hybridized to 250K_Nsp


title: KL_UM171_72h_2


title: MC-LR at 10 μg/L [ES6]


title: KL_UM171_72h_1


title: MC-LR at 10 μg/L [ES5]


title: mBL_53_hybridized to 250K_Nsp


title: KL_UM171_48h_3


title: Granulocytes_PrePMF_17


title: MC-LR at 10 μg/L [ES4]


title: mBL_52_hybridized to 250K_Nsp


title: KL_UM171_48h_2


title: mBL_50_hybridized to 250K_Nsp


title: mBL_55_hybridized to 250K_Nsp


title: MC-LR at 10 μg/L [ES3]


title: Granulocytes_PET_18


title: mBL_51_hybridized to 250K_Nsp


title: Granulocytes_PET_19


title: mBL_5_hybridized to 250K_Nsp


title: KL_UM171_48h_1


title: MC-LR at 10 μg/L [ES2]


title: KL_UM171_72h_3


title: KL_UM171_24h_3


title: Granulocytes_PET_17


title: MC-LR at 10 μg/L [ES1]


title: Granulocytes_PrePMF_16


title: mBL_49_hybridized to 250K_Nsp


title: KL_UM171_24h_2


title: mBL_48_hybridized to 250K_Nsp


title: mBL_44_hybridized to 250K_Nsp


title: Granulocytes_PPV_13

value: PPV


title: Granulocytes_PMF_27


title: Granulocytes_PMF_26


title: mBL_43_hybridized to 250K_Nsp


title: Granulocytes_PPV_14


title: KL_UM171_24h_1

value: sgKBTBD4 tagged with tRFP647


title: KL_DMSO_3

value: DMSO


title: solvent control group [ES154]

value: Negative control

value: HepaRG

value: solvent control

value: 2 hours


title: Granulocytes_PMF_25


title: solvent control group [ES156]


title: solvent control group [ES155]


title: mBL_42_hybridized to 250K_Nsp


title: mBL_41_hybridized to 250K_Nsp


title: mBL_40_hybridized to 250K_Nsp


title: KL_DMSO_2

value: shLuciferase tagged with GFP


title: solvent control group [ES153]


title: KL_DMSO_1


title: solvent control group [ES152]


title: AR_UM171_72h_3

value: sgAAVS1 tagged with tRFP647

value: shRCOR1 tagged with GFP


title: Granulocytes_PMF_24


title: mBL_38_hybridized to 250K_Nsp

value: lymphoma


title: Granulocytes_PMF_23


title: mBL_39_hybridized to 250K_Nsp

value: Adult


title: solvent control group [ES151]


title: AR_UM171_72h_2


title: AR_UM171_72h_1


title: solvent control group [ES111]


title: AR_UM171_48h_3


title: solvent control group [ES110]


title: solvent control group [ES112]


title: solvent control group [ES109]


title: AR_UM171_48h_1


title: mBL_37_hybridized to 250K_Nsp


title: solvent control group [ES108]


title: AR_UM171_24h_3


title: Granulocytes_PPV_11


title: Granulocytes_PMF_22

value: Overt-PMF


title: AR_UM171_48h_2


title: mBL_35_hybridized to 250K_Nsp


title: solvent control group [ES106]


title: mBL_36_hybridized to 250K_Nsp


title: Granulocytes_PMF_20

value: TN


title: AR_UM171_24h_1


title: Granulocytes_PMF_21


title: Granulocytes_PPV_10


title: solvent control group [ES107]


title: Granulocytes_PET_15

value: PET


title: mBL_28_hybridized to 250K_Nsp

value: Pediatric


title: AR_DMSO_3


title: mBL_34_hybridized to 250K_Nsp


title: Granulocytes_PET_16

value: CALR Type 1


title: Granulocytes_PPV_9

value: PPV


title: solvent control group [ES104]


title: mBL_31_hybridized to 250K_Nsp


title: Granulocytes_PET_14


title: AR_DMSO_2


title: mBL_27_hybridized to 250K_Nsp


title: solvent control group [ES103]


title: solvent control group [ES105]


title: mBL_33_hybridized to 250K_Nsp


title: Granulocytes_PMF_19


title: mBL_24_hybridized to 250K_Nsp


title: Granulocytes_PPV_8


title: AR_DMSO_1


title: AR_UM171_24h_2


title: solvent control group [ES101]


title: AL_TCP_24h_2

value: TCP


title: solvent control group [ES102]


title: AL_TCP_24h_3


title: solvent control group [ES64]


title: AL_TCP_24h_1


title: Granulocytes_PMF_17


title: mBL_26_hybridized to 250K_Nsp


title: mBL_25_hybridized to 250K_Nsp


title: mBL_23_hybridized to 250K_Nsp


title: Granulocytes_PMF_15


title: Granulocytes_PMF_18


title: Granulocytes_PMF_16


title: solvent control group [ES63]


title: AL_UM171_72h_3


title: solvent control group [ES62]


title: mBL_20_hybridized to 250K_Nsp


title: mBL_22_hybridized to 250K_Nsp


title: solvent control group [ES61]


title: AL_UM171_72h_2


title: Granulocytes_PrePMF_15

value: Pre-PMF


title: solvent control group [ES60]

value: Negative control


title: AL_UM171_72h_1


title: Granulocytes_PMF_14


title: AL_UM171_48h_3


title: mBL_2_hybridized to 250K_Nsp


title: mBL_19_hybridized to 250K_Nsp


title: solvent control group [ES59]

value: HepaRG


title: AL_UM171_48h_2


title: Granulocytes_PPV_12


title: OE

city: Tianjin

first: Xiaosu

address: 94 Weijin Road

institute: Nankai University

description: A549 cells - DCBLD2

data_processing:
mRNA sequencing by Illumina HiSeq: Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen)/RNeasy Mini Kit (Qiagen)/other kits. Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel. 1 μg total RNA with RIN value above 6.5 was used for following library preparation. Next generation sequencing library preparations were constructed according to the manufacturer’s protocol. The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and 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 by beads 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 beads, and fragments of ~420 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 13 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 beads, validated using an Qsep100 (Bioptic，Taiwan， China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).
Then libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA). Sequencing was carried out using a 2x150bp paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
The sequences were processed and analyzed by GENEWIZ.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw count and FPKM values

source_name: Human lung adenocarcinoma

extract_protocol:
Cells RNA was harvested using MagZol TM Reagent (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 NEBNext® Poly(A) mRNA Magnetic Isolation Module

value: Human lung adenocarcinoma cells

tag: condition

value: DCBLD2 overexpression


title: AL_UM171_48h_1

value: shLuciferase tagged with GFP


title: Vec

description: A549 cells - vector

value: vector


title: solvent control group [ES57]

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.19.1
read quality was checked for each sample using FastQC
raw reads were mapped to the transcript sequences of the human reference genome from NCBI using BWA default single-end read mapping protocol
Read count data were normalized and filtered out batch effects
Genome_build: GRCh38
Supplementary_files_format_and_content: Normalized and batch-adjusted read count in the tab-delimited text format

extract_protocol:
Cells were thawed in Qiazol lysis buffer (Qiagen, Hilden, DE) further homogenized (Bullet Blender Storm 24 mixer mill, Next Advance, Averill Park, NY) using the manufacturer’s recommended settings.  Approximately 250 µl of chloroform:isoamyl alcohol (24:1; Sigma-Aldrich Chemical Co., St. Louis, MO) was added to each tube, mixed by inversion, and vortexed and incubated at room temperature for 3 min and transferred to a 1.5 ml Heavy Phase Lock Gel microfuge tube (5Prime, Inc., Gaithersburg, MD), incubated on ice (10 min) and centrifuged at 14,200 g (5 min, room temperature (RT)). The supernatant was transferred to a microcentrifuge tube (Eppendorf North America, Hauppauge, NY) and mixed with an equal volume of 70% ethanol and put on a RNeasy® MinElute Clean Up kit 2.0 ml column (Qiagen) and processed according to the manufacturer’s protocol with DNase treatment (RNase-free DNase kit, Qiagen) prior to final cleanup and elution. RNA was quantified and quality was confirmed using an Agilent RNA 6000 Nano kit with a 2100 Bioanalyzer (Agilent Technologies, Inc., Wilmington, DE). Typical RIN scores were above 9.  RNA eluates were stored at -80 °C
Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep for NeoPrep kit (Illumina), following the manufacturer’s protocol. An input of 100 ng total RNA was used for each sample. Additional resuspension buffer was added to each library to obtain a final total volume of about 24 µL. The concentration of each library was determined using either the KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems) or the Qubit dsDNA HS Assay kit (Thermo Fisher Scientific).  Libraries were normalized to 10 nM and combined into pools of 8-16 samples. Dilutions of libraries for quantitation and pooling was done using 10 mM Tris-HCl, pH 8.5.

value: solvent control

value: 2 hours


title: AL_UM171_24h_3

value: sgAAVS1 tagged with tRFP647


title: shD5

description: A549 cells - shDCBLD2


title: mBL_17_hybridized to 250K_Nsp

value: lymphoma

value: Adult


title: solvent control group [ES56]


title: Granulocytes_PrePMF_14


title: Granulocytes_PET_13

value: PET


title: Granulocytes_PrePMF_13


title: AL_UM171_24h_2


title: solvent control group [ES58]


title: AL_UM171_24h_1


title: solvent control group [ES55]


title: solvent control group [ES54]


title: miR-20b 2

city: Eonyang-eup, Ulju-gun

first: Sounkou

last: Kim

state: Ulsan

department: Department of Biological Science

country: South Korea

institute: Ulsan National Institute of Science and Technology

data_processing:
Base calling was done by bcl2fastq2 Conversion Software v2.19
Sequenced reads were mapped to hg38 whole genome using HISAT version 2.1.0
Mapped sequences were assembled and merged using StringTie v2.1.1
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver HepG2 cells

growth_protocol: HepG2 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) containing 10 % fetal bovine serum (FBS) and 1 % penicillin/streptomycin at 37 °C under 5 % CO2 incubator.

extract_protocol:
Total mRNAs were isolated using TRIzol reagent purchased from Thermo Fisher Scientific. Reverse-transcription of the RNA (total RNA 1ug) was performed with ABI Reverse Transcription Kit
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: HepG2 cells were transfected with miR-20b or miRNA-negative control.

tag: transfection

value: hsa-miR-20b overexpression

tag: tissue

value: liver

value: Human hepatocellular carcinoma cells


title: AL_134_2

tag: cell line


title: solvent control group [ES53]

city: Durham

first: Weichun

institute: US EPA


title: mBL_12_hybridized to 250K_Nsp


title: miR-20b 1

tag: cell type


title: sc

description: A549 cells - scramble control

value: scramble control


title: solvent control group [ES52]


title: AL_134_1


title: control miRNA 3

value: Control miRNA


title: miR-20b 3


title: Granulocytes_PrePMF_8

value: Pre-PMF

value: MPL


title: Granulocytes_PrePMF_10

value: CALR Type 1


title: solvent control group [ES51]

value: Negative control

value: HepaRG


title: Granulocytes_PrePMF_11


title: mBL_15_hybridized to 250K_Nsp


title: AL_DMSO_3

value: shLuciferase tagged with GFP

value: DMSO


title: Granulocytes_PET_12

value: TN


title: Granulocytes_PrePMF_9


title: control miRNA 2


title: Granulocytes_PET_10


title: Granulocytes_PET_11


title: AL_134_3

value: sgAAVS1 tagged with tRFP647


title: solvent control group [ES50]

value: solvent control

value: 2 hours


title: mBL_16_hybridized to 250K_Nsp

value: lymphoma

value: Adult


title: AL_DMSO_2


title: control miRNA 1

value: liver


title: AL_DMSO_1


title: solvent control group [ES49]


title: mBL_29_hybridized to 250K_Nsp

value: Pediatric


title: scRNA-seq of MDA-MB-231, MCF7, T-47D, MDA-MB-452 and MEF cells

city: Shenzhen

first: Guipeng

last: Li

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology

data_processing:
Gene-cell matrices were determined using 10X Genomics Cellranger version 3.1.0 with default parameters (cellranger count).
Genome_build: concatenated hg38-mm10
Supplementary_files_format_and_content: h5 file produced by cellranger

organism:
Homo sapiens
Mus musculus

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium instrument. Reverse transcription was performed in droplet and library construction was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide
Library preparation was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide and using a custom CASB library preparation protocol.


title: solvent control group [ES48]

last: Huang

address: 109 TW Alexander Dr


title: mBL_13_hybridized to 250K_Nsp


title: Granulocytes_PET_9

value: PET


title: MAC_Obese

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Libraries were sequenced by Illumina NovaSeq Sequencing System.
fastq files were generated using Cellranger mkfastq (version 3.1.0). The raw reads were mapped to human reference genome (refdata-cellranger-mm10-3.0.0) using cellranger count.
Multiple samples were aggregated by cellranger aggr.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: human adipose cell

extract_protocol:
Cells were sorted by flow cytometry.
Library was generated by Chromium™ Single Cell 3’ Library Construction (10x Genomics).
scRNA-seq

value: adipose tissue

value: obese donor

value: Macrophage


title: solvent control group [ES47]


title: MAC_Lean

value: lean donor


title: Δnit-4 NaNO3 Biological Replicate 3

city: Ithaca

first: Lori

middle: B

last: Huberman

state: NY

address: 236 Tower Rd.

department: Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science

institute: Cornell University

data_processing:
Illumina Casava1.8 software used for base calling
Sequence reads were trimmed for adaptor sequence and aligned to the predicted transcripts from the N. crassa OR74A genome (v12) with HiSat2 v2.1.0 with the parameters --max-intronlen 5000 --dta-cufflinks
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using Cufflinks v2.2.1 with the parameters --library-type fr-unstranded -u -b -G --compatible-hits-norm --max-bundle-frags=10000000
FPKMs in the FPKM_Metafile.txt were generated by running all samples through cuffmerge v2.2.1; then cuffquant v2.2.1 with the parameters --library-type fr-unstranded --max-bundle-frags=10000000; then cuffnorm v2.2.1 with the parameters --library-type fr-unstranded.
Genome_build: Neurospora crassa OR74A genome v12
Supplementary_files_format_and_content: tab-deliminated text files include FPKM values for each sample

organism: Neurospora crassa

source_name: Neurospora crassa mycelia

growth_protocol: N. crassa conidia were inoculated into 3ml of Vogel's minimal media + 2% sucrose and incubated at 25C in constant light with constant shaking at 200rpm for 24h

extract_protocol:
Mycelia were filtered using Whatman paper #1 and flash frozen using liquid nitrogen. RNA was isolated by bead beating in Trizol reagent and then cleaned up using the Qiagen RNeasy kit.
RNA were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mycelia were washed in media lacking a carbon source (for mannose or carbon starvation) or media lacking a nitrogen source (for all others) and then transferred to 3ml of Vogel's minimal media with thie indicated carbon or nitrogen source and incubated at 25C in constant light with constant shaking at 200rpm for 4h prior to harvesting for RNAseq.

tag: genotype

tag: media

value: Vogel's minimal medium with 2% Sucrose and 50mM NaNO3


title: DC_Obese

value: Dendritic cell


title: CD200r_Positive_Obese

value: Innate lymphoid cell


title: Δnit-4 NaNO3 Biological Replicate 1


title: DC_Lean


title: Granulocytes_PMF_13

value: Overt-PMF

value: CALR Type 1


title: Epithelium_homeo_rep3

city: Cleveland

first: Thaddeus

last: Stappenbeck

state: OH

address: 9500 Euclid Ave

department: Inflammation and Immunity

institute: Lerner Research Institute

description: LCM-microarray analysis of the homeostatic villus epithelium

hyb_protocol: The balanced cDNAs were suspended in Agilent 2x gene expression buffer (55ul), Agilent 10x blocking agent (11ul), and Kreablock (6ul). The hybridization solutions were applied to Agilent Mouse v2 8x60K Microarrays (G4852B-074809). Hybridization was carried out at 65C for 20h. Washing procedures were conducted according to Agilent gene expression protocols.

scan_protocol: Slides were scanned on an Agilent C-class Microarray scanner to detect Cy5 fluorescence according to manufacturer's specifications. Gridding and analysis of images were performed using Feature Extraction v11.5.1.1 (Agilent Technologies).

data_processing: Raw data values (rProcessedSignal) were quantile-normalized and log2-transformed across all samples. Detectable genes were defined as those with values >5.0 in at least 50% of samples studied. Differentially expressed genes were deemed significant when fold-change >2.0 and p<0.01. Data processing was conducted using Partek Genomics Suite.

source_name: villus epithelium, homeostasis

label_protocol: RNA samples were amplified using the WTA2 kit (Sigma). Amplified cDNA products were purified with PCR purification columns (Qiagen), and quality was assessed with the Agilent 2100 Bioanalyzer. cDNAs were chemically labeled with the ULS cDNA labeling kit (Kreatech). Per reaction, 3ug of cDNA (+water=16ul) was mixed with Kreatech 10x labeling solution (2ul) and Cy5-ULS reagent (2ul). The reactions were incubated at 85C for 15min in the dark and placed on ice for 3min. Labeled cDNAs were purified with PCR purification columns (Qiagen) and quantitated on a Nanodrop spectrophotometer.

growth_protocol: 7-week-old C57BL/6J male mice obtained from the Jackson Laboratory were housed under specific-pathogen-free conditions unperturbed for at least one-week prior to experimental manipulations.

extract_protocol: Intestinal tissues were fixed in methacarn (60% methanol, 30% chloroform, 10% glacial acetic acid) for 4h at room temperature, washed in 70% ethanol, and processed for paraffin embedding. Paraffin blocks were sectioned at 7um on a microtome. Sections were de-paraffinized in xylene, rehydrated in a series of ethanol washes (70/95/100%), and briefly stained with methyl green (Vector Laboratories). Laser capture microdissection (LCM) was performed using CapSure Micro LCM Caps (Applied Biosystems) on the Arcuturus PixCell IIe system. RNA extraction was carried out with the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems).

treatment_protocol: Mice were given one intraperitoneal injection of 20mg/kg poly(I:C) HMW (InvivoGen) to induce villus atrophy in the proximal small intestine. An equivalent volume of saline (0.9% NaCl solution) was injected in control mice. Duodenal tissues were harvested 24h post-injection.

tag: strain

tag: gender

value: male

tag: age

value: 8 weeks

tag: region

value: duodenum

value: 24h after saline injection


title: Epithelium_homeo_rep2

tag: treatment


title: Granulocytes_PET_7

value: CALR


title: Epithelium_homeo_rep4


title: Granulocytes_PET_8

value: MPL


title: Δnit-4 NaNO3 Biological Replicate 2


title: CD200r_Positive_Lean

tag: group


title: Granulocytes_PMF_12

value: TN


title: Granulocytes_PPV_7

value: PPV


title: Δnit-2 50mM Tryptophan Biological Replicate 3

value: Vogel's minimal medium with 2% Sucrose and 50mM Tryptophan


title: Epithelium_atrophy_rep4

description: LCM-microarray analysis of the atrophic villus epithelium

source_name: villus epithelium, atrophy

value: 24h after poly(I:C) injection


title: CD200r_Negative_Obese

value: adipose tissue

value: obese donor

value: Natural killer cell


title: CD200r_Negative_Lean

value: lean donor


title: Granulocytes_PMF_10


title: Granulocytes_PET_6

value: PET


title: Epithelium_atrophy_rep3


title: Granulocytes_PET_5


title: Epithelium_atrophy_rep2


title: Δnit-2 50mM Proline Biological Replicate 3

value: Vogel's minimal medium with 2% Sucrose and 50mM Proline


title: post-chemoresistant stage, patient 2

city: Hefei

first: Wulin

last: Shan

state: Anhui

address: Huanhudong Road 107

institute: The First Affiliated Hospital of University of Science and Technology of China

description:
Sample 4
S04
P17092076512

data_processing:
The original image data was transformed into Sequenced Reads for Base Calling analysis using software BCL2FASTQ2 (V2.19.0)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using bowtie
The analysis method of miRNA expression abundance is to count according to the mapping position of read on the genome. It is necessary to verify whether the position of read is consistent with the mature sequence of known miRNA, and if the position is inconsistent, no statistics will be taken. Mirdeep2 software is used to analyze and process this part;S01(norm) : Counts per million reads after miRNA standardization in the S01 sample. The following header of the same format has the same meaning.
Genome_build: hg19
Supplementary_files_format_and_content: Abundance of miRNA expression of each sample

source_name: small cell lung cancer

extract_protocol:
plasma exosomes isolated from two small cell lung cancer patients. RNA from plasma exosomes was isolated using the Qiagen miRNeasy Serum Plasma Kit. The minimum requirement for detection of Agilent 2100 is 1μL 10 ng/μL sample
miRNAs libraries Starts from the RNA that has passed the quality inspection, the 3' -end adaptor is linked, the reverse primer is hybridized, the 5' -end adaptor is linked, the reverse transcription is made into DNA, and then PCR amplification is performed

tag: individual

value: patient 2

tag: disease state

value: small cell lung cancer

tag: Stage

value: post-chemoresistant stage

tag: sample type

value: plasma exosomes


title: Granulocytes_PMF_11

tag: disease

value: Overt-PMF

tag: driver mutation

value: CALR Type 1


title: Epithelium_homeo_rep1

value: male

value: 8 weeks

value: duodenum

value: 24h after saline injection


title: Epithelium_atrophy_rep1

value: 24h after poly(I:C) injection


title: Granulocytes_PMF_9


title: Δnit-2 50mM Tryptophan Biological Replicate 2

value: Vogel's minimal medium with 2% Sucrose and 50mM Tryptophan


title: pre-chemoresistant stage, patient 2

description:
Sample 3
S03
P17092076511

value: pre-chemoresistant stage


title: Δnit-2 50mM Tryptophan Biological Replicate 1


title: pre-chemoresistant stage, patient 1

description:
Sample 1
S01
P17090273758

value: patient 1


title: post-chemoresistant stage, patient 1

description:
Sample 2
S02
P17090273759


title: mBL_18_hybridized to 250K_Nsp

tag: tumor type

value: lymphoma

tag: age group

value: Adult


title: Δnit-2 50mM Isoleucine Biological Replicate 2

value: Vogel's minimal medium with 2% Sucrose and 50mM Isoleucine


title: Human_L861-01-N04

city: lanzhou

last: wang

address: No 204 Donggang West Road, Lanzhou city, Gansu province, China

institute: Lanzhou University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kitv3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina HiSeq X ten platform and reads were generated.
Quality control:Raw data of fastq format was firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. And reads were trimmed and cleaned by removing the sequences smaller than 15 nt or longer than 35 nt. At the same time, Q20, Q30, GC-content of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Comparative analysis:Use Bowtie tools soft, The Clean Reads respectively with Silva database, GtRNAdb database, Rfam database and Repbase database sequence alignment, filter ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA) and other ncRNA and repeats. The remaining reads were used to detect known miRNA and novel miRNA predicted by comparing with known miRNAs from miRBase v20.0. Randfold tools soft was used for novel miRNA secondary structure prediction.
Quantification of miRNA expression levels:miRNA expression levels were estimated for each sample: 1) sRNA were mapped back onto the precursor sequence;2) Readcount for each miRNA was obtained from the mapping results.
Genome_build: miRBase v20.0
Supplementary_files_format_and_content: Readcount

source_name: plasma

extract_protocol:
All samples in this study were enrolled from Gansu Provincial Hospital between October 2018 and March 2019. The cohort from this study was comprised of patients with lung adenocarcinoma and healthy peoples. We collected the plasma sample from research subjects that had been confirmed with tissue pathology. Also, all patients were not accepted any therapeutic strategies, such as surgery, chemoradiotherapy, targeted treatment and immunotherapy, and had no any complications or other history of cancer.Five milliliters of peripheral venous blood were collected in from each object with ethylenediaminetetraacetic acid (EDTA) anticoagulant tube, and then centrifuged (TD5G, Shanghai) at 1000 rpm for 10 minutes at room temperature immediately, followed by a 10 minutes high-speed centrifugation (Biofuge Frsco, Heraeus) at 12,000 rpm at 4°C, and finally, removed cell debris. The supernatant plasma was stored at -80 °C.A total amount of 2.5ng RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNextR UltraTM small RNA Sample Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, first of all, ligated the 3′ SR Adaptor. Mixed 3′ SR Adaptor for Illumina, RNA and Nuclease-Free Water, mixture system after incubation for 2 minutes at 70 degrees in a preheated thermal cycler. Tube was transfer to ice. Then, add 3′ Ligation Reaction Buffer (2X) and 3′ Ligation Enzyme Mix ligate the 3′ SR Adaptor. Incubated for 1 hour at 25°C in a thermal cycler. To prevent adaptor-dimer formation, the SR RT Primer hybridizes to the excess of 3′ SR Adaptor (that remains free after the 3′ ligation reaction) and transforms the single stranded DNA adaptor into a double-stranded DNA (dsDNA) molecule. dsDNAs are not substrates for ligation mediated. The second, ligated the 5′ SR Adaptor. Then, reverse transcription synthetic first chain. PCR amplification and Size Selection. PAGE gel was used to electrophoresis fragment screening purposes, rubber cutting recycling as the pieces get small RNA libraries. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: Sex

value: healthy


title: Δnit-2 50mM Proline Biological Replicate 2

tag: genotype

value: Vogel's minimal medium with 2% Sucrose and 50mM Proline


title: Δnit-2 50mM Isoleucine Biological Replicate 3

tag: media


title: Granulocytes_PMF_8

value: CALR Type 2


title: Human_L861-01-N03

value: female


title: Δnit-2 50mM NaNO3 Biological Replicate 3

value: Vogel's minimal medium with 2% Sucrose and 50mM NaNO3


title: Δnit-2 50mM NaNO3 Biological Replicate 2


title: Δnit-2 50mM NaNO3 Biological Replicate 1


title: Granulocytes_PET_4

value: PET

value: CALR Type 1


title: Granulocytes_PPV_6

value: PPV


title: Δamn-1 50mM Tryptophan Biological Replicate 3


title: Human_L861-01-N01

value: male


title: Granulocytes_PMF_7

value: Overt-PMF


title: Human_L861-01-N02


title: Granulocytes_PrePMF_7

source_name: Granulocytes from PrePMF peripheral blood

value: Pre-PMF

value: MPL


title: Human_L861-01-T06

value: lung adenocarcinoma


title: Granulocytes_PET_3


title: Granulocytes_PrePMF_6

value: TN


title: Human_L861-01-T05


title: Δnit-2 50mM Proline Biological Replicate 1


title: Human_L861-01-T04


title: Δamn-1 50mM Tryptophan Biological Replicate 2

value: Vogel's minimal medium with 2% Sucrose and 50mM Tryptophan


title: Δamn-1 50mM Tryptophan Biological Replicate 1


title: Δamn-1 50mM Proline Biological Replicate 3


title: Human_L861-01-T03


title: Human_L861-01-T02


title: snATAC-seq of HAP1 and MDA-MB-231 cells

data_processing:
peak-cell matrices were determined using 10X Genomics Cellranger-atac version 1.2.0 with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: h5 file produced by cellranger-atac

source_name: HAP1 and MDA-MB-231 cells

extract_protocol:
Single nuclei were extracted with nuclei extraction buffer (NUC101-1KT, Sigma-Aldrich), and transposed with the 10X Chromium ATAC Reagent Kit. Afterward, nuclei were subjected to 10X Chromium instrument for amplifiation of tagmented genomic DNA using 10X Chromium ATAC Reagent Kit.
Library preparation was performed according to the 10X Chromium ATAC Reagent Kit User Guide.

tag: cell line

value: HAP1 and MDA-MB-231


title: Granulocytes_PMF_6

source_name: Granulocytes from PMF peripheral blood


title: Δamn-1 50mM Proline Biological Replicate 2


title: Human_L861-01-T01


title: Granulocytes_PMF_5


title: Granulocytes_PPV_4


title: scRNA-seq of HAP1 cells

data_processing:
Gene-cell matrices were determined using 10X Genomics Cellranger version 3.1.0 with default parameters (cellranger count).
Genome_build: hg38
Supplementary_files_format_and_content: h5 file produced by cellranger

source_name: HAP1 cells


title: Granulocytes_PPV_5

data_processing: Partek® Genomics Suite® software, version 7.0 (Partek Inc., St. Louis, MO, USA) was used to normalize the probe level data and convert them into expression values by means of robust multiarray average (RMA). An exploratory principal component analysis (PCA) was performed and existing batch effect was removed by means of the specific tool implemented in Partek® GS®.


title: Granulocytes_PrePMF_4


title: Δamn-1 50mM Isoleucine Biological Replicate 3

value: Vogel's minimal medium with 2% Sucrose and 50mM Isoleucine


title: LMNA.SID-19999

city: Maastricht

first: Kasper

last: Derks

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Center

description:
LMNA.SID-19999
EMB

data_processing:
Bcl2fastq 1.20 used for base-calling and fastq generation
Alignment was performed using STAR, default settings
custom Rscript (as descibed and published in TTN paper) was used to groups samples and generate PCA plot
Genome_build: UCSC Hg38
Supplementary_files_format_and_content: tab delimeted raw reads per RefSeq annotated gene-transcript

extract_protocol:
miRVana
Illumina TruSeq LT stranded, Samples random pooled per 12.

tag: tissue

value: Heart biopsy

value: LMNA-DCM


title: Δamn-1 50mM Proline Biological Replicate 1

value: Vogel's minimal medium with 2% Sucrose and 50mM Proline


title: LMNA.SID-10282

description:
LMNA.SID-10282
EMB