title: PolII-S2__Ctcf-KO

description:
p-val. threshold 1e-10
PolII-S2__Ctcf-KO.bedgraph

value: mouse embryonic fibroblasts (MEFs)

value: Ctcf-KO


title: AB10926

status: Public on Mar 13 2023

type: SRA

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

library_source: transcriptomic

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Well-barcode-RMT are extracted from the 7 first base pairs in the R2 fastq sequences. Unique-molecular-identifier are extracted from the subsequent 8 base pairs in the R2 sequences. R1 contains the genomic sequences.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error.
Genome_build: mm10
Genome_build: The tail of gene Epo was elongated by 1kb chr5:137,481,020-137,485,852
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: Epo-secreting Norn cells

extract_protocol:
Kidney single cell suspension: renal capsule was removed and the tissue minced with razor blades into 1 mm pieces. Each minced kidney was placed in 1 ml DMEM medium containing collagenase IV (Worthington Biochemical Cat no. LS004188, final concentration 0.25 mg/ml), neutral protease (Worthington Biochemical Cat no. LS02106, final concentration 0.25 mg/ml), and DNase (Roche Cat. no. 10104159001, final concentration 2000 U/ml), and incubated in a thermomixer at 37°C, 300 RPM, for 25-30 min. During this time, the suspension was passed 10 times through a 18G syringe and 8 times a 21 G syringe.
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}

tag: strain

tag: organ

value: kidney

tag: cell type

value: Enriched gating for Epo-secreting Norn cells

tag: selection marker

value: Daily doses of tamoxifen for 5 days

value: 4 hours hypoxia induced by 0.1% CO

tag: mouse age

value: 6-8 weeks


title: F1(Express617 x G3D001 ),six-leaf stage,rep1 [20N1070_Rep1_L WGBS]

city: Wuhan

first: Hao

last: Wang

address: No. 1, Shizishan Street, Hongshan District

department: National Key Laboratory of Crop Genetic Improvement

country: China

institute: Huazhong Agricultural University

library_source: genomic

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using  fastp 0.23.1 and TrimGalore-0.6.6
Sequence reads were mapped to Express617 using Bismark 0.23.0
Alignments were then deduplicated with the "deduplicate_bismark"  tool  in Bismark 0.23.0
Methylated regions were extracted and converted to bed format with the  "bismark_methylation_extractor" and "bismark2bedGraph" tools from Bismark 0.23.0 respectively.
The "coverage2cytosine" tool from Bismark 0.23.0 was run to  determine the DNA methylation context. Regions in unassigned scaffolds were discarded
Assembly: Express617_v1

molecule: genomic DNA

organism: Brassica napus

source_name: leaf

growth_protocol: Express617, G3D001 and its F1 plants were planted in the natural environment of the potting field in Huazhong Agricultural University

extract_protocol:
DNA was extracted using CTAB method . 2.5 ug of total DNA was used for the construction of sequencing libraries.
DNA libraries for Bisulfite-seq were prepared using TruSeq Nano DNA LT Sample Prep Kit for Illumina following manufacturer's protocols.

tag: tissue

value: leaf

tag: genotype

value: F1(Express617 x G3D001 )

tag: time

value: six-leaf stage


title: PolII-S2__wt

city: Vienna

first: Roman

middle: R

last: Stocsits

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

description:
p-val. threshold 1e-10
PolII-S2__wt.bedgraph

data_processing:
Basecalling software: Illumina RTA
RNA polymerase II ChIP-Seq in mouse cells was performed without spike-in, and short-read sequencing data were mapped against the mm9 template using bowtie2
Illumina short read sequencing data for NIPBL/MAU2 were performed using calibration spike-ins (mouse) and aligned against a fusion genome template consisting of merged hg19 and mm9 assemblies.
NIPBL/MAU2 calibration by random subsampling of read counts after deduplication
Peak callings with MACS software versions 1.4 and 2 were applied on full, merged, filtered, and deduplicated replicate data sets of HA-tagged samples with corresponding depleted conditions (+dTAG) as input controls.
Genome_build: hg19
Genome_build: mm9
Supplementary_files_format_and_content: bigwig (*.bw) files containing ChIP-Seq profiles after full processing as described.
Supplementary_files_format_and_content: bedGraph (*.bedgraph) files containing ChIP-Seq profiles after full processing as described.

source_name: mouse embryonic fibroblasts

growth_protocol: HeLa Kyoto (RRID:CVCL_1922) were from Narumiya S (Kyoto University; Kyoto; Japan). MEFs were generated in the lab by 3T3 methods.

extract_protocol:
ChIP-Seq: Cells were cross-linked and scrapped of the plate. The DNA was fragmented and the protein of interest was immunoprecipitated with indicated antibodies; Adaptors were ligated to the 5' and 3' ends and the library was prepared for Illumina sequencing by a qPCR amplification step.
Libraries were prepared for sequencing using standard Illumina protocols. All antibodies used in this study were listed in Online Methods section 'Antibodies and Reagents'.

value: wildtype

tag: chip antibody

value: RNA polymerase II S2 (Abcam, ab5095)

tag: treatment


title: WT REPLICATE 3 (Polysome fraction)

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

country: USA

institute: FHCRC

data_processing:
Library strategy: Polysome-seq
Sequencing was performed using an Illumina HiSeq 2500 in Rapid Run mode and  employed a single-end, 50 base read length (SE50) sequencing strategy.
adaptor was trimmed from raw sequencing files, RRNA was removed from sequencing data using bowtie. Files were then aligned to mm10 using STAR2 and counts  per gene were generated using HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw values for each Sample.

molecule: total RNA

source_name: organoids

extract_protocol: Organoid cell lysates were layered only 10-50% sucrose gradient and fractionated. Polysome fraction was collected. RNA was prepared using RNeasy Mini Kit with DNase I (Qiagen). RNA concentration and quality (A260/A280) was measured using a NanoDrop 1000 Spectrophotometer (Thermo Scientific). RNA libraries were prepared for sequencing using standard Illumina protocols.

value: primary bladder urothlelial organoids

tag: genotype/variation

value: ARID1A WT


title: AB11062


title: CRC264_Mir_n4

city: Naples

first: Gennaro

last: Gambardella

address: Via Campi Flegrei 34,

country: Italy

institute: Telethon Institute of Genetics and Medicine (TIGEM)

data_processing:
trimming with bbduk
alignment with star
Expression quantification with htseq-count
Supplementary files format and content: hg38
Supplementary files format and content: tab-delimited text files include RAW counts for each Sample

organism: Homo sapiens

source_name: Colorectal cancer stem-like cells (Colorectosphere)

extract_protocol:
Cell pellets of growing spheres were lysed and RNA was extracted with Maxwell RSCmiRNA tissue kit (Promega) according to manufacturer's instructions.
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit  (Lexogen, Vienna, Austria) according to manufacturer's instructions
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the Illumina NovaSeq 6000 with a read length of 100 bp

value: colorectal


title: CRC264_Mir_n3

value: Colorectal cancer stem-like cells (Colorectosphere)


title: KO REPLICATE 2 (Polysome fraction)

value: ARID1A KO


title: AB10771


title: F0(Express617 x G3D001),30 days ovule,rep3 [F0_Rep3_E30]

data_processing:
Filter reads shorter than 18nt using seqtk 1.3
Sequence reads were mapped to Express617 and were quantified using ShortStack 3.8.5
Assembly: Express617_v1
Supplementary files format and content: Counts.txt

source_name: ovule

extract_protocol:
Small RNA was extracted using Plant miRNA kit . 1 ug of total RNA was used for the construction of sequencing libraries.
sRNA libraries for miRNA-seq were prepared using NEB Next Multiplex Small RNA Library Prep Set for Illumina following manufacturer's protocols.

value: ovule

value: F0(Express617 x G3D001)

value: 30 days after ovule fertilization


title: AB10770

value: kidney

value: Enriched gating for Epo-secreting Norn cells


title: WT REPLICATE 2 (Polysome fraction)


title: G3D001,six-leaf stage,rep1 [20N1067_Rep1_L WGBS]


title: F0(Express617 x G3D001),30 days ovule,rep2 [F0_Rep2_E30]


title: CRC264_Mir_n2


title: F0(Express617 x G3D001),30 days ovule,rep1 [F0_Rep1_E30]


title: WT REPLICATE 1 (Polysome fraction)


title: CRC264_Ctr_n3

value: WT


title: AB10768

value: Daily doses of tamoxifen for 5 days

value: 4 hours hypoxia induced by 0.1% CO

value: 6-8 weeks


title: NT, FLOW biol rep 1

city: WAUWATOSA

first: ZIQING

last: LIU

state: WI

address: 8701 W Watertown Plank Rd, BSB 5320

department: Biology

institute: Medical College of Wisconsin

data_processing:
Fastq data quality was checked by fastqc and no trimming was performed because the data quality looks great. Sequencing depth ~ 20-30 million paired end reads/sample.
Fastq reads were mapped to hg38 genome by STAR with mismatch =1. All files has over 80% mapping rate.
Aligned reads were counted by Htseq-count with union mode. Over 80% mapped reads are from mRNA.
Assembly: hg38
Supplementary files format and content: a csv file containing Htseq counts for all genes in all samples

source_name: Human umbilical vein endothelial cells (HUVEC)

growth_protocol: HUVEC were cultured in EBM-2 (Lonza) supplemented with Endothelial Growth Medium bullet kit (Lonza) and 1x antibiotic-antimycotic (Gibco) at 5% CO2 and 37°C

extract_protocol:
RNA was extracted using TRIzol (Invitrogen)
KAPA mRNA HyperPrep Kit (Roche) was used to construct stranded libraries

treatment_protocol: HUVEC were treated with indicated siRNA at ~80% confluency using Lipofectamine 2000 or 3000 (ThermoFisher) for 24 h. Cells were cultured onto µ-Slides (Ibidi) then exposed to either static conditions for 48h or 15dyn/cm2 shear stress for 72 h on an Ibidi flow pump.

value: Non-targeting siRNA

value: control

tag: stress

value: 72h shear stress at 15 dyn/cm2


title: KO REPLICATE 1 (Polysome fraction)

value: primary bladder urothlelial organoids


title: NT, FLOW biol rep 2

value: Human umbilical vein endothelial cells (HUVEC)


title: CRC264_Ctr_n4

value: colorectal


title: F1(Express617 x G3D001 ),six-leaf stage,rep2 [20N1084_Rep3_L WGBS]

value: leaf

value: F1(Express617 x G3D001 )

value: six-leaf stage


title: AB10769


title: AB10767


title: AB10772


title: KO REPLICATE 3 (Polysome fraction)

value: ARID1A KO


title: G3D001,30 days ovule,rep3 [20N1090_Rep3_E30]

value: ovule

value: 30 days after ovule fertilization


title: CRC264_Ctr_n2

value: Colorectal cancer stem-like cells (Colorectosphere)


title: Express617,30 days ovule,rep3 [20N1087_Rep3_E30]


title: AB10766

value: kidney

value: Enriched gating for Epo-secreting Norn cells


title: CRC264_Ctr_n1

value: WT


title: Express617,six-leaf stage,rep1 [20N1068_Rep1_L WGBS]


title: KO REPLICATE 3 (Subpolysome fraction)

extract_protocol: Organoid cell lysates were layered only 10-50% sucrose gradient and fractionated. Subpolysome fraction was collected. RNA was prepared using RNeasy Mini Kit with DNase I (Qiagen). RNA concentration and quality (A260/A280) was measured using a NanoDrop 1000 Spectrophotometer (Thermo Scientific). RNA libraries were prepared for sequencing using standard Illumina protocols.


title: AB10765

value: Daily doses of tamoxifen for 5 days

value: 4 hours hypoxia induced by 0.1% CO

value: 6-8 weeks


title: KO REPLICATE 3 (total mRNA)

extract_protocol: RNA was extracted from bladder epithelial organoids. Total RNA was prepared using RNeasy Mini Kit with DNase I (Qiagen). RNA concentration and quality (A260/A280) was measured using a NanoDrop 1000 Spectrophotometer (Thermo Scientific). RNA libraries were prepared for sequencing using standard Illumina protocols.


title: MIR327_n3


title: MIR327_n2


title: F1(Express617 x G3D001),30 days ovule,rep3 [20N1084_Rep3_E30]

value: F1(Express617 x G3D001)


title: WT REPLICATE 3 (Subpolysome fraction)

value: primary bladder urothlelial organoids

value: ARID1A WT


title: AB10461


title: MIR327_n1

value: colorectal


title: WT REPLICATE 3 (total mRNA)


title: F1(Express617 x G3D001),30 days ovule,rep2 [20N1073_Rep2_E30]


title: WT327_n3


title: WT327_n2


title: AB10454


title: AB10455


title: WT327_n1


title: WT REPLICATE 2 (Subpolysome fraction)


title: AB10460

value: tdT+


title: AB10453


title: WT REPLICATE 2 (total mRNA)


title: F1(Express617 x G3D001),30 days ovule,rep1 [20N1070_Rep1_E30]


title: KO REPLICATE 2 (total mRNA)


title: Express617,30 days ovule,rep1 [20N1068_Rep1_E30]


title: AB10451


title: AB10452


title: KO REPLICATE 1 (Subpolysome fraction)


title: Express617,30 days ovule,rep2 [20N1076_Rep2_E30]


title: F0(Express617 x G3D001),15 days ovule,rep3 [F0_Rep3_E15]

value: F0(Express617 x G3D001)

value: 15 days after ovule fertilization


title: KO REPLICATE 1 (total mRNA)

value: ARID1A KO


title: AB10450


title: AB10449


title: G3D001,30 days ovule,rep2 [20N1071_Rep2_E30]

value: ovule


title: KO REPLICATE 2 (Subpolysome fraction)


title: F0(Express617 x G3D001),15 days ovule,rep2 [F0_Rep2_E15]


title: WT REPLICATE 1 (Subpolysome fraction)


title: F0(Express617 x G3D001),15 days ovule,rep1 [F0_Rep1_E15]


title: 8000 Pa, replicate 3

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

data_processing:
After merging mutiple files,  paried-end reads were trimmed for nextera adapters using BBmap(version 36.59)
Sequencing reads mapping to ribosomal RNA were removed by matching all sequencing reads to ribosomal RNA sequences from the RefSeq database using BBmap (ver.36.59)
Alignment to GRch38 (with HISAT2 2.1.2) and summarization (Htseq 0.11.4) of the result  reads were performed.
After filtering (removing genes with <100 sequencing read counts in all replicates), expression count data were normalized using voom within the limma package.
Differentially expressed genes were identified using DESeq2.
Assembly: GRCh38
Supplementary files format and content: The processed data files include genes, RNA sequencing counts and TMM method normalized expression levels.

growth_protocol: Cells were maintained in DMEM/F12 (Gibco) media supplemented with 5% horse serum (Gibco), 10 mM HEPES (Gibco) and 0.029 M sodium bicarbonate (Gibco).

extract_protocol:
RNA was extracted using TRIzol reagent
Biological triplicate libraries were prepared from each treatment.

treatment_protocol: Cells were seeded on 10-cm Petrisoft easycoat dishes (Matrigen, stiffness 500 Pa or 8000 Pa.) conjugated in house with growth factor-reduced Matrigel (0.14 mg/ml, Corning). Cells were plated in growth media containing penicillin/streptomycin and fungizone. Media was changed on day four and RNA was isolated on day 5 after seeding.

tag: cell line

tag: rna

value: Cytosolic

tag: replicate

tag: stiffness

value: High stiffness (8000 Pa)


title: 8000 Pa, replicate 1


title: 500 Pa, replicate 3

value: Low stiffness (500 Pa)


title: 8000 Pa, replicate 2


title: AB10448

value: kidney

value: Enriched gating for Epo-secreting Norn cells


title: AB10347


title: G3D001,30 days ovule,rep1 [20N1067_Rep1_E30]

value: 30 days after ovule fertilization


title: GMP-MoP, bio rep 2 [ATAc-seq]

city: Hachioji

first: Kenichi

last: Asano

state: Tokyo

address: 1432-1 Horinouchi

department: Life Sciences

country: Japan

institute: Tokyo University of Pharmacy and Life Sciences

data_processing:
Sequencing reads were aligned to a mousereference genome in the Bowtie2 (version 2.3.5.1).
ATAC-seq data for GMP and MDP were retrieved from NCBI/GEO (GSE149762).
Peak identification and calculation of read counts per peak were performed using the HOMER software (version 4.11).
A catalog file of peak data was created and read count values were calculated by using the HOMER software.
The R package edgeR (version 3.32.1) was used for normalization of read counts and calculation of RPKM values for each peak.
Assembly: mm10
Supplementary files format and content: BED files include ATAC-seq peak regions and raw count values.かんがえる

source_name: BM

extract_protocol:
Five thousand progenitor cells were sorted into 1.5 mL tubes. Transposition reaction was performed by using Tagment DNA Enzyme and Buffer Kit (Illumina).
Sequence libraries wre prepared by PCR-amplification of the transposed genomic DNA (New England Biolabs) with indexed primers.

value: BM

value: BM progenitor cells

tag: sample group

value: GMP-MoP

tag: antibodies/tags

value: Illumina Tagment DNA Enzyme


title: G3D001,15 days ovule,rep3 [20N1090_Rep3_E15]


title: Express617,15 days ovule,rep3 [20N1087_Rep3_E15]


title: AB10346

tag: strain

tag: organ

value: 4 hours hypoxia induced by 0.1% CO

value: 6-8 weeks


title: WT REPLICATE 1 (total mRNA)

value: primary bladder urothlelial organoids

value: ARID1A WT


title: 500 Pa, replicate 2


title: 500 Pa, replicate 1


title: AB10345

tag: cell type

tag: selection marker


title: GMP-MoP, bio rep 1 [ATAc-seq]

tag: tissue


title: F1(Express617 x G3D001),15 days ovule,rep3 [20N1084_Rep3_E15]

tag: genotype

value: F1(Express617 x G3D001)

value: 15 days after ovule fertilization


title: Express617,15 days ovule,rep2 [20N1076_Rep2_E15]

value: ovule

tag: time


title: Human adjacent liver tissues [X-1b]

city: shanghai

first: Gui-Qi

last: zhu

address: shanghai

institute: zhongshan hospital

library_source: transcriptomic single cell

data_processing:
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell- geneexpression/software/pipelines/latest/what-is-cell-ranger) using default parameters. All downstream single-cell analyses were performed using Cell Ranger and Seurat unless mentioned specifically. In brief, for each gene and each cell Barcode (filtered by CellRanger), unique molecule identifiers were counted to construct digital expression matrices. Secondary filtration by Seurat: A gene with expression in more than 3 cells was considered as expressed, and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells. Cellranger count takes FASTQ files performs alignment, filtering, Barcode counting, and UMI counting. It uses the Chromium cellular Barcodes to generate feature Barcode matrices by cellranger count or cellranger aggr and reruns the dimensionality reduction, clustering, and gene expression algorithms using cellranger default parameter settings. Secondary Analysis of Gene Expression we use Seurat. The Seurat package was used to normalise data, dimensionality reduction, clustering,differential expression. we used Seurat alignment method canonical correlation analysis (CCA) for integrated analysis of datasets. For clustering, highly variable genes were selected and the principal components based on those genes used to build a graph, which was segmented with a resolution of 0.6.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Human adjacent liver tissues

extract_protocol:
approximately 5000 cells/ FACS-sorted cells were washed with 0.04% BSA DPBS for three times and were resuscitated to a concentration of 700~1200 cells/ul (viability over 85%). Cells were captured in droplets at a targeted cell recovery of cells.
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3ʹ Reagent Kits v3 (10x Genomics), according to the manufacturer’s instructions. Briefly, approximately 5000 cells/ FACS-sorted cells were washed with 0.04% BSA DPBS for three times and were resuscitated to a concentration of 700~1200 cells/ul (viability over 85%). Cells were captured in droplets at a targeted cell recovery of cells. After the reverse transcriptio step, emulsions were broken and Barcoded-cDNA was purified with Dynabeads, followed by PCR amplification. Amplified cDNA was then used for 3’gene expression library construction. For gene expression library construction, 50 ng of amplified cDNA was fragmented and end-repaired, double-size selected with SPRIselect beads, and sequenced on a NovaSeq platform (Illumia) to generate 150 bp paired-end Reads.

treatment_protocol: scRNA derived from 7 HBV-related HCC tissues

value: Human adjacent liver tissues

tag: virus affected

value: HBV

tag: tumor stage

value: BCLC-A


title: proNeu2, bio rep 2 [ATAc-seq]


title: proNeu2, bio rep 1 [ATAc-seq]


title: Human adjacent liver tissues [2b-0618]

value: BCLC-B


title: F1(Express617 x G3D001),15 days ovule,rep2 [20N1073_Rep2_E15]


title: AB10293

value: kidney

value: Enriched gating for Epo-secreting Norn cells

value: Daily doses of tamoxifen for 5 days

tag: mouse age


title: proNeu1, bio rep 2 [ATAc-seq]

value: BM

value: BM progenitor cells


title: Human adjacent liver tissues [1b-0618]


title: G3D001,15 days ovule,rep2 [20N1071_Rep2_E15]


title: AB10292


title: Human adjacent liver tissues [B-2b]


title: proNeu1, bio rep 1 [ATAc-seq]

value: Illumina Tagment DNA Enzyme


title: Express617,15 days ovule,rep1 [20N1068_Rep1_E15]


title: Human hepatocellular carcinoma tissues [1a-0831]

source_name: Human hepatocellular carcinoma tissues

value: Human hepatocellular carcinoma tissues


title: F1(Express617 x G3D001),15 days ovule,rep1 [20N1070_Rep1_E15]


title: AB10291

value: 4 hours hypoxia induced by 0.1% CO

value: 6-8 weeks


title: il17-egfp positive l4

city: Boston

first: jinzhi

last: duan

state: Massachusetts

address: 6th Floor, Room 641, NRB, 77 Louis Pasteur Avenue

institute: Brigham and Women' hospital

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR 2.7.3a  in partek software.
The reads were quantified with Quantify to annotation model (Partek E/M) with default setting.
Assembly: mm10
Supplementary files format and content: IL17 EGFP POSITIVE AND NEGATIVE text files include gene account values for each Sample.

source_name: small intestine epithelia cell

extract_protocol:
200 live cells was direactly sorted to 10 ul cell lysis buffer ( 0.2%  Triton X-100 and 2 U μl–1 RNase inhibitor).
RNA libraries were prepared for sequencing  following smart-seq2 protocol (Picelli, Faridani et al; Nat Protoc ;2014)


title: AB9464


title: AB10290


title: cMoP, bio rep 1 [ATAc-seq]

value: cMoP


title: Human hepatocellular carcinoma tissues [1a-0727]


title: cMoP, bio rep 2 [ATAc-seq]


title: AB10289

value: tdT+


title: Human hepatocellular carcinoma tissues [1a-0707]


title: AB10344


title: il17-egfp positive l3


title: Human hepatocellular carcinoma tissues [1a-0629]


title: Human hepatocellular carcinoma tissues [1a-0706]


title: G3D001,six-leaf stage,rep3 [20N1090_Rep3_L]

value: leaf

value: six-leaf stage


title: Express617,six-leaf stage,rep3 [20N1087_Rep3_L]


title: G3D001,15 days ovule,rep1 [20N1067_Rep1_E15]

value: ovule

value: 15 days after ovule fertilization


title: Human hepatocellular carcinoma tissues [1a-0618]

value: HBV


title: F1(Express617 x G3D001),six-leaf stage,rep3 [20N1084_Rep3_L]

value: F1(Express617 x G3D001)


title: il17-egfp positive l2


title: il17-egfp positive l1


title: AB9455

value: kidney


title: Human hepatocellular carcinoma tissues [2a-0706]

value: BCLC-B


title: 133M_NIPBL RNAi r2

description:
q-value (min. FDR) cutoff for significant regions is 0.05
HeLa_NIPBL-RNAi.bw

source_name: cervical carcinoma

value: HeLa Kyoto

value: NIPBL knockdown

tag: chip antibody

value: NIPBL (Peters laboratory A870 or 133M)

tag: treatment


title: il17-egfp negative l4


title: F1(Express617 x G3D001),six-leaf stage,rep2 [20N1073_Rep2_L]


title: il17-egfp negative l3


title: AB9454

value: Enriched gating for Epo-secreting Norn cells

value: Daily doses of tamoxifen for 5 days

value: normoxia


title: 133M_control r2

description:
q-value (min. FDR) cutoff for significant regions is 0.05
HeLa_ctrl.bw

tag: cell line

value: wildtype


title: AB9456

value: 4 hours hypoxia induced by 0.1% CO

value: 6-8 weeks


title: G3D001,six-leaf stage,rep2 [20N1071_Rep2_L]

value: leaf


title: MAU2-HA SCC1 knockdown r2

description:
q-value (min. FDR) cutoff for significant regions is 0.05
MAU2-HA_SCC1-kd_treat_pileup.bedgraph

value: SCC1 knockdown

value: HA (Abcam, ab9110)

value: HA-tagged


title: MAU2-HA control r2

description:
q-value (min. FDR) cutoff for significant regions is 0.05
MAU2-HA_ctrl_treat_pileup.bedgraph


title: il17-egfp negative l2


title: il17-egfp negative l1


title: AB9316


title: AB9317


title: F1(Express617 x G3D001),six-leaf stage,rep1 [20N1070_Rep1_L]

value: six-leaf stage


title: G3D001,six-leaf stage,rep1 [20N1067_Rep1_L]


title: Express617,six-leaf stage,rep1 [20N1068_Rep1_L]


title: AB9221


title: HA-NIPBL SCC1 knockdown r2

description:
q-value (min. FDR) cutoff for significant regions is 0.05
HA-NIPBL_SCC1-kd_treat_pileup.bedgraph


title: HA-NIPBL control r2

description:
q-value (min. FDR) cutoff for significant regions is 0.05
HA-NIPBL_ctrl_treat_pileup.bedgraph


title: Mcemp1-/- PCMC [YJ05]

city: Cleveland

first: Youn Jung

last: Choi

email: choiy4@ccf.org, younjung514@gmail.com

state: OH

address: 9500 Euclid Ave, NE2-251

department: Cancer biology

institute: Cleveland Clinic Lerner Research Institute

data_processing:
Fastq files were analyzed with Partek Flow (Build 10.0.21.1026). This includes quality control, alignment to mm10, peak filtering, normalization, and differential gene expression.
Genome_build: mm10

source_name: Peritoneal cell-derived mast cells (PCMC)

extract_protocol:
RNA from PCMC was extracted using RNeasy Micro Kit (74004) from QIAGEN.
The RNA-seq library was prepared using the KAPA mRNA HyperPrep Kit (KR1352), according to manufacturers’ instructions.

tag: culture timeline

value: 9 days


title: Mcemp1-/- PCMC [YJ06]

value: Peritoneal cell-derived mast cells (PCMC)


title: Mcemp1-/- PCMC [YJ04]


title: AB9220

value: kidney


title: RPE-1 p53KO + Reversine 3 (RNA-seq)

city: New York

first: Albert

middle: S

last: Agustinus

state: New York

address: 408 East 69th Street, Room 419-G

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Reads were processed using standard pipeline from www.Basepair.com using the website's Expression count (STAR) pipeline
Genome_build: hg38
Supplementary_files_format_and_content: TXT - FPKM values from STAR pipeline for genes and transcript

source_name: Retina (female)

growth_protocol: RPE-1 cells were grown in DMEM supplemented with 10% FBS and 1X Pen-Strep in 100 mm dish (Corning   Corning™ 100 mm TC-Treated Culture Dishes)

extract_protocol:
As described in the protocol for Rneasy Plus Mini Kit (Qiagen 74134)
Truseq stranded workflow

treatment_protocol: RPE-1 cells were treated with either 1:1000 DMSO (vehicle control) or 0.5 µM reversine for 48 hours, before passaging. This treatment was done long-term until passage #8)

tag: Sex

value: female

value: hTERT-immortalized retinal pigment epithelial cell line

value: p53 KO

value: Reversine 0.5 uM 48 hours before splitting, long-term


title: F0(Express617 x G3D001 ),30 days ovule,rep3 [F0_Rep3_E30 RNA-seq]

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using  fastp 0.23.1
Trimmed sequence reads were mapped to Express617 using hisat2 2.2.1
Read count extraction and normalization were performed using featurecounts 2.0.1
Assembly: Express617_v1
Supplementary files format and content: counts

extract_protocol:
RNA was extracted using TRIzol reagent kit . 0.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.

value: ovule

value: F0(Express617 x G3D001 )

value: 30 days after ovule fertilization


title: Express617,six-leaf stage,rep2 [20N1076_Rep2_L]


title: AB9453

value: Enriched gating for Epo-secreting Norn cells

value: Daily doses of tamoxifen for 5 days

value: normoxia


title: AB9218

value: 4 hours hypoxia induced by 0.1% CO

value: 6-8 weeks


title: Wild-type PCMC [YJ03]

value: Wild type


title: F0(Express617 x G3D001 ),30 days ovule,rep1 [F0_Rep1_E30 RNA-seq]


title: Wild-type PCMC [YJ02]


title: RPE-1 p53KO + Reversine 2 (RNA-seq)


title: AB9217


title: G3D001,30 days ovule,rep3 [20N1090_Rep3_E30 RNA-seq]


title: AB9216


title: RPE-1 p53KO + Reversine (RNA-seq)


title: Wild-type PCMC [YJ01]


title: Express617,30 days ovule,rep3 [20N1087_Rep3_E30 RNA-seq]


title: RPE-1 p53KO LMB2OE + Reversine 2 (RNA-seq)

value: p53 KO LMB2OE


title: AB9215


title: F1(Express617 x G3D001 ),30 days ovule,rep3 [20N1084_Rep3_E30 RNA-seq]

value: F1(Express617 x G3D001 )


title: AB9219


title: RPE-1 p53KO LMB2OE + Reversine 3 (RNA-seq)


title: AB9214


title: F0(Express617 x G3D001 ),30 days ovule,rep2 [F0_Rep2_E30 RNA-seq]


title: WT_liver_normal2

city: Los Angeles

first: Hidekazu

last: Tsukamoto

state: CA

address: 1333 San Pablo Street MMR414

department: Pathology

institute: University of Southern California

description: RNA

data_processing:
RNA-seq was analyzed with Partek Flow v6
Raw sequencing reads were trimmed based on quality score (Phred score>=20, minimum read length 25nt)
Trimmed reads were mapped to mm10 mouse genome with Gencode M11 as guidance using STAR aligner (v2.6.1) with default parameter settings
Gencode M11 was used to quantify the gene level the aligned reads using Partek E/M method
Read counts were normalized using Upper Quartile nomalization and subjected to differential expression analysis using Partek Gene Specific Analysis (GSA) method
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited GSA differential expression analysis result for all genes

source_name: Liver tissue

extract_protocol:
RNA extraction by PicoPure TRNA isolation kit
Libraries were prepared according to Ilumina TruSeq RNA Library Prep Kit v2 protocol

treatment_protocol: Injected with diethyl nitrosamine (10mg/kg) at 2 wk old and fed Western alcohol diet from 6 wk old for 4 months

value: Untreated


title: AB9213

extract_protocol:
Kidney single cell suspension: renal capsule was removed and the tissue minced with razor blades into 1 mm pieces. Each minced kidney was placed in 1 ml DMEM medium containing collagenase IV (Worthington Biochemical Cat no. LS004188, final concentration 0.25 mg/ml), neutral protease (Worthington Biochemical Cat no. LS02106, final concentration 0.25 mg/ml), and DNase (Roche Cat. no. 10104159001, final concentration 2000 U/ml), and incubated in a thermomixer at 37°C, 300 RPM, for 25-30 min. During this time, the suspension was passed 10 times through a 18G syringe and 8 times a 21 G syringe.
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}

value: kidney


title: F1(Express617 x G3D001 ),30 days ovule,rep2 [20N1073_Rep2_E30 RNA-seq]


title: RPE-1 p53KO LMB2OE + Reversine (RNA-seq)

value: female


title: WT_liver_normal3

description: RNA


title: WT_liver_normal1

description: RNA


title: KO_liver_DEN3

description: RNA

value: Treated with DEN and Western alcohol diet


title: RPE-1 p53KO LMB2OE + DMSO 3 (RNA-seq)

value: hTERT-immortalized retinal pigment epithelial cell line

value: DMSO 10 uL 48 hours before splitting, long-term


title: KO_liver_DEN2

description: RNA


title: Express617,30 days ovule,rep2 [20N1076_Rep2_E30 RNA-seq]

value: ovule


title: RPE-1 p53KO LMB2OE + DMSO 2 (RNA-seq)


title: RPE-1 p53KO LMB2OE + DMSO (RNA-seq)


title: KO_liver_DEN1

description: RNA


title: G3D001,30 days ovule,rep2 [20N1071_Rep2_E30 RNA-seq]


title: AB9212


title: RPE-1 p53KO + DMSO Rep 3 (RNA-seq)

value: p53 KO


title: AB9210


title: Express617,30 days ovule,rep1 [20N1068_Rep1_E30 RNA-seq]

value: 30 days after ovule fertilization


title: WT_liver_DEN3

description: RNA


title: RPE-1 p53KO + DMSO Rep 2 (RNA-seq)


title: G3D001,30 days ovule,rep1 [20N1067_Rep1_E30 RNA-seq]


title: WT_liver_DEN2

description: RNA


title: AB9209

value: Enriched gating for Epo-secreting Norn cells


title: AB9208


title: AB9207


title: WT_liver_DEN1

description: RNA


title: F0(Express617 x G3D001 ),15 days ovule,rep3 [F0_Rep3_E15 RNA-seq]

value: F0(Express617 x G3D001 )

value: 15 days after ovule fertilization


title: AB9206

value: 4 hours hypoxia induced by 0.1% CO


title: 4T1 Sorted primary nuclei rep2

data_processing:
Reads were mapped to mm10 using bowtie2 with the following parameters: -t -X2000 --no-mixed --no-discordant. Reads were filtered based on -F 1804 -q 30 using samtools and the MarkDuplicates function in Picard tools was used to remove PCR duplicates. Peak calling was done using macs2  callpeak function with the following parameters: -f BAM -g hs --nomodel --shift 37 --extsize 73 --keep-dup all -B --SPMR --call-summits -q 1e-2. Summit of peaks were extended by 250bp and merged across samples. IGVtools count function was used to generate TDF files for visualization.
Genome_build: mm10
Supplementary_files_format_and_content: BED - peak calls from MACS2
Supplementary_files_format_and_content: bigWig files for visualization in IGV

source_name: 4T1 Cells

growth_protocol: 4T1 cells were grown in RPMI media supplemented with 10% FBS and 1X Pen-Strep in 245x245 mm dish (Corning   Corning™ TC-Treated Culture Dishes)

extract_protocol:
According to Toufektchan E and Maciejowski J, STAR Protoc. 2021
Library prepared according to Buenrostro et. al. 2015 (Micronuclei adjusted to 20x of nuclei)

treatment_protocol: 4T1 cells were treated with 0.5 µM Reversine for 48 hours before micronuclei isolation (Toufektchan E and Maciejowski J, STAR Protoc. 2021)

value: BALB/c

value: 4T1 TNBC Breast Cancer Cells

value: Reversine 0.5 uM 48 hours


title: RPE-1 p53KO + DMSO (RNA-seq)


title: RPE-1 p53KO + Reversine 3

description: RPE-1 p53KO Reversine 3

data_processing:
Reads were mapped to hg38 using bowtie2 with the following parameters: -t -X2000 --no-mixed --no-discordant. Reads were filtered based on -F 1804 -q 30 using samtools and the MarkDuplicates function in Picard tools was used to remove PCR duplicates. Peak calling was done using macs2  callpeak function with the following parameters: -f BAM -g hs --nomodel --shift 37 --extsize 73 --keep-dup all -B --SPMR --call-summits -q 1e-2. Summit of peaks were extended by 250bp and merged across samples. IGVtools count function was used to generate TDF files for visualization.
Genome_build: hg38
Supplementary_files_format_and_content: BED - peak calls from MACS2
Supplementary_files_format_and_content: bigWig files for visualization in IGV

extract_protocol:
Extraction was performed according to Buenrostro et. al. 2015
Library prepared according to Buenrostro et. al. 2015

value: Reversine 0.5 uM 48 hours before splitting, long-term


title: AB9211

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Well-barcode-RMT are extracted from the 7 first base pairs in the R2 fastq sequences. Unique-molecular-identifier are extracted from the subsequent 8 base pairs in the R2 sequences. R1 contains the genomic sequences.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error.
Genome_build: mm10
Genome_build: The tail of gene Epo was elongated by 1kb chr5:137,481,020-137,485,852
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

value: 6-8 weeks


title: F0(Express617 x G3D001 ),15 days ovule,rep2 [F0_Rep2_E15 RNA-seq]


title: 4T1 Sorted primary nuclei rep1


title: F1(Express617 x G3D001 ),30 days ovule,rep1 [20N1070_Rep1_E30 RNA-seq]

value: F1(Express617 x G3D001 )


title: RPE-1 p53KO + Reversine

description: RPE-1 p53KO Reversine

value: female


title: AB9204

value: kidney


title: F0(Express617 x G3D001 ),15 days ovule,rep1 [F0_Rep1_E15 RNA-seq]


title: Express617,15 days ovule,rep3 [20N1087_Rep3_E15 RNA-seq]


title: 4T1 Sorted ruptured micronuclei rep 2


title: RPE-1 p53KO LMB2OE + Reversine 3

description: RPE-1 p53KO LMB2OE Reversine 3

value: hTERT-immortalized retinal pigment epithelial cell line

value: p53 KO LMB2OE


title: RPE-1 p53KO LMB2OE + Reversine 2

description: RPE-1 p53KO LMB2OE Reversine 2


title: 4T1 Sorted intact micronuclei rep 2


title: AB9202


title: Express617,15 days ovule,rep2 [20N1076_Rep2_E15 RNA-seq]

value: ovule


title: AB9203


title: AB9047

value: normoxia


title: F1(Express617 x G3D001 ),15 days ovule,rep2 [20N1073_Rep2_E15 RNA-seq]


title: 4T1 Sorted ruptured micronuclei rep 1


title: AB9205


title: RPE-1 p53KO + Reversine 2

description: RPE-1 p53KO Reversine 2

value: p53 KO


title: RPE-1 p53KO LMB2OE + DMSO 3

description: RPE-1 p53KO LMB2OE DMSO 3

value: DMSO 10 uL 48 hours before splitting, long-term


title: AB9046

value: Enriched gating for Epo-secreting Norn cells


title: 4T1 Sorted intact micronuclei rep 1


title: RPE-1 p53KO LMB2OE + DMSO 2

description: RPE-1 p53KO LMB2OE DMSO 2


title: G3D001,15 days ovule,rep2 [20N1071_Rep2_E15 RNA-seq]

value: 15 days after ovule fertilization


title: F1(Express617 x G3D001 ),15 days ovule,rep1 [20N1070_Rep1_E15 RNA-seq]


title: G3D001,15 days ovule,rep3 [20N1090_Rep3_E15 RNA-seq]


title: RPE-1 p53KO LMB2OE + DMSO

description: RPE-1 p53KO LMB2OE DMSO


title: AB9044

value: 4 hours hypoxia induced by 0.1% CO


title: RPE-1 p53KO + DMSO Rep 3

description: RPE-1 p53KO DMSO 3


title: AB9045


title: F1(Express617 x G3D001 ),15 days ovule,rep3 [20N1084_Rep3_E15 RNA-seq]


title: RPE-1 p53KO + DMSO Rep 2

description: RPE-1 p53KO DMSO 2


title: G3D001,15 days ovule,rep1 [20N1067_Rep1_E15 RNA-seq]


title: RPE-1 p53KO LMB2OE + Reversine

description: RPE-1 p53KO LMB2OE Reversine


title: AB9042


title: AB9041


title: GFP+ cells, E11.5 kidneys, Tbx18 (GFP/GFP), rep3

type: RNA

city: Hannover

first: Mark-Oliver

last: Trowe

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

country: Germany

institute: Medizinische Hochschule Hannover

hyb_protocol: cRNA fragmentation, hybridisation and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’, except that 200ng (samples M5062-M5089) and 400ng (samples M5717-M5718) of each fluorescently labelled cRNA were used for hybridization.

scan_protocol: Slides were scanned using the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by use of the extraction protocol file ‘GE1_107_Sep09.xml’.  Measurements of on-chip replicates were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.  Averaged gPS values were normalized by Quantile normalization first, followed by global linear scaling. For the latter approach all quantile normalized gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be finally normalized (‘Array I’ in the formula shown below). Accordingly, finally normalized gPS values for all samples (microarray data sets) were calculated by the following formula:  finally normalized gPSArray i = quantile normalized gPSArray i x (1500 / 75th PercentileArray i)  Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 10 finally normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 10.

label: Alexa Fluor 555

label_protocol: 20 ng of total RNA of samples M5062-M5065 and M5717-M5718, and 10 ng of samples M5088-M5089 were used to prepare aminoallyl-UTP-modified (aaUTP) cRNA (Amino Allyl MessageAmp™ II Kit; #AM1753; Thermo Fisher Scientific) applying one-round of amplification as directed by the company, except for a twofold downscaling of all reaction volumes. 14 ng of generated cDNA was used for aaUTP-cRNA synthesis. The labeling of aaUTP-cRNA was performed by use of Alexa Fluor 555 Reactive Dye (#A32756; Thermo Fisher Scientific) as recommended in the manual of the Amino Allyl MessageAmp™ II Kit (twofold downscaled reaction volumes).

extract_protocol: Extraction of total RNA was performed using peqGOLD RNAPure (VWR Peqlab) according to the manufacturer’s recommendations.

treatment_protocol: Mechanically dissected E11.5 kidney rudiments were homogenized, and single cell suspensions were subjected to FACS. GFP+ cells were collected and immediately frozen. Cells from successive rounds of FACS were later combined to obtain pools with around 100.000 cells each.

value: NMRI

value: pooled male and female

tag: developmental stage

value: kidney rudiment


title: GFP+ cells, E11.5 kidneys, Tbx18 (GFP/+), rep3


title: GFP+ cells, E11.5 kidneys, Tbx18 (GFP/GFP), rep2


title: G3D001,six-leaf stage,rep3 [20N1090_Rep3_L RNA-seq]

value: leaf

value: six-leaf stage


title: RPE-1 p53KO + DMSO

description: RPE-1 p53KO DMSO


title: F1(Express617 x G3D001 ),six-leaf stage,rep3 [20N1084_Rep3_L RNA-seq]

value: F1(Express617 x G3D001 )


title: AB9040

value: 6-8 weeks


title: Xbp1ΔIEC

data_processing:
Cellranger count 3.1.0
Genome_build: mm10
Supplementary_files_format_and_content: h5 Expression Matrices

source_name: small intestine cd4 cell

extract_protocol:
10k SI LP CD4 (CD45+CD4+TCRβ+) living cells from Germline free Xbp1ΔIEC and Xbp1fl/fl were FACS-sorted for sequencing.
The sorted live cells were separated into a single droplet using the Chromium Single Cell 3' v3 kit  according to the manufacturer’s instruction (10x Genomics) and RNA libraries were prepared for sequencing using standard protocols.

value: small intestine cd4 cell

value: Xbp1 delta


title: Express617,six-leaf stage,rep3 [20N1087_Rep3_L RNA-seq]


title: K562_4sU_IAA_1h

city: Xiamen

first: Chaoyong

last: Yang

state: Fujian

address: 422 Siming Road

institute: Xiamen University

data_processing:
Drop seq pipeline
Assembly: hg38
Supplementary files format and content: rds

growth_protocol: Human K562 cells and human colorectal cancer HCT116 cells were cultured in high glucose Dulbecco's modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (Gibco, catalog no. 11965) and 1× penicillin–streptomycin (Gibco, catalog no. 15140122; 100 U/ml of penicillin, 100 µg/ml of streptomycin) and maintained at 37 °C with 5% CO2.

extract_protocol:
K562 cells were centrifuged and collected for scRNA-seq. HCT116 cells were centrifuged and fixed by methanol before scRNA-seq.
The 3’-end enriched sequencing library was prepared by TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme Biotech, catalog no. TD503) according to the manufacturer’s instructions.

treatment_protocol: For Sample 7, 8, and 9, the cells were treated by 300 nM 5-AZA-CdR for 1, 2, and 3 days, respectively.

tag: disease type

value: human chronic myeloid leukemia

value: IAA treated 1h


title: K562_4sU_IAA_2h

value: IAA treated 2h


title: Xbp1fl/fl

tag: strain


title: AB9043

source_name: Epo-secreting Norn cells

tag: organ

value: kidney


title: K562_4sU_IAA_30min

value: IAA treated 30min


title: Express617,six-leaf stage,rep2 [20N1076_Rep2_L RNA-seq]

source_name: leaf


title: Irx3/5-het-P6 [S20]

city: Pok Fu Lam

first: Peikai

last: Chen

address: Sassoon Road 5

department: Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Data was aligned to mouse genome mm10 (reference v3.0.0 provided by 10X Genomics) by CellRanger (version 3.1.0)
Data was also aligned to a reference file of exogenous sequences, including tdTomato (1431bp),  WPRE (Woodchuck Hepatitis Virus (WHP) Posttranscriptional Regulatory Element; 592bp) and GFP (720), by CellRanger (version 3.1.0)
The resulting matrix files were integrated and further processed on Seurat (version 3).
Dimension reduction including CCA, PCA, tSNE and UMAP were perforedm.
Clustering were performed, and differentially expressed genes between one cluster and another (or all remaining clusters) were performed. A further filtering of abs(log2(fold-change)) > 1/2 and FDR <0.05 was applied to ensure higher specificity and correct for multiple testing.
Genome_build: mm10
Supplementary_files_format_and_content: gzip text file of gene expression file in mm10 or in exogenous genes

source_name: proximal and distal tibia_Irx3/5-het-P6

growth_protocol: The mice grow under normal condition.

extract_protocol:
RNA extraction from disassociated cells was done according to standard 10X Genomics Protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No special treatment is applied.

value: male

tag: age

tag: strain genotype

value: Col10a1Cre;Rosa26-Tdtomato;Irx3 +/Δ;Irx5 +/- (Irx3/5 heterozygous control)

value: proximal and distal tibia


title: GFP+ cells, E11.5 kidneys, Tbx18(cre/+);Hprt(Tbx18VP16), rep2

value: NMRI

tag: tissue


title: GFP+ cells, E11.5 kidneys, Tbx18 (GFP/GFP), rep1

tag: genotype

value: pooled male and female


title: G3D001,six-leaf stage,rep2 [20N1071_Rep2_L RNA-seq]

tag: time


title: Irx3/5-het-P6 [S19]


title: Express617,15 days ovule,rep1 [20N1068_Rep1_E15 RNA-seq]

value: ovule

value: 15 days after ovule fertilization


title: GFP+ cells, E11.5 kidneys, Tbx18(cre/+);Hprt(Tbx18VP16), rep1

value: kidney rudiment


title: F1(Express617 x G3D001 ),six-leaf stage,rep1 [20N1070_Rep1_L RNA-seq]

value: leaf

value: F1(Express617 x G3D001 )

value: six-leaf stage


title: Irx3/5-het-P6 [S18]


title: Irx3/5-het-P6 [S17]


title: Express617,six-leaf stage,rep1 [20N1068_Rep1_L RNA-seq]


title: GFP+ cells, E11.5 kidneys, Tbx18 (GFP/+), rep1


title: NCI-H520 cells, SIA-cIgG high, biol rep 2

city: Nanjing

first: Xinmei

last: Huang

address: Zhongshan Road

institute: Nanjing Drum Tower Hospital

data_processing:
Python3.8
For data analysis, the sgRNA spacer sequences were mapped by count_spacers.python.
The normalized sgRNA read counts of SIA-cIgG high and SIA-cIgG low were compared with MAGeCK.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include sgRNA distribution for each sample

source_name: cell line

growth_protocol: NCI-H520 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Genomic DNA was extracted from screening cells and amplification using the previously published protocol, primer sequences were obtained from the Zhangfeng lab.
PCR products were purified by TIANGEN PCR purification kit and quantified following manufacturer’s recommendations, and diluted libraries were sequenced on an IIlumina HiSeq X Ten.

treatment_protocol: A genome-wide CRISPR activation sgRNA library was transduced in NCI-H520 cells. The transduced cells were selected with 10 μg/mL blasticidin for 7 days. The drug resistant cells were passaged for the genome-wide screen by FACS sorting of SIA-cIgG high and SIA-cIgG low cells.

value: cell line

tag: cell type

value: lung squamous carcinoma cells

value: SIA-cIgG high

value: CRISPRa screen and FACS sorting


title: F1(Express617 x G3D001 ),six-leaf stage,rep2 [20N1073_Rep2_L RNA-seq]


title: NCI-H520 cells, SIA-cIgG high, biol rep 1


title: NCI-H520 cells, SIA-cIgG low, biol rep 2

value: SIA-cIgG low


title: G3D001,six-leaf stage,rep1 [20N1067_Rep1_L RNA-seq]


title: NCI-H520 cells, SIA-cIgG low, biol rep 1


title: High stiffness replicate 2

hyb_protocol: 2.5 ug of ssDNA target was then hybridized to Human Gene 1.0 ST Array in a GeneChip Hybridization Oven 645 (16h-18 h at 45° C).

scan_protocol: The arrays were washed and stained in a Gene Chip Fluidics Station 450 and finally scanned in an Affymetrix Gene Chip Scanner 3000 7G.

data_processing: DNA-microarray raw data (.cel files) were summarized to gene level expression values using the Oligo package. A custom cdf based on the entrez gene data base (version 25.0.0) was used as it provides improved precision and accuracy. Following normalization using the robust microarray average (RMA) method, 20513 unique genes were included.

label: biotin

label_protocol: A total of 200 ng of RNA was used to generate amplified sense strand DNA targets with Ambion WT Expression Kit followed by fragmentation and biotinylation with Affymetrix GeneChip WT Terminal Labeling Kit.

extract_protocol: The coverslip gels were removed from the culture dishes and edges were carefully wiped clean with a cotton swab. Cells were then lysed by placing the coverslip gel-side down in 500 µl Lysis solution/2-Mercaptoethanol mixture from the GenElute™ mammalian total RNA miniprep kit (Sigma-Aldrich) and RNA was isolated according to the manufacturer’s protocol.

treatment_protocol: MCF10CA1a cells were cultured for five days on low (400 Pa) or high (5000 Pa) 50 mm polyacrylamide-based hydrogels. Gels were prepared in house and were conjugated with growth factor-reduced Matrigel (0.14 mg/ml) prior to cell plating.

tag: stiffness

value: High stiffness (8000 Pa)


title: Sample 49 P81

status: Public on Mar 12 2023

city: Fort Collins

first: Henry

middle: J

last: Thompson

state: CO

address: 1173 Campus Delivery

institute: Colorado State University

data_processing:
CLC Genomics Workbench v 21.0.3
Raw sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC Genomics Workbench (parameters: Quality limit = 0.05; Maximum number of ambiguities = 2; automatic read-through adapter trimming; maximum length = 150; Trim end = 3'-end)
The resulting high-quality reads were mapped to Mus musculus genome reference, version GRCm38, using gene ontology associations (20150630)  in CLC Genomics Workbench
Read count extraction was performed using CLC Genomics Workbench
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files with total counts values for each sample and matrix file

source_name: Female, Liver, 0% Bean (Control)

extract_protocol:
Liver was harvested and snap frozen in liquid nitrogen. RNA was isolated from liver the RNeasy mini kit (Qiagen, Inc., USA).
RNA libraries were prepared for sequencing using standard Illumina protocols (Nugen Universal mRNA kit, Tecan Genomics, Inc., Redwood City, CA, USA)

value: Liver

value: WT

value: Female

tag: diet

value: 0% Bean (Control)


title: Sample 55 P90


title: Sample 53 P88

source_name: Female, Liver, 35% Bean

value: 35% Bean


title: Sample 59 P96


title: Sample 56 P92


title: Sample 48 P79

source_name: Female, Liver, 70% Bean

value: 70% Bean


title: Sample 57 P93


title: Sample 50 P83


title: Sample 60 P97


title: Sample 51 P84


title: DNA, GADD45A_enh_STARRSeq, plasmidPool

city: Albany

first: Morgan

middle: A

last: Sammons

state: NY

address: 1400 Washington Ave, Life Sciences 2075

department: Biological Sciences

institute: University at Albany - SUNY

description: PCR amplified plasmid DNA (STARR-seq DNA)

library_source: other

data_processing:
STARR-seq paired-end Illumina sequencing reads were first merged using bbmerge tool from bbtools (v37.62). All merged sequencing reads were then counted using fastx_collapser tool from fastx_toolkit (v0.0.14). Read counts were then collected by searching for exact match in the designed enhancer library pool sequences using a custom python script.
Assembly: GRCh38
Supplementary files format and content: Comma-delimited, raw read counts for each enhancer variant sequence in plasmid DNA pool and STARRSeq RNA from each cell type and treatment condition
Library strategy: STARR-seq

molecule: other

organism: synthetic construct

growth_protocol: HCT116 (WT or TP53-/-) were cultured in McCoy's 5A (modified) Medium (gibco, 16600082) supplemented 10% FBS (avantor, 89510-186) and 1% Pen/Strep (gibco, 15070-063) at 37oC and 5% CO2.

extract_protocol:
RNA extraction and processing was done as described in Neumayr, et al, 2019 with minor modifications. Total RNA was extracted using the Quick-RNA Miniprep Kit (Zymo, R1054), followed by polyA+ RNA selection using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, E7490S).
Library was constructed as described in Neumayr, et al, 2019.

treatment_protocol: HCT116 (WT or TP53-/-) were first transiently transfected with STARRSeq plasmid library pool. After 5h, media was replaced with fresh media supplemented  with either DMSO, 5uM Nutlin-3A or 2uM Tunicamycin for 6h.

tag: sample type

value: plasmidPool


title: Sample 54 P89


title: RNA, GADD45A_enh_STARRSeq, HCT116 p53KO, Tunicamycin

description: PCR amplified cDNA (STARR-seq transcript)

source_name: colon

value: colon

value: human colorectal carcinoma

tag: transfection

value: STARRSeq plasmid library pool

tag: treatment

value: Tunicamycin (6 hrs)


title: Sample 47 P78


title: High stiffness replicate 3

tag: cell line


title: RNA, GADD45A_enh_STARRSeq, HCT116 p53KO, DMSO

value: DMSO (6 hrs)


title: Sample 52 P86

tag: Sex


title: Sample 58 P94


title: GFP+ cells, E11.5 kidneys, Tbx18 (GFP/+), rep2

value: NMRI

value: pooled male and female

tag: developmental stage

value: kidney rudiment


title: High stiffness replicate 1


title: RNA, GADD45A_enh_STARRSeq, HCT116, Tunicamycin


title: Low stiffness replicate 3

value: Low stiffness (500 Pa)


title: Low stiffness replicate 2


title: Sample 46 P76


title: RNA, GADD45A_enh_STARRSeq, HCT116 p53KO, Nutlin-3A

value: Nutlin-3A (6 hrs)


title: Low stiffness replicate 1


title: RNA, GADD45A_enh_STARRSeq, HCT116, DMSO


title: Sample 44 P73

value: Liver


title: Sample 43 P71

value: WT


title: Sample 45 P74

value: Female


title: Sample 38 P63


title: Sample 39 P64


title: Sample 41 P68


title: siCtrl_for_siPAIP_2nd

city: Wuhan

first: Dong

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Qvalue < =0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

growth_protocol: HepG2 cells were cultured under standard conditions with Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, and 100 U/mL penicillin.

extract_protocol:
The RNA was treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were assessed by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of each RNA sample was further verified by 1.5% agarose gel electrophoresis.electrophoresis.
A total 1μg RNA for each sample was used for RNA-seq library preparation. PolyA mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Invitrogen, Carlsbad, CA, USA) before directional RNA-seq library preparation. The frag¬mented RNA wereend repaired and 5' adaptor ligation. Then, reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified, amplified, and stored at -80°C until they were used for sequencing.

treatment_protocol: To knockdown PAIP1, siRNA against human PAIP1 transfection of HepG2 cells was performed using lipofectAMINE 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. Transfected cells were harvested after 48 h for analysis.

value: transfected with non-target control siRNA


title: Sample 37 P61

value: 0% Bean (Control)


title: siPAIP1_1st

value: transfected with PAIP1 siRNA


title: siPAIP1_2nd


title: siCtrl_for_siPAIP_1st


title: siPAIP1_3rd


title: siCtrl_for_siPAIP_3rd


title: p-SCC primary cells

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

institute: RWTH Aachen University

description: Urinary bladder

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials according to the manufacturer's instructions: hybridization 45°C for 16 hours at 60 rpm; Fluidics Station Program FS_450_0001.

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

data_processing: Raw image data were analysed with Affymetrix® Expression Console™ Software (Affymetrix, USA), and gene expression intensities were normalized and summarized with SST robust multiarray average algorithm (Affymetrix): SST-RMA. Further analyses was performed using the Transcriptome Analysis Console (TAC) Software of Affymetrix.

label: Biotin

source_name: p-SCC primary cells

label_protocol: Fragmented, biotinylated cDNAs were prepared from 300 ng total RNA using GeneChip WT Plus Kit according to the manufacturer's instructions.

growth_protocol: p-SCC cells were cultured in mammary stem cell (MSC) medium23 as spheres in a 3D 50% Matrigel (Corning, 35423) environment or expanded in 2D on culture plates coated with 2% Matrigel, as described previously for BCSCs (see 47. Metzger E, Stepputtis SS, Strietz J, Preca BT, Urban S, Willmann D, et al. KDM4 Inhibition Targets Breast Cancer Stem-like Cells. Cancer Res. 2017; 77: 5900-5912). Cell lines (SCaBER and J82) were cultured in DMEM medium (Gibco, Paisley, UK) supplemented with 10% fetal bovine serum (Gibco).

extract_protocol: Total RNA was isolated from patient tumor material using the automated Maxwell 16 LEV simplyRNA Tissue Kit (Promega, AS1280) according to the manufacturer's instructions. RNA from primary cultured tumor cells and cell lines were extracted using the Nucleospin RNA Plus Kit (Macherey-Nagel, 740984.50) according to the manufacturer's instructions.

treatment_protocol: Cells were not treated.

value: Pool of squamous bladder cancer cells


title: SCaBER cell line

description: Urinary bladder

source_name: SCaBER cell line

value: SCaBER


title: SCC tumor tissue

description: Urinary bladder

source_name: SCC tumor tissue

value: Squamous bladder carcinoma


title: Sample 36 P59

value: 70% Bean


title: COVID-19 patient3, Sputum

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 (hg38) 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: hg38
Supplementary_files_format_and_content: .h5ad

source_name: COVID-19 patient Sputum

extract_protocol: Cells  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 V3 (10x Genomics, 120237) following the manufacturer’s instruction. Sequencing was operated on an Illumina HiSeq X Ten

value: Sputum

tag: disease

tag: disease state

value: mild


title: J82 cell line

description: Urinary bladder

source_name: J82 cell line


title: RNA, GADD45A_enh_STARRSeq, HCT116, Nutlin-3A

value: colon

value: human colorectal carcinoma

value: STARRSeq plasmid library pool


title: Sample 34 P56

tag: strain


title: Sample 42 P69


title: Sample 40 P66


title: COVID-19 patient1, Sputum

value: severe


title: COVID-19 patient2, Sputum


title: COVID-19 patient4, Sputum


title: Sample 35 P58

value: 35% Bean


title: PBMC

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: hg38

source_name: PBMC

growth_protocol: Cells get from COVID-19 patient

extract_protocol:
Cells  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 V3 (10x Genomics, 120237) following the manufacturer’s instruction. Sequencing was operated on an Illumina HiSeq X Ten

tag: subject status

value: COVID-19 patient

value: peripheral blood mononuclear cell (PBMC)


title: Sample 31 P51

value: Liver

value: WT

value: Female


title: Sample 30 P49

source_name: Male, Liver, 70% Bean

value: Male


title: Sample 29 P48

source_name: Male, Liver, 35% Bean


title: Sample 28 P46

source_name: Male, Liver, 0% Bean (Control)

value: 0% Bean (Control)


title: Sample 27 P44


title: Tfap4 KO 8

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6
Reads were aligned to the mouse genome using the Rsubread aligner version 2.0.1
Fragment (read-pair) counts were summarized by Ensembl Gene ID using the Rsubread featureCounts function
Genes were identified using Gencode annotation to the mm10 genome, version M25
Assembly: mm10
Supplementary files format and content: tab-delimited text files wre written from the R prompt; columns represent Ensembl Gene ID, total gene length (total base count of all exons) and the number of fragments mapping to that gene

source_name: Bone marrow

extract_protocol:
Pre-B cells isolated from the bone marrow were lysed in QIAzol Lysis Reagent (Qiagen) and total RNA was extracted using the Qiagen miRNeasy Mini Kit according to manufacturer's protocol including optional on-column DNAse digestion.
An input of 100ng total RNA was used to prepare mRNA libraries using the Illumina TruSeq RNA sample Prep Kit according to manufacturer's protocol.

value: Bone marrow

value: Pre-B cells


title: Tfap4 KO 5


title: Tfap4 KO 6


title: Tfap4 KO 3


title: Tfap4 KO 4


title: Sample 25 P41


title: Tfap4 KO 7


title: Sample 26 P43


title: Sample 24 P39

value: 70% Bean


title: Tfap4 KO 1


title: Sample 23 P38


title: Control 6

value: Control


title: Control 4


title: NAFLD_rep2

city: Guangzhou

first: Sijia

last: Liang

address: 74 Zhongshan 2 Rd

department: Pharmacology

institute: Sun Yat-Sen University

data_processing:
Quality control.Clean datas were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data through custom perl and python scripts.
The small RNA tags were mapped to reference sequence by Bowtie without mismatch to analyze their expression and distribution on the reference.  Known miRNA alignment.Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, mirdeep2 and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures.
Remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA.
Target gene of miRNA was predicted by psRobot_tar inmiRanda (Enright et al, 2003).
miRNA expression levels were estimated by CPM (counts per million). Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3).
Assembly: hg38
Supplementary files format and content: xlsx
Supplementary files format and content: miRNA expression read counts were included in excel file with CPM value.

source_name: liver cells

extract_protocol:
RNA degradation and contamination was monitored on 1% agarose gels.RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA).

value: liver cells

value: NAFLD

value: Untreated


title: Control 3


title: Sample 22 P36


title: NAFLD_rep1


title: human Pleura effusion

description: scRNA-seq

source_name: human Pleura effusion

growth_protocol: Cells from COVID-19 patient

extract_protocol:
polyA
Cells  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 V3 (10x Genomics, 120237) following the manufacturer’s instruction. Sequencing was operated on an Illumina HiSeq X Ten

value: Pleura effusion


title: Sample 21 P34


title: Control 2


title: Control 1


title: non-steatosis_rep1

value: non-steatosis


title: Ripk3 knock-out 6

data_processing:
The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6
Reads were aligned to the mouse genome by STAR version 2.5.3a
Fragment (read-pair) counts were summarized by Ensembl Gene ID using the Rsubread featureCounts function
Genes were identified using Gencode annotation to the mm10 genome, version M23
Assembly: mm10
Supplementary files format and content: tab-delimited text files wre written from the R prompt; columns represent Ensembl Gene ID, total gene length (total base count of all exons) and the number of fragments mapping to that gene

source_name: CD8 T-cell

extract_protocol:
RNA extraction was performed using the RNeasy® Mini Kit (Qiagen, Venlo, Netherlands)
An input of <500 pg of total RNA were prepared and indexed separately for illumina sequencing using the SMART-seq® v4 Ultra® low input RNA kit (Clontech, Takara-Bio, Shiga, Japan) as per manufacturer’s instructions. Each library was quantified using the Agilent Tapestation and the Qubit™ DNA BR assay kit for Qubit 3.0® Fluorometer (Thermo Fisher Scientific). The indexed libraries were pooled and diluted to 1.5 pM for paired end sequencing (2 x 81 cycles) on a NextSeq 500 instrument using the v2 150 cycle High Output kit (illumina) as per manufacturer’s instructions.

tag: batch

value: CD8 T-cell

value: Ripk3 knock-out


title: Sample 20 P33

tag: tissue

value: 35% Bean


title: Tfap4 KO 2

tag: genotype


title: Ripk3 knock-out 7


title: Ripk3 knock-out 4


title: Sample 19 P31

value: Liver


title: Ripk3 knock-out 5


title: Ripk3 knock-out 3


title: Hs islets_DFMO and Proinflammatory cytokines_Donor 5

city: Chicago

first: Raghavendra

last: Mirmira

state: IL

address: 900 E 57th St

institute: University of Chicago

data_processing:
ROSALIND RNA-seq method:
Reads were trimmed using cutadapt. Quality scores were assessed using FastQC.
Reads were aligned to the Homo sapiens genome build hg19 using STAR.
Individual sample reads were quantified using HTseq and normalized via Relative Log Expression (RLE) using DESeq2 R library.
DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction.
Assembly: hg19
Supplementary files format and content: tab-delimited text files

source_name: Human islets from cadaveric organ donors

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit Set A/B following manufacturer's protocols.

treatment_protocol: Upon receipt, human islets were cultured in fresh human islet medium and allowed to recover for 24 h. Hand-picked islets were distributed into culture wells for 4 conditions: Vehicle, 5 mM DFMO, proinflammatory cytokines (50 IU IL-1β + 1000 IU IFN-γ), and proinflammatory cytokines + 5 mM DFMO. The islets were pre-treated with 5 mM DFMO for 24 h prior to addition of proinflammatory cytokines. Incubation proceeded for another 24 h. After the completion of the treatments, the islets were washed twice with PBS. The pellets were then stored at -80°C until RNA-sequencing.

value: Treated with DFMO and IL-1β and IFN-γ for 24 hours


title: Hs islets_DFMO and Proinflammatory cytokines_Donor 4

value: Human islets from cadaveric organ donors


title: Ripk3 knock-out 2

value: Male


title: Hs islets_DFMO and Proinflammatory cytokines_Donor 3


title: Ripk3 knock-out 1


title: Control 5


title: Sample 17 P28

value: WT


title: Wild type 4

value: Female

value: Wild type


title: non-steatosis_rep2


title: Hs islets_DFMO and Proinflammatory cytokines_Donor 2


title: Wild type 3


title: Hs islets_DFMO and Proinflammatory cytokines_Donor 1


title: Wild type 2


title: Sample 16 P26

value: 0% Bean (Control)


title: Wild type 1


title: Sample 15 P24

value: 70% Bean


title: Mettl3-HKO rep3

city: Harbin

first: Zheng

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house  perl scripts. In this step, clean data (clean reads) were obtained by removing reads  containing adapter, reads containing ploy-N and low quality reads from raw data. At  the same time, Q20, Q30 and GC content the clean data were calculated. All the  downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from  genome website directly. Index of the reference genome was built using Hisat2 v2.0.5  and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.  We selected Hisat2 as the mapping tool for that Hisat2 can generate a database  of splice junctions based on the gene model annotation file and thus a better mapping  result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each  gene. And then FPKM of each gene was calculated based on the length of the gene  and reads count mapped to this gene. FPKM, expected number of Fragments Per  Kilobase of transcript sequence per Millions base pairs sequenced, considers the  effect of sequencing depth and gene length for the reads count at the same time, and is  currently the most commonly used method for estimating gene expression levels
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was  implemented by the clusterProfiler R package, in which gene length bias wascorrected.  GO terms with corrected Pvalue less than 0.05 were considered significantly enriched  by differential expressed genes.  KEGG is a database resource for understanding high-level functions and utilities  of the biological system, such as the cell, the organism and the ecosystem, from  molecular-level information, especially large-scale molecular datasets generated by  genome sequencing and other high-through put experimental technologies  (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the  statistical enrichment of differential expression genes in KEGG pathways.
Assembly: grcm38_p6
Supplementary files format and content: excel, gene_fpkm

source_name: Liver

growth_protocol: Mettl3flox/flox and HKO mice were fed with a normal chow diet for 8 weeks.

extract_protocol:
Livers were removed, flash frozen on liqid nitrogen, and total RNA was harvested using TriPure reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached  magnetic beads. Fragmentation was carried out using divalent cations under elevated  temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand  cDNA was synthesized using random hexamer primer and M-MuLV Reverse  Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently  performed using DNA Polymerase I and RNase H. Remaining overhangs were  converted into blunt ends via exonuclease/polymerase activities. After adenylation of  3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were  ligated to prepare for hybridization. In order to select cDNA fragments of  preferentially 250~300 bp in length, the library fragments were purified with AMPure  XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA)  was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5  min at 95 °Cbefore PCR. Then PCR was performed with Phusion High -Fidelity DNA  polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products  were purified (AMPure XP system) and library quality was assessed on the Agilent  Bioanalyzer 2100 system.


title: Hs islets_Proinflammatory cytokines_Donor 5

value: Treated with IL-1β and IFN-γ for 24 hours


title: Sample 18 P29


title: Sample 14 P23


title: Hs islets_Proinflammatory cytokines_Donor 4


title: Mettl3-HKO rep1


title: Mettl3 flox/flox rep3

value: Mettl3 flox/flox


title: Sample 12 P19


title: Mettl3 flox/flox rep2


title: Mettl3 flox/flox rep1


title: Human_ovary8_snATAC-seq

first: Chen

last: Jin

institute: Columbia University Medical Center

data_processing:
For snRNA-seq, fastq files were processed with Cellranger 3.1.0 by "count" function with pre mRNA reference generated from refdata-cellranger-GRCh38-3.0.0 by manufacture's instruction.
For snATAC-seq, fastq files were processed with CellrangerATAC 2.0.0 by "count" function with refdata-cellranger-atac-GRCh38-1.2.0
Assembly: GRCh38
Supplementary files format and content: Filtered barcode-feaure matrix(snRNA-seq) and Filtered barcode-peak matrix and fragment file(snATAC-seq)

source_name: ovary

extract_protocol:
The nuclei isolation was performed according to 10× Genomics protocol CG000212 (Rev B) with ~100 mg frozen human ovary sample.
10x Chromium Single Cell ATAC Reagent Kits (v1)

tag: age

tag: gender

value: female

value: ovary


title: Sample 11 P18


title: Human_ovary7_snATAC-seq


title: Human_ovary6_snATAC-seq


title: Hs islets_Proinflammatory cytokines_Donor 2


title: Human_ovary5_snATAC-seq


title: Hs islets_Proinflammatory cytokines_Donor 1


title: Sample 10 P16


title: Human_ovary4_snATAC-seq


title: Human_ovary3_snATAC-seq


title: Hs islets_DFMO_Donor 4

value: Treated with DFMO for 24 hours


title: Sample 9 P14


title: Sample 8 P13


title: Mettl3-HKO rep2


title: Hs islets_Proinflammatory cytokines_Donor 3


title: Sample 13 P21


title: Human_ovary2_snATAC-seq


title: Hs islets_DFMO_Donor 3


title: cell, infection, rep2

city: Bei Jing

first: Yuting

last: Shi

address: No. 97 Ma Chang, Tongzhou District,Beijing of China

institute: Beijing Chest Hospital, Capital Medical University

data_processing:
fastx (version:0.0.13)
The filtering main steps are as follows:1. Remove the joint sequence contained in reads;2.Remove bases with mass Q lower than 10 at the 3 'UTR, Q=-10logerror_ratio;3. Remove reads less than 10 in length.
Bowtie was used to compare 18-40nt clean reads with the reference genome, and the alignment process allowed 1 base mismatch
The number of reads compared to each miRNA was normalized by permanent TMM method, and then converted into TPM (formula: number of reads on a miRNA ×106/ number of total reads) for standardization of miRNA expression level
The edgeR was used to conduct miRNA analysis of differences among samples, and the p-value was obtained and corrected by multiple hypothesis testing. The threshold of p-value was determined by controlling FDR, and the corrected p-value was q-value. Meanwhile, the differential expression multiple was calculated according to TPM value, namely, Fold-change.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: blood

growth_protocol: THP-1 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (Cat# 74004, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer/Agilent 4200 TapeStation (Agilent technologies, Santa Clara, CA, US)/.Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
According to the experimental instructions, the purified Total RNA was subjected to 3 'end joint connection, 5' end joint connection, reverse transcription, amplification, size selection of cDNA library, purification and other steps to complete the construction of sequencing sample library.

treatment_protocol: THP1 cells (2×105/ml) were differentiated using 100μm/ml phorbol 12-myristate 13-acetate(PMA) for 36h.

value: blood

tag: cell type

value: Human myeloid leukemia mononuclear cells

value: untreated

value: M.tb (H37Rv) infection


title: cell, infection, rep3


title: cell, infection, rep1


title: Sample 7 P11

value: Liver

tag: diet


title: Human_ovary1_snATAC-seq


title: Sample 6 P09


title: Human_ovary8_snRNA-seq

molecule: nuclear RNA

extract_protocol:
The nuclei isolation was performed according to 10× Genomics protocol CG000393 (Rev A) with ~100 mg frozen human ovary sample.
10x Chromium Single Cell 3' Reagent Kits (v3)


title: Sample 5 P08

value: 35% Bean


title: cell, uninfection, rep3

value: uninfected


title: Hs islets_DFMO_Donor 1

value: Human islets from cadaveric organ donors


title: Hs islets_Unstimulated_Donor 5

value: Unstimulated control


title: Human_ovary7_snRNA-seq


title: Hs islets_DFMO_Donor 2


title: cell, uninfection, rep2

value: WT


title: Hs islets_DFMO_Donor 5


title: Sample 4 P06

value: Male

value: 0% Bean (Control)


title: Hs islets_Unstimulated_Donor 4


title: cell, uninfection, rep1


title: Human_ovary6_snRNA-seq


title: Human_ovary5_snRNA-seq


title: Sample 3 P04

value: 70% Bean


title: CAR T cells, 9 patients: 5xCR, 4xPD IP-3 Surface-2

city: Houston

first: Navin

last: Varadarajan

state: Texas

address: 4722 Calhoun Rd

department: Chemical and Biomolecular Engineering

institute: University of Houston

description: 10x Genomics

data_processing:
We processed gene expression FASTQ files generated with Illumina sequencer using the Cell Ranger pipeline (version 6.0.0, 10x Genomics) for read alignment and generation of feature-barcode matrices. The output files then were uploaded into R (version 4.0.1) for further processing using Seurat Package (version 4.1.0). We used the SAVER package first, to recover the gene expression profile in the data. Then we filtered out the cells with high mitochondrial gene expression (more than 15% of the read counts) and we ended up with 21,469 cells from nine patients with mean unique molecular identifier (UMI) of 7738. Demultiplexing was performed by comparing the reads of the hashtags (TotalSeq C anti-human hashtag 1,2 and 3 antibodies) for each cell.
Assembly: GRCh38
Supplementary files format and content: Compressed csv (csv.gz) of normalized gene expression for all the patients in a table

source_name: Human blood cells

extract_protocol:
CD19-targeted CAR T cells were washed out from infusion bags. Cells were resuspended in PBS solution containing 0.4% BSA and counted to measure cell concentration and viability.
We performed scRNA-seq for nine samples (5 CR and 4 PD) with enough number of residual cells. We first used dead cell removal kit (Miltenyi Biotec) containing MicroBeads for the magnetic labeling of dead cells and we then removed the dead cells by passing the resuspended cells through the magnetic field of a MACS separator. We performed library preparation process in three batches. For each batch, we used three different TotalSeq C anti-human Hashtag Antibodies (BioLegend, TotalSeq C anti-human hashtag 1,2 and 3 antibody) to multiplex the samples as per the manufacturer’s protocols. Next, we did transcriptome capturing using 10x Chromium platform (10x Genomics). We used Chromium single cell 5’ reagent v2 kit for gene expression profiling according to the manufacturer’s instructions.

value: T cells

value: Human blood cells

value: Blood T cells from patients with LBCL, transduced with CAR (chimeric antigen receptor)


title: Hs islets_Unstimulated_Donor 3


title: Human_ovary4_snRNA-seq

city: New York

value: female

value: ovary


title: Sample 32 P53

source_name: Female, Liver, 35% Bean

value: Female


title: Hs islets_Unstimulated_Donor 2


title: CAR T cells, 9 patients: 5xCR, 4xPD IP-3 Surface-1

description: 10x Genomics


title: Hs islets_Unstimulated_Donor 1


title: Sample 1 P01


title: Human_ovary3_snRNA-seq


title: CAR T cells, 9 patients: 5xCR, 4xPD IP-2

description: 10x Genomics


title: CAR T cells, 9 patients: 5xCR, 4xPD IP-2 Surface

description: 10x Genomics


title: sorted CD45-CD235a-CD271+ cells (MSC O1)

city: Lund

first: Stefan

last: Lang

address: Sölvegatan 17

department: Molecular Hematology

institute: Lund University

data_processing:
Raw 10 result folders were converted to fastq files using the cellranger mkfastq program. Version
fastq files were mapped against the human genome file human_GRCh38_gencode.v31.600. Versions: kallisto/0.46.0 bustools/0.39.3
The single quantified loom files were merged and the data was then exported  using scipy.sparse.csr_matrix
Genome_build: human_GRCh38_gencode.v31.600
Supplementary_files_format_and_content: CellRanger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: bone marrow

extract_protocol:
FACS-sorted BM-MNC cells were encapsulated into emulsion droplets as single cells using the Chromium Controller (10X Genomics).
scRNAseq libraries were constructed using the Chromium Single Cell Gene Expression 3’ v3 Reagent Kit according to the manufacturer’s instructions. Reverse transcription and library preparation were performed on a C1000 Touch Thermal Cycler (Bio-Rad). Amplified cDNA and final libraries concentrations were measured with a Qubit 4 Fluorometer (Invitrogen) using the dsDNA High Sensitivity Assay (Invitrogen). cDNA and library traces were evaluated on a TapeStation (Agilent) using High Sensitivity D5000 and D1000 Screen Tapes (Agilent). Individual libraries were diluted to 1.5 nM and pooled for sequencing. Pools were sequenced on a NovaSeq 6000 (Illumina) aiming for a sequencing depth of 50.000 reads per cell.
scRNAseq

value: bone marrow

value: non-hematopoietic cells

tag: cell subset

value: sorted CD45-CD235a-CD271+ cells


title: Human_ovary2_snRNA-seq


title: Sample 33 P54

source_name: Female, Liver, 70% Bean

extract_protocol:
Liver was harvested and snap frozen in liquid nitrogen. RNA was isolated from liver the RNeasy mini kit (Qiagen, Inc., USA).
RNA libraries were prepared for sequencing using standard Illumina protocols (Nugen Universal mRNA kit, Tecan Genomics, Inc., Redwood City, CA, USA)

value: Liver


title: MUSKARDIA, replicate 3, scRNAseq

city: Shanghai

first: Wenyong

last: Lin

address: No. 528, Zhangheng Road, Pudong New Area

department: Cardiovascular Research Institute of Traditional Chinese Medicine

institute: Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine

description: 10x Genomics

data_processing:
Reads were processed using the Cell Ranger 4.0 pipeline with default and recommended parameters. FASTQs generated from Illumina sequencing outputs were aligned to the mouse genome, version GRCm38, using the STAR algorithm. Next, gene barcode matrices were generated for each sample by counting the UMIs and filtering non-cell-associated barcodes. Finally, we generated a gene barcode matrix containing barcoded cells and gene expression counts. This output was then imported into the Seurat (v3.2.0) R toolkit for quality control and downstream analysis of the single-cell RNA-seq data
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: heart

extract_protocol:
Mice hearts were harvested and frozen after sacrificing them. Frozen tissue samples were cut into pieces <0.5 cm and homogenized using a glass Dounce tissue grinder (Sigma, cat. no. D8938). The tissue was homogenized 25 times with pestle A and 25 times with pestle B in 2 ml of ice-cold nuclei EZ lysis buffer. The sample was then incubated in ice for 5 min with 3 ml of cold EZ lysis buffer. Nuclei were centrifuged at 500 g for 5 min at 4°C, washed with 5 ml ice-cold EZ lysis buffer, and incubated on ice for 5 min. After centrifugation, the nuclear pellet was washed with 5 ml nuclei suspension buffer (NSB; consisting of 1% PBS, 0.01% BSA, and 0.1% RNase inhibitor (Clontech, cat. no. 2313A)). Isolated nuclei were resuspended in 2 ml NSB, filtered through a 35 μm cell strainer (Corning-Falcon, cat. no. 352235) and counted. A final concentration of 1,000 nuclei per μl was used for loading onto a 10x channel.
Beads with a unique molecular identifier (UMI) and cell barcodes were loaded close to saturation such that each cell was paired with a bead in a gel beads-in-emulsion. After exposure to the cell lysis buffer, polyadenylated RNA molecules were hybridized into the beads. Beads were retrieved in a single tube for reverse transcription. For complementary deoxyribonucleic acid (cDNA) synthesis, each cDNA molecule was tagged on the 5’ end (that is, the 3’ end of a messenger RNA transcript) with UMI and a cell label indicating its cell of origin. Briefly, 10× beads were subjected to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked to the cell barcode and UMI. All remaining procedures, including library construction, were performed according to the standard manufacturer’s protocol (Chromium Single Cell 3ʹ v3). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and Qubit high- sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina) using 2 × 150 chemistry.

value: heart

value: Gavage with MUSKARDIA solution for 7 days before operation, LAD ligation for 30 minutes, followed by recanalization for 24 hours.


title: CAR T cells, 9 patients: 5xCR, 4xPD IP-1 Surface

description: 10x Genomics


title: CAR T cells, 9 patients: 5xCR, 4xPD IP-3

description: 10x Genomics


title: MUSKARDIA, replicate 2, scRNAseq

description: 10x Genomics


title: Mpfc3, PBS

first: Shuang-Qi

last: Gao

address: tianhe road 600

institute: Third Affiliated Hospital of Sun Yat-sen University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: brain

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: brain

value: PBS


title: I/R, replicate 3, scRNAseq

description: 10x Genomics

value: Gavage with vehicle for 7 days before operation, LAD ligation for 30 minutes, followed by recanalization for 24 hours.


title: MUSKARDIA, replicate 1, scRNAseq

description: 10x Genomics


title: sorted CD45-CD235a-CD271+ cells (MSC O2)


title: sorted CD45-CD235a-CD271+ cells (MSC Y3)


title: CAR T cells, 9 patients: 5xCR, 4xPD IP-1

description: 10x Genomics


title: sorted CD45-CD235a-CD271+ cells (MSC Y2)


title: sorted CD45-CD235a- cells (BM O2)

value: sorted CD45-CD235a- cells


title: I/R, replicate 2, scRNAseq

description: 10x Genomics


title: Sample 2 P03

data_processing:
CLC Genomics Workbench v 21.0.3
Raw sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC Genomics Workbench (parameters: Quality limit = 0.05; Maximum number of ambiguities = 2; automatic read-through adapter trimming; maximum length = 150; Trim end = 3'-end)
The resulting high-quality reads were mapped to Mus musculus genome reference, version GRCm38, using gene ontology associations (20150630)  in CLC Genomics Workbench
Read count extraction was performed using CLC Genomics Workbench
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files with total counts values for each sample and matrix file

value: WT

value: Male

value: 35% Bean


title: I/R, replicate 1, scRNAseq

description: 10x Genomics


title: Mpfc1, PBS


title: sham, replicate 3, scRNAseq

description: 10x Genomics

value: Gavage with vehicle for 7 days before operation, needles only, no ligation.


title: Mpfc4, TSP1


title: Mpfc3, TSP1


title: sorted CD45-CD235a- cells (HS BM 2)


title: sham, replicate 2, scRNAseq

description: 10x Genomics


title: Mpfc2, TSP1


title: Mpfc1, TSP1


title: F - Cre control  [4047]

status: Public on Mar 11 2023

city: Blacksburg

first: Hehuang

last: Xie

state: VA

address: 1015 Life Science Cir

department: Department of Biomedical Sciences and Pathobiology

institute: Virginia Tech

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore-3.8.2 (parameter --paired --phred33 --fastqc --illumina -q 30 --length 30)
Trimmed sequence reads were mapped to GRCm38 using STAR 2.7.9  (parameters- default settings)
Read count is extracted using STAR-2.7.9 --quant mode
Assembly: GRCm38
Supplementary files format and content: comma-delimited text files from the second column of STAR-2.7.9 quant output
Supplementary files format and content: sample information of the read count table

source_name: pituitary

extract_protocol:
RNA extraction was performed using Rneasy mini kit (Qiagen). 1.5 ug of total RNA was used for non-stranded RNA-seq.
non-stranded RNA-seq

value: pituitary

value: endocrine


title: Human_ovary1_snRNA-seq

value: female

value: ovary


title: F - Cre control  [4046]

value: Female


title: sorted CD45-CD235a- cells (BM O1)

value: bone marrow

value: non-hematopoietic cells


title: F - Cre control  [4048]


title: M - Cre control  [4051]


title: sham, replicate 1, scRNAseq

description: 10x Genomics

value: heart


title: CL1-0_Stable-expreesing shMITF_shRNA3

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

description: Gene expression data from CL1-0 stable-expressing MITF

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 plus 2.0 GeneChip on Affymetrix Hybridization Oven 645, 60 RPM, then washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The expression data were analyzed by GeneSpring GX 13.0 (Silicon Genetics, Redwood City, CA). The Affymetrix CEL files were transformed by GC-RMA algorithm, and each probe set was summarized using the median of the corresponding probes.

source_name: CL1-0_stably-expressing MITF gene

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)(Santa Clara, CA, USA, http://www.affymetrix.com).

growth_protocol: The human lung cancer cell line, CL1-0, was grown in RPMI-1640 media supplemented with 10% FBS. All cell lines were incubated at 37°C in a humidified 20% O2/5% CO2 environment.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: CL1-0 cells were individually transfected with three scrembles and shMITF, respectively. The stable-expressing cells were maintained in complete media with puromycin.

tag: tumor type

value: human lung cancer cell line

tag: cell line source  ethnicity

value: Asian

tag: cell line source age

value: 64 years

tag: cell line source gender

value: male

tag: genotype/variation

value: stably-expressing MITF gene


title: sorted CD45-CD235a-CD271+ cells (Y1)

value: sorted CD45-CD235a-CD271+ cells


title: CL1-0_Stable-expreesing shMITF_shRNA2

tag: cell line


title: CL1-0_Stable-expreesing shMITF_shRNA1


title: Mpfc2, PBS

value: brain

tag: treatment

value: PBS


title: M - Cre control  [4052]

value: Male


title: CL1-0_Stable-expressing scramble_vector2

description: Gene expression data from CL1-0 stable-expressing an pEF-V5 empty vector

source_name: CL1-0_stably-expressing scramble_vector

value: stably-expressing scramble_vector


title: M - Cre control  [4049]

value: pituitary

value: endocrine


title: F - complete wild type  [4055]


title: CL1-0_Stable-expressing scramble_vector3


title: M - complete wild type  [4054]


title: F - complete wild type  [4056]


title: M - complete wild type  [4053]


title: F - complete wild type  [4045]


title: F - Egr1cKO [4946]


title: M - complete wild type  [4042]


title: F - Egr1cKO [4944]


title: sorted CD45-CD235a- cells (HS BM 1)

value: sorted CD45-CD235a- cells


title: CL1-0_Stable-expressing scramble_vector1


title: M - Egr1cKO [4948]


title: F - Egr1cKO [4954]

value: Female


title: M - Egr1cKO [4937]


title: M - Egr1cKO [4947]


title: F - Egr1cKO control  [4951]


title: F - Egr1cKO control  [4953]


title: F - Egr1cKO control  [4952]


title: M - Egr1cKO control  [4935]


title: M - Egr1cKO control  [4950]