title: Hepatocytes NTsi rep2

city: Ottawa

first: Ruth

last: McPherson

state: Ontario

address: 40 Ruskin

institute: UOHI

description: Expression console values

hyb_protocol: Samples were hybridized with HuGene-2_0-st  arrays (Affymetrix) and scanned at the Centre for Applied Genomics (TCAG), Toronto

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Relative expression changes assessed by Expression Console (RMA)

label: Biotin

source_name: Hepatocyte

label_protocol: Standard Affymetrix protocol

growth_protocol: HepG2/HuH-7:  Low glucose DMEM supplemented with 10% serum; media left unchanged throughout procedure. Primary human hepatocytes: Obtained from Sigma and grown in William's E media with supplements (MED-HHCM: Sigma), which was replaced daily.

extract_protocol: Cells were lysed with TriPure Isolation Reagent (Roche) and the total RNA was isolated using the Direct-zol RNA Miniprep (hepatoma cells) or Microprep (hepatocyte) Kits (Zymo Research).  One repeat from HuH7  (COP1si) had low RNA quality (low RIN) and was excluded from the analysis.

treatment_protocol: 30-40% confluent hepatoma or 70-80 % conluent primary hepatocyes were transfected for 96 h with 10 nM of a RFWD2/COP1 silencing RNA.  Treatment was continuous but for primary cells, media was changed daily.

value: Human Hepatocyte (cryopreserved)

tag: transfected with

value: NTsi


title: Hepatocytes NTsi rep3

status: Public on Nov 01 2022

type: RNA

country: Canada

description: Expression console values

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: cell line


title: Hepatocytes NTsi rep1

description: Expression console values


title: control.24hr.1

city: South San Francisco

first: Josh

last: Kaminker

state: CA

address: 1 DNA Way

department: Bioinformatics and Computational Biology

country: USA

institute: Genentech

hyb_protocol: 750 ng of the labeled cRNA was fragmented and hybridized to arrays as described in manufacturer’s hybridization kit

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent’s Feature Extraction software 11.0 was used to analyze acquired array images

organism: Mus musculus

source_name: RNA purified from cultured neurons

label_protocol: Briefly, total RNA sample was converted to double-stranded cDNA and then to Cy-dye labeled cRNA using Agilent’s Quick Amp Labeling Kit. The labeled cRNA was purified using RNeasy mini kit (Qiagen, San Diego, CA). cRNA yield and Cy-dye incorporation was determined using ND-1000 spectrophotometer (Thermo Scientific)

growth_protocol: DIV 21 dissociated mouse hippocampal neurons in 6 well plates were treated by Vehicle, 100 μM AP5, 100 nM NVP-AAM077 or 1 μM Ro25-4891 for 24 hours in a cell culture incubator

extract_protocol: Total RNA was isolated using RNeasy plus kit (Qiagen)

tag: tissue

value: neurons

source_name: universal mouse reference (Stratagene, La Jolla, CA)

value: universal mouse reference


title: Hepatocytes COP1si rep3

description: Expression console values


title: ATAC Day_5_Veh_2

type: SRA

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

library_source: genomic

data_processing:
Sequenced samples were trimmed with Trimmomatic, mapped using Bowtie2 and replicate mapped files merged with SAM tools. Coverage files were generated with deepTools. Open chromatin chromatin was detected with MACS2 using a p value < 1x10-7 and a q value of less than 0.1 and differentially regulated regions identified with DiffBind using a 2-fold enrichment threshold and lower than 0.01 p value. Bed files were analyzed with Bedtools, and visualized alongside coverage files on IGV and Sparkpy.
Assembly: hg38
Supplementary files format and content: Genomic tracks as BigWig files

molecule: genomic DNA

source_name: LNCaP

extract_protocol:
Libraries were prepared using the Nextera DNA library Prep Kit (Illumina) adapting a published protocol. Cells were washed in PBS and then lysed for 3 min in 10 mM Tris-HCl, pH 7.4,10 mM NaCl, 3 mM MgCl2 and 0.1% Igepal CA-630, 0.1% Tween-20, 0.01% Digitonin, 1% BSA (all SIGMA). Cold wash buffer (same as lysis buffer without Igepal and digitonin) was added to the lysate and mixed three times by inverting the tubes and immediately spun 500 x g for 5 min, 4°C. Supernatant was discarded and nuclei resuspended in 2.5 μl TDE1 (Nextera Tn5, 100 nM final), 0.5 μl 1% Digitonin (0.01% final), 0.5ul 10% Tween-20 (1% final) 16.5 μl PBS and 5 μl water and incubated for 30 min at 37°C with gentle mixing (1000 RPM).
DNA was purified with the QIAGEN MinElute PCR Purification Kit (Thermo Fisher Scientific). PCR amplification was performed with the NEBNext High-Fidelity 2x PCR Master Mix (New England Labs) using custom Nextera PCR Primers containing barcodes. Adaptors were removed with AMPure XP beads according to manufacturer’s protocol. Libraries were quantified with the Qubit and sequenced with a NovaSeq 6000 (Illumina).

value: LNCaP

tag: treatment

value: Vehicle

tag: time point

value: Day 5


title: control.24hr.3


title: Hepatocytes COP1si rep1

description: Expression console values


title: Ro25.24hr.3


title: control.24hr.4


title: HuH7 NTsi rep 3

description: Expression console values

value: Human Hepatocyte carcinoma cell line


title: Ro25.24hr.5


title: Hepatocytes COP1si rep2

description: Expression console values


title: Ro25.24hr.4


title: control.24hr.5


title: ATAC Day_26_Veh_1

value: Day 26


title: control.24hr.2


title: NVP.24hr.5


title: Ro25.24hr.1


title: HuH7 NTsi rep 2

description: Expression console values


title: NVP.24hr.4


title: Ro25.24hr.2


title: HuH7 NTsi rep 1

description: Expression console values


title: ATAC Day_5_Veh_1


title: ATAC Day_5_R1881_1


title: A375-PPAP2.2 cells, Blue light, 6 hour

city: Bunkyo-Ku

first: Yoshibumi

last: Ueda

state: Tokyo

address: 7-3-1 Hongo

department: Chemistry

country: Japan

institute: The University of Tokyo

library_source: transcriptomic

data_processing:
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh38 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Skin

growth_protocol: A375-PPAP2.2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using cell scrapers and extracted by Rneasy mini plus kit (Qiagen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: The medium was replaced with DMEM containing 1% FBS for serum starvation 3 h before blue light irradiation (6 and 24 hours)

value: Skin

value: epithelial

tag: disease

value: melanoma

value: Blue light

value: 6 hours


title: A375-PPAP2.2 cells, Blue light, 24 hour

value: 24 hours


title: 200gLib_TeloHAEC_Dialout_2.2

city: Stanford

first: Jesse

last: Engreitz

address: 240 Pasteur Drive

institute: Stanford University

description:
dialout for 2 of 2 biological replicates. Technical replicate library #2.
Dialout library to link CBCs to guides

data_processing:
Fastq files were de-multiplexed by index primer
Demultiplexed fastq files for the same sample, with the same index, and from the same sequencing run were concatenated
Note, for each scRNAseq library, there were four 10xGenomics index primers for each library, designated SAMPLEID_1 _2 _3 & _4 (for 50 gene library fastq files) or _a, _b, _c & _d (for 200 gene library files)
See the Sample Information column, for information about cases where libraries were resequenced, or where multiple libraries were made from the same sample
1) We ran CellRanger (which maps reads to the human genome, assigns reads to the distinct CellBarcodes (CBCs) for each droplet, and counts reads in each droplet for all transcripts in the human genome.
1) CellRanger distinguishes droplets with true cells from droplets with debris or ambient RNA, and generates a matrix of genes by CBCs (the filtered feature barcode matrix), which was used for downstream analysis.
2) Dialout libraries linking CBCs to guides were sequenced to saturation (~40x coverage) using either Illumina NextSeq or Novaseq (as detailed in the Sample Information column).
2) Dialout read 1 covers the 10x Genomics barcode/CBC and UMI. Read 2 covers 24 invariant bases of U6 promoter sequence before reading into the guide protospacer sequence
Dialout analysis: 1) dialout reads with fewer than 4 exact duplicate were removed to reduce noise from PCR chimeras, 2) for each cell barcode x guide combination, the number of distinct Unique Molecular Identifiers (UMIs) was counted. The guide with the highest number of UMIs, plus 2nd, 3rd and 4th place guides were recorded.
Processed dialout data was used to assign whether each CellRanger cell barcode had one cell (singlet) or multiple cells (multiplet). Singlet status & the ID of top guides for singlets is available in the …calls.tsv files associated with each scRNAseq sample (also described further, under "processed data files format")
For the Supplementary files: 200gLib_TeloHAEC_DE_{p.values,log2fcs}.txt, we subset the cell ranger genes x barcodes matrix to only those barcodes corresponding to singlet cells (1 cell & 1 guide, as defined by in the calls.tsv files for each library), & combined the data from both bioreps. We then applied edgeR to the RDS genes x singlets table, to detect differentially expressed genes for singlet cells with guides to each target (up to 15 guides) versus singlet cells with non-targeting or safe targeting guides. Individual edgeR results tables for each contrast were then aggregated to give genes x perturbation tables of log2 fold changes & p.values, respectively.
Assembly: hg19
Supplementary files format and content: Matrix files (.mtx). Filtered feature barcode matrices with rows=genes and columns=cell barcodes, and values=read counts, for all high quality cells called by CellRanger. Includes all reads from each sample (both Novaseq runs). To read, in R, do: library(Matrix);mymatrix=readMM("filename")
Supplementary files format and content: Barcodes files (barcodes.tsv). The list of cell barcodes (CBCs) for high quality cells. Use for column names of the extracted matrix file.
Supplementary files format and content: Features files (features.tsv). Tab delimited table of gene names (symbols & ENSEMBL gene numbers) quantified by CellRanger. User for row names of the extracted matrix file. Features should be the same for all sample matrices.
Supplementary files format and content: Singlet calls files (calls.tsv). Tab delimited table, with header row, with columns: CBC_10x (cell barcode, in the same order as barcodes.tsv), Guide (guide protospacer sequence), Gene(gene/target of top guide), UMI_count (# of UMIs for guide with most UMIs), Good_singlet (1 if cell is a singlet, 0 otherwise), Multiplet (1 if singlet, 2, 3 or 4 for doublet, triplet or quadruplet, 0 or NA if no guide was assigned to the cell. Specific column names may vary by file, but denote these same things. For the 50 gene library singlets were defined as cells that had 6+ UMIs for the top guide and less than 1/5th of this for the 2nd most abundant guide. For the 200 gene library, singlets were defined as cells with 4+ UMIs for the top guide and <1/5th this for the 2nd most abundant guide.

source_name: Vascular

growth_protocol: Eahy926 cells (a HUVEC-A549 hybrid cell line, commonly used as an endothelial cell culture model), was grown in DMEM +10% FBS. Telomerase-immortalized human aortic endothelial cells (TeloHAEC) and were purchased from ATCC, and grown in Lifeline VEGF endothelial cell media with 1x Penn/Strep. TeloHAEC were plated at a density of 0.5-1.0 x 106 cells per 10cm plate and split before reaching 4 x 106/plate (3 to 4 days).

extract_protocol:
Cells were either loaded at the maximum recommended concentration (16,000 cells/lane, "16k"), or "superloaded" at 150,000 cells per 10X Chromium controller lane ("150k"). 1 lane was used for each cell line/loading condition for the 50gene library, and 2 per cell line (superloading only) for the 200 gene library. scRNA-seq and dialout libraries were prepared as described below.
1) scRNA-seq libraries were prepared using 3’ scRNA-seq V3 kits (10X Genomics), according to manufacturer instructions. For the Eahy926 50 gene 150k loading, three techical replicate libraries were made from the amplified cDNA from a single lane (denoted "scRNAseq.1, .2 or .3, in library names & "_A2", "_A3" & "_A4" in fastq filenames). Note that the 10x Indexes were a mix of 4 oligos for each library (each starting with a different base to avoid sequencing biases). Thus each scRNAseq library has 4 fastq files for each read direction (denoted _1, _2, _3 & _4 in fastq file names).
2) From the initial amplified cDNA, we used a two stage PCR protocol to generate “dialout” libraries, for each lane. Because the CROP-seq vector expresses a PolII polyadenylated transcript that ends just downstream of the guide sequence, the dialout libraries identify the sgRNA sequences associated with each droplet.

treatment_protocol:
1) To create the TeloHAEC CRISPRi line, cells were transduced with lentiviral vectors containing 1) dox-inducible (tetracycline operator controlled) dCas9-KRAB-BFP (CRISPRi machinery, which targets epigenetic repressors to efficiently silence enhancers or promoters58–60) and 2) rtTA (tetracycline activator) with a hygromycin marker. After hygromycin selection (250ug/ml for 4 days), cells were treated with 1 ug/ml doxycycline (dox, a stable tetracycline analogue) for 3 days before FACS sorting for the top 15% of BFP positive cells, and after a period in culture without dox, treated again with dox and re-sorted.  CRISPRi Eahy926 were created the same way, except that the rtTA vector bore puromycin resistance & was selected for that marker, and only one round of FACS sorting was performed.
2) For Perturb-seq CRISPRi TeloHAEC & Eahy926 were transduced with a Lentivirus library carrying guide RNAs against the promoters of ~50 genes (the "50gene" library, 3 guides per target + 9 control guides),  in a CROP-opti-blast backbone, selected for blasticidin resistance (15ug/ml) for 3 to 4 days, and then treated for 7 days with 1ug/ml doxycycline to induce the CRISPRi machinery. Additionally, the CRISPRi TeloHAEC line was transduced with a Lentivirus library carrying guide RNAs against the promoters of ~200 genes (the "200gene" library, with 15 guide per target), followed by the same steps. Guides and targets for each library are listed in the supplementary files: 200gLib_targets_n_guides.txt & 50gLib_targets_n_guides.txt.

value: Vascular

value: CRISPRi TeloHAEC

value: Endothelial

value: Transduced with "200gene" guide library (see supplementary files)


title: A375-PPAP2.2 cells, Control, 0 hour

value: Control

value: 0 hour


title: NVP.24hr.3

value: neurons

value: universal mouse reference


title: 200gLib_TeloHAEC_Dialout_1.2

description:
dialout for 1 of 2 biological replicates. Technical replicate library #2.
Dialout library to link CBCs to guides


title: bermudagrass heat-7d rep2

city: Wuhan

first: Zhulong

last: Chan

state: Hubei Province

address: No. 1, Shizishan St, Nanhu

department: College of Horticulture and Forestry Sciences

country: China

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for base calling.
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, Q30and 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 Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat 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.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then RPKM of each gene was calculated.
Differential expression analysis of two treatment/control (two biological replicates per condition) was performed using the DESeq R package (1.18.0). DESeq 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 DESeq were assigned as differentially expressed

organism: Cynodon dactylon

source_name: leaf

extract_protocol:
The leaves of control and stress treated bermudagrass plants were collected for RAN isolation following the standard Qiagen RNeasy mini kit protocol. RNA purity and integrity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA), respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: leaf

tag: treatment time

value: 7d after heat treatment

tag: genotype

value: WT


title: 200gLib_TeloHAEC_scRNAseq_2

description:
2 of 2 biological replicates
3' mRNA scRNAseq
200gLib_TeloHAEC_scRNAseq_2_matrix.mtx
200gLib_TeloHAEC_scRNAseq_2_barcodes.tsv
200gLib_TeloHAEC_scRNAseq_2_features.tsv
200gLib_TeloHAEC_scRNAseq_2_calls.tsv

library_source: transcriptomic single cell


title: bermudagrass heat-7d rep1


title: NVP.24hr.2


title: HepG2 NTsi rep 3

description: Expression console values

value: Human Hepatocyte carcinoma cell line

value: NTsi


title: HuH7 COP1si rep 1

description: Expression console values


title: NVP.24hr.1


title: 200gLib_TeloHAEC_scRNAseq_1

description:
1 of 2 biological replicates
3' mRNA scRNAseq
200gLib_TeloHAEC_scRNAseq_1_matrix.mtx
200gLib_TeloHAEC_scRNAseq_1_barcodes.tsv
200gLib_TeloHAEC_scRNAseq_1_features.tsv
200gLib_TeloHAEC_scRNAseq_1_calls.tsv


title: bermudagrass submergence-7d rep1

value: 7d after submergence treatment


title: HepG2 NTsi rep 1

description: Expression console values


title: HepG2 COP1si rep 3

description: Expression console values


title: DonorC, FFPE, probes

city: Cambridge

first: Anna

last: Lyubetskaya

address: 100 Binney St

institute: Bristol-Myers Squibb

description:
Illumina Novaseq 6000
Visium for FFPE ST library

library_source: other

data_processing:
All sequencing outputs were processed using SpaceRanger-1.2.1 (10x Genomics) with rat (Rnor6.0ERCC-ensembl98), mouse (mm10-2020-A), and human (GRCh38-2020-A) references.
Assembly: Rnor6.0ERCC-ensembl98, mm10-2020-A, GRCh38-2020-A
Supplementary files format and content: 10x Genomics SpaceRanger output files: filtered_feature_bc_matrix.h5, raw_feature_bc_matrix.h5, scalefactors_json.json, tissue_hires_image.png, tissue_positions_list.csv
Supplementary files format and content: Full scale TIFF images
Library strategy: ST RNAseq (Visium and Visium for FFPE)

molecule: other

source_name: Pancreatic cancer

growth_protocol: B16F10 and MC38 mouse tumor samples were grown by subcutaneous implantation of 1e6 or 1.5e6 B16F10 or MC38 cells, respectively, into the flank of female C57BL/6 mice. Tumors were harvested 10 days (d10) or 16 days (d16) post-implantation.

extract_protocol:
Rat colons were collected from 6-8 week-old Sprague-Dawley rats and were rinsed with ice-cold PBS before O.C.T. or FFPE embedding. Mouse syngeneic tumors were collected in ice-cold PBS before O.C.T. embedding. O.C.T. embedding was accomplished by placing tissue in a cryomold with ice-cold TissueTek O.C.T. Compound on an aluminum block pre-cooled in a dry ice ethanol bath. FFPE tissues were first placed in 10% neutral buffered formalin for 24-hour fixation, after which tissue was processed for embedding in a Sakura VIP automated system with vacuum/pressue cycles, dehydrating in graded alcohols to xylene and then paraffin, and embedded into blocks for sectioning.  All tumor resection smples were obtained with informed concesnt from BioIVT and Discovery Life Sciences. The Donor-A tumor (BioIVT) was divided prior to fixation, one half was O.C.T. embedded, the other half was FFPE embedded.
All mouse B16F10 and MC38 samples, and fresh-frozen (FF) rat colon and Donor-A PDAC samples were processed with the Visium Spatial Gene Expression kit (10X Genomics, PN-1000184) according to manufacturer protocol (10X Genomics, CG000160 Rev A and CG000238 Rev D for sectioning/staining and library preparation, respecitvely). Rat colon FF samples with a coverslip (wCS) were coverslipped during imaging, according to manufacturer protocol (10X Genomics, CG000160 RevA). Rat colon and Donor-A FFPE polyA-capture (FFPE-pA) samples were processed as described in Villacampa, et al., Cell Genomics 2021, using reagents from the Visium Spatial gene Expression kit (10X Genomics, PN-1000184), with a modified permeabilization, using 2X permeabilization enzyme for 60 minutes (permebailization enzyme was dissovled at 4 mg/ml (4X) in 0.1 N HCl and diluted to 2X in 0.1 N HCl). Donor A-C FFPE probe samples (FFPE-probes) were processed according to the Visium FFPE Regeant kit with Human Transcriptome Probe kit (10X Genomics, PN-100362 and PN-1000364) according to manufacturer protocol (10X Genomics, CG000409 Rev A and CG000407 Rev A for sectioning/staining and library preparation, respectively).

value: Pancreatic cancer


title: HepG2 NTsi rep 2

description: Expression console values


title: HuH7 COP1si rep 2

description: Expression console values


title: AP5.24hr.3


title: miR-142 KO CML LSK, from KO CML males [852]

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

data_processing:
Illumina NovaSeq6000
RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic and polyA tails using FASTP.
The processed reads were mapped to the mouse genome mm10 using STAR (v. 2.6.0.a), and gene expression levels were summarized by HTSeq-count v.0.11.1.
Gene expression raw counts were normalized using TMM normalization method and differential expression analysis was conducted using log likelihood ratio test implemented in “edgeR”.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: BM Lin-Sca-1+c-Kit+ (LSK)

extract_protocol:
RNA was extracted using the miRNeasy Micro Kit (Qiagen, Valencia, CA).
RNA sequencing libraries were prepared with Kapa mRNA HyperPrep kit (Kapa Biosystems, Cat KR1352) according to the manufacturer's protocol. The final libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit.
RNA-seq was performed on Illumina NovaSeq6000 with S4 Reagent kit v1.5 (Illumina, Cat 20028313) at Tgen with the sequencing length of 2x101. Real-time analysis (RTA) 3.4.4 software was used to process the image analysis.

value: BM Lin-Sca-1+c-Kit+ (LSK)

tag: Sex

value: male

value: Mir142 KO BCR-ABL+


title: AP5.24hr.5


title: miR-142 KO CML LSK, from KO CML males [834]


title: HepG2 COP1si rep 1

description: Expression console values


title: HepG2 COP1si rep 2

description: Expression console values


title: DonorB, FFPE, probes


title: bermudagrass salt-7d rep2

value: 7d after salt treatment


title: miR-142 KO CML LSK, from KO CML females [859]

value: female


title: AP5.24hr.4


title: AP5.24hr.2


title: bermudagrass salt-7d rep1


title: DonorA, FFPE, probes


title: miR-142 KO CML LSK, from KO CML males [851]


title: bermudagrass submergence-7d rep2


title: miR-142 KO CML LSK, from KO CML females [855]


title: bermudagrass drought-7d rep2

value: 7d after drought treatment


title: Clone 19 of HeLa-Cas9 cell line with SNAPC4-Knockdown polyA, RNA

city: Rockville

first: May Christine

middle: V

last: Malicdan

state: MD

address: 5625 Fisher's Ln

department: National Human Genome Research Institute

institute: National Institutes of Health

data_processing:
For polyA RNA-Seq, the data was processed using RTA version 3.4.4. Reads were then aligned to GRCh37 using HISAT2, and reads were assembled and counted using StringTie and counts were generated using DESeq2.
For small RNA-Seq, reads were then aligned to GRCh37 by BGI and reads were assembled and counted using StringTie. Next, counts were generated using DESeq2
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include counts values for each Sample

source_name: Cervix

extract_protocol:
For polyA RNA-Seq, total RNA was extracted from HeLa cells using the Maxwell RSC simplyRNA Cells Kit (AS1390, Promega), and from patient-derived fibroblasts using the Maxwell RSC miRNA from Tissue Kit (AS1460, Promega), according to the manufacturer’s specifications.
For small RNA-seq total RNA was extracted from HeLa cells and patient-derived fibroblasts using the Maxwell RSC miRNA from Tissue Kit (AS1460, Promega) according to the manufacturer’s specifications.
For polyA RNA-seq, stranded poly-A selected mRNA libraries were constructed from 1 µg total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490, New England Biolabs) and NEBNext Ultra II Directional RNA Library Prep for Illumina with Sample Purification Beads (E7765, New England Biolabs). Amplification was performed using 8 cycles of PCR to avoid over-amplification. Unique dual-indexed barcode adapters were applied to each library.
Small RNA-seq library construction was carried out by BGI Genomics (Shenzhen, China).

value: Cervix

value: HeLa line stably expressing Cas9


title: Clone 12 of HeLa-Cas9 cell line with SNAPC4-Knockdown, polyA RNA


title: bermudagrass drought-7d rep1


title: bermudagrass control-7d rep2

value: 7d control


title: CML LSK, from CML males [259]

value: BCR-ABL+


title: CML LSK, from CML males [260]


title: Parental HeLa-Cas9 cell line, polyA RNA


title: Control skin fibroblast cell line 3, polyA RNA

value: Skin

value: Primary Skin Fibroblasts


title: AP5.24hr.1

value: neurons

value: universal mouse reference


title: bermudagrass control-7d rep1

value: leaf

value: WT


title: Control skin fibroblast cell line 2, polyA RNA


title: CML LSK, from CML males [258]


title: Control skin fibroblast cell line 1, polyA RNA


title: Individual 6, Skin biopsy-derived fibroblasts, polyA RNA

value: Derived from skin biopsy


title: Individual 4, Skin biopsy-derived fibroblasts, polyA RNA


title: CML LSK, from CML females [287]

value: BM Lin-Sca-1+c-Kit+ (LSK)


title: CML LSK, from CML females [290]


title: Individual 3, Skin biopsy-derived fibroblasts, polyA RNA


title: CML LSK, from CML females [286]


title: miR-142 KO LSK, from KO males [394]

value: male

value: Mir142 KO


title: 34.Post

city: Houston

first: Sreyashi

last: Basu

address: 7455 Fannin Street

institute: MDACC

description:
3663-Post
NR
FFPE

hyb_protocol: Digital detection and direct molecular barcoding of target molecules through the use of a color coded probe pair. Magnetic beads derivatized with short nucleic acid sequences that are complementary to the Capture Probe and the Reporter Probes are used sequentially. First, the hybridization mixture is allowed to bind to the magnetic beads by the Capture Probe. Wash steps are performed and excess Reporter Probes and non-target cellular transcripts are removed during wash steps. After washing, the Capture Probes and Target/Probe complexes are eluted off of the beads and are hybridized to magnetic beads complementary to the Reporter Probe. Wash steps are performed and excess Capture Probes are washed away. Finally, the purified Target/Probe complexes are eluted off and are immobilized in the cartridge for data collection. 300ng of each RNA sample was added to the CodeSet in hybridization buffer and incubated at 65¬∞C for 16 hours. 12 samples were processed per cartridge. Each cartridge was subjected to a 3 hour automated processing  on the Prep Station

scan_protocol: Data Collection was carried out in theGEN2 nCounterTM Digital Analyzer. Digital images were processed and the barcode counts are tabulated in a comma separated value (CSV) format. Raw target counts were collected using the NanoString data collection software, nSolver.

data_processing: Six positive control probes (POS A-F) and their corresponding RNA targets at various concentrations from 128 fM to 0.5 fM were included in the assay to account for systematic variation introduced by pipetting, sample purification, and imaging. Negative control probes (with no corresponding targets, NEG A-H) were included to control for non-specific background noise, i.e. non-specific carryover of reporter probes. The raw target counts were background corrected, normalized to the mean of the positive control probes for each assay, and then normalized to the geometric mean of the reference genes (B2M, PGK1, and RPLP0). nSolver computes a normalization factor for each assay based on the average of positive control counts for the whole data set. NanoString recommends that for optimal results positive control normalization factors range between 0.3 and 3.0 for all assays.

source_name: MIBC

extract_protocol: On average, 5 um-thick FFPE sections were prepared for the extraction of total RNA from tumor cell-rich areas, which were identified by a immunopathologist (JB)

value: MIBC


title: 34.Pre

description:
3663-Pre
NR
FFPE


title: 35.Post

description:
3674-Post
NR
FFPE


title: 35.Pre

description:
3674-Pre
NR
FFPE


title: 32.Post

description:
3629-Post
NR
FFPE


title: miR-142 KO LSK, from KO females [424]

value: female


title: miR-142 KO LSK, from KO females [423]


title: MM6, shNS, mRNA, rep2

city: Guangzhou

first: Hengyou

last: Weng

state: Guangdong

address: Room 304, Building D, 190 Kaiyuan Ave,

institute: Guangzhou Laboratory

description:
MM6_shNS_mRNA
RNA-seq

data_processing:
The raw reads of ribo-seq were first quality checked by FastQC and then adaptors trimmed by Cutadapt with the following parameters: -a AACTGTAGGCACCATCAAT -m 25 -M 34. Any processed reads that mapped to tRNA, snRNA and rRNA were discarded by using bowtie and then the remained reads were mapped to the human transcriptome by use of STAR with following parameters: --outFilterMultimapNmax 20 --outFilterMismatchNoverReadLmax 0.08.
The aligned results were then passed to RSEM to estimate the read counts of genes.
To obtain the raw read count and background expression levels of genes measured with Transcript Per Million (TPM), we processed the mRNA sequencing reads by mapping with STAR and estimating with RSEM, which were similar with RNA-seq analysis.
To avoid the over-normalization, we then normalized the read count of genes from ribo-seq and RNA-seq by using the sequencing depth of libraries and the median-of-ratio method, respectively.
Assembly: hg38
Supplementary files format and content: Normalized read count

molecule: polyA RNA

source_name: Human AML cell MonoMac6

growth_protocol: MonoMac-6 (MM6) cells were cultured in RPMI-1640 medium supplemented with 2 mM L-Glutamine, 1× Non-Essential Amino Acid, 1 mM sodium pyruvate, and 9 mg/ml insulin.

extract_protocol:
For input samples, RNA was isolated using Trizol reagent. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. For ribo-seq samples, ribosome profiling was performed using Epi™ Ribosome Profiling Kit (Epibiotek, R1814). Subsquently, RPFs (ribosome-protected RNA fragments) was extracted using RNA clean&ConcentratorTM-5 kit (ZYMO, R1016).
For input samples, VAHTS Stranded mRNA-seq Library Prep Kit for Illumina V2 (Vazyme Biotech, NR612-02) was used for library preparation according to the instructions. For ribo-seq sample, EpiTM RiboRNA Depletion Kit (Human/Mouse/Rat) (Epibiotek, R1805) was used for rRNA depletion. Sequencing libraries were constructed using QIAseq miRNA Library kit (QIAGEN, 1103679).

treatment_protocol: MM6 cells were transduced with shNS or shIGF2BP2 lentiviruses for 48h, followed by puromycin seletion for 2 days. 1×106 cells from each samples were collected for total RNA extraction, and taken as input control for ribo-seq. 10×106 cells in 10 ml medium were treated with 100 mg/mL cycloheximide. After gentle shaking to mix thoroughly, incubate the cells  at 37°C and 5% CO2 for 15 min. Cells were then harvested and washed with ice-cold PBS supplemented with 100 mg/mL cycloheximide twice. Cell pellets were flash frozen in the liquid nitrogen and stored at 80°C before being subjected for ribo-seq.

value: Human acute myeloid leukemia (AML) cells

value: shNS


title: 28.Post

description:
3552-Post
NR
FFPE


title: miR-142 KO LSK, from KO females [422]


title: miR-142 KO LSK, from KO males [418]


title: WT LSK, from wt males [M3]


title: 22.Pre

description:
3424-Pre
NR
FFPE


title: miR-142 KO CML LSK, from KO CML females [837]

value: Mir142 KO BCR-ABL+


title: WT LSK, from wt males [603]


title: 19.Post

description:
3378-Post
NR
FFPE


title: 18.Pre

description:
3312-Pre
NR
FFPE


title: MM6, shBP2-1, mRNA, rep2

description:
MM6_shBP2B_mRNA
RNA-seq


title: 31.Pre

description:
3580-Pre
NR
FFPE


title: 13.Pre

description:
3171-Pre
NR
FFPE


title: Individual 1, Skin biopsy-derived fibroblasts, polyA RNA


title: MM6, shNS, mRNA, rep1

description:
MM6_shNS_mRNA
RNA-seq


title: miR-142 KO LSK, from KO males [399]


title: Individual 2, Skin biopsy-derived fibroblasts, polyA RNA


title: WT LSK, from wt females [639]


title: 28.Pre

description:
3552-Pre
NR
FFPE


title: MM6, shNS, ribo, rep2

description:
MM6_shNS_ribo
ribo-seq

data_processing:
The raw reads of ribo-seq were first quality checked by FastQC and then adaptors trimmed by Cutadapt with the following parameters: -a AACTGTAGGCACCATCAAT -m 25 -M 34. Any processed reads that mapped to tRNA, snRNA and rRNA were discarded by using bowtie and then the remained reads were mapped to the human transcriptome by use of STAR with following parameters: --outFilterMultimapNmax 20 --outFilterMismatchNoverReadLmax 0.08.
The aligned results were then passed to RSEM to estimate the read counts of genes.
To obtain the raw read count and background expression levels of genes measured with Transcript Per Million (TPM), we processed the mRNA sequencing reads by mapping with STAR and estimating with RSEM, which were similar with RNA-seq analysis.
To avoid the over-normalization, we then normalized the read count of genes from ribo-seq and RNA-seq by using the sequencing depth of libraries and the median-of-ratio method, respectively.
Assembly: hg38
Supplementary files format and content: Normalized read count
Library strategy: Ribo-seq


title: WT LSK, from wt females [605]


title: MM6, shBP2-2, mRNA, rep2

description:
MM6_shBP2D_mRNA
RNA-seq


title: MM6, shNS, ribo, rep1

description:
MM6_shNS_ribo
ribo-seq


title: MM6, shBP2-1, mRNA, rep1

description:
MM6_shBP2B_mRNA
RNA-seq


title: MM6, shBP2-2, ribo, rep2

description:
MM6_shBP2D_ribo
ribo-seq


title: 9.Post

description:
3091-Post
NR
FFPE


title: 9.Pre

description:
3091-Pre
NR
FFPE


title: 13.Post

description:
3171-Post
NR
FFPE


title: 4.Post

description:
2928-Post
NR
FFPE


title: MM6, shBP2-2, ribo, rep1

description:
MM6_shBP2D_ribo
ribo-seq


title: Isolated single nuclei from hippocampus of 9-month-old P301S-APOEKO mouse treated with antibiotic cocktail

city: St. Louis

first: Jason

last: Ulrich

state: MO

address: 660 S Euclid

department: Neurology

institute: Washington University

description: TEKO-ABX

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v3.0.2)
sample de-multiplexing, Cell Ranger Single Cell Software Suite (v3.0.2)
barcode processing, Cell Ranger Single Cell Software Suite (v3.0.2)
single-cell 3' gene counting, Cell Ranger Single Cell Software Suite (v3.0.2)
alignment, Cell Ranger Single Cell Software Suite (v3.0.2)
Assembly: mm10+ human APOE
Supplementary files format and content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

source_name: hippocampus

extract_protocol:
Mice were randomly assigned to antibiotic cocktail (4 mg/mL kanamycin, 0.35 mg/mL gentamicin, 8,500 U/mL colistin, 2.15 mg/mL metronidazole, 0.45 mg/mL vancomycin) or water group. Antibiotic cocktail (100 uL) or water were administered daily for one week at 2 weeks of age via oral gavage. Mice were then aged to 40 weeks. Upon tissue harvest, mice were euthanized and perfused with 1U/ml heparin in PBS. Left hemisphere of the brains were dissected out and flash frozen on dry ice. Flash frozen brain tissue was homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice 15 minutes. The suspension was filtered through a 30 um filter to remove debris and pelleted at 500 x g 5 min at 4o C. Nuclei were washed and filtered twice with Nuclei Wash (1% BSA in PBS with 0.2 U/uL RNasin (Promega)). Nuclei pellets were resuspended in 500 uL Nuclei Wash and 900 uL 1.8 M Sucrose. This 1400 uL mixture was carefully layered on top of 500 uL 1.8 M sucrose and centrifuged at 13,000 x g 45 min 4oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in Nuclei wash at 1200 nuclei/uL and filtered through a 40 um FlowMi Cell Strainer.
Isolated single nuclei were subjected to droplet-based 3’ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5’ Reagent Kits as per manufacturer’s instructions (10x Genomics) The generated scRNAseq libraries were sequenced using an Illumina sequencer.

tag: mouse genotype

value: P301S APOE-KO

tag: strain

value: kanamycin, gentamicin, colistin, metronidazole, vancomycin

value: nuclei of brain


title: Isolated single nuclei from hippocampus of 9-month-old P301S-APOEKO mouse treated with water

value: water


title: 4.Pre

description:
2928-Pre
NR
FFPE


title: MM6, shBP2-1, ribo, rep1

description:
MM6_shBP2B_ribo
ribo-seq


title: WT LSK, from wt females [F3]


title: Isolated single nuclei from hippocampus of 9-month-old P301S-APOE4 mouse treated with antibiotic cocktail

value: P301S APOE4


title: 37.Pre

description:
3705-Pre
R
FFPE


title: MM6, shBP2-2, mRNA, rep1

description:
MM6_shBP2D_mRNA
RNA-seq


title: 36.Pre

description:
3695-Pre
R
FFPE


title: Isolated single nuclei from hippocampus of 9-month-old APOE4 mouse treated with antibiotic cocktail


title: Isolated single nuclei from hippocampus of 9-month-old APOE4 mouse treated with water


title: Isolated single nuclei from hippocampus of 9-month-old P301S-APOE3 mouse treated with antibiotic cocktail

value: P301S APOE3


title: MM6_shNS_NA_rep3

description: rna_seq_raw_gene_read_count.xlsx: MM6_YTHDF2_shNS_rep3

data_processing:
The raw RNA-seq reads were quality checked by FastQC (version 0.11.5) and then adaptors trimmed by Cutadapt (version 3.4). The processed reads were mapped to human transcriptome built with gene annotations (hg38, GENCODE v37) by STAR (version 2.7.2b) with parameters recommended by ENCODE project.
The aligned results were then passed to RSEM (version 1.2.31) to estimate the read count of genes.
Finally, the estimated read counts of genes were analyzed by DESeq2 (version 1.32.0) to identify differentially expressed genes with following parameters: sfType=poscounts, test=Wald and lfcShrink(type=none).
Assembly: hg38
Supplementary files format and content: Raw read gount of genes and processed results from DESeq2

growth_protocol: MonoMac-6 cells were cultured in RPMI-1640 medium supplemented with 2 mM L-Glutamine, 1× Non-Essential Amino Acid, 1 mM sodium pyruvate, and 9 mg/ml insulin.

extract_protocol:
Total RNA from MonoMac6 cells with different treatments was isolated using the TRIzol reagent (Thermo fisher Scientific).
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: MonoMac6 cells were treated with DMSO or CWI1-2 (0.5uM) for 48h before collection for RNA extraction. For YTHDF2 KO, MonoMac6 cells were transduced with shNS or shYTHDF2 lentiviruses for 48h, followed by puromycin selection for 3 days, and then subjected to RNA extraction.


title: MM6_shNS_NA_rep1

description: rna_seq_raw_gene_read_count.xlsx: MM6_YTHDF2_shNS_rep1


title: MM6_shYTHDF2_NA_rep1

description: rna_seq_raw_gene_read_count.xlsx: MM6_YTHDF2_shRNA_rep1


title: MM6_shYTHDF2_NA_rep3

description: rna_seq_raw_gene_read_count.xlsx: MM6_YTHDF2_shRNA_rep3


title: Isolated single nuclei from hippocampus of 9-month-old APOE3 mouse treated with water


title: Isolated single nuclei from hippocampus of 9-month-old P301S-APOE3 mouse treated with water


title: MM6_shYTHDF2_NA_rep2

description: rna_seq_raw_gene_read_count.xlsx: MM6_YTHDF2_shRNA_rep2


title: 25.Pre

description:
3496-Pre
R
FFPE


title: Isolated single nuclei from hippocampus of 9-month-old APOE3 mouse treated with antibiotic cocktail


title: MM6, shBP2-1, ribo, rep2

description:
MM6_shBP2B_ribo
ribo-seq


title: MM6_DMSO_48h_rep3

description: rna_seq_raw_gene_read_count.xlsx: MM6_DMSO_48h_rep3

value: DMSO

value: 48 hours


title: MM6_DMSO_48h_rep2

description: rna_seq_raw_gene_read_count.xlsx: MM6_DMSO_48h_rep2


title: Tet2/3 DKO WGBS replicate 2, hair matrix keratinocytes, P4.5

city: Boston

first: Andrey

last: Sharov

state: Massachusetts

address: 609 Albany Street

department: Dermatology

institute: Boston University School of Medicine

data_processing:
Low qualitiy reads and adaptors were trimmed by using trim-galore with default paramaters.
Trimmed reads were aligned, deduplicated and methylation extracted with bismark.
Differential methylated regions were called with BSseq package in R language.
Assembly: GRCm38/mm10
Supplementary files format and content: bigwig, txt

source_name: primary cells

extract_protocol:
DNA was isolated from 400 K cells and sheared to 300 - 500 bp. Mmethylation conversion was performed with EZ DNA Methylation-Gold kit (Zymo, #5005) follow product manual.
DNA libraries are prepared by using ACCEL-NGS® Methyl-seq DNA Library kit (Swift Biosciences, #30024 and #x6024) with 7 - 9 cycles’ PCR amplification as the manual described.

value: primary cells

value: hair matrix keratinocytes

value: Tet2/Tet3 DKO, Krt14-Cre


title: 25.Post

description:
3496-Post
R
FFPE


title: 23.Pre

description:
3481-Pre
R
FFPE


title: 24.Pre

description:
3491-Pre
R
FFPE


title: MM6_DMSO_48h_rep1

description: rna_seq_raw_gene_read_count.xlsx: MM6_DMSO_48h_rep1


title: Isolated single nuclei from hippocampus of 9-month-old P301S-APOE4 mouse treated with water


title: 15.Post

description:
3238-Post
R
FFPE


title: Tet2/3 DKO WGBS replicate 1, hair matrix keratinocytes, P4.5


title: 11.Post

description:
3123-Post
R
FFPE


title: Wild type WGBS replicate 2, hair matrix keratinocytes, P4.5

value: WT


title: MM6_shNS_NA_rep2

description: rna_seq_raw_gene_read_count.xlsx: MM6_YTHDF2_shNS_rep2


title: 11.Pre

description:
3123-Pre
R
FFPE

value: MIBC


title: 23.Post

description:
3481-Post
R
FFPE


title: MM6_05uM_48h_rep3

description: rna_seq_raw_gene_read_count.xlsx: MM6_05uM_48h_rep3


title: Wild type WGBS replicate 1, hair matrix keratinocytes, P4.5


title: MM6_05uM_48h_rep2

description: rna_seq_raw_gene_read_count.xlsx: MM6_05uM_48h_rep2


title: MC38, day 16, mouse 8, rep D, experiment 3

description:
Illumina NextSeq 500 and NextSeq 550 (merged)
Visium ST library

source_name: MC38 syngeneic tumor

value: MC38 syngeneic tumor


title: Tet2/3 DKO HiC, hair matrix keratinocytes, P4.5

data_processing:
Hi-C reads were analyzed in one click system Juicer with default paramaters, and differentially changed peaks were called with hiccups.
Hi-C results were viewed with JuicerBox.
Assembly: GRCm38/mm10
Supplementary files format and content: hic, bedpe

extract_protocol:
DNA is extracted with Arima and procedure is followed with the manual.  Briefly DNA are digested with Arima enzymes and  labeled with biotin and re-ligated again. Biotin-labeled DNA is sheared to 300 - 500 bp, and enriched with enrichment beads.
DNA libraries are prepared by using Swift Biosciences Accel-NGS 2S Plus DNA Library Kit with a 5-7 cycles’ amplification. DNA libraries of the samples for paired-end sequencing are performed in the Illumina NovaSeq 6000 system (2 × 150 bp).


title: 15.Pre

description:
3238-Pre
R
FFPE


title: Wild type HiC, hair matrix keratinocytes, P4.5


title: 12.Pre

description:
3119-Pre
R
FFPE


title: 10.Pre

description:
3121-Pre
R
FFPE


title: MM6_05uM_48h_rep1

description: rna_seq_raw_gene_read_count.xlsx: MM6_05uM_48h_rep1

value: Human acute myeloid leukemia (AML) cells


title: MC38, day 16, mouse 6, rep D, experiment 2

description:
Illumina NextSeq 500, NextSeq 550, and NovaSeq 6000 (merged)
Visium ST library


title: 8.Pre

description:
3073-Pre
R
FFPE


title: Experiment_1_con_3

city: Hannover

first: shuyong

last: zhu

state: Lower Saxony

address: OE 5230, Carl-Neuberg-Str. 1, 30625

department: Institute of Virology

country: Germany

institute: Hannover Medical School

data_processing:
raw reads was confirmed by FastQC
aligned to the human reference genome GRCh38 using STAR
counted per gene by employing the 'quantmode GeneCounts' option
Fold changes and FDRs for each gene were estimated with DESeq2
differentially expressed genes were selected by FDR < 0.001 and absolute log2foldChange value >= 1

source_name: human neurons differentiated from neural precursor cells

growth_protocol: The smNPCs were grown on Matrigel (Corning, 354263) coated dishes, fed with N2/B27 medium (48% (vol/vol) DMEM/F12, 48% (vol/vol) Neurobasal, 2% (vol/vol) B27 minus AO, 0.5% (vol/vol), N2 supplement, 1% (vol/vol) Penicillin/streptomycin, and 1% (vol/vol) GlutaMAX™ Supplement) containing 3 μM CHIR 99021 (Axon Medchem, Groningen, The Netherlands), 0.5 μM purmorphamine (PMA, Alexis, Farmingdale, NY), and 150 μM L-Ascorbic acid (Sigma).The day 60 human neurons were grown on on Matrigel (Corning, 354263) coated dishes, fed with N2/B27 medium (48% (vol/vol) DMEM/F12, 48% (vol/vol) Neurobasal, 2% (vol/vol) B27 minus AO, 0.5% (vol/vol) N2 supplement, 1% (vol/vol) Penicillin/streptomycin, and 1% (vol/vol) GlutaMAX™ Supplement) containing 25, 10, 10 ng/ml of NGF, BDNF, and GDNF, respectively.

extract_protocol:
Total RNA was isolated from day 60 hiNeurons and smNPCs, followed by removal of ribosomal RNA and transfer RNA using Macherey Nagel RNA isolation kit.
The RNA population containing messenger RNA (mRNA), pre-processed RNA and regulatory RNA molecules were reverse transcribed into short double-strained DNA fragments to construct the cDNA library for sequencing.

value: hiPSC derived neurons

tag: origin

value: hiPSC derived from cord bood


title: Experiment_1_con_1


title: Experiment_1_con_2


title: 2_smNPC_P59

source_name: neural precursor cells

value: hiPSC derived neural precursor cells


title: 3.Pre

description:
2902-Pre
R
FFPE


title: MC38, day 10, mouse 5, rep D, experiment 2


title: MC38, day 10, mouse 5, rep C1 and C2, experiment 1

description:
Illumina NextSeq 550
Visium ST library


title: 2.Post

description:
2707-Post
R
FFPE


title: 3_smNPC_P59


title: B16, day 16, mouse 3, rep C, experiment 3

source_name: B16F10 syngeneic tumor

value: B16F10 syngeneic tumor


title: 1_smNPC_P59


title: 2.Pre

description:
2707-Pre
R
FFPE


title: B16, day 16, mouse 2, rep C, experiment 2


title: B16, day 16, mouse 3, rep A, experiment 3


title: B16, day 10, mouse 1, rep C, experiment 2


title: TGF 2

city: Columbus

first: Michael

last: Tranter

state: OH

address: 2255 Kenny Road

department: Molecular Medicine and Therapeutics

institute: The Ohio State University

data_processing:
All read mapping and analysis was performed using the CLC Genomics Workbench v20.0.2 (CLC Bio-Qiagen).
Reads were mapped using the following parameters:  min. read length fraction = 0.8, min. read similarity fraction = 0.8. mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = both, Maximum number of hits for a read=10, Expression value= Transcripts per million (TPM).
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: TPM

source_name: Isolated cardiac fibroblasts

extract_protocol:
Primary isolated cells were cultured until 80% confluency, treated with 0.1M 4-SU at 20 and 4 hrs prior to crosslinking +/- TGFbeta, cross-linked at 200000 uJ/sq.cm using 368nm light, and total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: 12 weeks

value: wild-type

value: 10 ng/ml TGFbeta

value: Isolated cardiac fibroblasts


title: neoadjuvant hormonal therapy sensitivity 5

city: Jinan

first: Jing

last: Hu

address: Wenhua xi road

department: Department of Pathology

institute: Shandong University

description:
mirna expression profile
ZDS

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human miRNA Microarrays (8*60K) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Arrays were scanned using an Agilent Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um . Dye channel was set to Green and Green PMT is set to 100%.

data_processing: The generated image files were analyzed using Agilent Feature Extraction Software (v 11.0.1.1). Using GemeSpring v12.1 software(Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: prostate cancer

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA Extraction was performed using TRIZOL following the manufacturer's recommendations.

value: prostate cancer

tag: phenotype


title: TGF 1


title: Vehicle 2

value: vehicle control


title: Transcriptional profiling of peripheral neutrophils from Healthy Control 10

city: Beijing

first: Wenjie

last: Zheng

address: No1 ShuaiFuYuan，Dong Cheng District ，Beijing, Beijing, CN

institute: Peking Union Medical College Hospital

description: Healthy Controls

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.
Assembly: hg38
Supplementary files format and content: count_matrix.csv concludes combined csv file of matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: sample_info.csv concludes sample information

source_name: peripheral blood

extract_protocol:
RNA was harvested using Trizol reagent.A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Peripheral neutrophils were isolated from blood by density gradient centrifugation and then resuspended in PBS

value: peripheral blood

value: peripheral neutrophil

value: HC

tag: batch

value: female

tag: oral ulcer

value: No

tag: genital ulcer

tag: gastrointestinal involvement

tag: erythema nodule

tag: ocular involvement

tag: vascular involvement

tag: cns involvement

tag: arthritis


title: Transcriptional profiling of peripheral neutrophils from Healthy Control 8

description: Healthy Controls

tag: tissue

tag: cell line

tag: cell type

tag: treatment

value: male


title: CRC, GDT, CITE-seq

city: Leiden

first: Natasja

middle: de

last: Vries

address: Albinusdreef 2

country: Netherlands

institute: Leiden University Medical Center

description: 10x Genomics Antibody-derived oligonucleotide (ADT) and Hashtag-derived oligonucleotide (HTO)

data_processing:
Reads were aligned to the human reference genome (GRCh38) and quantified using Cell Ranger (version 3.1.0).
Downstream analysis was performed using Seurat (version 3.1.5) according to the author’s instructions.
Cells that had less than 200 detected genes and genes that were expressed in less than six cells were excluded.
The resulting 5669 cells were demultiplexed based on HTO enrichment using the MULTIseqDemux algorithm.
Cells with a mitochondrial gene content greater than 10% and cells with outlying numbers of expressed genes (>3000) were filtered out from the analysis, resulting in a final dataset of 4442 cells.
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output file: filtered_feature_bc_matrix.h5

source_name: Colon cancer

extract_protocol:
Single-cell digests of MMR-deficient colon cancer specimens were thawed, stained with cell surface flow cytometry antibodies and HTOs, and washed. Single, live CD45+ EPCAM– CD3+ TCRγδ+ cells were sorted on a FACS Aria III 4L (BD Biosciences). After sorting, the samples were pooled.
scRNA-seq libraries were prepared using the Chromium Single Cell 5’ Reagent Kit v1 chemistry (10X Genomics) following the manufacturer’s instructions. The construction of 5’ Gene Expression libraries allowed the identification of γδ T cell subsets according to Vδ and Vγ usage. Libraries were sequenced on a HiSeq X Ten using paired-end 2x150 bp sequencing (Illumina).

value: Colon cancer

value: naive

value: Gamma-delta T cells

tag: library type

value: HTO and ADT

tag: antibodies/tags

value: TotalSeq-C anti-CD45RA (clone HI100, BioLegend), TotalSeq-C anti-CD45RO (clone UCHL1, BioLegend), TotalSeq-C CD298/β2m hashtag antibodies HTO1, HTO6, HTO7, HTO8, HTO9 (clone LNH-94/2M2, BioLegend)


title: Vehicle 1

tag: strain

tag: age

value: 12 weeks

tag: genotype


title: CRC, GDT, scRNA-seq

description: 10x Genomics RNA

value: RNA


title: neoadjuvant hormonal therapy sensitivity 4

description:
mirna expression profile
SGX

tag: phenotype


title: neoadjuvant hormonal therapy resistance 5

description:
mirna expression profile
LQT

value: neoadjuvant hormonal therapy resistance


title: 16 weeks after cercarial infection [TCR]

city: Tianjin,China

first: Zhuo

last: Yue

address: Qixiangtai Road

institute: Tianjin medical university

data_processing:
Raw sequencing data were processed using the 10X Genomics Cell Ranger pipline
Genome_build: mm10 and GRCm38
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and cell ,TCR/BCR clonotype information

source_name: Spleen

extract_protocol:
Mice were sacrificed under anesthesia and spleens were harvested. Spleen tissue was minced in a sterile Petri plate. The erythrocytes were lysed in ACK buffer and a single-cell suspension of murine splenocytes was prepared by passing cells through 70 μm strainers.
Single cell RNA libraries were prepared using Chromium Single cell 5' Library & gel bead kit and coupled Chromium single cell V(D)J enrichment kit&scT/BCR library according to the manufacturer's protocol

treatment_protocol: BALB/c mice were percutaneously infected with 30±2 cercariae of S. japonicum. Successful infection was confirmed by detecting serum specific antibody or identifying parasitic eggs in fecal samples after infection.

value: Immune cell

tag: agent

value: S. japonicum

tag: time point

value: 16 weeks

value: BALB/c

tag: Sex


title: neoadjuvant hormonal therapy sensitivity 3

description:
mirna expression profile
LKL

value: prostate cancer


title: neoadjuvant hormonal therapy sensitivity 2

description:
mirna expression profile
FSH


title: neoadjuvant hormonal therapy sensitivity 1

description:
mirna expression profile
BRX


title: Transcriptional profiling of peripheral neutrophils from Healthy Control 9

description: Healthy Controls

value: peripheral blood

value: peripheral neutrophil

value: HC

tag: batch

tag: oral ulcer

tag: genital ulcer

tag: gastrointestinal involvement

tag: erythema nodule

tag: ocular involvement


title: Transcriptional profiling of peripheral neutrophils from Healthy Control 7

description: Healthy Controls

tag: tissue

tag: cell line

tag: cell type

value: male

value: No

tag: vascular involvement

tag: cns involvement

tag: arthritis


title: 12 weeks after cercarial infection [TCR]

tag: strain

value: female


title: neoadjuvant hormonal therapy resistance 3

description:
mirna expression profile
ZJS

tag: phenotype


title: 6 weeks after cercarial infection [TCR]

tag: agent

value: 6 weeks


title: 22- EGD15

city: Grand Forks

first: Sandeep

middle: K

last: Singhal

state: NORTH DAKOTA

address: 1301 N Columbia Rd Stop 9037

department: Pathology

institute: University of North Dakota

data_processing:
RNA-seq raw reads were stored in fastq format files containing the sequence data for this cohort study (11 patients). Each file was explored using fastQC (18) and fastp (19) for improving their quality variables. After pre-processing and quality control, STAR aligner v.2.5.2b, the trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL (20). The normalized distribution of the counts was checked to identify the outliers.
Assembly: GRCh38

source_name: Proximal Jejunum

extract_protocol: Frozen tissue was embedded in optimal cutting temperature compound and 8 µm sections were frozen sectioned a microtome-cryostat.  Sections were mounted on to a PET membrane steel frame slides (1.4 µm, RNase-free, Leica LMD slides, NCI, Inc. Brooklyn Park, MN) and sectioned slides were stored at -80oC.  Applied 50 µl of RNase Inhibitor (ProtectRNA 500x R7397, Sigma-Aldrich) was added to all staining jars (per 25 ml of the following ethanol and isopropanol jars, not in xylene jar).  Frozen slide was immediately submerged into 95% ethanol for 30 sec. with frequent dipping up and down.  Hematoxylin stain was directly applied to the tissue sections on the slides for 60 sec.  De-stained in 100% isopropanol, 10 dips for 15 sec. Eosin stain was applied directly to tissue sections on the slide for 2 sec and de-stained in 100% isopropanol for 10 dips for 30 sec.  The slides were then de-stained subsequently in 75% ethanol for 5 dips for 15 sec, then 95% ethanol for 10 dips, then 100% ethanol for 10 dips for 10 sec. A final submersion of the slide in anhydrous 100% ethanol for 30 sec.  Then the slide was repeatedly dipped in xylene for 15 sec with a final submersion for 10 min.  Slide was air-dried for 2 min.  Laser capture microscopy immediately followed in which two sections were cut of about 10-30 intestinal epithelial cells along with the villi and collected into the collection cap (Leica LMD 6, Deer Park, IL).  Sectioned cells were lysed with 5µl of lysis buffer the Tecan LCMSeq kit and tubes were stored at -80oC.  RNA library was prepared using the Tecan Ovation SoLo RNA-Seq library preparation kit per manufacturer’s instructions. Libraries were quantified using Quant-iT PicoGreen dsDNA assay kit and read on BioTek FLx800 fluorescence microplate reader. Libraries were pooled equal molar and the sample pool was quantified using Biorad ddPCR. Libraries were sequenced using Illumina HiSeq X Ten at Psomagen (Rockville, MD).

value: Proximal Jejunum

value: Enterocyte

tag: time point

value: post-bypass (endoscopically sampled)

tag: treatment

value: LCM dissected


title: 21- GBP15

value: gastric bypass (sampled at time of surgery)


title: 20- EGD12


title: Transcriptional profiling of peripheral neutrophils from Healthy Control 6

description: Healthy Controls

tag: genotype

tag: batch

tag: age

tag: Sex


title: MC38, day 16, mouse 7, rep D, experiment 3

data_processing:
All sequencing outputs were processed using SpaceRanger-1.2.1 (10x Genomics) with rat (Rnor6.0ERCC-ensembl98), mouse (mm10-2020-A), and human (GRCh38-2020-A) references.
Assembly: Rnor6.0ERCC-ensembl98, mm10-2020-A, GRCh38-2020-A
Supplementary files format and content: 10x Genomics SpaceRanger output files: filtered_feature_bc_matrix.h5, raw_feature_bc_matrix.h5, scalefactors_json.json, tissue_hires_image.png, tissue_positions_list.csv
Supplementary files format and content: Full scale TIFF images
Library strategy: ST RNAseq (Visium and Visium for FFPE)

value: MC38 syngeneic tumor


title: neoadjuvant hormonal therapy resistance 2

description:
mirna expression profile
WG

value: neoadjuvant hormonal therapy resistance


title: neoadjuvant hormonal therapy resistance 4

description:
mirna expression profile
ZSF


title: 19- GBP12


title: 4 weeks after cercarial infection [TCR]

value: Immune cell

value: S. japonicum

value: 4 weeks


title: Transcriptional profiling of peripheral neutrophils from Healthy Control 5

description: Healthy Controls

value: peripheral blood

tag: oral ulcer

tag: genital ulcer

tag: gastrointestinal involvement

tag: erythema nodule


title: naive mouse [TCR]

tag: cell type

value: BALB/c


title: 18- EGD11

tag: tissue


title: 17- GBP11


title: neoadjuvant hormonal therapy resistance 1

description:
mirna expression profile
STJ

value: prostate cancer


title: 16- EGD09


title: Transcriptional profiling of peripheral neutrophils from Healthy Control 2

description: Healthy Controls

tag: cell line

value: peripheral neutrophil

value: HC

value: male

tag: ocular involvement

tag: vascular involvement

tag: cns involvement


title: Transcriptional profiling of peripheral neutrophils from Healthy Control 1

description: Healthy Controls

value: No

tag: arthritis


title: 6 weeks after cercarial infection [BCR]

tag: agent

tag: time point

value: 6 weeks

tag: strain

value: female


title: 12 weeks after cercarial infection [BCR]

value: 12 weeks


title: Transcriptional profiling of peripheral neutrophils from BD patinet 10

description: BD patients

tag: genotype

tag: treatment

value: BD

tag: batch

value: Yes


title: 13- GBP08

value: Proximal Jejunum

value: Enterocyte

value: gastric bypass (sampled at time of surgery)

value: LCM dissected


title: naive mouse [BCR]

value: Immune cell

tag: Sex


title: 16 weeks after cercarial infection [BCR]

value: S. japonicum

value: 16 weeks


title: 14- EGD08

value: post-bypass (endoscopically sampled)


title: 12- EGD06


title: 4 weeks after cercarial infection [BCR]

value: 4 weeks

value: BALB/c


title: Transcriptional profiling of peripheral neutrophils from Healthy Control 3

description: Healthy Controls

value: peripheral blood

value: peripheral neutrophil

value: HC

tag: age

value: male

tag: oral ulcer

tag: genital ulcer


title: Transcriptional profiling of peripheral neutrophils from BD patinet 9

description: BD patients

tag: cell type

value: female

value: No

tag: gastrointestinal involvement

tag: erythema nodule


title: Transcriptional profiling of peripheral neutrophils from BD patinet 8

description: BD patients

tag: tissue

tag: cell line

value: BD

value: Yes

tag: ocular involvement


title: Transcriptional profiling of peripheral neutrophils from BD patinet 7

description: BD patients

tag: vascular involvement

tag: cns involvement

tag: arthritis


title: 12 weeks after cercarial infection

tag: agent

tag: time point

value: 12 weeks

tag: strain


title: Transcriptional profiling of peripheral neutrophils from Healthy Control 4

description: Healthy Controls

tag: genotype

tag: treatment

tag: batch


title: 10- EGD05

value: Proximal Jejunum

value: Enterocyte


title: 15- GBP09

value: gastric bypass (sampled at time of surgery)

value: LCM dissected


title: 6 weeks after cercarial infection

value: Immune cell

value: S. japonicum

value: 6 weeks

tag: Sex


title: Transcriptional profiling of peripheral neutrophils from BD patinet 6

description: BD patients

tag: age

tag: oral ulcer

tag: genital ulcer


title: 9- GBP05

tag: cell type


title: Transcriptional profiling of peripheral neutrophils from BD patinet 4

description: BD patients

tag: tissue

tag: gastrointestinal involvement

tag: erythema nodule


title: AdAC direct #4

city: Berlin

first: Andranik

last: Ivanov

address: Chariteplatz 1

department: Core Unit Bioinformatics

institute: Berlin Institute of Health

data_processing:
Illumina bcl2fastq v2.20 software was used for basecalling
RNA-seq reads were mapped to mouse genome (GRCm38/p5) with STAR (version 2.7.3a) using the following parameters:  --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000
Reads were assigned to genes with featureCounts (-t exon -g gene_id, version 2.0.1) using Gencode GRCm38/vM12 gene annotation
Genome_build: GRCm38/p5
Supplementary_files_format_and_content: Tab delimited text file with raw read counts per gene for each sample

source_name: directly snap-frozen adult astrocytes

growth_protocol: Astrocytes generated from embryonic stem cells (AGES) were differentiated from neural stem cells (NSCs) using BMP4. Adult and neonatal astrocytes were isolated from mouse brains using magnetic activated cell sorting (ABDK Kit, Miltenyi).

extract_protocol:
Total RNA from frozen cell pellets or astrocytic cultures was isolated using the NucleoSpin miRNA kit (Macherey Nagel, 740971-250)
RNA sequencing libraries were prepared using the TruSeq™ Stranded mRNA Library Prep kit (20020594, Illumina) starting from 100 ng of total RNA (RIN ≥7) on an epMotion® 5075 TMX workstation (Eppendorf)


title: 4 weeks after cercarial infection

value: 4 weeks

value: BALB/c


title: 6- EGD03

value: post-bypass (endoscopically sampled)


title: Transcriptional profiling of peripheral neutrophils from BD patinet 5

description: BD patients

value: peripheral blood

tag: cell line

value: peripheral neutrophil

tag: ocular involvement

tag: vascular involvement


title: naive mouse

value: female


title: 8- EGD04


title: 4- EGD02


title: 16 weeks after cercarial infection

tag: agent

value: 16 weeks


title: Transcriptional profiling of peripheral neutrophils from BD patinet 3

description: BD patients

value: BD

value: male

value: No

tag: cns involvement

tag: arthritis


title: AdAC direct #3

tag: strain


title: 11- GBP06

value: Proximal Jejunum

tag: time point

tag: treatment


title: 5- GBP03

value: Enterocyte


title: Transcriptional profiling of peripheral neutrophils from BD patinet 1

description: BD patients

tag: genotype

tag: batch

tag: Sex

value: Yes


title: ATAC-Seq SK-N-BE(2) shARID1A/B.4.2 rep3

city: Barcelona

first: Carlos

last: Jimenez

state: Barcelona

address: Pg. Vall dHebron 119-129, Edificio Collserola, lab 207

department: Pediatric Oncology

country: Spain

institute: Vall d'Hebron Institut de Recerca

description: Alignment reference genome GRCh38

data_processing:
ATAC-seq analysis was performed with nf-core pipeline (c.1.2.1, using GRCh38.104 as reference genome.
Differentially accessible peaks were determined with DESeq2.
Assembly: GRCh38.104
Supplementary files format and content: BigWig genomic coverage files for merged replicates of the same conditions.
Supplementary files format and content: Tab-delimited file with consesus peaks detected by ATAC-Seq in all samples
Supplementary files format and content: Tab-delimited files containint results of DESeq2 differential accessibility analysis, comparisons of each condition with control

growth_protocol: SK-N-BE(2) cells were cultured in Iscove's Modified Dulbecco's Medium supplemented with 20% heat-inactivated fetal bovine serum and insulin transferrin selenium.

extract_protocol:
ATAC-Seq procedures (Tagmentation reaction and PCR amplification for library generation) were performed as described in Buenrostro et al. Nat Methods 2013, with minor modification.
Library were constructed by PCR amplification with primers i5 and i7 (IDT, Newark, NJ, USA) from genomic DNA tagmented with linker oligonucleotides Tn5ME-A/Tn5MErev and Tn5ME-B/Tn5MErev (Picelli et al. Genome Res. 2014).

treatment_protocol: SK-N-BE(2) cells were transduced with lentiviral supernatant from HEK293T cells transfected with envelope and packaging plasmids and different shRNA-encoding plasmids.

value: ARID1A and ARID1B silencing


title: AdAC direct #1


title: AdAC direct #2


title: AdAC CellC #4

source_name: cultured adult astrocytes


title: ATAC-Seq SK-N-BE(2) shARID1A/B.4.2 rep2

description: Alignment reference genome GRCh38


title: 7- GBP04

value: gastric bypass (sampled at time of surgery)

value: LCM dissected


title: ATAC-Seq SK-N-BE(2) shARID1A/B.2.3 rep3

description: Alignment reference genome GRCh38


title: 1- GBP01


title: 2- EGD01


title: AdAC CellC #1


title: ATAC-Seq SK-N-BE(2) shARID1A/B.4.2 rep1

description: Alignment reference genome GRCh38


title: 3- GBP02


title: Transcriptional profiling of peripheral neutrophils from BD patinet 2

description: BD patients

tag: age

tag: oral ulcer

tag: genital ulcer


title: AdAC CellC #2


title: AdAC CellC #3


title: WT LSK, from wt males [634]

data_processing:
Illumina NovaSeq6000
RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic and polyA tails using FASTP.
The processed reads were mapped to the mouse genome mm10 using STAR (v. 2.6.0.a), and gene expression levels were summarized by HTSeq-count v.0.11.1.
Gene expression raw counts were normalized using TMM normalization method and differential expression analysis was conducted using log likelihood ratio test implemented in “edgeR”.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: BM Lin-Sca-1+c-Kit+ (LSK)

extract_protocol:
RNA was extracted using the miRNeasy Micro Kit (Qiagen, Valencia, CA).
RNA sequencing libraries were prepared with Kapa mRNA HyperPrep kit (Kapa Biosystems, Cat KR1352) according to the manufacturer's protocol. The final libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit.
RNA-seq was performed on Illumina NovaSeq6000 with S4 Reagent kit v1.5 (Illumina, Cat 20028313) at Tgen with the sequencing length of 2x101. Real-time analysis (RTA) 3.4.4 software was used to process the image analysis.

tag: cell type

value: BM Lin-Sca-1+c-Kit+ (LSK)

value: WT


title: 49 (RPL 3)

city: Wuhan

first: Yuehan

last: Li

address: Jiefang Ave.

department: Tongji Medical School

institute: Huahzong University of Science and Technology

data_processing:
The main steps of applying Seqtk for filtering raw reads in order to get clean reads which are applicable for data processing are as follows: 1. Remove the sequence of joints contained in reads; 2. Remove bases with 3 'end mass Q less than 20, that is, the base error rate is less than 0.01, among which ,Q= -10 log error_ratio; 3. Remove reads with length less than 25; 4. Remove ribosome RNA reads of the species
Spliced mapping algorithm of Hisat2 (version:2.0.4) was applied to conduct genome mapping of preprocessed reads. Default parameters were taken. The alignment results generated by Mapping are BAM files.
Application Stringtie (version: 1.3.0)in Hisat2 than after each gene Fragments could count to count, and then use TMM (trimmed mean of M values) normalization method, finally calculated using perl script FPKM value of each gene.
In order to make gene expression levels between different genes and samples comparable, reads were transformed into FPKM (Fragments Per Kilobase of exon model Per Million mapped reads) to standardize gene expression
EdgeR was used for gene analysis of differences between samples, and multiple hypothesis test and correction were carried out after p-value was obtained. The threshold value of p-value was determined by controlling FDR (False Discovery Rate), and the p-value after correction was q-value. Meanwhile, we calculate Fold-change according to FPKM.
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: abundance measurements

source_name: decidual tissue_RPL

extract_protocol:
Total RNA was extracted using RNAiso Plus Total RNA extraction reagent  (Cat#9109, TAKARA)following the manufacturer’ s instructions and checked for a  RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (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).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Decidua tissue from the control group was also collected during the procedure ofdilation and curettage (D&C). The surgical procedure was conducted under strict sterile condition, the samples were immediately snap-frozen and stored in liquid nitrogen for later processing.

tag: subject status

value: recurrent pregnancy loss (RPL)

tag: tissue

value: decidua


title: 47 (RPL 2)


title: neoAC direct #3

source_name: directly snap-frozen neonatal astrocytes


title: 50 (RPL 4)


title: ATAC-Seq SK-N-BE(2) shARID1B.3 rep3

description: Alignment reference genome GRCh38

tag: cell line

value: ARID1B silencing


title: neoAC direct #4


title: 46 (RPL 1)


title: neoAC direct #2


title: ATAC-Seq SK-N-BE(2) shARID1B.3 rep2

description: Alignment reference genome GRCh38


title: neoAC direct #1


title: 45 (control 3)

source_name: decidual tissue_control

value: control


title: 42 (control 1)


title: B16, day 16, mouse 4, rep C, experiment 3

city: Cambridge

first: Anna

last: Lyubetskaya

address: 100 Binney St

institute: Bristol-Myers Squibb

extract_protocol:
Rat colons were collected from 6-8 week-old Sprague-Dawley rats and were rinsed with ice-cold PBS before O.C.T. or FFPE embedding. Mouse syngeneic tumors were collected in ice-cold PBS before O.C.T. embedding. O.C.T. embedding was accomplished by placing tissue in a cryomold with ice-cold TissueTek O.C.T. Compound on an aluminum block pre-cooled in a dry ice ethanol bath. FFPE tissues were first placed in 10% neutral buffered formalin for 24-hour fixation, after which tissue was processed for embedding in a Sakura VIP automated system with vacuum/pressue cycles, dehydrating in graded alcohols to xylene and then paraffin, and embedded into blocks for sectioning.  All tumor resection smples were obtained with informed concesnt from BioIVT and Discovery Life Sciences. The Donor-A tumor (BioIVT) was divided prior to fixation, one half was O.C.T. embedded, the other half was FFPE embedded.
All mouse B16F10 and MC38 samples, and fresh-frozen (FF) rat colon and Donor-A PDAC samples were processed with the Visium Spatial Gene Expression kit (10X Genomics, PN-1000184) according to manufacturer protocol (10X Genomics, CG000160 Rev A and CG000238 Rev D for sectioning/staining and library preparation, respecitvely). Rat colon FF samples with a coverslip (wCS) were coverslipped during imaging, according to manufacturer protocol (10X Genomics, CG000160 RevA). Rat colon and Donor-A FFPE polyA-capture (FFPE-pA) samples were processed as described in Villacampa, et al., Cell Genomics 2021, using reagents from the Visium Spatial gene Expression kit (10X Genomics, PN-1000184), with a modified permeabilization, using 2X permeabilization enzyme for 60 minutes (permebailization enzyme was dissovled at 4 mg/ml (4X) in 0.1 N HCl and diluted to 2X in 0.1 N HCl). Donor A-C FFPE probe samples (FFPE-probes) were processed according to the Visium FFPE Regeant kit with Human Transcriptome Probe kit (10X Genomics, PN-100362 and PN-1000364) according to manufacturer protocol (10X Genomics, CG000409 Rev A and CG000407 Rev A for sectioning/staining and library preparation, respectively).

value: B16F10 syngeneic tumor


title: neoAC CellC #4

source_name: cultured neonatal astrocytes


title: ATAC-Seq SK-N-BE(2) shARID1B.2 rep3

description: Alignment reference genome GRCh38


title: ATAC-Seq SK-N-BE(2) shARID1A/B.2.3 rep2

description: Alignment reference genome GRCh38


title: neoAC CellC #3


title: ATAC-Seq SK-N-BE(2) shARID1A/B.2.3 rep1

description: Alignment reference genome GRCh38


title: 2.5_n6_f_30

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

data_processing:
Expression values were computed using STAR and featureCounts.
Genome_build: Bos taurus UMD_v3.1
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include raw counts.

organism: Bos taurus

source_name: Embryo

extract_protocol: The libraries were prepared following Illumina TruSeq stranded mRNA protocol. The quality of the RNA and final libraries was determined using an Agilent 4200 TapeStation System. The libraries were pooled equimolecularly and sequenced in an Illumina NovaSeq sequencer (single-end 100 bp) with a depth of around 20 Mio reads per sample.

value: Embryo

tag: developmental stage

value: Day 15 of pregnancy

value: maternal omega-6 diet

tag: size

value: short


title: 4.9_n6_f_28


title: ATAC-Seq SK-N-BE(2) shARID1B.2 rep1

description: Alignment reference genome GRCh38


title: AGES #4

source_name: Astrocytes generated from embryonic stem cells

value: Derived from murine ESC (GSC-5003, MTI-GlobalStem)


title: ATAC-Seq SK-N-BE(2) shARID1A.4 rep3

description: Alignment reference genome GRCh38

value: ARID1A silencing


title: AGES #3


title: ATAC-Seq SK-N-BE(2) shARID1A.4 rep2

description: Alignment reference genome GRCh38


title: 1.4_n6_f_25


title: ATAC-Seq SK-N-BE(2) shARID1B.3 rep1

description: Alignment reference genome GRCh38


title: 44 (control 2)


title: ATAC-Seq SK-N-BE(2) shARID1A.4 rep1

description: Alignment reference genome GRCh38


title: LAD2 mast cells, IL-33 treatment, replicate 6 [R1964]

city: Southampton

last: Willis

address: Southampton General Hospital, Tremona Road

country: United Kingdom

institute: University of Southampton

data_processing:
Alignment of RNA-seq data was performed using HISAT2
Counts data was extracted from HISAT2 output using SAMtools
Assembly: hg38
Supplementary files format and content: .csv file, raw counts

source_name: LAD2 Mast Cell

extract_protocol:
RNA was extracted using a Monarch total RNA miniprep kit
RNA libraries for RNA-seq were prepared using Novogenes's library construction protocol

value: LAD2 Mast Cell

value: Mast cell


title: LAD2 mast cells, IL-33 treatment, replicate 5 [R1954]


title: neoAC CellC #1


title: ATAC-Seq SK-N-BE(2) shARID1B.2 rep2

description: Alignment reference genome GRCh38


title: 5_n6_m_23


title: AGES #1


title: AGES #2


title: ATAC-Seq SK-N-BE(2) shARID1A.2 rep2

description: Alignment reference genome GRCh38


title: 4.5_n6_m_24


title: LAD2 mast cells, IL-33 control, replicate 6 [R1961]

value: Control


title: 7.7_n6_f_26


title: NSC #4

source_name: Neural stem cell


title: 3.7_n6_m_22


title: LAD2 mast cells, IL-33 treatment, replicate 4 [R1944]


title: LAD2 mast cells, IL-33 control, replicate 5 [R1951]


title: ATAC-Seq SK-N-BE(2) shARID1A.2 rep1

description: Alignment reference genome GRCh38


title: LAD2 mast cells, IL-33 control, replicate 4 [R1941]


title: 2.5_n6_m_21


title: NSC #3


title: ATAC-Seq SK-N-BE(2) Control rep3

description: Alignment reference genome GRCh38


title: 2.1_n6_f_20


title: NSC #2


title: ATAC-Seq SK-N-BE(2) Control rep2

description: Alignment reference genome GRCh38


title: 2.3_n6_f_19


title: ATAC-Seq SK-N-BE(2) shARID1A.2 rep3

description: Alignment reference genome GRCh38


title: NSC #1


title: F1 Kidney Control Replicate 3

city: Salt Lake City

first: Clement

last: Chow

state: UT

address: EIHG 5200 15 North 2030 East

institute: University of Utah

data_processing:
Fastq files were trimmed by using seqtk v1.2 software.
Parental RNA-seq reads were aligned to strain specific reference genomes using Bowtie2 v2.2.9
F1 reads were aligned to masked genomes using STAR v2.6 software.
Alignment files were sorted and converted using samtools v1.12
The Deseq2 default normalization method (median of ratios) was used to normalize counts using Deseq2 v1.28.1
Genome_build: GRCmm39, CAST_EiJ_v1
Supplementary_files_format_and_content: Matrix table with normalized counts for every gene and every sample

source_name: Kidney

extract_protocol:
Tissues were removed and placed on dry ice and stored at -80°C. RNA was harvested using Trizol reagent and Direct-zol RNA MiniPrep Kit Rna column extraction protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols. Illumina TruSeq Stranded Total RNA Library Prep Ribo-Zero Gold.

treatment_protocol: Control treatment mice were injected with DMSO using IP injection. TM treatment mice were injected with TM dissolved in DMSO using IP injection (final concentration of 1mg TM per 1kg mouse weight). Mice were euthanized 24 hours later.

value: 15-23 weeks

value: Male

value: DMSO

tag: replicate

value: Replicate 3


title: 2.3_n6_m_18


title: 6.4_n3_f_17

value: maternal omega-3 diet


title: LAD2 mast cells, IL-33 treatment, replicate 2 [R1924]


title: LAD2 mast cells, IL-33 control, replicate 3 [R1931]


title: SK-N-BE(2) shARID1A/B.4.2 rep3

data_processing:
Alignment with STAR v2.5.3a
Gene quantification with RSEM v1.3.0
Differential analysis with DESeq2 v1.26.0
Assembly: GRCh38
Supplementary files format and content: Normalized raw RNA counts for each transcript and sample (Gene_expression_rawdata.txt)
Supplementary files format and content: Differential expression analysis between silencing and control (shARID1A_vs_control_results.txt; shARID1B_vs_control_results.txt; shARID1A_B_vs_control_results.txt)

extract_protocol:
Total RNA was extracted with miRNeasy mini extraction kit (Qiagen) with and additional in-column step of DNAse I treatment. Total RNA was eluted in 20 ul of nuclease-free water.
Libraries were prepared following the TruSeq Stranded mRNA LT Sample Prep Kit protocol (Illumina).

value: ARID1A and ARID1B silencing


title: LAD2 mast cells, IL-33 control, replicate 2 [R1921]


title: F1 Kidney TM Replicate 3

value: TM


title: 11.7_n3_f_16

value: long


title: SK-N-BE(2) shARID1A/B.4.2 rep1


title: CAST Kidney Control Replicate 3

value: CASTEiJ


title: 6_n3_m_15

value: Embryo

value: Day 15 of pregnancy


title: LAD2 mast cells, IL-33 treatment, replicate 1 [R1914]


title: LAD2 mast cells, IL-33 control, replicate 1 [R1911]


title: LAD2 mast cells, IL-33 treatment, replicate 3 [R1934]


title: 0.4_n3_m_14

value: short


title: CAST Kidney TM Replicate 3


title: SK-N-BE(2) shARID1A/B.2.3 rep3


title: AML2_sgUTX_4_SGC0946_Rep2

city: Birmingham

first: xinyue

last: zhou

state: Alabama

address: WTI 510G 1824 6th Ave S

department: hematology and oncology

institute: university of alabama at birmingham

data_processing:
The paired-end reads were mapped to the human genome (hg19) using STAR (v2.5.1b) with default parameters.
Assembly: hg19
Supplementary files format and content: txt, raw read counts

growth_protocol: Cells were cultured in RPMI with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was isolated using RNeasy kit (Qiagen, Germany).
RNA-seq libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs), following the manufacturer’s protocol. The quality and concertation of the libraries were examined by Bioanalyzer High Sensitivity DNA Chip (Agilent). The multiplexed RNA-Seq libraries were paired-end sequenced for 150 bp on the Illumina HiSeq 4000 platform.

treatment_protocol:
Cells were lentivirally infected with indicated sgRNA for gene knockout
Cells were treated with DMSO or 1µM SGC0946 for 6 days.

value: Acute myeloid leukemia cells

value: UTX knockout

value: DOT1L inhibitor SGC0946

tag: time

value: Day 6


title: B6 Kidney Control Replicate 3

tag: strain


title: B6 Kidney TM Replicate 3


title: 1.3_n3_f_13


title: AML2_sgUTX_4_SGC0946_Rep1


title: ATAC-Seq SK-N-BE(2) Control rep1

description: Alignment reference genome GRCh38

value: Control


title: SK-N-BE(2) shARID1A/B.2.3 rep1


title: SK-N-BE(2) shARID1A/B.4.2 rep2


title: AML2_sgUTX_2_SGC0946_Rep2


title: 2.6_n3_m_12


title: SK-N-BE(2) shARID1B.3 rep3

value: ARID1B silencing


title: F1 Kidney Control Replicate 2

value: 15-23 weeks

value: Male

value: Replicate 2


title: 9.5_n3_m_11

value: maternal omega-3 diet


title: F1 Kidney TM Replicate 2


title: SK-N-BE(2) shARID1B.3 rep2


title: AML2_sgUTX_2_SGC0946_Rep1


title: 11.3_n3_m_10


title: AML2_sgLuc_SGC0946_Rep2

value: WT


title: 4.4_n3_f_08


title: AML2_sgLuc_SGC0946_Rep1


title: CAST Kidney Control Replicate 2

value: DMSO


title: SK-N-BE(2) shARID1B.2 rep3


title: SK-N-BE(2) shARID1B.3 rep1


title: SK-N-BE(2) shARID1A/B.2.3 rep2

value: ARID1A and ARID1B silencing


title: B6 Kidney Control Replicate 2


title: AML2_sgUTX_4_DMSO_Rep2


title: SK-N-BE(2) shARID1B.2 rep2


title: 13.2_n3_f_07

value: long


title: 10.5_n3_m_06

value: Embryo


title: B6 Kidney TM Replicate 2

value: TM


title: AML2_sgUTX_4_DMSO_Rep1


title: SK-N-BE(2) shARID1B.2 rep1


title: 2.1_n3_m_05

value: Day 15 of pregnancy

value: short


title: AML2_sgUTX_2_DMSO_Rep2

value: Acute myeloid leukemia cells

value: UTX knockout


title: SK-N-BE(2) shARID1A.4 rep3

value: ARID1A silencing


title: F1 Kidney TM Replicate 1

value: Replicate 1


title: F1 Kidney Control Replicate 1


title: 12.9_n3_m_04


title: SK-N-BE(2) shARID1A.4 rep2


title: AML2_sgUTX_2_DMSO_Rep1

value: Day 6


title: CAST Kidney TM Replicate 2

value: CASTEiJ

value: 15-23 weeks


title: CAST Kidney Control Replicate 1

value: Male


title: AML2_sgLuc_DMSO_Rep2


title: 5.5_n3_f_03

value: maternal omega-3 diet


title: SK-N-BE(2) shARID1A.4 rep1


title: SK-N-BE(2) shARID1A.2 rep3


title: SK-N-BE(2) shARID1A.2 rep2


title: 8_n3_m_02


title: SK-N-BE(2) shARID1A.2 rep1


title: CAST Kidney TM Replicate 1


title: B6 Kidney Control Replicate 1


title: GIST430/654/CCND1 fusion, palbociclib, recpliate 1

first: Inga-Marie

last: Schaefer

state: MA

address: 75 Francis Street

institute: Brigham and Women's Hospital

data_processing:
The samples were sequenced using a 2x150bp Paired End (PE) configuration and overall read amount per HiSeq lane of ~350 M
Trimmed reads were mapped to the Homo Sapiens GRCh38 (hg38) reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2
Gene expression between the groups was compared using DESeq2. The Wald test was used to generate P values and log2 fold changes. Genes with adjusted P values < 0.05 and absolute log2 fold changes > 1 were called as differentially expressed genes for each comparison.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Excel file includes FKPM values for each sample in separate columns

source_name: cell line

growth_protocol: Cells were maintained in IMDM media containing 3% FBS

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen)
A sequencing library was prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA)

treatment_protocol: Cells were treated wtith palbociclib (31.25 nM) versus DMSO control for 24h

value: cell line

value: GIST

value: palbiclib 31.25 nM


title: AML2_sgLuc_DMSO_Rep1

value: WT

value: DMSO


title: Patient Derived Xenograft model BCM-15100

city: Houston

middle: T

last: Lewis

state: TX

address: 1 Baylor Plaza N1210

department: Breast Center

institute: Baylor College of Medicine

description: RNAseq of human ER+ tumor tissue graft on mouse mammary fat pad

data_processing:
Raw reads were split into human/epithelial (graft) and murine/stromal (host) reads using Xenome v1.0.1
Human and Mouse reads were aligned to hg38 and mm10 reference genomes respectively using RSEM/STAR v2.5.3a_modified
The above STAR run was run internally by rsem-calculate-expression (RSEM v1.2.31), which then quantified transcripts and genes, producing isoform and gene level results.
Genome_build: hg38/mm10
Supplementary_files_format_and_content: A matrix file was generated using expected counts values from RSEM results. Each row represents a gene and each column represents a xenograft model

organism:
Homo sapiens
Mus musculus

source_name: Patient-Derived Xenograft

extract_protocol:
PDX tumor were harvested from mice and trimmed of excess fat pad tissue. Representative tumor fragments were snap frozen in liquid nitrogen. Tumor was homogenized and RNA extracted using the RNeasy Mini Kit from Qiagen.
NuGEN Ovation RNA-Seq v2 Kit (protocol p/n 7102, kit p/n 7102-08) along with ThermoFisher’s ERCC RNA Spike-In Control Mixes Protocol (publication number 4455352, rev. D) and the Rubicon ThruPlex DNA-Seq (protocol: QAM-108-002, kit p/n R400428) library preparation protocolss

treatment_protocol: Not applicable

value: Human breast tumor tissue graft on mouse mammary fat pad

tag: tumor subtype

value: human ER+ tumor

value: SCID/Bg mouse host

value: untreated


title: F1 Liver Control Replicate 3

source_name: Liver

tag: treatment

value: Replicate 3


title: B6 Kidney TM Replicate 1

value: TM


title: GIST430/654/CCND1 fusion, DMSO, replicate 2

city: Boston

tag: genotype


title: SK-N-BE(2) Control rep3

value: Control


title: CAST Liver Control Replicate 3


title: Patient Derived Xenograft model BCM-15057


title: GIST430/654/CCND1 fusion, DMSO, replicate 1


title: GIST430/654/CCND1 fusion, palbociclib, recpliate 2


title: SK-N-BE(2) Control rep2


title: CAST Liver TM Replicate 3


title: 20.3_n3_m_01

value: Embryo

value: Day 15 of pregnancy

value: long


title: Patient Derived Xenograft model BCM-15046

description: RNAseq of human TNBC tumor tissue graft on mouse mammary fat pad

value: human TNBC tumor


title: Patient Derived Xenograft model BCM-15115


title: GIST430/654/RB1-, palbociclib, recpliate 1


title: B6 Liver Control Replicate 3

value: 15-23 weeks

value: Male


title: GIST430/654/RB1-, palbociclib, recpliate 2

value: cell line

value: GIST


title: Patient Derived Xenograft model BCM-15034

description: RNAseq of human ER+/HER2+ tumor tissue graft on mouse mammary fat pad

value: human ER+/HER2+ tumor


title: Patient Derived Xenograft model BCM-15030


title: Patient Derived Xenograft model BCM-15051


title: MM6_shRNA-3_rep1

city: Guangzhou

first: Hengyou

last: Weng

address: Room 304, Building D, 190 Kaiyuan Ave,

institute: Guangzhou Laboratory

description: rna-seq_raw_gene_read_count.xlsx: MM6_IGF2BP2_shRNA-3_rep1

data_processing:
The raw RNA-seq reads were quality checked by FastQC (version 0.11.5) and then adaptors trimmed by Cutadapt (version 3.4). The processed reads were mapped to human transcriptome built with gene annotations (hg38, GENCODE v37) by STAR (version 2.7.2b) with parameters recommended by ENCODE project.
The aligned results were then passed to RSEM (version 1.2.31) to estimate the read count of genes.
Finally, the estimated read counts of genes were analyzed by DESeq2 (version 1.32.0) to identify differentially expressed genes with following parameters: sfType=poscounts, test=Wald and lfcShrink(type=none).
Assembly: hg38
Supplementary files format and content: Raw read gount of genes and processed results from DESeq2

source_name: Human AML cell MonoMac6

extract_protocol:
Total RNA from MonoMac6 cells with or without IGF2BP2 knockdown was isolated using the TRIzol reagent (Thermo fisher Scientific).
Library construction of 1 µg RNA per sample was made using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Human acute myeloid leukemia (AML) cells


title: MM6_shRNA-3_rep2

description: rna-seq_raw_gene_read_count.xlsx: MM6_IGF2BP2_shRNA-3_rep2


title: MM6_shRNA-3_rep3

description: rna-seq_raw_gene_read_count.xlsx: MM6_IGF2BP2_shRNA-3_rep3


title: GIST430/654/RB1-, DMSO, replicate 1

value: DMSO


title: GIST430/654 parental, palbociclib, recpliate 2

value: parental

value: palbiclib 31.25 nM


title: F1 Liver TM Replicate 2

value: Replicate 2


title: Patient Derived Xenograft model BCM-15029

value: Human breast tumor tissue graft on mouse mammary fat pad

value: SCID/Bg mouse host

value: untreated


title: GIST430/654/RB1-, DMSO, replicate 2


title: B6 Liver TM Replicate 3

value: TM

value: Replicate 3


title: MM6_shRNA-2_rep3

description: rna-seq_raw_gene_read_count.xlsx: MM6_IGF2BP2_shRNA-2_rep3


title: GIST430/654 parental, palbociclib, recpliate 1


title: CAST Liver Control Replicate 2

value: CASTEiJ


title: Patient Derived Xenograft model BCM-5438

value: human TNBC tumor


title: SK-N-BE(2) Control rep1

value: Control


title: MM6_shRNA-2_rep2

description: rna-seq_raw_gene_read_count.xlsx: MM6_IGF2BP2_shRNA-2_rep2


title: CAST Liver TM Replicate 2

value: 15-23 weeks

value: Male


title: Patient Derived Xenograft model BCM-4849


title: GIST430/654 parental, DMSO, replicate 2

value: cell line

value: GIST


title: F1 Liver Control Replicate 2


title: MM6_shRNA-2_rep1

description: rna-seq_raw_gene_read_count.xlsx: MM6_IGF2BP2_shRNA-2_rep1

value: Human acute myeloid leukemia (AML) cells


title: B6 Liver Control Replicate 2

value: DMSO


title: Patient Derived Xenograft model BCM-4400


title: MM6_shRNA-1_rep3

description: rna-seq_raw_gene_read_count.xlsx: MM6_IGF2BP2_shRNA-1_rep3


title: GIST430/654 parental, DMSO, replicate 1

value: parental


title: F1 Liver Control Replicate 1

value: Replicate 1


title: Patient Derived Xenograft model BCM-4169

description: RNAseq of human HER2+ tumor tissue graft on mouse mammary fat pad

value: human HER2+ tumor


title: F1 Liver TM Replicate 1


title: CAST Liver TM Replicate 1


title: MM6_NS_rep3

description: rna-seq_raw_gene_read_count.xlsx: MM6_IGF2BP2_shNS_rep3

value: shNS


title: MM6_shRNA-1_rep2

description: rna-seq_raw_gene_read_count.xlsx: MM6_IGF2BP2_shRNA-1_rep2


title: Patient Derived Xenograft model BCM-3472

value: Human breast tumor tissue graft on mouse mammary fat pad

value: SCID/Bg mouse host