title: Skin, Lesion_ST, rep1

city: Tainan City

first: Yi-Kai

last: Hong

state: Please select an option below

address: No.1, Daxue Rd., East Dist.

country: Taiwan

institute: National Cheng Kung University

description: 10x Genomics

data_processing:
library strategy: spatial transcriptomics (ST)
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skin

extract_protocol:
After removal of the adipose tissues, samples were minced with scissors into 1 mm2 piece and transferred into gentleMACS C tubes, and then incubated at 37°C for 2.5 h in Whole Skin Dissociation Kit of Human (Miltenyi Biotec, California, USA). Mechanical dissociation was performed on gentleMACS™ Octo Dissociator using ‘h_skin_01’ program. Cell suspension was passed through a 70-μm and then 40-μm filter for removal of large clump fragments. The cells were washed twice with PBS and resuspended in cold DMEM supplemented with 10% FBS. Erythrocytes were removed by red blood cell lysis solution (Miltenyi Biotec). Live cells of single suspension were stained by 0.4 % trypan blue and counted by TC20 Automated Cell Counter (Bio-Rad, California, USA).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Whole cells

value: Skin

value: Asia, male

value: 40 years old


title: 17897X3 EPHB2-WT-3

status: Public on Apr 10 2024

type: SRA

city: Salt Lake City

first: Patrice

last: Mimche

state: Utah

address: 26 North Medical Dr

country: USA

institute: University of Utah

library_source: transcriptomic

data_processing:
The human GRCh38 genome and gene annotation files were downloaded from Ensembl release 98
Trimmed reads were aligned to the reference database using STAR version 2.7.2c in two pass mode to output a BAM file sorted by coordinates
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.26.0
Assembly: hg38; H_sapiens_Dec_2013; GRCh38
Supplementary files format and content: FeatureCount output files combined into a single tab-delimited matrix

molecule: total RNA

organism: Homo sapiens

source_name: skin

growth_protocol: Dermal fibroblasts lines were cultured in the fibroblast growth kit-low serum (ATCC, VA) constituted with the following ingredients: Fibroblast basal medium, ascorbic acid, fetal bovine serum, rhFGF-basic, L-glutamine, and hydrocortisone.

extract_protocol:
Total RNA was extracted using RNA Stat60® (Tel-Test Inc, USA) following standard phenol-chloroform procedure, and further purified using the NucleoSpin RNA-II purification kit (Machery-Nagel) following the manufacturer’s instructions.
Total RNA samples (100-500 ng) were hybridized with Ribo-Zero Gold to substantially deplete cytoplasmic and mitochondrial rRNA from the samples.  Stranded RNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded Total RNA Library Prep Gold kit (20020598) with TruSeq RNA UD Indexes (20022371).  Purified libraries were qualified on an Agilent Technologies 4150 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 1.30 nM in preparation for Illumina sequence analysis.  Sequencing libraries (1.3 nM) were chemically denatured and applied to an Illumina NovaSeq flow cell using the NovaSeq XP chemistry workflow (20021665).  Following transfer of the flowcell to an Illumina NovaSeq instrument, a 2 x 151 cycle paired end sequence run was performed using a NovaSeq S2 reagent Kit (20012860).

treatment_protocol: Human dernal fibroblasats (70% confluency) were transfected with EPHB2 Mission®-esiRNA (Sigma Aldrich, USA) delivered into the cells using the lipofectamine® RNAiMAX (Invitrogen, USA) according to the manufacturer’s instruction. After 48H incubation, transfected fibroblast were stimulated with recombinant human TGF-β1 at 10 ng/ml for another 24H.

tag: tissue

value: skin

tag: cell line

value: Primary cell

tag: cell type

value: Human dermal fibroblast

tag: genotype

value: Wild type

tag: treatment


title: rep2_prep2_MPRALibC6cyclesPCR

city: Memphis

first: Daniel

last: Savic

state: TN

address: 262 Danny Thomas pl.

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

description:
Plasmid DNA
barcodes.txt

library_source: other

data_processing:
Following next-generation sequencing, the MPRA sequence data was trimmed to contain only barcode sequences without allowing for any mismatches and read counts were determined for all barcodes. To identify significant allele-specific effects mpralm (69) was performed on RNA and DNA barcode counts after merging RNA or DNA counts across all barcodes for each allele.
Assembly: .txt file containing SNV-barcode associations
Supplementary files format and content: .txt file containing SNV-barcode associations
Supplementary files format and content: .txt file containing analysis of all cell lines x all SNVs MPRA data
Library strategy: MPRA

molecule: other

organism: synthetic construct

source_name: MPRA library control

growth_protocol: RPMI 1640 + 10% serum

extract_protocol: MPRA Oligo design :Oligo libraries were designed by following previous work with modified protocols (1-4). MPRA oligos ordered from Agilent (230 bp) were structured as follows: 5'-Primer1-enh-Kpnl-Xbal-barcode-primer2-3' where primer1 and primer2 are universal primer sites, enh denotes the 175bp variant containing region to test for enhancer activity, Kpnl and Xbal denote recognition sequences for cut sites, and barcode denotes 10-bp tag sequence (see Sup File 6). Agilent oligos were resuspended in 100 ul nuclease free water. All 10-bp barcodes for each variant allele used in MPRA are provided in Supplemental File 7. MPRA Plasmid Cloning-Input (DNA) Library construction: For plasmid cloning, oligo libraries were amplified by 20 cycles of emulsion PCR (Micellula DNA Emulsion & Purification Kit #E3600, EURx Molecular Biology Products) using Herculase II fusion DNA polymerase (#600675, Agilent), forward and reverse primers (see Sup File 3) to introduce SfiI restriction enzyme sites (GGCCNNNNNGGCC) (NEB) and homology arms to the pMPRA1 plasmid (Cat: #49349, Addgene). Purified PCR products were separated on a 2-4% agarose gel to verify the expected amplification size of 281bp. The pMPRA1 backbone vector was Sfil digested overnight and size selected on a 1% agarose gel. Vector backbone gel extraction was done with the Qiagen gel extraction kit and QIAquick PCR purification kit (28706X4 and 28104).  Gibson assembly was used to clone oligos into vector using 79 ng of inserts, 100 ng of digested vector, and 20 ul Gibson assembly 2x master mix (# E2611S, NEB). The reaction was purified using MinElute PCR purification column (Qiagen), and drop analysis was performed with Millipore filters (Type VSWP 0.25 um Millipore #VSWP02500). For the transformation step, we aimed to obtain 10x CFU bacterial cells than the distinct promoter-tag combinations (unique sequences) in the oligo library. We transformed the Gibson assembly reactions into MegaX DH10B electrocompetent bacteria (#C6400-03, Invitrogen) using GenePulser II electroporator (Bio-Rad). Plasmids were extracted with Qiagen Maxi Prep Kit. For quality control studies, an aliquot of the isolated plasmid library was digested with SfiI and run on 1 % agarose gel to confirm the presence of inserts. To generate linear enhancer-barcode backbone sequences for reporter insertion, 2 ug of plasmid was digested with KpnI/XbaI. A minimal promoter + truncated eGFP was then ligated to the linearized enhancer-barcode backbone and purified using the Qiagen MilEute PCR purification kit. The ligation was then transformed into 1 vial of MegaX electrocompetent bacteria (#C6400-03, Invitrogen) as before. Plasmids were then extracted using a Qiagen Maxiprep kit as before and the elution was verified as a single size band by gel electrophoresis. MPRA library transfection and sequencing MPRA plasmid library (10 µg) transfections were done in 10 ALL cell lines having at >95% cell viability (45 million cells x 4 replicates x 10 cell lines) using electroporation with the Neon Transfection system (Thermofisher). Next day, RNA-was harvested using the RNeasy plus mini kit (Cat: #74134, Qiagen) using 4 columns per sample. Once the RNA was isolated, we performed additional DNase digestion using RQ1 RNase-free DNase (Cat: # M6101, Promega). All tubes from the same replicates were combined and added 1 volume of 70% ethanol to the combined lysate and mixed well by pipetting. The DNase treated RNA was again purified with RNeasy mini kit and eluted in 60 ul RNase free water. Total RNA was quantified using DeNovix Ds-11 FX instrument. We yielded 16µg-112µg of total RNA from each replicate depending on the cell line used. mRNA purification was performed using Dynabeads mRNA purification kit (Cat: #61006, Invitrogen). mRNA concentration was measured using Qubit HS RNA (Cat: #Q32852, Invitrogen). We yielded from 0.75-2 ug of mRNA in average from each replicate. cDNA was synthesized using three primers (2 uM) cDNA P1, cDNA P4, and cDNA 6, with the Superscript III first-strand synthesis system (Cat: #18080051, Invitrogen) (see Sup File 6). Final multiplexing of 50ng cDNA and input plasmid DNA (4 aliquots of MPRA plasmid pool that were independently prepared for next-generation sequencing) was carried out using Q5 Hot Start 2x Master Mix (NEB #M0494S), index primers, and Multiplexing primer 1 for 15 cycles of PCR. The reactions were size selected using AMPure XP beads (Cat: #A63881, Beckman Coulter, Indianapolis, IN) and eluted in 20 ul nuclease free water. The final library concentration was measured using Qubit DNA HS. 20-40 ng of each library was sequenced on the Illumina NovaSeq (200 million x 150bp paired-end reads per sample) at the Hartwell Center for Bioinformatics and Biotechnology at St. Jude Children's Research Hospital. MPRA sequencing analysis Following next-generation sequencing, the MPRA sequence data was trimmed to contain only barcode sequences without allowing for any mismatches and read counts were determined for all barcodes. To identify significant allele-specific effects mpralm (5) was performed on RNA and DNA barcode counts after merging RNA or DNA counts across all barcodes for each allele.  1. P. Kheradpour et al., Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Genome Res 23, 800-811 (2013).  2. A. Melnikov et al., Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay. Nature biotechnology 30, 271-277 (2012).  3. A. Melnikov, X. Zhang, P. Rogov, L. Wang, T. S. Mikkelsen, Massively parallel reporter assays in cultured mammalian cells. JoVE (Journal of Visualized Experiments), e51719 (2014).  4. J. Choi et al., Massively parallel reporter assays of melanoma risk variants identify MX2 as a gene promoting melanoma. Nat Commun 11, 2718 (2020).  5. L. Myint, D. G. Avramopoulos, L. A. Goff, K. D. Hansen, Linear models enable powerful differential activity analysis in massively parallel reporter assays. BMC Genomics 20, 209 (2019).

value: MPRA library control


title: rep1_prep2_MPRALibC6cyclesPCR

description:
Plasmid DNA
barcodes.txt


title: Patient 25 TCR Post-Denosumab TP2

city: San Francisco

first: Mark

last: Bridge

state: CA

address: 513 Parnassus Ave

institute: UCSF

description: bulk TCR-seq

data_processing:
mixcr-3.0.13 was used to analyze amplicons for each sample R1 R2 with flags: --species hs --starting-material rna --5-end v-primers --3-end j-primers --adapters adapters-present
TRB output files were collected and matched against UMIs extracted from the input fastq sequences, and combined with the TRB data into a TRB with UMI file (TRB_w_umi.txt file) for each TRB
Assembly: N/A (raw reads used)
Supplementary files format and content: TRB.txt - TCR amplicon clonotype mixcr analysis file
Supplementary files format and content: TRB_w_umi.txt - TRB with UMI
Library strategy: VDJ-seq

molecule: polyA RNA

source_name: blood

extract_protocol:
Cryopreserved PBMCs were thawed and 250,000 cells were extracted for RNA using the Invitrogen RNAqueous-Micro Total RNA Isolation Kit (Thermo Fisher #AM1931).
10.4ng of RNA was used for reverse transcription (RT) and cDNA generation, following the Smart-seq2 protocol with modifications. The oligo-dT primer was biotinylated at the 5’ end. A barcode, unique molecular modifiers, and biotin were added to the 5’ end of the TSO primer. Maxima H Minus Reverse Transcriptase (Thermo Fisher #EP0753) was used for reverse transcription. Barcoded RT product was then pooled together using a DNA Clean & Concentrator-5 Kit (Zymo Research, #D4013). 16 cycles were used for cDNA amplification. cDNA was then enriched for alpha and beta TCR receptors separately and used for Illumina library generation.
Modified Smartseq-2 with UMIs and barcodes and targeted TCR alpha and beta amplification.

tag: individual

value: Patient 25

value: blood

value: Immune cells

tag: library type

value: VDJ

value: Denosumab TP2

tag: additional treatment

value: No Chemo No Steroid


title: 17897X1 EPHB2-WT-1


title: PDXMPRA1137Rep3

data_processing:
Following next-generation sequencing, the MPRA sequence data was trimmed to contain only barcode sequences without allowing for any mismatches and read counts were determined for all barcodes. To identify significant allele-specific effects mpralm (5) was performed on RNA and DNA barcode counts after merging RNA or DNA counts across all barcodes for each allele.
Assembly: .txt file containing SNV-barcode associations
Supplementary files format and content: .txt file containing SNV-barcode associations
Supplementary files format and content: .txt file containing analysis of all cell lines x all SNVs MPRA data
Library strategy: MPRA

source_name: PDX

extract_protocol:
MPRA Oligo design
Oligo libraries were designed by following previous work with modified protocols (1-4). MPRA oligos ordered from Agilent (230 bp) were structured as follows: 5’-Primer1-enh-Kpnl-Xbal-barcode-primer2-3’ where primer1 and primer2 are universal primer sites, enh denotes the 175bp variant containing region to test for enhancer activity, Kpnl and Xbal denote recognition sequences for cut sites, and barcode denotes 10-bp tag sequence (see Sup File 6). Agilent oligos were resuspended in 100 ul nuclease free water. All 10-bp barcodes for each variant allele used in MPRA are provided in Supplemental File 7.
MPRA Plasmid Cloning-Input (DNA) Library construction
For plasmid cloning, oligo libraries were amplified by 20 cycles of emulsion PCR (Micellula DNA Emulsion & Purification Kit #E3600, EURx Molecular Biology Products) using Herculase II fusion DNA polymerase (#600675, Agilent), forward and reverse primers (see Sup File 3) to introduce SfiI restriction enzyme sites (GGCCNNNNNGGCC) (NEB) and homology arms to the pMPRA1 plasmid (Cat: #49349, Addgene). Purified PCR products were separated on a 2-4% agarose gel to verify the expected amplification size of 281bp. The pMPRA1 backbone vector was Sfil digested overnight and size selected on a 1% agarose gel. Vector backbone gel extraction was done with the Qiagen gel extraction kit and QIAquick PCR purification kit (28706X4 and 28104).  Gibson assembly was used to clone oligos into vector using 79 ng of inserts, 100 ng of digested vector, and 20 ul Gibson assembly 2x master mix (# E2611S, NEB). The reaction was purified using MinElute PCR purification column (Qiagen), and drop analysis was performed with Millipore filters (Type VSWP 0.25 um Millipore #VSWP02500). For the transformation step, we aimed to obtain 10x CFU bacterial cells than the distinct promoter-tag combinations (unique sequences) in the oligo library. We transformed the Gibson assembly reactions into MegaX DH10B electrocompetent bacteria (#C6400-03, Invitrogen) using GenePulser II electroporator (Bio-Rad). Plasmids were extracted with Qiagen Maxi Prep Kit. For quality control studies, an aliquot of the isolated plasmid library was digested with SfiI and run on 1 % agarose gel to confirm the presence of inserts. To generate linear enhancer-barcode backbone sequences for reporter insertion, 2 ug of plasmid was digested with KpnI/XbaI. A minimal promoter + truncated eGFP was then ligated to the linearized enhancer-barcode backbone and purified using the Qiagen MilEute PCR purification kit. The ligation was then transformed into 1 vial of MegaX electrocompetent bacteria (#C6400-03, Invitrogen) as before. Plasmids were then extracted using a Qiagen Maxiprep kit as before and the elution was verified as a single size band by gel electrophoresis.
MPRA library transfection and sequencing
MPRA plasmid library (10 µg) transfections were done in 10 ALL cell lines having at >95% cell viability (45 million cells x 4 replicates x 10 cell lines) using electroporation with the Neon Transfection system (Thermofisher). Next day, RNA-was harvested using the RNeasy plus mini kit (Cat: #74134, Qiagen) using 4 columns per sample. Once the RNA was isolated, we performed additional DNase digestion using RQ1 RNase-free DNase (Cat: # M6101, Promega). All tubes from the same replicates were combined and added 1 volume of 70% ethanol to the combined lysate and mixed well by pipetting. The DNase treated RNA was again purified with RNeasy mini kit and eluted in 60 ul RNase free water. Total RNA was quantified using DeNovix Ds-11 FX instrument. We yielded 16µg-112µg of total RNA from each replicate depending on the cell line used. mRNA purification was performed using Dynabeads mRNA purification kit (Cat: #61006, Invitrogen). mRNA concentration was measured using Qubit HS RNA (Cat: #Q32852, Invitrogen). We yielded from 0.75-2 ug of mRNA in average from each replicate. cDNA was synthesized using three primers (2 uM) cDNA P1, cDNA P4, and cDNA 6, with the Superscript III first-strand synthesis system (Cat: #18080051, Invitrogen) (see Sup File 6).
Final multiplexing of 50ng cDNA and input plasmid DNA (4 aliquots of MPRA plasmid pool that were independently prepared for next-generation sequencing) was carried out using Q5 Hot Start 2x Master Mix (NEB #M0494S), index primers, and Multiplexing primer 1 for 15 cycles of PCR. The reactions were size selected using AMPure XP beads (Cat: #A63881, Beckman Coulter, Indianapolis, IN) and eluted in 20 ul nuclease free water. The final library concentration was measured using Qubit DNA HS. 20-40 ng of each library was sequenced on the Illumina NovaSeq (200 million x 150bp paired-end reads per sample) at the Hartwell Center for Bioinformatics and Biotechnology at St. Jude Children’s Research Hospital.

value: PDX


title: rep3_prep1_MPRALibC6cyclesPCR

description:
Plasmid DNA
barcodes.txt


title: Patient 26 TCR Post-Denosumab TP4

description: bulk TCR-seq

value: Patient 26

value: Denosumab TP4


title: Patient 26 TCR Post-Denosumab TP2

description: bulk TCR-seq


title: Patient 25 TCR Pre-Denosumab TP1

description: bulk TCR-seq

value: No Denosumab TP1


title: PDXMPRA1137Rep1


title: Patient 24 TCR Post-Denosumab TP4

description: bulk TCR-seq

value: Patient 24

value: Chemo and Steroid


title: Patient 24 TCR Post-Denosumab TP2

description: bulk TCR-seq

value: Steroid only


title: Patient 25 TCR Post-Denosumab TP3

description: bulk TCR-seq

value: Denosumab TP3


title: PDXMPRA4420Rep1


title: rep1_prep1_MPRALibC6cyclesPCR

description:
Plasmid DNA
barcodes.txt


title: rep2_prep2_MPRALibC10cyclesPCR

description:
Plasmid DNA
barcodes.txt


title: Patient 22 TCR Post-Denosumab TP4

description: bulk TCR-seq

value: Patient 22


title: PDCoV_virion_rep2

city: Wuhan

first: Dengguo

last: Wei

state: Hubei Province

address: Huazhong Agricultural University, Hongshan District, Wuhan City, Hubei Province

department: College of Veterinary Medicine

country: China

institute: Huazhong Agricultural University

data_processing:
Data cleaning
Sequence alignment
Identification and visualization of valid chimeric reads
Secondary structure prediction
Assembly: PDCoV CHN-HN-2014 (GenBank accession: KT336560)
Supplementary files format and content: The HIC file displays the interaction matrix of the virus genome structure for different sets of PDCoV data
Supplementary files format and content: The CT file displays the entire genome structure of PDCoV
Library strategy: vRIC-seq

organism: Sus scrofa

source_name: Renal

extract_protocol:
After completing the proximity-ligated, the RNA was extracted by proteinase K, Trizol and chloroform according to the manufacturer’s instruction.
BioMag®Plus Concanavalin A beads was used to capture virions, 500 μL purified virus was added to the 150 μL washed beads with ConA Binding buffer, and incubated for 10 min at room temperature. The beads was washed with ConA Binding buffer for three times and PBST buffer for once (1 × PBS, 0.1% Tween 20), and resuspended in 1 mL PBST buffer. The final concentration of 1% formaldehyde was used to fix the RNA-RNA interaction, and final concentration 0.125 M glycine was added to quench the formaldehyde.

value: Renal


title: Patient 22 TCR Post-Denosumab TP2

description: bulk TCR-seq


title: Patient 22 TCR Post-Denosumab TP3

description: bulk TCR-seq


title: PDXMPRA1137Rep2


title: Patient 21 TCR Post-Denosumab TP4

description: bulk TCR-seq

value: Patient 21


title: PDCoV_virion_rep1


title: Patient 23 TCR Pre-Denosumab TP1

description: bulk TCR-seq

value: Patient 23


title: Patient 22 TCR Pre-Denosumab TP1

description: bulk TCR-seq

value: blood


title: Patient 26 TCR Post-Denosumab TP3

description: bulk TCR-seq

value: Immune cells


title: Patient 21 TCR Post-Denosumab TP3

description: bulk TCR-seq

value: VDJ


title: rep1_prep2_MPRALibC10cyclesPCR

description:
Plasmid DNA
barcodes.txt

value: MPRA library control


title: rep3_prep2_MPRALibC10cyclesPCR

description:
Plasmid DNA
barcodes.txt


title: SFB_03102022_BCR

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

description:
10x 5' BCR
SFB_03102022_filtered_contig_annotations.csv
SFB_03102022_airr_rearrangement.tsv

data_processing:
Base calls were processed to FASTQs using Cell Ranger mkfastq v. 6.1.1.
FASTQs for gene expression were aligned to the GRCm38 mouse reference genome using STAR as implemented in Cell Ranger v. 6.1.1, and collapsed to UMI counts per 10x barcode.
FASTQs for feature barcode quantification were aligned to the hashtag feature reference and collapsed to UMI counts per 10x barcode, using Cell Ranger v. 6.1.1.
FASTQs for BCR sequence were aligned to the GRCm38 mouse V(D)J reference using Cell Ranger v. 6.1.1.
Assembly: GRCm38
Supplementary files format and content: Processed data for gene expression and feature barcode counts are in .h5 10x sparse matrix format; each row is a gene or feature barcode, each column is a sample. Processed data for BCR sequence data are .csv and .tsv format; each row is a sequence from a single BCR chain.
Supplementary files format and content: feature_reference.csv  (Each HTO corresponds to one mouse, with the mouse number indicated by "M#".  So HTO_M1 was used to label cells from mouse 1, HTO_M2 for cells from mouse 2, etc.  All cells from each mouse were hashtagged prior to pooling, so any non-B cells that were incidentally included in sequencing were also labeled with the mouse-specific hashtags.)
Library strategy: scTCR-seq

organism: Mus musculus

source_name: B cells from Peyer's patch

growth_protocol: Ten wild-type B6 mice were de novo colonized for 21 days with segmented filamentous bacteria (SFB).

extract_protocol:
A single cell suspension was prepared from pooled sorted cells and loaded onto one channel on the 10x Chromium Controller according to the manufacturer’s protocol, with a target capture of 10,000 cells per channel.
Sequencing libraries were generated using the NextGEM Single Cell 5' Kit v2. Gene expression, BCR, and feature barcoding libraries were pooled and treated with Illumina Free Adapter Blocking Reagent.
Sequencing of pooled libraries was carried out on a NextSeq 2000 sequencer, using a NextSeq P2 flowcell, with target depths of 40000, 5000, and 5000 raw reads per cell for gene expression, BCR, and feature barcode libraries, respectively.

treatment_protocol: Peyer’s patch leukocytes were separately stained with oligo-hashtagged antibodies, prior to pooling, staining, and FACS isolation of SFB3340+ B cells.

tag: strain

value: de novo colonized for 21 days with SFB

value: Peyer's patch

value: SFB-specific B cells

tag: fraction

value: BCR RNA


title: rep2_prep1_MPRALibC10cyclesPCR

description:
Plasmid DNA
barcodes.txt


title: rep2_prep1_MPRALibC6cyclesPCR

description:
Plasmid DNA
barcodes.txt


title: Patient 21 TCR Post-Denosumab TP2

description: bulk TCR-seq

value: Denosumab TP2

value: No Chemo No Steroid


title: Patient 21 TCR Pre-Denosumab TP1

description: bulk TCR-seq

value: No Denosumab TP1


title: SFB_03102022_FB

description:
10x 5' feature barcode
SFB_03102022_sample_feature_bc_matrix.h5
SFB_03102022_feature_reference.csv

data_processing:
Base calls were processed to FASTQs using Cell Ranger mkfastq v. 6.1.1.
FASTQs for gene expression were aligned to the GRCm38 mouse reference genome using STAR as implemented in Cell Ranger v. 6.1.1, and collapsed to UMI counts per 10x barcode.
FASTQs for feature barcode quantification were aligned to the hashtag feature reference and collapsed to UMI counts per 10x barcode, using Cell Ranger v. 6.1.1.
FASTQs for BCR sequence were aligned to the GRCm38 mouse V(D)J reference using Cell Ranger v. 6.1.1.
Assembly: GRCm38
Supplementary files format and content: Processed data for gene expression and feature barcode counts are in .h5 10x sparse matrix format; each row is a gene or feature barcode, each column is a sample. Processed data for BCR sequence data are .csv and .tsv format; each row is a sequence from a single BCR chain.
Supplementary files format and content: feature_reference.csv  (Each HTO corresponds to one mouse, with the mouse number indicated by "M#".  So HTO_M1 was used to label cells from mouse 1, HTO_M2 for cells from mouse 2, etc.  All cells from each mouse were hashtagged prior to pooling, so any non-B cells that were incidentally included in sequencing were also labeled with the mouse-specific hashtags.)

molecule: protein

value: DNA oligo tags


title: SFB_03102022_GEX

description:
10x 5' gene expression
SFB_03102022_sample_feature_bc_matrix.h5

library_source: transcriptomic single cell

value: total RNA


title: rep1_prep1_MPRALibC10cyclesPCR

description:
Plasmid DNA
barcodes.txt


title: Patient 20 TCR Post-Denosumab TP4

description: bulk TCR-seq

value: Patient 20

value: Denosumab TP4

value: Chemo and Steroid


title: Patient 20 TCR Post-Denosumab TP2

description: bulk TCR-seq


title: VC-treated group of immature Sertoli cells [V3]

city: jingzhou

first: wu

middle: zi

last: wei

state: Hubei

department: Animal Science

institute: yangtze university

data_processing:
Illumina Casava1.7 software used for basecalling.
Using Bowtie1 to build the reference genome index, and then mapping the clean reads to the genome. Bowtie1 is fast and accurate, and has good performing in short reads alignment.
Mapping reads to mature miRNA and hairping which recorded in miRBase (release 21) to identiy known-miRNA. After excluded the reads mapped to known miRNA/ncRNA/repeat region/mRNA region, the remaining reads were used to predict novel miRNA, the keys of prediction is hairping structure and stability. The software for identification and prediction is miRDeep2.
After got the count of mature miRNA in miRDeeo2, TPM（Transcripts Per Million）was used for estimationand normalization.
For animals, miRanda and TargetScan were used for predicting target genes of known or novel miRNA, at least two software intersection.
Genome_build: Sus scrofa11.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: iSCs were cultured in Minimum Essential Medium (MEM) with Eagle's balanced salt solution (HyClone, USA), supplementing with 10% fetal bovine serum (Clark, Australia) and 1% penicillin-streptomycin (Gibco, USA), in a 5% CO2 incubator at 37°C.

extract_protocol:
Trizol reagent (Sigma) was used to isolate the total RNA of samples collected from three controls (C1, C2 and C3) and three AA2P-treated (V1, V2 and V3) iSC cells.
The libraries were constructed and sequenced on an Illumina NovaSeq 6000 (Illumina, San Diego, CA, USA) in a single lane.

treatment_protocol: The cells were seeded at a density of approximately 1×10^5 cells/mL, and cultured for 6h, before treated with the L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate (AA2P, Sigma, USA) at 250μM.

tag: age

value: 80 to 90 days gestation

value: Testis

value: immature sertoli cells


title: Patient 20 TCR Pre-Denosumab TP1

description: bulk TCR-seq

value: blood

value: Immune cells

value: VDJ


title: Patient 20 TCR Post-Denosumab TP3

description: bulk TCR-seq

value: Denosumab TP3


title: Patient 19 TCR Post-Denosumab TP4

description: bulk TCR-seq

value: Patient 19

value: Steroid only


title: SCN,PND30,rep2

city: Lübeck

first: Kristian

last: Händler

address: Ratzeburger Allee 160

department: Human Genetics

country: Germany

institute: UKSH

data_processing:
count matrices were generated via Cellranger v5.0.1 (10X Genomics) using the Mouse reference transcriptome mm10-2020-A (10x Genomics)
Seurat v4 was employed to normalize, filter, merge and visualize data
Filter criteria: count_p_gene≥5, cell_p_gene≥10, 750≤count_p_cell≤50000, 500≤gene_p_cell≤10000, maxpct_mt:0.025,  maxpct_rb:0.03
scrublet-0.2.3: npcs_scrublet:25, exp_db_rate:0.06, threshold:0.15
trajectory analysis was performed using monocle 2.4.0
Assembly: mm10

source_name: SCN

growth_protocol: C57BL6/J (WT) Females of 2-4 months of age were group-housed and kept in LD12:12 at 22 ± 2 °C and a relative humidity of 60 ± 5 % with ad-libitum access to food and water. Estrous cycle was synchronized adding male bedding to the cage, after 4 days (when they reach proestrus) females were individually housed overnight (ON) in presence of a fertile male. The next day was considered GD0.5 if a vaginal plug was present. Females were separated, single housed and left undisturbed until the appropriate GD/PND to obtain the SCN sample.

extract_protocol:
To reduce sex bias and litter effects, SCNs were collected from only 1 male and 1 female fetus/pup per mother of at least 5 different mothers. Then 10 samples were pooled per developmental timepoint. Brains were dissected and sliced in 250 μm coronal sections with vibratome in ice cold HBSS 1X. SCN was dissected with a scalpel under the microscope and snap frozen in liquid N2. Single nuclei were extracted from pooled fresh frozen SCN tissue (from 10 fetus/pup) per timepoint.
Chromium Next GEM Single Cell 3ʹ Kit v3.1, 4 rxns PN-1000269 with dual indexing was used following manufacturers protocols

value: SCN

tag: developmental stage

value: WT


title: rep3_prep1_MPRALibC10cyclesPCR

description:
Plasmid DNA
barcodes.txt

value: MPRA library control


title: Patient 19 TCR Post-Denosumab TP3

description: bulk TCR-seq


title: VC-treated group of immature Sertoli cells [V1]

value: L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate


title: Patient 19 TCR Post-Denosumab TP2

description: bulk TCR-seq

value: Denosumab TP2


title: Patient 19 TCR Pre-Denosumab TP1

description: bulk TCR-seq

value: No Denosumab TP1


title: Patient 17 TCR Post-Denosumab TP3

description: bulk TCR-seq

value: Patient 17

value: No Chemo No Steroid


title: SCN,PND10,rep1


title: control group of immature Sertoli cells [C3]

source_name: control group of immature Sertoli cells

value: 80 to 90 days gestation

value: none (control)


title: Patient 18 TCR Pre-Denosumab TP1

description: bulk TCR-seq

value: Patient 18

value: Chemo and Steroid


title: SCN,PND10,rep2


title: control group of immature Sertoli cells [C2]

value: 80 to 90 days gestation

value: Testis

value: immature sertoli cells


title: Patient 16 TCR Pre-Denosumab TP1

description: bulk TCR-seq

value: Patient 16

value: blood

value: Immune cells

value: VDJ


title: SCN,PND02,rep1

value: SCN

value: WT


title: control group of immature Sertoli cells [C1]


title: Patient 15 TCR Pre-Denosumab TP1

description: bulk TCR-seq

value: Patient 15


title: Patient 15 TCR Post-Denosumab TP2

description: bulk TCR-seq

value: Denosumab TP2


title: ONT-seq, NGN3m, day 5, rep 3

city: Berlin

first: Dr. Andreas

last: Mayer

address: Ihnestraße 63-73

institute: Max-Plack-Institute for Molecular Genetics

data_processing:
ONT-seq data was processed using the IsoTV pipeline (Annaldasula et al, 2021). In short, the data were basecalled using Guppy 3.2.4 with parameters corresponding to the used flowcell and kit. Low quality reads (mean Q<5) were filtered out using Filtlong. Then the full-length transcripts were identified and oriented using Pychopper with the options "-x", "-b", "-S", "-a", "-u", and "-l". To de novo assemble the transcriptome, we applied Pinfish to full-length transcripts from all samples with the following parameters: cluster_gff used "-c=3", "-d=5", "-e=50", and "-p", collapse_partials used "-d=5", "-e=50", and "-f=500", and polish_clusters used "-a" and "-c=1". Then, the clustered and polished transcripts were compared to the human reference genome annotation, Gencode Version 32, using GffCompare (Pertea & Pertea, 2020) with the following parameters: "-r", "-R", "-A", and "-K". To obtain the transcript expression, all the reads with Q>10 were aligned to the constructed transcriptome using Minimap2 (Li, 2018) with the following parameter "-uf".
Assembly: GRCh38_p12
Supplementary files format and content: Gene annotation file from ONT-seq data analysis
Supplementary files format and content: Differential transcript usage analysis with ONT-seq data
Supplementary files format and content: Classification of transcript isoforms detected in ONT-seq
Supplementary files format and content: Raw transcript counts from ONT-seq data
Library strategy: ONT-seq

source_name: PGP1 iPSC line

growth_protocol: On the plating day 15,000-20,000 cells/cm2 cells were plated onto Matrigel® coated plates in mTeSR™1 media with Y-27632 RHO/ROCK pathway inhibitor (ROCKi) (StemCell Technologies), to a final concentration of 3,3 µg/ml and grown for 24 h. The following day media was exchanged, and cells were grown in mTeSR™1 media.

extract_protocol:
Cell pellets were lysed in 700 µL QIAzol™ and total RNA was isolated using the miRNeasy Micro Kit (Qiagen), including DNase treatment  according to the manufacturer’s instructions for RNA isolation including smaller RNA species >17nt. (Qiagen).
ONT-seq libraries were prepared using the direct cDNA sequencing (SQK-DCS109) kit from Oxford Nanopore Technologies according to the manufacturer’s protocol.

treatment_protocol: The second day after plating, doxycycline (0,5 µg/mL) was added to the culture media to induce Neurogenin-3 expression and cell differentiation. Media was changed every 24 hours by mTeSR™1 with doxycycline for 5 consecutive days. Samples were collected every day in precise 24 h intervals: before the addition of doxycycline (D0) and every 24 h for 5 days (D1-D5).

value: Adult dermal fibroblasts

value: PGP1 iPSC line

tag: time

value: Day 5

value: Induction of NGN3 expression


title: Patient 15 TCR Post-Denosumab TP4

description: bulk TCR-seq

value: Denosumab TP4

value: No Chemo No Steroid


title: Patient 15 TCR Post-Denosumab TP3

description: bulk TCR-seq

value: Denosumab TP3


title: Patient 14 TCR Pre-Denosumab TP1

description: bulk TCR-seq

value: Patient 14

value: No Denosumab TP1


title: Patient 13 TCR Post-Denosumab TP3

description: bulk TCR-seq

value: Patient 13

value: Chemo and Steroid


title: Patient 13 TCR Post-Denosumab TP2

description: bulk TCR-seq

value: blood

value: Immune cells


title: SCN,GD17.5,rep1

value: SCN


title: VC-treated group of immature Sertoli cells [V2]

value: 80 to 90 days gestation

value: Testis

value: immature sertoli cells

value: L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate


title: SCN,PND30,rep1

value: WT


title: ONT-seq, NGN3m, day 5, rep 1

value: Adult dermal fibroblasts

value: PGP1 iPSC line

value: Day 5


title: Patient 13 TCR Pre-Denosumab TP1

description: bulk TCR-seq

value: VDJ


title: Head and Neck Squamous cell tumor, Drug+XRT_Wk2_miRNA74

type: RNA

city: Bethesda

first: Michelle

last: Bylicky

state: Maryland

address: 10 Center Drive

department: Radiation Oncology Branch

institute: National Cancer Institute

description: miRNA 2 weeks post treatment start, Animals received 2 weeks of Onalespib (5 days per week, 55mg/kg) and 1 week of radiation (3 x 2 Gy).

hyb_protocol: mRNA: 1 µg of purified cRNA was fragmented to uniform size and applied to Agilent Human 8x60 (v3) Gene Expression Microarrays Design ID 072363 (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, washed at 42° C for 30 min, and stained with Streptavidin-Alexa555.     miRNA: labeled target was applied to Agilent Human miRNA 8x60 v21.0 arrays (design ID 070156) in hybridization buffer.  Arrays were hybridized at 55° C for 20 hrs in a rotating incubator, washed at 37° C for 10 min.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2505C Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

source_name: FaDu human squamous cell carcinoma

label_protocol: mRNA: Labeled cRNA was prepared from total RNA samples. Briefly, the Poly(A)+ RNA population within total RNA was amplified using MessageAMP II (Applied Biosystems, Foster City, CA).  After a second round of reverse transcription, second-strand cDNA synthesis, and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of Biotin-11-UTP.  The quantity and quality of the cRNA was assayed by spectrophotometry and on the Agilent Bioanalyzer.   miRNA: Total RNA samples were dephosphorylated, denatured, and end-labeled with Cy-3.

growth_protocol: The human squamous cell carcinoma from the pharynx (FaDu) was used for this study. Prior to injection FaDu cells were cultured in DMEM, 10% FBS. These cells were injected into right flank of athymic mice at a concentration of 1 x 10^6 cells.

extract_protocol: Tumor samples were bathed in liquid nitrogen and pulverized into a fine powder using a mortar and pestle. Approximately 100 µg of powdered sample was lysed with 700 µl of QIAzol lysis buffer (Cat # 79306, QIAGEN) and homogenized by passing the solution through QIAshredder spin columns (Cat # 79654, QIAGEN). RNA isolation was performed using standard miRNeasy mini kits (Cat # 217004, QIAGEN) according to the manufacturer’s protocol. Quality and quantity of the RNA samples were assessed using a DeNovix DS-11 nanodrop spectrophotometer (DeNovix, DE, US) and Agilent Bioanalyzer with the RNA6000 Nano Lab Chip (Agilent Technologies, Santa Clara, CA). by spectrophotometry and on the Agilent Bioanalyzer.

treatment_protocol: Six-week old Athymic nude nu/nu female mice were injected with FaDu cells in right flank. FaDu cells were allowed to grow to tumor size 200mm3 before treatment started. Mice were divided into 4 groups beyond the initial Control on D1: Untreated (UT), x-ray irradiation only (Rad), Onalespib drug treated only (Drug), and both (Rad + Drug). Mice received i.p injections 5 days per week of control vehicle or Onalespib. Mice received Drug through week 1 and week 2. Mice in the Drug+Rad group had a second week of Drug. In animals receiving Onalespib and radiation, animals were injected with Onalespib 2-3 hours prior to radiation. Mice in Rad groups received 6Gy total radiation 2Gy every other day (2Gy x 3) for the first week. Mice receiving treatments were euthanized at the end of week 1 and at the end of week 2. Animals receiving radiation were euthanized approximately 4 hours post radiation. Control mice were euthanized at the beginning of treatment (D1), and Untreated (vehicle only) at the end of week 1 and Day 8 of treatment schedule due to excessive tumor size. Tumor samples were analyzed at Day 1 at end of Week 1 and Week 2 (indicated in figure 1A, below). Additional mice were followed for tumor growth delay. Longer term tumor samples were not available as this was not the primary purpose of this study.

tag: tumor type

value: Head and Neck Squamous cell tumor

tag: tumor origin

value: hypopharyngeal

tag: mouse strain

value: Athymic nude mice (nu/nu)

tag: biological sex

value: Female

tag: age of mice

value: 6 weeks old

value: Drug+XRT


title: Patient 17 TCR Pre-Denosumab TP1

description: bulk TCR-seq

value: Patient 17

tag: tissue

value: blood

value: Immune cells

value: No Denosumab TP1

value: No Chemo No Steroid


title: Patient 10 TCR Post-Denosumab TP3

description: bulk TCR-seq

value: Patient 10

tag: cell type

value: Denosumab TP3


title: ONT-seq, NGN3m, day 3, rep 2

value: Adult dermal fibroblasts

tag: cell line

value: Day 3

value: Induction of NGN3 expression


title: Patient 12 TCR Pre-Denosumab TP1

description: bulk TCR-seq

value: Patient 12

value: VDJ

tag: treatment


title: Head and Neck Squamous cell tumor, Drug+XRT_Wk2_miRNA72

value: Head and Neck Squamous cell tumor

value: hypopharyngeal


title: Head and Neck Squamous cell tumor, Drug+XRT_Wk2_miRNA71

value: Athymic nude mice (nu/nu)

value: Female


title: Patient 09 TCR Post-Denosumab TP4

description: bulk TCR-seq

tag: individual

value: Patient 09

value: Denosumab TP4

value: Chemo only


title: ONT-seq, NGN3m, day 3, rep 3

value: PGP1 iPSC line


title: Patient 11 TCR Pre-Denosumab TP1

description: bulk TCR-seq

value: Patient 11

value: blood

value: Immune cells

tag: library type

value: No Denosumab TP1


title: Head and Neck Squamous cell tumor, Drug+XRT_Wk2_miRNA73

value: 6 weeks old

value: Drug+XRT


title: Head and Neck Squamous cell tumor, XRT_Wk2_miRNA70

description: miRNA  2 weeks after treatment start, mice received radiation the 1st week (3 x 2 Gy) and no subsequent treatment the second week

value: XRT


title: Patient 10 TCR Post-Denosumab TP2

description: bulk TCR-seq

value: Patient 10

value: Denosumab TP2

tag: additional treatment

value: No Chemo No Steroid


title: Head and Neck Squamous cell tumor, XRT_Wk2_miRNA67

value: Head and Neck Squamous cell tumor

value: hypopharyngeal


title: Patient 07 TCR Post-Denosumab TP3

description: bulk TCR-seq

value: Patient 07

value: VDJ

value: Denosumab TP3

value: Steroid only


title: ONT-seq, NGN3m, day 5, rep 2

value: Adult dermal fibroblasts

value: PGP1 iPSC line

value: Day 5

value: Induction of NGN3 expression


title: Patient 10 TCR Pre-Denosumab TP1

description: bulk TCR-seq

value: blood

value: Immune cells

value: No Denosumab TP1


title: ONT-seq, NGN3m, day 3, rep 1

value: Day 3


title: Patient 09 TCR Post-Denosumab TP3

description: bulk TCR-seq

value: Patient 09


title: Patient 09 TCR Post-Denosumab TP2

description: bulk TCR-seq

value: Denosumab TP2


title: Head and Neck Squamous cell tumor, XRT_Wk2_miRNA69

value: Athymic nude mice (nu/nu)

value: Female

value: 6 weeks old

value: XRT


title: Patient 07 TCR Post-Denosumab TP2

description: bulk TCR-seq

value: Patient 07

value: VDJ

value: No Chemo No Steroid


title: Patient 07 TCR Pre-Denosumab TP1

description: bulk TCR-seq


title: Head and Neck Squamous cell tumor, XRT_Wk2_miRNA68

value: Head and Neck Squamous cell tumor

value: hypopharyngeal


title: Patient 06 TCR Post-Denosumab TP4

description: bulk TCR-seq

value: Patient 06

value: Denosumab TP4


title: ONT-seq, NGN3m, day 0, rep 2

value: Adult dermal fibroblasts

value: PGP1 iPSC line

value: Day 0

value: Induction of NGN3 expression


title: Head and Neck Squamous cell tumor, Drug_Wk2_miRNA65

description: miRNA 2 weeks after treatment start, animals received IP injection of Onalespib 55mg/kg for 5 days on both weeks including day of euthanasia

value: Drug


title: Patient 09 TCR Pre-Denosumab TP1

description: bulk TCR-seq

value: Patient 09

value: blood

value: Immune cells

value: No Denosumab TP1


title: Patient 06 TCR Post-Denosumab TP2

description: bulk TCR-seq

value: Denosumab TP2


title: Patient 08 TCR Post-Denosumab TP4

description: bulk TCR-seq

value: Patient 08

value: Chemo and Steroid


title: Patient 08 TCR Post-Denosumab TP2

description: bulk TCR-seq

value: VDJ


title: Amphioxus_21hpf_ATACseq rep2

city: Barcelona

first: Arnau

last: Sebe-Pedros

address: Dr. Aiguader 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation

library_source: genomic

data_processing:
ATAC-seq: Reads were mapped into the Branchiostoma lanceolatum genome using bwa 0.7.17. The resulting BAM files were (i) filtered using alignmentSieve (from the deeptools 3.5.1 package) to exclude weak alignments MAPQ > 30), (ii) corrected to shift the left and right ends of reads, to account for ATAC mapping biases (+4/−5 bp in the positive and negative strands, using the --ATACshift flag in alignmentSieve), and (iii) filtered to only include nucleosome-free alignments (--maxFragmentLength 120 with alignmentSieve). Duplicated reads were marked with biobambam2 2.0.87, coordinate-sorted, and removed to produce filtered BAM files. Then, we concatenated the BAM files stage-wise. Normalized coverage for each stage was reported as bins per million mapped reads (BPM),  calculated using the bamCoverage tool in deeptools.
Branchiostoma lanceolatum genome v3 (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02808-6#Sec10)

molecule: genomic DNA

organism: Branchiostoma lanceolatum

source_name: 21hpf embryos

extract_protocol:
ATAC-seq was perform as detailed in the OmniATAC protocol (doi.org/10.1038/nmeth.4396). Around 50,000 cells were used for each tagmentation reaction.
21hpf embyos (19C) were dissociated and pooled before sorting single-cells for scRNAseq or ATAC-seq experiments.

value: 21hpf embryos

tag: genotype

value: Wild type


title: Patient 07 TCR Post-Denosumab TP4

description: bulk TCR-seq

value: Patient 07

value: Steroid only


title: Patient 06 TCR Pre-Denosumab TP1

description: bulk TCR-seq

value: Patient 06

value: No Chemo No Steroid


title: Patient 10 TCR Post-Denosumab TP4

description: bulk TCR-seq

value: Patient 10

value: Denosumab TP4


title: Amphioxus_21hpf_ATACseq rep1


title: Head and Neck Squamous cell tumor, Drug_Wk2_miRNA63

value: Head and Neck Squamous cell tumor

value: hypopharyngeal

value: Athymic nude mice (nu/nu)

value: Female

value: 6 weeks old

value: Drug


title: Head and Neck Squamous cell tumor, Drug_Wk2_miRNA66


title: Amphioxus_21hpf_scRNAseq S2

data_processing:
scRNA-seq: Read_1 files were mapped into Branchiostoma lanceolatum genome v3 (doi.org/10.1186/s13059-022-02808-6) using STARR, using default parameters. Demultiplexing and UMI counting (UMI and cell barcodes are in read 2) was performed using the pipeline described in Keren-Shaul et al. 2019 (10.1038/s41596-019-0164-4). Pipeline can be found: http://compgenomics.weizmann.ac.il/tanay/?page_id=672
Branchiostoma lanceolatum genome v3 (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02808-6#Sec10)

extract_protocol:
MARS-seq was performed as described in Keren-Shaul et al. 2019 (10.1038/s41596-019-0164-4). All 40 plates (a total of 15,384 single cell libraries) were prepared using the same conditions and reagents. Using a Bravo automated liquid handling platform (Agilent), mRNA was reverse transcribed into cDNA using the lysis oligonucleotide containing unique molecular identifiers (UMIs) and cell barcodes. Residual, unused oligonucleotides were removed by treatment with Exonuclease I (NEB). cDNAs were pooled and linearly amplified using T7 in vitro transcription. The resulting RNA was fragmented and ligated to an oligo containing the pool barcode and Illumina sequences, using T4 ssDNA:RNA ligase. RNA was reverse transcribed into DNA and PCR-amplified with 14 cycles.
21hpf embyos (19C) were dissociated and pooled before sorting single-cells for scRNAseq or ATAC-seq experiments.


title: Amphioxus_21hpf_ATACseq rep4


title: Patient 04 TCR Post-Denosumab TP3

description: bulk TCR-seq

value: Patient 04

value: blood

value: Immune cells

value: Denosumab TP3

value: Chemo only


title: Head and Neck Squamous cell tumor, Ctrl_Wk2_miRNA62

description: miRNA 10 days post treatment start in sham animals, early euthanasia due to tumor size

value: Ctrl


title: ONT-seq, NGN3m, day 0, rep 3

value: Adult dermal fibroblasts

value: PGP1 iPSC line

value: Day 0

value: Induction of NGN3 expression


title: Patient 04 TCR Pre-Denosumab TP1

description: bulk TCR-seq

value: VDJ

value: No Denosumab TP1


title: Amphioxus_21hpf_ATACseq rep3

value: 21hpf embryos

value: Wild type


title: Patient 04 TCR Post-Denosumab TP2

description: bulk TCR-seq

value: Denosumab TP2


title: Head and Neck Squamous cell tumor, Drug_Wk2_miRNA64

value: Head and Neck Squamous cell tumor

value: hypopharyngeal

value: Athymic nude mice (nu/nu)

value: Female

value: 6 weeks old


title: Patient 03 TCR Post-Denosumab TP4

description: bulk TCR-seq

value: Patient 03

value: blood

value: Immune cells

value: Denosumab TP4

value: No Chemo No Steroid


title: ONT-seq, NGN3m, day 0, rep 1

value: Adult dermal fibroblasts

value: PGP1 iPSC line

value: Day 0


title: Patient 06 TCR Post-Denosumab TP3

description: bulk TCR-seq

value: Patient 06

value: VDJ

value: Denosumab TP3


title: Patient 03 TCR Post-Denosumab TP2

description: bulk TCR-seq

value: Denosumab TP2


title: Patient 05 TCR Pre-Denosumab TP1

description: bulk TCR-seq

value: Patient 05

value: No Denosumab TP1


title: Amphioxus_21hpf_scRNAseq S1

value: 21hpf embryos

value: Wild type


title: Canine cutaneous histiocytoma, group 3 according to Cockerell & Slauson 1979, lymphocyte enriched, FFPE, 5

first: Alina

middle: Katharina

last: Loriani Fard

address: Robert-von-Ostertag Straße 15

department: Department of Veterinary Medicine

institute: Freie Universität Berlin

description: male

hyb_protocol: 150 to 250ng of total RNA were hybridized to the nCounter Canine IO Panel XT CodeSets (NanoString Technologies, Inc., Seattle, WA, USA). Hybridized samples were processed following the manufacturer’s protocols (protocol ID: MAN-10023-11, MAN-10056-06) and loaded onto the nCounter MAX Analysis System’s (NanoString) Prep Station for purification and immobilization on sample cartridges.

scan_protocol: These were transferred to the Digital Analyzer for data collection following the manufacturer’s user manual (protocol ID: MAN-C0035-08).

data_processing:
Following the workflow described in the manufacturer’s user manuals (MAN-C0019-08, MAN-C0011-04), the reporter library files (RLF) and reporter code count (RCC) files were imported into the nSolver 4.0 Analysis Software. Quality control and normalization followed default settings. DGE analysis was achieved using the R 3.3.2-based nCounter Advanced Analysis 2.0 plug-in (version 2.0.134) with recommended statistical settings.
Nanostring canine IO standard for normalization: 20220420_AL03_Standard_12.RCC

organism: Canis lupus familiaris

source_name: FFPE tumor tissue, group 3

extract_protocol: Total RNA was extracted utilizing the PureLink FFPE Total RNA Isolation Kit (Thermo Fisher Scientific Inc.). After DNase I treatment 150 to 250ng total RNA was used for library construction.

tag: pooled sample

value: no

tag: breed

value: Jack Russell Terrier

tag: age (years)


title: Patient 01 TCR Pre-Denosumab TP1

description: bulk TCR-seq

value: Patient 01

value: blood


title: Patient 03 TCR Post-Denosumab TP3

description: bulk TCR-seq

value: Patient 03

value: Immune cells


title: Patient 02 TCR Pre-Denosumab TP1

description: bulk TCR-seq

value: Patient 02

value: No Chemo No Steroid


title: OP9M2_IR_24h_4

city: Tel Aviv

first: Michael

last: Milyavsky

address: 35 Klatzkin st, TAU Faculty of Medicine, Room 435

department: Pathology

country: Israel

institute: Tel Aviv University

data_processing:
Poly-A/T stretches and Illumina adapters were trimmed from the reads using cutadapt
resulting reads shorter than 30bp were discarded. Reads were mapped to the H. sapiens reference genome GRCh38 using STAR, supplied with gene annotations downloaded from Ensembl (and with EndToEnd option and outFilterMismatchNoverLmax was set to 0.04).
Expression levels for each gene were quantified using htseq-count
Differentially expressed genes were identified using DESeq2, with the betaPrior, cooksCutoff and independentFiltering parameters set to False
Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg
Assembly: GRCh38
Supplementary files format and content: processed data files are in tsv format, with 2 <columns annotationa><count>.
Supplementary files format and content: precessed data files shows read counts before and after UMI correction

source_name: Cord Blood

growth_protocol: OP9M2 Mesenchymal Stromal Cells (MSCs) were plated (30,000 cells/ cm2) on tissue culture treated wells in MSC media (MEMα + 20% FBS + 1% Pen/Strep + 1% Glutamine) , 24 hours before co-culture. To collect OP9M2 conditioned media, MSC media was replaced with HSC media [StemSpan SFEM II + SFT cytokines (SCF, FLT3, TPO - 25ng/ml) + 1% P/S + 1% Glutamine]

extract_protocol:
CD34+CD38-CD45RA- cells cultured in indicated conditions were sorted directly into TRIzol Reagent (Thermo Fisher), and RNA was extracted.
Sequencing Libraries were prepared using MARSeq. Single reads were sequenced on 1 lane(s) of an Illumina NOvaSeq_sp. The output was ~15 million reads per sample

treatment_protocol: Cord Blood CD34+ cells were cultured in HSC media for (4hr or 24hr), OP9M2 conditioned media (4hr or 24hr) or co-cultured with OP9M2 MSCs (4hr or 24hr)

value: Cord Blood

value: Hematopoietic Stem and Progenitor cells

value: WT

value: Co-cultured on top of OP9M2 MSCs


title: OP9M2_IR_24h_3


title: OP9M2_IR_24h_2


title: Head and Neck Squamous cell tumor, Drug+XRT_Wk1_miRNA58

description: miRNA 1 week post Onalespib (5 days, 55mg/kg) and radiation treatment (3 x 2 Gy)

value: Head and Neck Squamous cell tumor

value: hypopharyngeal

value: Athymic nude mice (nu/nu)

value: Female

value: 6 weeks old

value: Drug+XRT

tag: time


title: Head and Neck Squamous cell tumor, Ctrl_Wk2_miRNA59

tag: tumor type

value: Ctrl


title: Canine cutaneous histiocytoma, group 3 according to Cockerell & Slauson 1979, lymphocyte enriched, FFPE, 4

description: male

value: no

value: Bullterrier


title: Head and Neck Squamous cell tumor, Ctrl_Wk2_miRNA60

tag: tumor origin


title: Canine cutaneous histiocytoma, group 3 according to Cockerell & Slauson 1979, lymphocyte enriched, FFPE, 3

description: male

value: Pug


title: OP9M2_IR_24h_1


title: Head and Neck Squamous cell tumor, XRT_Wk1_miRNA55

description: miRNA 1 week after treatment start, animals received radiation every other day for 3 days, 2 Gy each day, total 6Gy. Animals irradiated day of euthanasia

tag: mouse strain

value: XRT


title: Head and Neck Squamous cell tumor, Drug+XRT_Wk1_miRNA57

tag: biological sex


title: Patient 03 TCR Pre-Denosumab TP1

description: bulk TCR-seq

value: Patient 03

value: blood

value: Immune cells

value: VDJ

value: No Denosumab TP1


title: OP9M2_NT_24h_2

value: Cord Blood

value: Hematopoietic Stem and Progenitor cells

value: WT

value: Co-cultured on top of OP9M2 MSCs


title: OP9M2_NT_24h_4


title: OP9M2_NT_24h_3


title: OP9M2_NT_24h_1


title: Canine cutaneous histiocytoma, group 3 according to Cockerell & Slauson 1979, lymphocyte enriched, FFPE, 1

description: male neutered

value: Rottweiler


title: OP9M2_IR_4h_3


title: Head and Neck Squamous cell tumor, XRT_Wk1_miRNA54

value: Head and Neck Squamous cell tumor

value: hypopharyngeal

value: Athymic nude mice (nu/nu)

value: Female

tag: age of mice

value: 6 weeks old


title: OP9M2_IR_4h_1

tag: tissue


title: Head and Neck Squamous cell tumor, XRT_Wk1_miRNA52


title: Canine cutaneous histiocytoma, group 2 according to Cockerell & Slauson 1979, lymphocyte enriched, FFPE, 6

description: male, female, male

source_name: FFPE lymphocyte enriched tissue, group 2

value: yes (3 individuals)

value: Bordeaux Mastiff, French Bulldog, Labradoodle


title: Head and Neck Squamous cell tumor, Drug+XRT_Wk1_miRNA56

value: Drug+XRT


title: Canine cutaneous histiocytoma, group 2 according to Cockerell & Slauson 1979, lymphocyte enriched, FFPE, 5

description: female, male, male neutered, female

value: yes (4 individuals)

value: Flat Coated Retriever, n/s, Boxer, Bernese Mountain Dog


title: Head and Neck Squamous cell tumor, XRT_Wk1_miRNA53

value: XRT


title: OP9M2_IR_4h_4

tag: cell type


title: CM_IR_24h_1

value: OP9M2 MSC conditioned medium


title: Canine cutaneous histiocytoma, group 3 according to Cockerell & Slauson 1979, lymphocyte enriched, FFPE, 2

description: female

value: no

value: Beagle


title: OP9M2_NT_4h_4

value: Cord Blood

value: Hematopoietic Stem and Progenitor cells

value: WT


title: Head and Neck Squamous cell tumor, Drug_Wk1_miRNA48

description: miRNA 1 week after treatment start, animals received IP injection of Onalespib 55mg/kg for 5 days including day of euthanasia

value: Head and Neck Squamous cell tumor

value: Drug


title: OP9M2_IR_4h_2

value: Co-cultured on top of OP9M2 MSCs


title: Head and Neck Squamous cell tumor, Drug_Wk1_miRNA49

value: hypopharyngeal

value: Athymic nude mice (nu/nu)

value: Female


title: Canine cutaneous histiocytoma, group 2 according to Cockerell & Slauson 1979, lymphocyte enriched, FFPE, 3

description: female, female, male, male

value: Rhodesian Ridgeback, French Bulldog, French Bulldog, Dachshund


title: Head and Neck Squamous cell tumor, Drug_Wk1_miRNA51

value: 6 weeks old


title: OP9M2_NT_4h_2


title: CM_NT_24h_4


title: Head and Neck Squamous cell tumor, Drug_Wk1_miRNA50


title: CM_IR_24h_3


title: CM_NT_24h_3


title: Canine cutaneous histiocytoma, group 2 according to Cockerell & Slauson 1979, lymphocyte enriched, FFPE, 2

description: female neutered

value: Pug


title: OP9M2_NT_4h_3


title: Canine cutaneous histiocytoma, group 2 according to Cockerell & Slauson 1979, tumor cell enriched, FFPE, 4

description: female neutered

source_name: FFPE tumor cell enriched tissue, group 2

value: Doberman


title: Head and Neck Squamous cell tumor, Ctrl_Wk1_miRNA46

description: miRNA from untreated tumors 1 week post treatment start, sham animals

value: Ctrl


title: CM_IR_24h_4

value: OP9M2 MSC conditioned medium


title: Canine cutaneous histiocytoma, group 2 according to Cockerell & Slauson 1979, lymphocyte enriched, FFPE, 1

description: female

value: no

value: Akita


title: Head and Neck Squamous cell tumor, Ctrl_Wk2_miRNA61


title: CM_NT_24h_1

value: Cord Blood


title: Canine cutaneous histiocytoma, group 2 according to Cockerell & Slauson 1979, tumor cell enriched, FFPE, 5

description: male

value: Mix


title: Canine cutaneous histiocytoma, group 2 according to Cockerell & Slauson 1979, lymphocyte enriched, FFPE, 4

description: male, male neutered, female, n/s

value: yes (4 individuals)

value: Doberman, French Bulldog, Jack Russel Mix, n/s


title: CM_NT_24h_2

value: Hematopoietic Stem and Progenitor cells

value: WT


title: OP9M2_NT_4h_1

value: Co-cultured on top of OP9M2 MSCs


title: CM_IR_24h_2


title: CM_IR_4h_4


title: Canine cutaneous histiocytoma, group 2 according to Cockerell & Slauson 1979, tumor cell enriched, FFPE, 3

description: female

value: Hovawart


title: Head and Neck Squamous cell tumor, Ctrl_Wk1_miRNA47

value: Head and Neck Squamous cell tumor

value: hypopharyngeal

value: Athymic nude mice (nu/nu)

value: Female


title: CM_IR_4h_2


title: CM_NT_4h_3


title: Canine cutaneous histiocytoma, group 2 according to Cockerell & Slauson 1979, tumor cell enriched, FFPE, 2

description: male neutered

value: English Bulldog


title: CM_NT_4h_4


title: Canine cutaneous histiocytoma, group 2 according to Cockerell & Slauson 1979, tumor cell enriched, FFPE, 1

description: male

value: Bavarian Mountain Hound


title: CM_NT_4h_2

value: OP9M2 MSC conditioned medium


title: CM_IR_4h_1


title: CM_NT_4h_1


title: Head and Neck Squamous cell tumor, Ctrl_Wk1_miRNA45

value: 6 weeks old

value: Ctrl


title: Head and Neck Squamous cell tumor, Ctrl_Wk1_miRNA44


title: SFT_IR_24h_4

value: Cord Blood

value: SFEM media with cytokines (SCF, FLT3, TPO - 25ng/ml)


title: SFT_IR_24h_3


title: Head and Neck Squamous cell tumor, Ctrl_Day1_miRNA43

description: miRNA Day 1 of experiment


title: Canine cutaneous histiocytoma group 1 according to Cockerell & Slauson 1979, FFPE, 5

description: female

source_name: FFPE tumor tissue, group 1

value: no

value: French Bulldog


title: SFT_IR_24h_2

value: Hematopoietic Stem and Progenitor cells


title: Canine cutaneous histiocytoma, group 1 according to Cockerell & Slauson 1979, FFPE, 3

description: n/s

value: Terrier

value: n/s


title: Head and Neck Squamous cell tumor, Ctrl_Day1_miRNA40

description: miRNA Day 1 of experiment


title: CM_IR_4h_3

value: WT


title: Canine cutaneous histiocytoma, group 1 according to Cockerell & Slauson 1979, FFPE, 2

description: male

value: Goldendoodle


title: SFT_NT_24h_4


title: SFT_IR_24h_1


title: Head and Neck Squamous cell tumor, Ctrl_Day1_miRNA41

description: miRNA Day 1 of experiment

value: Head and Neck Squamous cell tumor

value: hypopharyngeal


title: SFT_NT_24h_2


title: SFT_NT_24h_3


title: WS5

city: Abu Dhabi

first: Andre

middle: Sanches

last: Barreiros

state: Abu Dhabi

address: Hamdan street

country: United Arab Emirates

institute: Khalifa University

description: Wild-type strain 5 hrs. under 37C + serum

data_processing:
Clean filtered sequence reads were mapped to the reference genome using HISAT (hierarchical indexing for spliced alignment of transcripts) to perform the genome mapping step.
Reads were mapped to theC.albicansstrain SC5314 reference genome (assembly 21) (http://www.candidagenome.org)
Clean reads were mapped to reference transcripts using Bowtie2 v2.2.5.
Gene expression levels in each sample were calculated using RSEM v1.2.12.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

organism: Candida albicans

source_name: Yeast extract-peptone-dexrose

extract_protocol:
RNA extraction was performed using Rneasy Micro Kit (Qiagen GmbH, Germany), following the manufacturer's instructions
RNA sequencing was performed by the BGI Group, Shenzen, China with 8 samples extracted belonging to two different strains, DK218 and MAY34.

value: Yeast extract-peptone-dexrose

tag: temperature

tag: strain

value: Serum

value: 5 hrs


title: WT_rep3, RNA-seq

city: Shanghai

first: Wenhao

last: Xie

state: Shanghai

address: No. 2005, Songhu Road

department: School of Life Science

institute: Fudan University

description:
Oryza sativa Nipponbare
WT_rep3

data_processing:
Raw reads were trimmed to remove the adapters and take out the reads with low sequencing quality score using Cutadapt.
The reads with high quality score were aligned to the rice reference genome (MSU7) using Hisat2.
Reads mapped to the nuclear genome were preserved and SAMtools was used to obtain high quality alignments.
FeatureCounts was used to calculate the reads count of genes.
Differentially expressed TEs (Transposable Elements) were identified using TEtranscripts.
Assembly: MSU7
Supplementary files format and content: Binary bw files (bigwig).
Supplementary files format and content: Tab-delimited text files including featureCounts value and TPM (Transcripts per million) for each Sample.

organism: Oryza sativa Japonica Group

source_name: 14-day-old seedlings

growth_protocol: Rice were grown in artificial growth chambers under an SD photoperiod for 14 days.

extract_protocol:
RNA was extracted using an RNAprep pure Plant Kit (Tiangen Biotech).
The strand-specific RNA-seq libraries were constructed by following the KAPA stranded mRNA-seq Kit instructions (Illumina® Platforms, KR0960-v5.17), according to the manufacturer’s instructions.

value: 14-day-old seedlings

tag: cultivar

value: Nipponbare

value: wild-type

tag: treatment

value: no treatment


title: WS3

description: Wild-type strain 3 hrs. under 37C + serum

value: 3 hrs


title: SFT_IR_4h_4

value: Cord Blood

value: SFEM media with cytokines (SCF, FLT3, TPO - 25ng/ml)


title: Head and Neck Squamous cell tumor, Ctrl_Day1_miRNA42

description: miRNA Day 1 of experiment

value: Athymic nude mice (nu/nu)

value: Female

value: 6 weeks old

value: Ctrl


title: Canine cutaneous histiocytoma, group 1 according to Cockerell & Slauson 1979, FFPE, 4

description: male neutered

value: no

value: Boxer


title: SFT_NT_24h_1

value: Hematopoietic Stem and Progenitor cells

value: WT


title: SFT_IR_4h_2


title: WC5

description: Wild-type strain 5 hrs. under 30C control

value: Yeast extract-peptone-dexrose


title: WT_rep2, RNA-seq

description:
Oryza sativa Nipponbare
WT_rep2


title: SFT_IR_4h_3


title: Head and Neck Squamous cell tumor, Ctrl_Day1_miRNA38

description: miRNA Day 1 of experiment

value: Head and Neck Squamous cell tumor

value: hypopharyngeal


title: WT_rep1, RNA-seq

description:
Oryza sativa Nipponbare
WT_rep1

value: 14-day-old seedlings

value: Nipponbare


title: SFT_NT_4h_4


title: WC3

description: Wild-type strain 3 hrs. under 30C control


title: SFT_NT_4h_3


title: osino80_rep3, RNA-seq

description:
Oryza sativa Nipponbare
osino80_rep3

value: no treatment


title: SFT_IR_4h_1


title: PS5

description: ppg1D/D strain at 5 hrs. under 37C + serum

value: Serum

value: 5 hrs


title: Head and Neck Squamous cell tumor, Ctrl_Day1_miRNA39

description: miRNA Day 1 of experiment


title: SFT_NT_4h_1

value: Cord Blood

value: SFEM media with cytokines (SCF, FLT3, TPO - 25ng/ml)


title: osino80_rep2, RNA-seq

description:
Oryza sativa Nipponbare
osino80_rep2


title: Skin, Lesional, rep2

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skin

extract_protocol:
After removal of the adipose tissues, samples were minced with scissors into 1 mm2 piece and transferred into gentleMACS C tubes, and then incubated at 37°C for 2.5 h in Whole Skin Dissociation Kit of Human (Miltenyi Biotec, California, USA). Mechanical dissociation was performed on gentleMACS™ Octo Dissociator using ‘h_skin_01’ program. Cell suspension was passed through a 70-μm and then 40-μm filter for removal of large clump fragments. The cells were washed twice with PBS and resuspended in cold DMEM supplemented with 10% FBS. Erythrocytes were removed by red blood cell lysis solution (Miltenyi Biotec). Live cells of single suspension were stained by 0.4 % trypan blue and counted by TC20 Automated Cell Counter (Bio-Rad, California, USA).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Whole cells

value: Skin

value: Asia, male

tag: age

value: 34 years old


title: osino80_rep1, RNA-seq

description:
Oryza sativa Nipponbare
osino80_rep1

tag: genotype


title: Skin, Lesional, rep1

description: 10x Genomics

value: 40 years old


title: Skin, Nonlesional, rep1

description: 10x Genomics


title: PC5

description: ppg1D/D strain at 5 hrs. under 30C control


title: Canine cutaneous histiocytoma, group 1 according to Cockerell & Slauson 1979 , FFPE, 1

description: male neutered

tag: pooled sample

value: no

value: French Bulldog


title: RNA-seq, NGN3m, day 5, rep 6

data_processing:
For gene and transcript expression quantification, we used RSEM (Li & Dewey, 2011) in the paired-end mode. All RNA-seq datasets were aligned to the human reference transcriptome using Bowtie (Langmead, 2010). The human reference transcriptome was built using the human reference genome GRCh38 version p12 and the corresponding Gencode annotation version 28.
Assembly: GRCh38_p12
Supplementary files format and content: Quantification of gene expression for each RNA-seq sample by RSEM
Supplementary files format and content: Quantification of isoform expression for each RNA-seq sample by RSEM
Supplementary files format and content: Differential transcript usage analysis with RNA-seq data

extract_protocol:
Cell pellets were lysed in 700 µL QIAzol™ and total RNA was isolated using the miRNeasy Micro Kit (Qiagen), including DNase treatment  according to the manufacturer’s instructions for RNA isolation including smaller RNA species >17nt. (Qiagen).
RNA-seq libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (Roche) according to the manufacturer’s instructions.

value: Adult dermal fibroblasts

tag: cell line

value: PGP1 iPSC line

value: Day 5

value: Induction of NGN3 expression


title: PC3

description: ppg1D/D strain at 3 hrs. under 30C control

value: Yeast extract-peptone-dexrose

value: 3 hrs


title: YFP_YFP_rep4, ChIP-seq

description:
Oryza sativa Nipponbare
YFP_YFP_rep4

data_processing:
Raw reads were trimmed to remove the adapters and take out the reads with low sequencing quality score using Cutadapt.
The reads with high quality score were aligned to the rice reference genome (MSU7) using Bowtie2.
Reads mapped to the nuclear genome were preserved and SAMtools was used to obtain high quality alignments.
After deduplication, SICER was used to call peaks by comparing the IP and the input.
Reads were normalized as reads per kilobase per million mapped reads (RPKM) in windows of 10 bp using the bamCoverage tool in deepTools. To obtain the enrichment signal around the gene body, TSS and TTS, computeMatrix tool in deepTools was employed.
Assembly: MSU7
Supplementary files format and content: bigWig

extract_protocol:
Rice seedlings were harvested and fixed with the buffer containing 0.4 M sucrose, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 1% formaldehyde, and 1 mM PMSF. Chromatin was sonicated into DNA fragments around 200~500-bp in size using lysis buffer containing 50 mM HEPES (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1 mM PMSF, 1% SDS, 0.1% Na deoxycholate, 1% Triton X-100 and Protease Inhibitor cocktail.
The ChIP-seq libraries were constructed by following the manufacturer’s instructions of VAHTSTM Universal DNA Library Prep Kit (Vazyme).

value: 14-day-old seedlings

value: Nipponbare

value: no treatment

tag: antibody

value: YFP


title: YFP_YFP_rep3, ChIP-seq

description:
Oryza sativa Nipponbare
YFP_YFP_rep3


title: RNA-seq, NGN3m, day 5, rep 4

tag: time


title: RNA-seq, NGN3m, day 5, rep 1


title: RNA-seq, NGN3m, day 3, rep 5

value: Day 3


title: YFP_YFP_rep2, ChIP-seq

description:
Oryza sativa Nipponbare
YFP_YFP_rep2


title: YFP_YFP_rep1, ChIP-seq

description:
Oryza sativa Nipponbare
YFP_YFP_rep1


title: RNA-seq, NGN3m, day 3, rep 1


title: RNA-seq, NGN3m, day 3, rep 3


title: s-E15.5-XHET-13B

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

data_processing:
Small RNA-seq reads were trimmed using fastx 0.0.14 and cutadapt 1.8.3: zcat ${FILE}.fastq.gz | fastx_trimmer -f 5 -i - -o ${FILE}.tmp.fastq cutadapt --format="fastq" --front=GTTCAGAGTTCTACAGTCCGACGATCNNNN --adapter=NNNNTGGAATTCTCGGGTGCCAAGG --error-rate=0.075 --times=2 --overlap=14 --minimum-length=12 --max-n=0.1 --output="${FILE}.fastq" --trim-n --match-read-wildcards ${FILE}.tmp.fastq
Trimmed reads were mapped to mouse (mm10) genome using STAR 2.7.3a with following parameters: STAR --readFilesIn ${FILE}.fastq.gz --genomeDir ${GENOME_INDEX} --runThreadN 12 --genomeLoad NoSharedMemory --limitBAMsortRAM 20000000000 --readFilesCommand unpigz –c --outFileNamePrefix ${FILENAME} --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outFilterMultimapNmax 99999  --outFilterMismatchNoverLmax 0.1 --outFilterMatchNminOverLread 0.66 --alignSJoverhangMin 999 --alignSJDBoverhangMin 999
Genome browser coverage tracks in bigWig format were produced using bedtools v2.29.2 and wigToBigWig v 4 from UCSC: genomeCoverageBed -ibam ${FILE} -bg -split > ${FILE}.bedGraph wigToBigWig ${FILE}.bedGraph chrNameLength.txt ${FILE}.bw
Assembly: mm10
Supplementary files format and content: coverage genome browser tracks files: - .bigWig format - generated in a non-stranded mode.  - not normalized for library size

source_name: whole embryos

extract_protocol:
Embryos were homogenized in Qiazol lysis reagent (Qiagen) and total RNA was isolated by Qiazol-chloroform extraction and ethanol precipitation method.
Small RNA libraries were constructed using Nextflex Small RNA-seq kit v3 for Illumina (Perkin Elmer) according to the manufacturer’s protocol; 3′ adapter ligation was performed overnight at 20 °C, 15 cycles were used for PCR amplification and NextFlex beads were used for size selection.

treatment_protocol: E15.5 embryos were removed from the uterus and washed in PBS. The yolk sac was taken for genotyping and embryos were transferred into RNAlater (Thermo Fisher Scientific)

value: whole embryos

value: Dicer X/wt

tag: fraction

value: small RNA

tag: replicate

value: biol rep 2


title: SFT_NT_4h_2

value: Cord Blood

value: Hematopoietic Stem and Progenitor cells

value: WT

value: SFEM media with cytokines (SCF, FLT3, TPO - 25ng/ml)


title: RNA-seq, NGN3m, day 5, rep 2

value: Adult dermal fibroblasts

value: PGP1 iPSC line

value: Day 5


title: RNA-seq, NGN3m, day 3, rep 2

value: Induction of NGN3 expression


title: s_E15.5_XHOM_7B (re-analyzed)

description: re-analysis of GSM5870277

value: Dicer X/X

value: biol rep 5


title: PS3

description: ppg1D/D strain at 3 hrs. under 37C + serum

value: Yeast extract-peptone-dexrose

value: Serum

value: 3 hrs


title: s-E15.5-XHET-7

value: whole embryos

value: biol rep 1


title: YFP_input_rep3, ChIP-seq

description:
Oryza sativa Nipponbare
YFP_input_rep3

value: 14-day-old seedlings

value: Nipponbare

value: no treatment


title: RNA-seq, NGN3m, day 2, rep 5

value: Day 2


title: YFP_input_rep2, ChIP-seq

description:
Oryza sativa Nipponbare
YFP_input_rep2


title: RNA-seq, NGN3m, day 2, rep 4


title: s_E15.5_XHOM_4 (re-analyzed)

description: re-analysis of GSM5870276

value: small RNA

value: biol rep 4


title: YFP_input_rep1, ChIP-seq

description:
Oryza sativa Nipponbare
YFP_input_rep1


title: RNA-seq, NGN3m, day 2, rep 2

value: Adult dermal fibroblasts


title: s_E15.5_XHOM_3B (re-analyzed)

description: re-analysis of GSM5870275

value: biol rep 3


title: RNA-seq, NGN3m, day 2, rep 3

value: PGP1 iPSC line


title: RNA-seq, NGN3m, day 2, rep 1

value: Induction of NGN3 expression


title: WT_YFP_rep1, ChIP-seq

description:
Oryza sativa Nipponbare
WT_YFP_rep1

value: wild-type

value: YFP


title: RNA-seq, NGN3m, day 5, rep 5

value: Day 5


title: s-E15.5-XHET-2B

value: Dicer X/wt


title: RNA-seq, NGN3m, day 1, rep 5

value: Day 1


title: WT_input_rep4, ChIP-seq

description:
Oryza sativa Nipponbare
WT_input_rep4


title: RNA-seq, NGN3m, day 1, rep 4


title: s_E15.5_XHOM_10B_r2 (re-analyzed)

description: re-analysis of GSM5870273

value: whole embryos

value: Dicer X/X


title: WT_input_rep2, ChIP-seq

description:
Oryza sativa Nipponbare
WT_input_rep2

value: 14-day-old seedlings


title: RNA-seq, NGN3m, day 1, rep 1


title: RNA-seq, NGN3m, day 0, rep 5

value: Day 0


title: RNA-seq, NGN3m, day 0, rep 4


title: s_E15.5_WT_8B (re-analyzed)

description: re-analysis of GSM5870272

value: Dicer wt/wt


title: RNA-seq, NGN3m, day 0, rep 3


title: WT_input_rep1, ChIP-seq

description:
Oryza sativa Nipponbare
WT_input_rep1

value: Nipponbare

value: no treatment


title: RNA-seq, NGN3m, day 0, rep 2


title: s_E15.5_WT_1 (re-analyzed)

description: re-analysis of GSM5870270

value: small RNA

value: biol rep 1


title: WT_input_for_YFP_rep1, ChIP-seq

description:
Oryza sativa Nipponbare
WT_input_for_YFP_rep1


title: GCs,ob,mutant, rep3

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

data_processing:
Base calling software.  Quality of raw reads was evaluated by means of FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
After adapter and quality trimming using Trim Galore (v0.6.2), RNA-seq data was mapped to mouse genome GRCm38 using HISAT2 v2.1.0.
Assembly: GRCm38
Supplementary files format and content: Raw counts per gene were calculated in R using the org.Mmu.eg.db package.

source_name: Ovaries

extract_protocol:
RNA was harvested using G&T protocol - beads for poly A tail pooled down the RNA, followed by reverse transcription and amplification
All libraries were prepared from 100-200 pg of cDNA using the Nextera XT Kit (Illumina) following manufacturer's protocol.

value: Ovaries

value: Granulosa cells (GCs)

tag: developmental stage

value: GCs from Antral follicle

value: ob/ob -/-

tag: state

value: Mutant


title: RNA-seq, NGN3m, day 0, rep 1

value: Adult dermal fibroblasts

value: PGP1 iPSC line

value: Induction of NGN3 expression


title: GCs,ob,mutant, rep2


title: WT_H3_rep2, ChIP-seq

description:
Oryza sativa Nipponbare
WT_H3_rep2

value: wild-type


title: CaPaX503

city: Nantes

first: Christophe

last: Blanquart

address: 8 Quai Moncousu

country: France

institute: INSERM UMR 1307/CNRS UMR 6075

data_processing:
Pipeline details have been published by Charpentier E et al. 2018 (10.21203/rs.3.pex-1336/v1)
Assembly: Hg19
Supplementary files format and content: Matrix table of raw gene counts for all genes in all samples

growth_protocol: Cells were grown as multicellular spheroids (MCTS) in low adherence 96-well plates in DMEM medium supplemented with 10% FCS

extract_protocol:
Nucleospin RNA kit, Macherey-Nagel
Libraries were prepared according to NovaSeq 6000 Sequencing Sytem's instructions accompanying the NovaSeq 6000 SP Reagent Kit (Ref# 20028401). Libraries were sequenced on the NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: MCTS were treated with carboplatin-paclitaxel or -gemcitabine combinations according to clinic schedule of administration consisting on three repetitions of treatments (one combination and two single treatments (paclitaxel or gemcitabine)).

value: Lung cancer cells

value: Chemotherapies


title: CaPa503


title: CaPaX502


title: WT_H3_rep1, ChIP-seq

description:
Oryza sativa Nipponbare
WT_H3_rep1

value: 14-day-old seedlings


title: CaPa502


title: s_E15.5_XHOM_2 (re-analyzed)

description: re-analysis of GSM5870274

value: whole embryos

value: Dicer X/X

value: biol rep 2


title: GCs,ob,mutant, rep1


title: CaGeX503


title: CaPa501


title: WT_H3K9me2_rep3, ChIP-seq

description:
Oryza sativa Nipponbare
WT_H3K9me2_rep3

value: Nipponbare

value: no treatment


title: CaGeX502


title: CaGeX501


title: s_E15.5_WT_6 (re-analyzed)

description: re-analysis of GSM5870271

value: Dicer wt/wt

value: small RNA


title: WT_H3K9me2_rep2, ChIP-seq

description:
Oryza sativa Nipponbare
WT_H3K9me2_rep2


title: CaGe501


title: GCs,ob,control, rep2

value: Ovaries

value: Granulosa cells (GCs)

value: GCs from Antral follicle

value: ob/ob +/+

value: Wild type


title: WT_H3K9me2_rep1, ChIP-seq

description:
Oryza sativa Nipponbare
WT_H3K9me2_rep1


title: CTX6


title: CTX5


title: RNA-seq, NGN3m, day 1, rep 3

value: Adult dermal fibroblasts

value: PGP1 iPSC line

value: Day 1

value: Induction of NGN3 expression


title: CTX3

value: Lung cancer cells


title: WT_H3K4me3_rep2, ChIP-seq

description:
Oryza sativa Nipponbare
WT_H3K4me3_rep2

value: 14-day-old seedlings

value: wild-type


title: GCs,db,mutant, rep4

value: db/db -/-

value: Mutant


title: CTX2


title: GCs,db,mutant, rep3


title: CT8


title: GCs,db,mutant, rep2


title: WT_H3K4me2_rep2, ChIP-seq

description:
Oryza sativa Nipponbare
WT_H3K4me2_rep2

value: Nipponbare

value: no treatment


title: WT_H3K4me3_rep1, ChIP-seq

description:
Oryza sativa Nipponbare
WT_H3K4me3_rep1


title: CT6


title: CT7


title: CT5


title: WT_H3K4me2_rep1, ChIP-seq

description:
Oryza sativa Nipponbare
WT_H3K4me2_rep1


title: CaGe502

value: Chemotherapies


title: CT9


title: WT_H3K36me3_rep2, ChIP-seq

description:
Oryza sativa Nipponbare
WT_H3K36me3_rep2


title: CT4


title: GCs,db,mutant, rep1

value: Ovaries


title: GCs,db,control, rep4

value: Granulosa cells (GCs)

value: db/db +/+


title: WT_H3K36me3_rep1, ChIP-seq

description:
Oryza sativa Nipponbare
WT_H3K36me3_rep1


title: CT1


title: GCs,db,control, rep3

value: GCs from Antral follicle


title: WT_H3K27me3_rep3, ChIP-seq

description:
Oryza sativa Nipponbare
WT_H3K27me3_rep3


title: Kelly xenograft, STM, 14D, RIP, rep1

city: Chicago

first: Susan

middle: L

last: Cohn

state: IL

address: 5721 S. Maryland Ave.

department: Pediatrics

institute: University of Chicago

description: mouse xenograft, pulldown (meRIP-Seq)

data_processing:
Raw read quality for all sequencing data was assessed with fastqc (version 0.11.5)
Trimmomatic (version 0.36) was used to trim leading and trailing bases below quality 3 and remove reads less than 36 base pairs in length
Reads were aligned to GRCh38 using Hisat2 (version 2.1.0).
Reads were counted across exons (-exon flag) using featureCounts of subread (version 1.5.3).
bigWig files normalized to reads per kilobase million (RPKM) were generated with deepTools (version 2.0).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample
Supplementary files format and content: bigWig files normalized to RPKM
Library strategy: meRIP-Seq

source_name: Kelly

growth_protocol: Kelly and NGP cells were grown at 5% CO2 in RPMI1640 (Life Technologies) supplemented with 10% heat-inactivated FBS, 2 mmol/L l-glutamine, and 1% penicillin/streptomycin. For mouse xenograft studies, male and female nude mide (Harlan) were subcutaneously injected with 1 x 10^7 Kelly neuroblastoma cells dissolved in 200 uL including cultrex basement memberane extract per manufacturer's instructions (R&D Systems, 3632-005-02).

extract_protocol:
Total RNA was harvested from cells using the TRIzol reagent (Invitrogen). Poly(A) RNA was extracted using the Dynabeads mRNA DIRECT Purification kit following the manufacturer's protocol.
1 μg of poly(A) RNA was used for each sample. m6A and non-m6A spikein RNA from the EpiMark N6-Methyladenosine Enrichment Kit (NEB) were added as the normalization controls for m6A level analysis. RNA was diluted to 100 μl and fragmented by 30 cycles of sonication. 1μg of m6A antibody from the same kit was incubated with 25 μl of protein G beads at 4 °C for 30 minutes with rotation. Beads were then washed with reaction buffer (150 mM NaCl, 10 mM Tris-HCl, 0.1 % NP-40), rotated with RNA samples at 4 °C for 1 hour, washed with reaction buffer, low salt wash buffer (50 mM NaCl, 10 mM Tris-HCl, 0.1 % NP-40), high salt wash buffer (500 mM NaCl, 10 mM Tris-HCl, 0.1 % NP-40), and eluted with 100 μl of RLT buffer (QIAGEN). Enriched RNA (meRIP-Seq) as well as input RNA (RNA-Seq) was purified by RNA Clean & Concentrator Kits (Zymo Research) and cDNA libraries were constructed using the SMART® cDNA Library Construction Kit (Takara) following the manufacturer’s instructions.

treatment_protocol: Kelly and NGP cells were treated with either 8 uM STM2457 or DMSO for 1 or 6 days. In the mouse Kelly cell neuroblastoma xenograft model, mice were injected with 50 mg/kg STM2457 or vehicle alone peritoneally once daiily for 14 days

value: Kelly

value: neuroblastoma cell line, MYCN-amplified

value: WT


title: GCs,db,control, rep2

value: Wild type


title: Kelly xenograft, STM, 14D, RIP, rep2

description: mouse xenograft, pulldown (meRIP-Seq)


title: Kelly xenograft, DMSO, 14D, RIP, rep2

description: mouse xenograft, pulldown (meRIP-Seq)

value: DMSO


title: WT_H3K27me3_rep2, ChIP-seq

description:
Oryza sativa Nipponbare
WT_H3K27me3_rep2


title: Kelly xenograft, STM, 14D, input, rep2

description: mouse xenograft, input (RNA-Seq)

data_processing:
Raw read quality for all sequencing data was assessed with fastqc (version 0.11.5)
Trimmomatic (version 0.36) was used to trim leading and trailing bases below quality 3 and remove reads less than 36 base pairs in length
Reads were aligned to GRCh38 using Hisat2 (version 2.1.0).
Reads were counted across exons (-exon flag) using featureCounts of subread (version 1.5.3).
bigWig files normalized to reads per kilobase million (RPKM) were generated with deepTools (version 2.0).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample
Supplementary files format and content: bigWig files normalized to RPKM


title: WT_H3K27me3_rep1, ChIP-seq

description:
Oryza sativa Nipponbare
WT_H3K27me3_rep1


title: Kelly xenograft, STM, 14D, input, rep1

description: mouse xenograft, input (RNA-Seq)


title: GCs,db,control, rep1


title: Clone13_Minus [ATAC-seq]

city: Boston

first: David

middle: T

last: Scadden

state: MA

address: 185 Cambridge St

department: Center for Regenerative Medicine

institute: MGH

description: ATAC-Seqdata in ER-Hoxb8 cells

data_processing:
Illumina software used for basecalling.
Raw sequences of ATAC-seq data were mapped with a Bowtie2 mapper with a default setting to the mouse genome (mm10).
Genome_build: mm10
Supplementary_files_format_and_content: peaks

source_name: Mouse Bone Marrow ER-Hoxb8 monocytic cells

growth_protocol: ER-HoxB8 cells were maintained in RPMI medium supplemented with 10% FBS, penicillin/streptomycin, and SCF.

extract_protocol: ATAC-seq samples were performed as previously described (Buenrostro et al., 2015)

value: ER-Hoxb8 cells


title: Kelly xenograft, DMSO, 14D, input, rep2

description: mouse xenograft, input (RNA-Seq)


title: WT_H2AZ_rep2, ChIP-seq

description:
Oryza sativa Nipponbare
WT_H2AZ_rep2

value: 14-day-old seedlings


title: Kelly xenograft, DMSO, 14D, input, rep1

description: mouse xenograft, input (RNA-Seq)


title: Clone12_Minus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: CT3

value: Lung cancer cells


title: WT_H2AZ_rep1, ChIP-seq

description:
Oryza sativa Nipponbare
WT_H2AZ_rep1

value: wild-type


title: NGP cells, STM, 6D, RIP, rep3

description: pulldown (meRIP-Seq)

source_name: NGP

value: NGP


title: NGP cells, STM, 6D, RIP, rep2

description: pulldown (meRIP-Seq)


title: CTX1


title: NGP cells, STM, 6D, RIP, rep1

description: pulldown (meRIP-Seq)


title: Clone11_Minus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: Clone10_Minus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: NGP cells, DMSO, 6D, RIP, rep3

description: pulldown (meRIP-Seq)


title: WT_H2Aub_rep2, ChIP-seq

description:
Oryza sativa Nipponbare
WT_H2Aub_rep2

value: Nipponbare


title: NGP cells, DMSO, 6D, RIP, rep2

description: pulldown (meRIP-Seq)


title: Kelly xenograft, DMSO, 14D, RIP, rep1

description: mouse xenograft, pulldown (meRIP-Seq)


title: Clone9_Minus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: WT_H2Aub_rep1, ChIP-seq

description:
Oryza sativa Nipponbare
WT_H2Aub_rep1

value: no treatment


title: NGP cells, DMSO, 6D,  RIP, rep1

description: pulldown (meRIP-Seq)


title: NGP cells, STM, 6D,  input, rep3

description: input (RNA-Seq)


title: Clone8_Minus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: OsINO80-YFP_YFP_rep1, ChIP-seq

description:
Oryza sativa Nipponbare
OsINO80-YFP_YFP_rep1

value: YFP


title: RNA-seq, NGN3m, day 1, rep 2

value: Adult dermal fibroblasts

value: PGP1 iPSC line

value: Day 1

value: Induction of NGN3 expression


title: NGP cells, STM, 6D, input, rep2

description: input (RNA-Seq)


title: WT_H2A, ChIP-seq

description:
Oryza sativa Nipponbare
WT_H2A


title: NGP cells, STM, 6D, input, rep1

description: input (RNA-Seq)


title: NGP cells, DMSO, 6D, input, rep3

description: input (RNA-Seq)


title: Clone7_Minus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: NGP cells, DMSO, 6D, input, rep2

description: input (RNA-Seq)


title: OsINO80-YFP_input_rep1, ChIP-seq

description:
Oryza sativa Nipponbare
OsINO80-YFP_input_rep1


title: NGP cells, DMSO, 6D, input, rep1

description: input (RNA-Seq)


title: Clone6_Minus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: osino80_input_rep4, ChIP-seq

description:
Oryza sativa Nipponbare
osino80_input_rep4


title: Kelly cells, STM, 6D, RIP, rep3

description: pulldown (meRIP-Seq)

value: Kelly


title: Kelly cells, STM, 6D, RIP, rep2

description: pulldown (meRIP-Seq)

value: neuroblastoma cell line, MYCN-amplified


title: Clone5_Minus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: Kelly cells, STM, 6D, RIP, rep1

description: pulldown (meRIP-Seq)

value: WT


title: osino80_input_rep3, ChIP-seq

description:
Oryza sativa Nipponbare
osino80_input_rep3


title: Clone4_Minus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: Kelly cells, DMSO, 6D, RIP, rep3

description: pulldown (meRIP-Seq)


title: Kelly cells, DMSO, 6D, RIP, rep2

description: pulldown (meRIP-Seq)


title: osino80_input_rep2, ChIP-seq

description:
Oryza sativa Nipponbare
osino80_input_rep2


title: Clone3_Minus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: Kelly cells, DMSO, 6D,  RIP, rep1

description: pulldown (meRIP-Seq)


title: osino80_input_rep1, ChIP-seq

description:
Oryza sativa Nipponbare
osino80_input_rep1


title: Kelly cells, STM, 6D, input, rep2

description: input (RNA-Seq)


title: Clone2_Minus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: Kelly cells, DMSO, 6D, input, rep3

description: input (RNA-Seq)


title: osino80_H3_rep2, ChIP-seq

description:
Oryza sativa Nipponbare
osino80_H3_rep2


title: Clone1_Minus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: osino80_H3_rep1, ChIP-seq

description:
Oryza sativa Nipponbare
osino80_H3_rep1


title: Clone13_Plus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells

source_name: Mouse Bone Marrow ER-Hoxb8 GMP cells


title: Kelly cells, STM, 6D,  input, rep3

description: input (RNA-Seq)


title: Kelly cells, DMSO, 6D, input, rep1

description: input (RNA-Seq)


title: osino80_H3K9me2_rep3, ChIP-seq

description:
Oryza sativa Nipponbare
osino80_H3K9me2_rep3


title: Kelly cells, STM, 1D, RIP, rep2

description: pulldown (meRIP-Seq)


title: Kelly cells, STM, 1D, RIP, rep1

description: pulldown (meRIP-Seq)


title: Clone12_Plus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: osino80_H3K9me2_rep2, ChIP-seq

description:
Oryza sativa Nipponbare
osino80_H3K9me2_rep2


title: Clone11_Plus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: WT_input_rep3, ChIP-seq

description:
Oryza sativa Nipponbare
WT_input_rep3


title: Kelly cells, DMSO, 1D, RIP, rep2

description: pulldown (meRIP-Seq)


title: Kelly cells, DMSO, 1D, RIP, rep1

description: pulldown (meRIP-Seq)


title: Clone10_Plus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: Kelly cells, STM, 1D, input, rep2

description: input (RNA-Seq)


title: Kelly cells, STM, 6D, input, rep1

description: input (RNA-Seq)


title: Kelly cells, STM, 1D, input, rep1

description: input (RNA-Seq)


title: Clone9_Plus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: Kelly cells, STM, 1D, input, rep3

description: input (RNA-Seq)


title: Kelly cells, DMSO, 6D, input, rep2

description: input (RNA-Seq)


title: osino80_H3K4me3_rep1, ChIP-seq

description:
Oryza sativa Nipponbare
osino80_H3K4me3_rep1


title: Kelly cells, DMSO, 1D, input, rep3

description: input (RNA-Seq)


title: Kelly cells, DMSO, 1D, input, rep2

description: input (RNA-Seq)


title: osino80_H3K4me2_rep2, ChIP-seq

description:
Oryza sativa Nipponbare
osino80_H3K4me2_rep2


title: Kelly cells, STM, 1D, RIP, rep3

description: pulldown (meRIP-Seq)


title: Clone8_Plus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: Clone7_Plus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: NGP cells, STM, 6D, 6h, rep2

data_processing:
Raw read quality for all sequencing data was assessed with fastqc (version 0.11.5)
Trimmomatic (version 0.36) was used to trim leading and trailing bases below quality 3 and remove reads less than 36 base pairs in length
Reads were aligned to GRCh38 using Hisat2 (version 2.1.0).
Reads were counted across exons (-exon flag) using featureCounts of subread (version 1.5.3).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

growth_protocol: Kelly and NGP cells were grown at 5% CO2 in RPMI1640 (Life Technologies) supplemented with 10% heat-inactivated FBS, 2 mmol/L l-glutamine, and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was harvested from cells using the TRIzol reagent (Invitrogen). Poly(A) RNA was extracted using the Dynabeads mRNA DIRECT Purification kit following the manufacturer's protocol.
RNA was purified by RNA Clean & Concentrator Kits (Zymo Research) and cDNA libraries were constructed using the SMART® cDNA Library Construction Kit (Takara) following the manufacturer’s instructions.

treatment_protocol: Kelly and NGP cells were treated with either 8 uM STM2457 or DMSO for 3 or 6 days. Kelly and NGP cells were then treated with Actinomycin D (Sigma A1410) at a concentration of 10 μg/ml for 0, 3, or 6 hours. Total RNA was then extracted as below.

value: 6h actinomycin D


title: Kelly cells, DMSO, 1D, input, rep1

description: input (RNA-Seq)

value: DMSO


title: osino80_H3K4me2_rep1, ChIP-seq

description:
Oryza sativa Nipponbare
osino80_H3K4me2_rep1


title: Clone6_Plus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells

value: ER-Hoxb8 cells


title: Kelly cells, DMSO, 1D, RIP, rep3

description: pulldown (meRIP-Seq)


title: NGP cells, STM, 6D, 6h, rep1


title: NGP cells, STM, 6D, 3h, rep2

value: 3h actinomycin D


title: osino80_H3K9me2_rep1, ChIP-seq

description:
Oryza sativa Nipponbare
osino80_H3K9me2_rep1

value: 14-day-old seedlings


title: osino80_H3K36me3_rep2, ChIP-seq

description:
Oryza sativa Nipponbare
osino80_H3K36me3_rep2


title: NGP cells, DMSO, 6D, 6h, rep2


title: osino80_H3K4me3_rep2, ChIP-seq

description:
Oryza sativa Nipponbare
osino80_H3K4me3_rep2


title: NGP cells, DMSO, 6D, 6h, rep1


title: NGP cells, DMSO, 6D,  3h, rep2


title: osino80_H3K36me3_rep1, ChIP-seq

description:
Oryza sativa Nipponbare
osino80_H3K36me3_rep1


title: NGP cells, STM, 6D,  3h, rep1


title: NGP cells, STM, 6D, 0h, rep2

value: 0h actinomycin D


title: Clone4_Plus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: NGP cells, STM, 6D, 0h, rep1

value: NGP


title: osino80_H3K27me3_rep3, ChIP-seq

description:
Oryza sativa Nipponbare
osino80_H3K27me3_rep3

value: Nipponbare


title: Clone3_Plus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: NGP cells, DMSO, 6D, 3h, rep1


title: NGP cells, DMSO, 6D, 0h, rep2


title: Clone2_Plus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: NGP cells, STM, 3D, 6h, rep2


title: NGP cells, DMSO, 6D, 0h, rep1


title: osino80_H3K27me3_rep1, ChIP-seq

description:
Oryza sativa Nipponbare
osino80_H3K27me3_rep1

value: no treatment


title: NGP cells, STM, 3D, 6h, rep1


title: osino80_H2AZ_rep2, ChIP-seq

description:
Oryza sativa Nipponbare
osino80_H2AZ_rep2


title: Clone1_Plus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells