title: Veh N rep3

city: Amsterdam

last: Van den Bossche

address: De Boelelaan 1108

department: Molecular Cell Biology and Immunology

country: Netherlands

institute: Amsterdam UMC, VUmc

data_processing:
Reads were aligned to the mouse genome mm10 by STAR 2.5.2b with default settings.
Differential expression was analyzed using the R package DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: Table with raw gene counts for every gene and every sample

source_name: BMDMs

extract_protocol:
RNA of bone marrow-derived macrophages was harvested using the Qiagen RNeasy kit. RNA was used to construct strand-specific libraries with the KAPA mRNA Hyper-Prep kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow-derived macrophages

value: Vehicle pre-treatment 1h, Vehicle 24h


title: untreated_Run1_BCABCO_Rep1_Gemcitabine_ReadsPerGene

status: Public on Jun 24 2022

type: SRA

city: Heidelberg

first: Lukas

last: Mathur

address: Meyerhofstraße 1

department: Genome Biology

country: Germany

institute: EMBL

description:
Droplets with drug (treated) were mixed with DMSO droplets (untreated) to test "leackage" of the drugs to the DMSO droplets. 14 drugs with corresponding DMSO controls, 3 replicates each, plus 3 additional separate DMSO controls.
drug_exchage_matrix

library_source: transcriptomic

data_processing:
CASANA software was used for basecalling
Read1 (Barcode) was used to demultiplex read 2 according to treatment conditions using Je Debarcode version 2.0.beta allowing a maximum of 6 mismatches per barcode sequence,
Sequences were aligned to Homo_sapiens.GRCh38.84. using STAR version 2.4.2a
Created matrix with all alignments (treatment conditions) and remove genes with 0 read counts in all samples
Supplementary files format and content: Matrix containing read counts for all samples and replicate

molecule: total RNA

organism: Homo sapiens

source_name: K562 cells

growth_protocol: K562 cells were cultures in DMEM media supplemented with 10% BSA and 1% Penicillin Streptomycin

extract_protocol:
Cells were lysed and the released mRNA was reversed transcribed using barcoded poly-dT primers.
Biotin on the poly-dT primer was used to purify cDNA. Priming sites introduced over the poly-dT primers and the template switching oligonucleotide were used to amplify the cDNA. Subsequently, cDNA was fragmented using a hyperactive Tn5 transposase.

treatment_protocol: Cells were encapsulated into picoliter sized droplts along with 420 unique combinatorial treatment conditions. Droplets with cells were incubated for 12h/24h at 37 degrees Celsius

tag: cell type

value: Myelogenous leukemia cells

tag: genotype

value: bcr:abl fusion gene

tag: treatment

value: Cells were treated with 14 different drugs in droplets, each treatment has a corresponding DMSO control


title: ur-20_(miRNA-4-0)_prostate-cancer_N0M0

type: RNA

city: Moscow

first: Anton

last: Zhiyanov

address: 20 Myasnitskaya ulitsa

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

hyb_protocol: The procedure was performed according to the manufacturer's instructions

scan_protocol: GeneChips were scanned using the affymetrix GeneChip2 Scanner 3000 7G.

data_processing: RNA was analyzed using GeneChip miRNA 4.0 (Affymetrix), detecting all noncoding and mi- nor RNA from miRBase database, including mature miRNA and pre-miRNA. CEL files were processed using the oligo R package in the default mode to obtain the normalized expression values.

label: biotin

label_protocol: biotin

extract_protocol: Isolation of RNA from 200 µl of each plasma specimen was carried out using miRNeasy Serum/Plasma Kit (Qiagen) according to the instruction.

treatment_protocol: Blood was collected in S-Monovette EDTA-KE tubes, 8 ml (Sarstedt). Plasma was separated by 2-step  centrifugation on a 5810R centrifuge (Eppendorf) at ambient temperature. Step 1 centrifugation was carried out at 2000g for 1 min at medium acceleration  and inhibition velocity. The upper liquid phase was then transferred into a new tube and step 2 centrifugation was carried out at 4000g, after which plasma was  carefully collected, only 10% volume was left at the bottom of the tube.

tag: disease state

value: prostate cancer

tag: age

tag: gleason

tag: tnm

tag: psa

tag: group

value: Low risk


title: Veh N rep1

first: Jan

organism: Mus musculus

tag: strain

tag: tissue


title: ur-14_(miRNA-4-0)_prostate-cancer_NxM0

value: High risk


title: Veh N rep2


title: neocortex_Bcl6_mutant_rep4

city: Ulm

first: Christoph

last: Wiegreffe

address: Albert-Einstein-Allee 11

institute: Ulm University

description: knockout tissue

hyb_protocol: 2µg of total RNA were used for the One-Cycle target labeling assay, further processed and hybridized to the GeneChip® Mouse 430 2.0 array from Affymetrix according to manufacturer’s instructions.

scan_protocol: The Arrays were washed using Affymetrix fluidics station FS450, and scanned using the Gene Chip Scanner 3000.

data_processing: BRB Array Tools

source_name: neocortex tissue P5

label_protocol: One Cycle Target Labelling Protocol

growth_protocol: Fresh frozen dissected tissue was kept at -80°C until laser-microdissection.

extract_protocol: Extraction of total RNA was performed with the Rneasy kit according to the manufacturer's instructions (Qiagen).

treatment_protocol: Tissue was dissected in ice-cold phosphate buffer (pH7.2).

value: neocortex

tag: developmental stage

value: Postnatal day 5

value: Bcl6 mutant


title: Veh LPS rep3

value: Vehicle pre-treatment 1h, LPS 24h


title: neocortex_Bcl6_control_rep3

description: control tissue

value: Bcl6 control


title: untreated_Run1_BCABCO_Rep1_EPIRUBICIN_ReadsPerGene


title: neocortex_Bcl6_mutant_rep2

description: knockout tissue


title: neocortex_Bcl6_control_rep4

description: control tissue


title: neocortex_Bcl6_control_rep2

description: control tissue


title: ur-11_(miRNA-4-0)_prostate-cancer_N0M0


title: untreated_Run1_BCABCO_Rep1_Baricitinib_ReadsPerGene


title: ur-12_(miRNA-4-0)_prostate-cancer_N0M0


title: ur-13_(miRNA-4-0)_prostate-cancer_N0M0


title: neocortex_Bcl6_mutant_rep3

description: knockout tissue


title: ur-8_(miRNA-4-0)_prostate-cancer_N0M0


title: Veh LPS rep2


title: untreated_Run1_BCABCO_Rep1_AT9283_ReadsPerGene


title: D2HG LPS rep3

value: D2HG pre-treatment 1h, LPS 24h


title: Blastocyst-H2AZ-KD-RNA-6

city: Wuhan

first: Jing-Jing

last: Zhang

state: Hubei

address: 1 Lion Rock Street

department: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction

country: China

institute: Huazhong Agricultural University

data_processing:
All RNA-seq data were aligned to the mouse reference genome mm10 using STAR.
Gene FPKM (Fragments per kilobase of transcript per million mapped reads) values were quantified using Stringtie (version 2.1.4).
Gene differential expression analysis using DESeq2 (version 1.30.1) based on the reads count file obtained by featureCounts (version 1.6.2).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: FPKM.txt: Tab-delimited text file includes FPKM values for each gene.

molecule: polyA RNA

source_name: embryo

extract_protocol:
The RNA-seq libraries were generated using the Smart-seq2 protocol as previously described with some modifications. Briefly, 15 embryos from H2A.Z knockdown and control groups were harvested at the 2-cell, morula and blastocyst stages. After zona pellucidae removal in 0.5% pronase E and three washes in 0.05% PVA, embryos were transferred into lysis buffer containing Triton X-100, oligo-dT primer, dNTP (Thermo Fisher Scientific) and RNase inhibitor (Takara). After 72℃ incubation for 3 min, reverse transcription mix (100 U SuperScript II reverse transcriptase, 10 U RNase inhibitor, 1× Superscript II first-strand buffer, 5 mM DTT, 1 M betaine, 6 mM MgCl2, 1 μM TSO) was added into sample lysis buffer, followed by 42℃ incubation for 90 min to obtain cDNA.
cDNA was preamplification for 16-18 cycles by using KAPA HiFi HotStart ReadyMix (KK2601, Roche) and IS PCR primers, followed by PCR purification by AMPure XP beads (A63881, Beckman). Finally, amplified cDNA was fragmented and RNA-seq library was constructed by using TruePrep DNA Library Prep Kit (TD502, Vazyme) according to the manufacturer’s instructions. Paired-end 150-bp sequencing was performed on the Illumina HiSeq X-Ten.

treatment_protocol: Small interference RNAs (siRNAs) against mouse H2A.Z were designed and synthesized for three pairs by GenePharma, Shanghai, China. All three pairs of siRNAs for each gene were diluted and mixed in nuclease-free water with a working concentration of 20 μM. Mouse zygotes at the pronuclear stage 3 (20-22 h post hCG injection) were injected with approximately 10 pl of siRNAs using a PiezoXpert micromanipulator (Eppendorf), and cultured in G1-plus medium at 37℃ under 5% CO2 in air. The injected embryos were observed at 44 h, 55 h, 68 h, 78 h and 94 h post hCG injection to summary the developmental phenotypes.

value: Blastocyst

value: H2A.Z KD


title: treated_Run1_BCABCO_Rep3_Wortmannin_ReadsPerGene


title: treated_Run1_BCABCO_Rep3_YM155_ReadsPerGene


title: D2HG LPS rep2


title: Veh LPS rep1


title: ur-6_(miRNA-4-0)_prostate-cancer_N0M0


title: neocortex_Bcl6_mutant_rep1

description: knockout tissue


title: treated_Run1_BCABCO_Rep3_Triciribine_ReadsPerGene


title: ur-5_(miRNA-4-0)_prostate-cancer_N0M0


title: neocortex_Bcl11a_control_rep4

description: control tissue

source_name: neocortex tissue P2

value: Postnatal day 2

value: Bcl11a control


title: Blastocyst-H2AZ-KD-RNA-1


title: neocortex_Bcl6_control_rep1

description: control tissue


title: Blastocyst-H2AZ-KD-RNA-5


title: Blastocyst-H2AZ-KD-RNA-4


title: neocortex_Bcl11a_mutant_rep4

description: knockout tissue

value: Bcl11a mutant


title: treated_Run1_BCABCO_Rep3_SB747651_ReadsPerGene

value: Myelogenous leukemia cells


title: Femur tissues from a sham operation group rat

city: Dalian

first: Hao

last: Li

email: lihao0362@sina.com, lih@dmu.edu.cn, lh1362230894@outlook.com, lihao7y6@foxmail.com

state: Liaoning Province

address: lunshun nanlu

department: Department of pharmacy

institute: Dalian Medical University, Dalian, China

description:
Wistar rat,  Sham, 16 week
Young_1

data_processing:
The original Image data files were converted to original Sequenced Reads by Base Calling (v1.4.1).
For the original data, the software FastQC [1](Version: 0.11.5) was used for quality control processing
For data filtering, cutAdapter [2] (Version 1.11) is used, and parameters are: -A R1_adpter -A R2_adpter -m 20 -- max-N 0.05-q 20.
For the evaluation of Clean Data, the software FastQC [1](Version: 0.11.5) was used for quality control processing.
Clean reads data were compared to the reference genome using HISat2 software [3](version: 2.0.1-beta)
The stringtie software [4](Version: 2.0.4) was used to reconstruct the transcript by comparing the information of all samples.
FeatureCounts [5] software (version: V1.6.0) was used to count the number of reads that landed on genes according to the annotated file of the genome
Assembly: rn4
Supplementary files format and content: xls format file include logFC, logCPM, P values, and FDR values for each Sample;
Supplementary files format and content: xls format file include FPKM values for each Sample;

organism: Rattus norvegicus

source_name: Femur tissue

growth_protocol: The rats were housed in pathogen-free facilities under a 12/12 h light/dark cycle and the temperature during the experiment was maintained at around 23 ± 2°C. The rats were fed with the standard laboratory diet and drink deionized water freely.

extract_protocol:
RNA was harvested using TRIzol reagent (Sigma, St. Louis, USA). 2.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Female rats were undergoing either bilateral oophorectomy or bilateral sham operation after pentobarbital sodium anesthesia. One week later, the surviving rats were divided into the Oophorectomy group (OVX) and Control group (SHAM).

value: Femur tissue

value: Wistar

value: WT

value: Sham operation


title: neocortex_Bcl11a_mutant_rep3

description: knockout tissue


title: D2HG LPS rep1

value: Bone marrow-derived macrophages


title: PMA-treated THP-1, shDNMT1

type: genomic

city: Seoul

first: Junyoung

last: Park

address: 84, Heukseok-ro

department: Department of Life Science

country: South Korea

institute: Chung-Ang University

description:
THP-1_shDNMT1_PMA
modified THP-1 cell line

hyb_protocol: The whole-genome amplification process requires 250ng of input bisulfite-converted gDNA, MA1 and creates a sufficient quantity of DNA (1000X amplification) to be used on a single BeadChip in the infinium methylation assay (Illumina RPM and MSM). After amplification, the product is fragmented using a proprietary reagent (FMS), precipitated with 2-propanol (plus precipitating reagent; PM1), and resuspended in formamide-containing hybridization buffer (RA1). The DNA samples were denatured at 95 °C for 20 min, then placed in a humidified container for a minimum of 16 h at 48 °C allowing CpG loci to hybridize to the 50mer capture probes.

scan_protocol: Standard Illumina procedures using Illumina iScan scanner

data_processing: Each methylation data point is represented by fluorescent signals from the M (methylated) and U (unmethylated) alleles. Background intensity computed from a set of negative controls was subtracted from each analytical data point. The ratio of fluorescent signals was then computed from the two alleles ß = (max(M, 0))/(|U| + |M| + 100). The ß-value reflects the methylation level of each CpG site. A ß-value of 0~1 was reported signifying percent methylation, from 0% to 100%, respectively, for each CpG site.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: THP-1 cell, DNMT1 knockdown, PMA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA (gDNA) was extracted from each sample using Promega Wizard® Genomic DNA Purification Kit. Quality of extracted gDNA was checked with NanoDrop® ND-2000 UV-Vis Spectrophotometer. Then samples were electrophoresed on agarose gels. Samples with intact gDNA showing no smearing on agarose gel electrophoresis were selected for experiment. Intact gDNA was diluted to 50 ng/㎕ concentration based on Quant-iT Picogreen (Invitrogen) quantitation. Concentrations were adjusted based on these results. All prepared samples were bisulfite-converted according to the Zymo EZ DNA methylation kit protocols.

value: Acute myeloid leukemia

tag: cell line

value: DNMT1 knockdown

value: PMA


title: PMA-treated THP-1, shUHRF1

description:
THP-1_shUHRF1_PMA
modified THP-1 cell line

source_name: THP-1 cell, UHRF1 knockdown, PMA

value: UHRF1 knockdown


title: treated_Run1_BCABCO_Rep3_TRAMETINIB_ReadsPerGene

value: bcr:abl fusion gene

value: Cells were treated with 14 different drugs in droplets, each treatment has a corresponding DMSO control


title: neocortex_Bcl11a_control_rep3

description: control tissue

value: neocortex


title: Femur tissues from a ovariectomy-induced osteoporosis rat

description:
Wistar rat, Ovariectomy, 16 week
Old_2

value: Bilateral ovariectomy


title: Blastocyst-control-RNA-5

value: Blastocyst

value: control


title: neocortex_Bcl11a_mutant_rep2

description: knockout tissue

value: Postnatal day 2

value: Bcl11a mutant


title: treated_Run1_BCABCO_Rep3_Sangivamycin_ReadsPerGene

value: Myelogenous leukemia cells


title: Blastocyst-control-RNA-6


title: treated_Run1_BCABCO_Rep3_Pomalidomide_ReadsPerGene


title: AS2

city: New York

first: Caghan

last: Kizil

state: NY

country: USA

institute: Columbia University Irving Medical Center

description: 10X Chromium, single-cell sequencing

data_processing:
The fastq files were aligned to zebrafish transcript (Ensembl Version 95)by using STAR. The BAM files were as input for Cell Ranger (10X genmoics) to generate processed data files that include gene names (row names) and cell names (column names) and counts. Further analysis done by using Seurat package in R.
Genome_build: danRer11
Supplementary_files_format_and_content: tab-delimited file, with gene names in rows and cell names and counts in columns.

organism: Danio rerio

source_name: telencephalon

growth_protocol: Fish were kept at 28 °C water system with 14/10 hours light/dark cycles

extract_protocol: Cells from telencephalon were dissociated and cell tracking dye positve cells were sorted.  The library preparation was performed by 10X Genomics as per manufactur protocol

treatment_protocol: Zebfrafish brains were injected with neutral cell tracking dye and 5-6 min post-injection fish were sacrificed.

tag: tag

value: wilt type


title: neocortex_Bcl11a_control_rep2

description: control tissue

value: Bcl11a control


title: treated_Run1_BCABCO_Rep3_NMS1286937_ReadsPerGene


title: DMSO-treated THP-1, shDNMT3B

description:
THP-1_shDNMT3B_DMSO
modified THP-1 cell line

source_name: THP-1 cell, DNMT3B knockdown, DMSO

value: DNMT3B knockdown

value: DMSO


title: Blastocyst-control-RNA-4


title: OBPri2

first: Chen

address: Meibergdreef 9

institute: Amsterdam UMC

data_processing:
For Read alignment and gene counts STAR 2.6.1d was used using the ENSEMBL hg38 reference build from Illumina iGenomes.
The quality control is done using FastQC 0.11.4 and MultiQC v1.8 for summarization of the quality metrics.
For the differential gene expression and normalization the DESeq2 R package was used in combination with pheatmap for the heatmaps
Significant differences between samples are expressed with False Discovery Rate (FDR) value less than 0.05.
Further analysis with significantly different expression genes was performed with Metascape gene ontology (https://metascape.org/gp/index.html#/main/step1) to investigate biological gene functions and interactions.
Assembly: HG38
Supplementary files format and content: read count per gene in plain text format

source_name: bone

extract_protocol:
RNA was isolated with Quick-RNA MiniPrep (Zymo Research, Irvine, USA)
RNA libraries were prepared according to the manufacturer’s instructions for the Illumina TruSeq Stranded mRNA library prep kit (Illumina, Inc., California, USA).

value: bone

value: primary

value: osteoblasts

value: healthy


title: OBC3D21

source_name: skin

value: skin

value: differentiated fibroblasts

value: osteogenic transdifferentiation


title: treated_Run1_BCABCO_Rep3_Gemcitabine_ReadsPerGene

value: bcr:abl fusion gene

value: Cells were treated with 14 different drugs in droplets, each treatment has a corresponding DMSO control


title: Morula-H2AZ-KD-RNA-6

value: Morula

value: H2A.Z KD


title: OBPri1


title: 052821_94 [MW256_S94]

city: Tampa

first: Prahathees

last: Eswara

state: Florida

address: 4202 E Fowler Ave ISA2015

institute: University of South Florida

data_processing:
Quality control and adapter trimming was performed with bcl2fastq
Read mapping was performed with HISAT2
Read quantification was performed using Subread’s featureCounts functionality
Mapping statistics can be found in the ‘alignment.tsv’ file.  Raw, quantified counts are available in the “hisat2_counts.tsv” file
Read counts loaded into R and were normalized using edgeR’s Trimmed Mean of M values (TMM) algorithm. Subsequent values were then converted to counts per million (cpm).
Supplementary files format and content: Differential expression analysis was performed using edgeR’s exact test for differences between two groups of negative-binomial counts with an estimated dispersion value of .1.  The file “All Quantified Genes.tsv” contains the results of the exact test for all genes in addition to the normalized counts per million.  The file “Differentially Expressed Genes.tsv” is a subset of the aforementioned file with |logFC| > 1 and p < .05.

organism: Bacillus subtilis PY79

growth_protocol: Overnight cultures of B. subtilis strains were grown at 22 °C in lysogeny broth (LB) and diluted 1:10 in fresh LB before being grown at 37 °C to mid-log phase (OD600nm= 0.5-0.8). Cultures were then standardised to OD600nm= 0.1 in fresh LB. Where induction of genes under IPTG required, a final concentration of 1 mM IPTG was added when cultures were standardised, and the cultures were then grown for 2 h at 37 °C. For RNA-seq preparation, cultures were treated with RNAprotect Bacteria (Qiagen) before RNA was extracted utilising the RNeasy Mini Kit (Qiagen).

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Samples were sent to Microbial Genome Sequencing Center (MiGS) for processing

treatment_protocol: The inducer, IPTG, was added at the final concentration of 1 mM to overexpress mraZ/mraZ-R15A (MW189/MW256).

value: mraZ R15A overexpression (MW256)


title: treated_Run1_BCABCO_Rep3_Imatininb_ReadsPerGene

value: Myelogenous leukemia cells


title: Blastocyst-control-RNA-1

value: Blastocyst

value: control


title: Morula-H2AZ-KD-RNA-2


title: OBC1D21


title: 052821_93 [MW192_S93]

value: del-mraZ (MW192)


title: treated_Run1_BCABCO_Rep3_EPIRUBICIN_ReadsPerGene


title: neocortex_Bc11a_control_rep1

description: control tissue

value: neocortex

value: Postnatal day 2

value: Bcl11a control


title: untreated_Run1_BCABCO_Rep1_Dovitinib_ReadsPerGene


title: treated_Run1_BCABCO_Rep3_Dovitinib_ReadsPerGene


title: DMSO-treated THP-1, shDNMT1

description:
THP-1_shDNMT1_DMSO
modified THP-1 cell line

source_name: THP-1 cell, DNMT1 knockdown, DMSO

value: Acute myeloid leukemia

value: DNMT1 knockdown

value: DMSO


title: PMA-treated THP-1, shDNMT3B

description:
THP-1_shDNMT3B_PMA
modified THP-1 cell line

source_name: THP-1 cell, DNMT3B knockdown, PMA

value: DNMT3B knockdown

value: PMA


title: DMSO-treated THP-1, shNC

description:
THP-1_shNC_DMSO
modified THP-1 cell line

source_name: THP-1 cell, control, DMSO


title: Morula-control-RNA-8


title: FBC1D21

value: skin

value: primary

value: fibroblasts

value: healthy


title: neocortex_Bcl11a_mutant_rep1

description: knockout tissue

value: Bcl11a mutant


title: Morula-control-RNA-7

value: Morula


title: treated_Run1_BCABCO_Rep3_DMSO_ReadsPerGene

value: Myelogenous leukemia cells

value: bcr:abl fusion gene

value: Cells were treated with 14 different drugs in droplets, each treatment has a corresponding DMSO control


title: treated_Run1_BCABCO_Rep3_Baricitinib_ReadsPerGene


title: 052821_92 [MW189_S92]

value: mraZ overexpression (MW189)


title: Morula-control-RNA-2

value: control


title: treated_Run1_BCABCO_Rep3_AT9283_ReadsPerGene


title: DMSO-treated THP-1, shUHRF1

description:
THP-1_shUHRF1_DMSO
modified THP-1 cell line

source_name: THP-1 cell, UHRF1 knockdown, DMSO

value: UHRF1 knockdown


title: 2-cell-H2AZ-KD-RNA-4

value: H2A.Z KD


title: 2-cell-H2AZ-KD-RNA-2


title: D24 melanoma cells treated with Vemurafenib

city: Bundoora

first: Dao

last: Nguyen

state: Victoria

address: 289 McKimmies Rd

department: School of Science and Health and Biomedical Science

country: Australia

institute: Royal Melbourne Institute of Technology

description:
Test
SAMPLE 13

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://rotor-gene-q.software.informer.com/2.3/
For the normalization it uses housekeeping gene: GAPDH.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
Fold Change worksheet reports test/control (i.e., treated sample/untreated sample) ratios.

label: SYBR Green

source_name: D24 [Human melanoma] (RRID:CVCL_W871)

label_protocol: The qPCR was performed on a Qiagen Rotor-Gene Q (Qiagen, Germany) and analysed with inbuilt software (version 2.3.1.49). The thermal cycling conditions were as follows: initial activation at 95°C for 2 min, 45 cycles of 95°C 5 s, 60°C for 10 s, 72°C for 15 s, and melting curve from 65°C to 95°C

extract_protocol: Total RNA was extracted using TRIzol™ Reagent (Life Technologies, Melbourne, Australia) as per the manufacturer’s protocol

value: Cancer cell line

tag: activation agent

value: Vemurafenib

tag: time

value: 3 days


title: Morula-H2AZ-KD-RNA-1


title: 2-cell-H2AZ-KD-RNA-1


title: 2-cell-control-RNA-5


title: Untreated HaCaTcells

description:
Control
SAMPLE 9

source_name: HaCaT (RRID:CVCL_0038)

value: Spontaneously immortalized cell line

value: Control


title: HaCaT cells treated with water extract

description:
Test
SAMPLE 10

value: Water extract of M. cochinchinensis seeds


title: PMA-treated THP-1, shNC

description:
THP-1_shNC_PMA
modified THP-1 cell line

source_name: THP-1 cell, control, PMA

value: Acute myeloid leukemia

value: PMA


title: FBC3D21

value: skin

value: primary

value: fibroblasts

value: healthy


title: 2-cell-control-RNA-2


title: 052821_91  [PY79_S91]

value: WT (PY79)


title: treated_Run1_BCABCO_Rep2_Wortmannin_ReadsPerGene

source_name: K562 cells

value: Myelogenous leukemia cells

value: bcr:abl fusion gene

value: Cells were treated with 14 different drugs in droplets, each treatment has a corresponding DMSO control


title: Morula-Srcap-KD-2

library_source: genomic

data_processing:
All reads were mapped to the mouse reference genome mm10 or pig reference genome susScr11 using Bowtie2 (version 2.4.1).
The Samtools (version ) was used to remove low quality reads (MAPQ < 30) and Picard (version 1.9) was used to remove PCR duplicates.
The MACS2 (version 2.2.7.1) software calls the ChIP-seq peak with the parameters “--nolambda –nomodel --broad”
RPKM-normalized bigwig files were generated by bamCoverage subcommand in deepTools (version 3.5.0) and the tracks were visualized with Integrative Genomics Viewer (IGV, version 2.6.2).
Genome_build: mm10 (GRCm38) or susScr11 (Sscrofa11.1)
Supplementary_files_format_and_content: bigWig files

source_name: embryo

extract_protocol:
ULI-NChIP-seq was performed as previously described with some modifications. Embryos and cells were then added into 20 μL Nuclear Isolation buffer and 30 μL 10 U/ mL MNase Master mix to digest chromatin for 7 min at 25℃, and added 5.5 μL 100 mM EDTA and 5.5 μL 1% Triton X-100 plus 1% deoxycholate solution to finish digestion. Next, samples were incubated with antibody-bead complexes in 130 μL Complete Immunoprecipitation buffer overnight at 4°C. After two washes with 200 μL Low Salt Wash buffer and 200 μL High Salt Wash buffer, chromatin was dissolved in 100 μL ChIP Elution buffer for 2 h at 65℃.
DNA was then extracted by 100 μL phenol-chloroform-isoamyl alcohol (25:24:1), and used for library generation by using KAPA HyperPrep Kit (KK8504, Roche) following the manufacturer’s instructions. Paired-end 150-bp sequencing was performed on Illumina HiSeq X-Ten.

value: Morula

value: Srcap KD

tag: chip antibody


title: Morula-control-RNA-1

value: control


title: treated_Run1_BCABCO_Rep2_Sangivamycin_ReadsPerGene

tag: cell type


title: treated_Run1_BCABCO_Rep2_Gemcitabine_ReadsPerGene

tag: genotype


title: 2-cell-control-RNA-1

tag: treatment


title: treated_Run1_BCABCO_Rep2_Pomalidomide_ReadsPerGene


title: treated_Run1_BCABCO_Rep2_TRAMETINIB_ReadsPerGene


title: Morula-Anp32e-KD-2

value: Anp32e KD


title: Morula-Srcap-KD-1


title: treated_Run1_BCABCO_Rep2_SB747651_ReadsPerGene


title: treated_Run1_BCABCO_Rep2_EPIRUBICIN_ReadsPerGene


title: Morula-Anp32e-KD-1


title: treated_Run1_BCABCO_Rep2_YM155_ReadsPerGene


title: treated_Run1_BCABCO_Rep2_Imatininb_ReadsPerGene


title: treated_Run1_BCABCO_Rep2_Triciribine_ReadsPerGene


title: MM418-C1 melanoma cells treated with 50% EtOH extract

description:
Test
SAMPLE 7

source_name: MM418-C1 (RRID:CVCL_C843)

value: Cancer cell line

value: 50% EtOH extract of M. cochinchinensis seeds

value: 3 days


title: D24 melanoma cells treated with water extract

description:
Test
SAMPLE 2

value: Water extract of M. cochinchinensis seeds


title: HaCaT cells treated with 100% EtOH extract

description:
Test
SAMPLE 12

value: Spontaneously immortalized cell line

value: 100% EtOH extract of M. cochinchinensis seeds


title: MM418-C1 melanoma cells treated with water extract

description:
Test
SAMPLE 6


title: Untreated MM418-C1 melanoma cells

description:
Control
SAMPLE 5


title: treated_Run1_BCABCO_Rep2_NMS1286937_ReadsPerGene


title: MM418-C1 melanoma cells treated with 100% EtOH extract

description:
Test
SAMPLE 8


title: t20_control

city: Leuven

first: Rob

last: Lavigne

address: Kasteelpark Arenberg 21

department: Biosystems

country: Belgium

institute: KU Leuven

data_processing:
Library strategy: ONT-cappable-seq
Live basecalling and demultiplexing by PromethION 24 device
Identification and orientation of full-length reads using Pychopper (v2.5.0)
Read trimming using Cutadapt (v2.7)
Mapping of reads against reference genomes of P. aeruginosa US449 and LUZ7 using minimap2
Peak calling using termseq-peaks script
Genome_build: CP091880; NC_013691.1
Supplementary_files_format_and_content: Narrowpeak files generated by peak calling

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa

growth_protocol: P. aeruginosa cells were grown to exponential phase in LB medium and infected with phage LUZ7 at an MOI of 50 to ensure synchronous infection. Culture samples were collected at 0 minutes, and 5, 10 and 20 minutes post-infection.

extract_protocol:
Total RNA was extracted using hot-phenol extraction, followed by DNAse treatment. The enriched samples were subjected to an enrichment procedure based on streptavidin beads to enrich for primary transcripts. For the control samples the enrichment steps were omitted.
Total RNA was enriched for primary transcripts using an adapted version of the (SMRT)-cappable-seq enrichment protocol. In parallel, control samples were not enriched but subjected to similar environmental conditions. The RNA was reverse transcribed, PCR amplified and barcoded according to Oxford Nanopore Technology cDNA-PCR protocol (SQK-PCS109 combined with SQK-PBK004). The amplified cDNA samples were pooled together in a final library and loaded on a promethION flowcell.

tag: infection

value: Pseudomonas virus LUZ7

value: 20 minutes post-infection

value: no enrichment


title: 2-cell-control-RNA-4


title: D24 melanoma cells treated with 50% EtOH extract

description:
Test
SAMPLE 3


title: treated_Run1_BCABCO_Rep2_Dovitinib_ReadsPerGene


title: MM418-C1 melanoma cells treated with Vemurafenib

description:
Test
SAMPLE 14

value: Vemurafenib


title: D24 melanoma cells treated with 100% EtOH extract

description:
Test
SAMPLE 4


title: Untreated D24 melanoma cells

description:
Control
SAMPLE 1

value: Control


title: treated_Run1_BCABCO_Rep2_Baricitinib_ReadsPerGene

value: Myelogenous leukemia cells

value: bcr:abl fusion gene


title: treated_Run1_BCABCO_Rep2_AT9283_ReadsPerGene

value: Cells were treated with 14 different drugs in droplets, each treatment has a corresponding DMSO control


title: HaCaT cells treated with 50% EtOH extract

description:
Test
SAMPLE 11


title: t20_enriched

value: enriched for primary RNAs


title: Morula-H2AZ-KD-Pol2-1

value: Morula

value: H2A.Z KD


title: t10_control

value: 10 minutes post-infection


title: Morula-H2AZ-KD-H3K27me3-2


title: t10_enriched


title: Morula-H2AZ-KD-Pol2-2


title: Morula-H2AZ-KD-H3K27me3-1


title: Morula-H2AZ-KD-input

description:
Input
H2AZ_KD_Morula_input.bw


title: t5_control

value: 5 minutes post-infection


title: t5_enriched


title: treated_Run1_BCABCO_Rep2_DMSO_ReadsPerGene


title: Morula-H2AZ-KD-H3K4me3-3


title: treated_Run1_BCABCO_Rep1_Wortmannin_ReadsPerGene


title: Morula-H2AZ-KD-H3K4me3-4


title: treated_Run1_BCABCO_Rep1_TRAMETINIB_ReadsPerGene


title: Morula-H2AZ-KD-H2AZ-2


title: treated_Run1_BCABCO_Rep1_Triciribine_ReadsPerGene


title: Morula-H2AZ-KD-H2AZ-1


title: Morula-control-input

description:
Input
control_Morula_input.bw

value: control


title: T, replicate 3, scRNAseq

city: Paris

first: Paul

last: Gueguen

address: 26 rue D'Ulm

department: Inserm U932

country: France

institute: Institut Curie

description:
3' RNA
10x Genomics

library_source: transcriptomic single cell

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 genes, barcodes and matrix files

source_name: breast TNBC

extract_protocol:
Samples from tumor and juxta tumor were gently dissociated and enzymatically digested by an incubation of 30-40-minutes, at 37°C in agitation, in CO2-indipendent medium, supplemented by Collagenase I (2mg/mL), (Sigma) Hyaluronidase (2mg/mL) (Sigma), and DNase (25ug/mL) (Roche). Afterwards, single cell suspensions were obtained by disrupting the fragments with a syringe plunger over a 40uM cell strainer, washing with PBS (Gibco) supplemented by 2mM EDTA (Gibco) and 1% of human serum (BioWest). Cell suspension was obtained after 10’ of centrifugation. After isolation of total tissue-infiltrating cells, cells were counted in CO2-indipendent medium plus 5% of FBS, washed and resuspeded in PBS. HLA-DR+CD11c+ myeloid cells from tumor and juxta tumor-infiltrating cells were FACS sorted (ARIA-BD Bioscience) and collected in  in PBS supplemented with 0.04% w/v BSA. DAPI solution (BD- Bioscience) used for dead cells exclusion. CD11c, HALDR, CD45, CD3-CD56-CD19 were included for the staining. Single-cell suspension was loaded into a Chromium Single Cell Chip (10X Genomics) according to the manufacturer’s instructions.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, sorted-myeloid cells 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 a 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.

value: myeloid cells

tag: disease state

value: tumor

tag: cell marker

value: HLADR+CD11C+ double positive cells

value: breast TNBC


title: T, replicate 4, scRNAseq

description:
3' RNA
10x Genomics


title: treated_Run1_BCABCO_Rep1_Pomalidomide_ReadsPerGene


title: treated_Run1_BCABCO_Rep1_YM155_ReadsPerGene


title: T, replicate 2, scRNAseq

description:
3' RNA
10x Genomics


title: treated_Run1_BCABCO_Rep1_NMS1286937_ReadsPerGene


title: Morula-control-Pol2-2


title: T, replicate 1, scRNAseq

description:
3' RNA
10x Genomics


title: treated_Run1_BCABCO_Rep1_Imatininb_ReadsPerGene


title: Morula-control-Pol2-1


title: JT, replicate 2, scRNAseq

description:
3' RNA
10x Genomics

source_name: breast

value: Juxta tumor

value: breast


title: treated_Run1_BCABCO_Rep1_EPIRUBICIN_ReadsPerGene


title: treated_Run1_BCABCO_Rep1_Gemcitabine_ReadsPerGene


title: t0_control

value: Pre-infection

value: no enrichment


title: JT, replicate 3, scRNAseq

description:
3' RNA
10x Genomics


title: JT, replicate 1, scRNAseq

description:
3' RNA
10x Genomics


title: treated_Run1_BCABCO_Rep1_SB747651_ReadsPerGene

value: Myelogenous leukemia cells


title: Morula-control-H3K4me3-2


title: t0_enriched


title: Morula-control-H3K27me3-2


title: treated_Run1_BCABCO_Rep1_Dovitinib_ReadsPerGene

value: bcr:abl fusion gene


title: TNBC3_coculture_FAP_CD29

data_processing:
Aligned files were processed using Curie pipeline v3.1.8 https://github.com/bioinfo-pf-curie/RNA-seq. The pipeline is built using Nextflow and processes RNA-seq from raw sequencing reads to count table for downstream analysis
Briefly, the overall quality of raw sequencing data is first checked using FastQC. Reads were then aligned on a ribosomal RNAs database and on the genome reference using STAR 2.6.1a to the hg38 human reference genome.
Additional controls on aligned data are performed to infer strandness, complexity, gene-based saturation, read distribution or duplication level. The aligned data are then used to generate a final count matrix with all genes and all samples.
Assembly: hg38
Supplementary files format and content: Comma-separated text files including TPM values for each sample, the sample plan and the ENSEMBL gene convertion table.

extract_protocol: A step of DNase I digestion (RNase-Free Dnase Set-Qiagen) was added. Total RNA was analyzed using Agilent RNA 6000 Pico Kit on the Bioanalyzer 2100 Bioanalyzer system. RNA quality was checked by RNA Integrity Number (RIN). RNA sequencing libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Clontech/Takara)

treatment_protocol: After 3 hours of culture FACS-sorted monocytes were isolated by FACS-ARIA III (BD) cell sorter directly collected on lysing TCL buffer (Qiagen) containing 1%-mercatpoethanol before storage at -80°. RNA extraction was performed from ex vivo circulating isolated CD14+ and FAP+ CD29+ co-cultured monocytes by Single Cell RNA purification Kit (Norgen#, 51800) according to the manufacturer’s protocol.

value: monocyte

value: TNBC

value: FAP / CD31


title: C2 CSM

city: HONGO, BUNKYO-KU

first: Taku

last: Saito

state: TOKYO

department: Orthopaedic Surgery, Faculty of Medicine

country: Japan

institute: The University of Tokyo

data_processing:
Illumina HiSeq 4000 System
The raw sequence data were filtered using Trimmomatic (ver. 0.39) to remove adapter sequences, low-quality reads, N-rich sequences, and reads less than 50 bp in length.
The filtered data were aligned against the human reference genome (GRCh38.p13) using STAR (ver. 2.7.3a).
Gene expression counts and transcripts per million value were calculated using RSEM (ver. 1.3.3).
Genome_build: GRCh38.p13

source_name: yellow ligament

extract_protocol:
Total RNA was extracted using the Direct-zol RNA Kit (#R2062, Zymo Research, CA, USA) in accordance with the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: CSM


title: Morula-control-H3K27me3-1

value: Morula


title: treated_Run1_BCABCO_Rep1_Sangivamycin_ReadsPerGene

value: Cells were treated with 14 different drugs in droplets, each treatment has a corresponding DMSO control


title: treated_Run1_BCABCO_Rep1_DMSO_ReadsPerGene


title: TNBC2_coculture_FAP_CD29

value: FAP / CD30


title: Morula-control-H3K4me3-1

value: control


title: Morula-control-H2AZ-2


title: C1 CSM


title: treated_Run1_BCABCO_Rep1_Baricitinib_ReadsPerGene


title: TNBC1_coculture_FAP_CD29

value: FAP / CD29


title: Morula-control-H2AZ-1


title: TNBC3

value: Untreated


title: ESC

description:
Input
H2AZ_ESC.bw

value: ESC

value: WT


title: 22s000162_Trametinib_DMSO_countsPerGene

description:
5 replicates for each sample with different cell numbers
ERCC_spike_in_matrix

value: untreated or Trametinib treated cells with ERCC spike-ins


title: TNBC2


title: ESC-input

description: ESC-input.bw


title: 2-cell-PA-input

description:
Input
C57_2-cell_PA_input.bw

value: PA


title: 22s000161_Trametinib_DMSO_countsPerGene


title: TNBC1


title: HD3_coculture_FAP_CD29

value: healthy


title: HD2_coculture_FAP_CD29


title: 2-cell-PA-1


title: 2-cell-PA-2


title: treated_Run1_BCABCO_Rep1_AT9283_ReadsPerGene

value: Myelogenous leukemia cells


title: ChIP_AFF1_UD_2

city: Evanston

first: Xiaomin

last: Bao

state: IL

address: 633 Clark Street

department: Molecular Biosciences

institute: Northwestern University

data_processing:
[RNA-seq]  Reads were aligned using HiSat2. Number of Raw reads at each gene was calculated using htseq-count, and DESeq2 was used for differential expression analysis in R
[ChIP-seq]  Reads were aligned using Bowtie2. Peaks were called with MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq data is in format of table containing counts at each gene and DESeq output information.  ChIP-seq data are peaks files.

source_name: primary human neonatal keratinocytes

growth_protocol: neonatal keratinocyte were isolated from discarded foreskin, cultured in KSF and 154 keratinocyte medium

extract_protocol:
For  RNA-seq, RNA was extracted using Quick-RNA™ MiniPrep (Zymo Research)
For RNA-seq, NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina was used for library construction. For ChIP-seq, NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) was used for library construction.

treatment_protocol: To induce differentiaiton, keratinocytes were seeded in confluence and cultured with the addition of 1.2mM of calcium to growth medium. 10 uM of siRNA for each target were nucleofected (Lonza to keratinocytes)

value: undifferentiated keratinocytes

value: Rabbit anti-AFF1, source:Dr. Ali Shilatifard Lab Northwestern University, Lin et. al 2011


title: ChIP_AFF1_UD


title: 22s000160_Trametinib_DMSO_countsPerGene

value: bcr:abl fusion gene


title: RNA_TPA_Ctrl2

value: DMSO


title: 22s000162_DMSO_DMSO_countsPerGene


title: HD1_coculture_FAP_CD29

value: monocyte


title: 22s000160_DMSO_DMSO_countsPerGene


title: 22s000161_DMSO_DMSO_countsPerGene


title: O2 OPLL

value: OPLL


title: O1 OPLL


title: 2-cell-IVF-input

description:
Input
C57_2-cell_IVF_input.bw

value: C57BL/6 x DBA2

value: IVF


title: RNA_TPA_1hrTPA2

value: 1-hour TPA


title: HD3


title: 2-cell-IVF-2


title: RNA_TPA_Ctrl1


title: HD2


title: RNA_TPA_1hrTPA1


title: 22s000159_Trametinib_DMSO_countsPerGene


title: TE-input

description:
Input
TE-input.bw

value: TE (Blastocyst)

value: IVO


title: RNA_HEXIM1KD_sh2

value: HEXIM1 shRNA knockdown


title: 2-cell-IVF-1


title: 22s000158_DMSO_DMSO_countsPerGene


title: ChIP_HEXIM1_UD

value: Rabbit anti-HEXIM1, Abcam, Cat#ab25388


title: 22s000159_DMSO_DMSO_countsPerGene

value: untreated or Trametinib treated cells with ERCC spike-ins


title: TE-1


title: RNA_HEXIM1KD_Ctrl2

value: nontargeting control shRNA


title: 22s000158_Trametinib_DMSO_countsPerGene


title: ICM-input

description:
Input
ICM-input.bw

value: ICM (Blastocyst)


title: RNA_AFF4KD_sh2

value: AFF4 shRNA knockdown


title: 22s000157_Trametinib_DMSO_countsPerGene

value: Myelogenous leukemia cells


title: M7 [scATAC-seq]

city: Philadelphia

first: Pablo

last: Camara

state: PA

address: 3700 Hamilton Walk

department: Genetics

institute: University of Pennsylvania

description: snATAC_PF_EPN_Seurat.rds.gz, snATAC_PF_EPN_peak_frags.mtx.gz, snATAC_PF_EPN_cell_barcodes.tsv.gz, snATAC_PF_EPN_features.tsv.gz, snATAC_PF_EPN_meta_data.tsv.gz

library_source: genomic single cell

data_processing:
We used Cell Ranger ATAC (version 2.0) to map the FASTQ files to the human reference genome (GRCh38) and de-multiplex by their cell barcode.
We used Signac to call and quantify peaks. We selected high-quality cells based on the number (>1,500 and <35,000) and percentage (>20%) of fragments in peaks, the ratio of mono-nucleosomal to nucleosome-free fragments (<3), and the transcription start site (TSS) enrichment score (>2). In addition, we filtered out cells based on the percentage of mitochondrial fragments (>10%) and the percentage of fragments overlapping targeted sites (<20% or <25%, depending on the sample). We removed peaks overlapping the ENCODE blacklisted regions.
To integrate the single-nucleus ATAC-seq. data into a consolidated representation, we created a union peak set by merging intersecting peaks across samples using the reduce function from the GenomicRanges package (version 1.38.0). We removed peaks whose width was more than 3 standard deviations greater than the mean peak length and concatenated the union peak sets from each sample. For normalization and dimensionality reduction, we used latent semantic indexing (LSI). To do this, we used peaks that were open in at least 90% of the cells for term frequency-inverse document frequency (TF-IDF) normalization. The top 30 dimensions were integrated with Harmony (with parameters lambda = 0.5 and theta = 1). After removing the first dimension, the top 30 harmony dimensions were clustered using Louvain community detection and visualized with UMAP.
Assembly: GRCh38

source_name: Ependymoma biopsy, Metastasis, PFA-1

extract_protocol:
Nuclei were isolated from flash-frozen tumors following the 10x Genomics demonstrated protocol for Mouse Brain Tissue, with the following modifications: the first incubation in the lysis buffer was decreased to 45 seconds, and the second incubation, after pipet mixing, was 90 seconds. A 40 µm nylon cell strainer and a 30 µm MACS SmartStrainer (Miltenyi Biotec, cat. #130-098-458) were used in place of the suggested 70 µm and 40 µm tip strainers.
Single-nulcei ATAC-seq cDNA libraries were prepared using the Chromium Single Cell Platform (10x Genomics) by the Center for Applied Genomics of the Children’s Hospital of Philadelphia and sequenced on an Illumina NovaSeq 6000 sequencer using two 100-cycle SP flow cells.

value: Ependymoma biopsy, Metastasis, PFA-1


title: ICM-3


title: M8 [scATAC-seq]

source_name: Ependymoma biopsy, Metastasis, PFA

value: Ependymoma biopsy, Metastasis, PFA


title: TE-3


title: 22s000156_Trametinib_DMSO_countsPerGene

data_processing:
CASANA software was used for basecalling
Read1 (Barcode) was used to demultiplex read 2 according to treatment conditions using Je Debarcode version 2.0.beta allowing a maximum of 6 mismatches per barcode sequence,
Sequences were aligned to Homo_sapiens.GRCh38.84. using STAR version 2.4.2a
Created matrix with all alignments (treatment conditions) and remove genes with 0 read counts in all samples
Supplementary files format and content: Matrix containing read counts for all samples and replicate

extract_protocol:
Cells were lysed and the released mRNA was reversed transcribed using barcoded poly-dT primers.
Biotin on the poly-dT primer was used to purify cDNA. Priming sites introduced over the poly-dT primers and the template switching oligonucleotide were used to amplify the cDNA. Subsequently, cDNA was fragmented using a hyperactive Tn5 transposase.

value: bcr:abl fusion gene


title: RNA_AFF4KD_sh1

value: undifferentiated keratinocytes


title: I4 [scATAC-seq]

source_name: Ependymoma biopsy, Initial, PFB

value: Ependymoma biopsy, Initial, PFB


title: ICM-1


title: I5 [scATAC-seq]

source_name: Ependymoma biopsy, Initial, PFA-1

value: Ependymoma biopsy, Initial, PFA-1


title: RNA_HEXIM1KD_Ctrl1


title: I3 [scATAC-seq]

source_name: Ependymoma biopsy, Initial, PFA-2

value: Ependymoma biopsy, Initial, PFA-2


title: 22s000157_DMSO_DMSO_countsPerGene


title: HD1

value: monocyte

value: healthy

value: Untreated


title: I2 [scATAC-seq]

source_name: Ependymoma biopsy, Initial, PFA

value: Ependymoma biopsy, Initial, PFA


title: RNA_HEXIM1KD_sh1

value: HEXIM1 shRNA knockdown


title: RNA_AFF4KD_Ctrl1


title: Morula-07-594

value: Morula

value: IVO


title: Morula-ab4174


title: RNA_AFF4KD_Ctrl2

value: nontargeting control shRNA


title: T-4

city: shanghai

first: Song

address: No.415 Fengyang Road

institute: shanghai chagnzheng hospital

data_processing:
(mRNA and lncRNA)
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
(circRNA)
Circular RNA was predicted based on the sequencing data with ACFS circRNA prediction pipeline. Unmapped Reads was collected utilizing BWA-mem (bwa mem -t 1 -k 16 -T 20) for circRNA identification: head-to-tail junction was identified and highest splicing strength score was calculated by MaxEntScan33 with a filtering criterion greater than or equal to 10. Base on the re-alignment of the unmapped reads on the circular RNA candidates, Reads that mapped to the circular RNA back splicing junction (with an overhang of at least 6 nt) were counted for each circRNA.
count counting
Assembly: GRCh38
Supplementary files format and content: TXT file contain counts for each sample

source_name: bone

growth_protocol: Experimental tissue samples came from surgically excised tumour tissue from patients with GCTB, while the control bone tissue samples were from surgically respected para tumour tissue from the same individuals. GCTB and adjacent normal tissues were confirmed by histopathology.

extract_protocol:
After tissue collection, all specimens were preserved with RNA Fixer sample preservation solution and stored at -80℃
The amount and quality of total RNA were evaluated using Agilent 2200 instrument after total RNA were extracted using the Magen kit. According to the manufacturer's operating guide, the rRNA were extracted from the total RNA using the Vazyme Ribosome Removal Kit (Vazyme Biotech Co., Ltd). The Preparation Kit of The TruSeq Strand Total RNA Library was used to create RNA libraries utilising rRNA-depleted RNA (Illumina)

value: bone

tag: age

tag: Sex

value: female

tag: tumor stage

value: stage I


title: T-5

tag: tissue

value: male

value: stage II


title: RNA_AFF1KD_Ctrl1

value: undifferentiated keratinocytes


title: T-1


title: A-5

value: normal tissue


title: Morula-input

description:
Input
Morula-input.bw

tag: developmental stage

tag: strain


title: 22s000156_DMSO_DMSO_countsPerGene

first: Lukas

value: Myelogenous leukemia cells

value: bcr:abl fusion gene

value: untreated or Trametinib treated cells with ERCC spike-ins


title: 22s000154_Trametinib_DMSO_countsPerGene


title: T-3


title: 22s000155_DMSO_DMSO_countsPerGene


title: RNA_AFF1KD_Ctrl2


title: 22s000152_Trametinib_DMSO_countsPerGene


title: RNA_AFF1KD_sh1

value: AFF1 shRNA knockdown


title: RNA_AFF1KD_sh2


title: RNA_3hrKL_KL2_2

value: 3-hour KL2


title: 22s000153_DMSO_DMSO_countsPerGene


title: T-2


title: 22s000155_Trametinib_DMSO_countsPerGene


title: 22s000154_DMSO_DMSO_countsPerGene


title: Morula-2


title: 8-cell-input

description:
Input
8-cell-input.bw


title: Morula-1


title: RNA_3hrKL_KL2_1


title: 22s000153_Trametinib_DMSO_countsPerGene


title: A-4


title: Morula-ab150402


title: 8-cell-2


title: A-3


title: A-2


title: RNA_3hrKL_KL1_2

value: 3-hour KL1


title: 4-cell-input

description:
Input
4-cell-input.bw


title: 8-cell-1


title: 22s000151_Trametinib_DMSO_countsPerGene


title: A-1


title: 22s000151_DMSO_DMSO_countsPerGene


title: 4-cell-2


title: RNA_3hrKL_KL1_1


title: 22s000150_Trametinib_DMSO_countsPerGene.


title: 22s000150_DMSO_DMSO_countsPerGene


title: 22s000152_DMSO_DMSO_countsPerGene


title: RNA_3hrKL_Ctrl2

description:
RNA_KL1_3hr_AllInfo.csv
RNA_KL2_3hr_AllInfo.csv

value: 3-hour DMSO


title: 22s000149_Trametinib_DMSO_countsPerGene


title: RNA_24hrKL_KL2_2

value: 24-hour KL2


title: 2-cell-2

value: IVO


title: 4-cell-1


title: C_TH10785_1

city: Solna

first: Julian

middle: J

last: Albers

address: Tomtebodavägen 23

department: Department of Oncology and Pathology

country: Sweden

institute: Karolinska Institutet, Science for Life Laboratory

description: U2OS - TH10785 + PNKP1i

data_processing:
The quality of raw reads was first assessed using Novogene in-house script.
Clean reads were obtained for further analysis after removing reads with low quality, adapter sequence and poly-Ns.
Clean Reads were aligned to the human genome (Homo Sapiens, GRCh38/hg38) with HiSat2 (v2.0.5)
The number of mapped reads was determined with HTSeq (v0.6.1)
Gene Counts were normalized using DESeq2 (v1.30.1, default settings)
Genome_build: hg38
Supplementary_files_format_and_content: raw_gene_count_matrix (csv)
Supplementary_files_format_and_content: DESeq2-normalized_gene_count_matrix (csv)

source_name: U2OS cell line

growth_protocol: U2OS cells were cultured in DMEM (Lonza or Gibco) growth medium supplemented with 10% of fetal bovine serum (Biowest) and 100 U/ml penicillin-streptomycin (Gibco) and grew at 37°C in a 5% CO2 atmosphere.

extract_protocol:
RNA was extracted from cultured cells using TRIzol® Reagent (Thermo Fisher Scientific)
Library preparation and library sequencing was performed by Novogene Co., LTD (Beijing China). Briefly, library prep was performed using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following the manufacturer’s instructions to construct 250~300 bp insert cDNA libraries. Libraries were sequenced by the Novogene Bioinformatics Institute as 150-bp paired-end reads on an Illumina Novaseq 6000 platform.

treatment_protocol: U2OS cells were treated with respecitve compounds at the indicated concentrations or DMSO for 24h.

value: 10uM TH10785 + 10uM PNKP1i


title: RNA_3hrKL_Ctrl1


title: TH10785_3

description: U2OS - TH10785


title: C_TH10785_3

description: U2OS - TH10785 + PNKP1i


title: C_TH10785_2

description: U2OS - TH10785 + PNKP1i


title: 2-cell-input

description:
Input
2-cell-input.bw


title: TH10785_2

description: U2OS - TH10785


title: RNA_24hrKL_KL1_2

value: 24-hour KL1


title: 2-cell-1


title: 22s000148_Trametinib_DMSO_countsPerGene

institute: EMBL


title: 22s000149_DMSO_DMSO_countsPerGene


title: RNA_24hrKL_KL1_1


title: TH10785_1

description: U2OS - TH10785


title: PNKP1i_3

description: U2OS - PNKP1i

value: 10uM PNKP1i


title: 22s000076_DMSO_DMSO_countsPerGene


title: 22s000148_DMSO_DMSO_countsPerGene


title: early-2-cell-2

value: Early 2-cell


title: RNA_24hrKL_Ctrl2

description:
RNA_KL1_24hr_AllInfo.csv
RNA_KL2_24_AllInfo.csv

value: 24-hour DMSO


title: RNA_24hrKL_KL2_1


title: Zygote-input

description:
Input
Zygote-input.bw

value: Zygote


title: R338W TOP3B RIP sample

city: Bethesda

first: Lorinc

last: Pongor

state: MD

address: 37 Convent Dr,

department: DTB

institute: NIH

data_processing:
Raw reads were processed with cutadapt (v1.18) to remove adapters, followed by low quality read trimming using trimmomatic (v0.3).
Reads were aligned to the hg38 genome using STAR aligner (v2.6.1) using the gencode v24 gene annotation.
Gene expression levels were quantified using RSEM (v1.2.31).
Genome_build: hg38
Supplementary_files_format_and_content: Expression data for the two samples is summarized in "Expression_data.txt"

source_name: Human embryonic kidney 293 cells (HEK293 cell line)

growth_protocol: HEK293 cell lines were grown in Dulbecco's modified Eagle's medium (Life Technologies, Carlsbad, CA) supplemented with 10% Fetal Bovine Serum (Gemini, West Sacramento, CA) and 1% penicillin-streptomycin (ThermoFisher Scientific, 15140122) at 37°C in humidified 5% CO2 chamber according to the instructions from ATCC.

extract_protocol:
HEK293 cells transfected with FLAG tagged R338W TOP3B were lysed by resuspending in RIP lysis buffer (Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit, Millipore, Cat# 17-700) and R338W TOP3B-RNA complexes were immunoprecipitated using antibody against FLAG. We followed instruction of Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit, Millipore, Cat# 17-700  for extraction of RNA.
TruSeq Stranded Total  RNA Library Prep

tag: passages

tag: cell line

value: Monoclonal ANTI-FLAG® M2 antibody, Sigma-Aldrich, Cat# F1804


title: PNKP1i_1

description: U2OS - PNKP1i


title: 22s000074_Trametinib_DMSO_countsPerGene

city: Heidelberg

source_name: K562 cells


title: Zygote-1

source_name: embryo


title: early-2-cell-1


title: 22s000074_DMSO_DMSO_countsPerGene


title: 22s000076_Trametinib_DMSO_countsPerGene


title: DMSO_1

description: U2OS - DMSO control

value: DMSO


title: early-2-cell-input

description:
Input
early-2-cell-input.bw


title: DMSO_3

description: U2OS - DMSO control


title: R338W TOP3B INPUT sample


title: Zygote-2


title: IFN2

city: Atlanta

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

description: rRNA depletion RNA-seq

data_processing:
All total reads were mapped to hg38 by TopHat2 with default parameter followed by gene expression quantification and differential expression analysis using Cuffdiff.
Assembly: hg38
Supplementary files format and content: fpkm table

growth_protocol: The BE(2)-M17 human neuroblastoma line and SH-SY5Y line (both are from ATCC) were propagated in DMEM/F12 medium containing 10% fetal bovine serum (FBS) (HyClone).

extract_protocol:
Cultured cells were harvested then centrifuged at 1,500 g and cell pellets were used for RNA isolation. Cell pellet was homogenized in TRIzol using a hand-held pestle homogenizer and incubated in TRIzol for at least 5 minutes. Chloroform (1:5 ratio) was added, mixed well and incubated at room temperature for 15 minutes. Samples were then centrifuged at 12,000 g for 15 minutes at 4°C. The top aqueous layer was transferred to a clean tube, and the RNA was precipitated in 3 M NaAc pH 5.2 (10:1 ratio), 4 ml of glycogen (5 mg/ml), 100% isopropanol (1:1 ratio) overnight at -80°C. The next day, the samples were centrifuged at 20,000 g for 20 minutes at 4°C. The resulting RNA pellet was washed once in 75% ethanol, centrifuged at 7,500 g for 10 minutes at 4°C. The washed RNA pellet was dissolved in nuclease-free water. RNA was quantified by NanoDrop and the quality was confirmed by agarose gel.
An amount of 1ug total RNA per sample was processed for library preparation using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations. Libraries were sequenced on a HiSeq with a read length configuration of 150 PE, targeting 100M total reads per sample.

treatment_protocol: Cells were treated with IFN-γ (NOVUS biologicals, 285-IF-100) at the concentration of 10ng/ml for 24h.


title: patient_23 C1D+1 [c29_TCR]

city: Columbus

first: Bradley

middle: Wayne

last: Blaser

state: OH

address: 400 W 12th Ave

department: Comprehensive Cancer Center

institute: Ohio State University

data_processing:
*.fastq:  standard paired end fastq files from gene expression and TCR libraries.  If either "tcr" or "TCR" appears in the file name this is a TCR library.  Otherwise it is a gene expression library.  Fastq files without either "tcr/TCR" or "gex/GEX" are also gene expression libraries.
demultiplexing and fastq generation:  cellranger mkfastq (v5.0.1)
generation of cell barcode matrices:  cellranger multi (v5.0.1)
analysis of single cell data:  custom software available at doi:10.5061/dryad.1c59zw3vs and https://github.com/blaserlab/carson_ibr_trial
Genome_build: GRCh38-2020-A
Supplementary_files_format_and_content: *_filtered_feature_bc_matrix.h5:  gene-cell barcode matrices in hdf5 format.  Filtering was performed using default parameters in cellranger.
Supplementary_files_format_and_content: *_filtered_contig_annotations.csv:  cell barcodes annotated with TCR clonotype data.  Standard output from cellranger multi using default parameters.
Supplementary_files_format_and_content: *_clonotypes.csv:  aggregated TCR clonotype data.  Standard output from cellranger multi using default parameters.

source_name: PBMC

growth_protocol: Fresh PBMC were cryopreserved, thawed in batches and counted prior to loading on the 10X microfluidics chip.

extract_protocol:
Cell-barcoded cDNA was generated and TCR sequences were enriched using the 10X genomics Single Cell 5' Immune Profiling kit, V1.1.
Libraries were constructed from amplified cell-barcoded cDNA and TCR sequences using using the 10X Genomics Single Cell 5' Immune Profiling kit, v1.1 according to the manufacturers instructions.

treatment_protocol: No treatments were performed on the cells.

tag: subject id

tag: treatment/time point

value: PBMC


title: DMSO_2

description: U2OS - DMSO control


title: PNKP1i_2

description: U2OS - PNKP1i


title: 22s000073_DMSO_DMSO_countsPerGene

last: Mathur

address: Meyerhofstraße 1

tag: cell type

value: Myelogenous leukemia cells

value: bcr:abl fusion gene


title: RNA_24hrKL_Ctrl1

value: undifferentiated keratinocytes


title: patient_23 C1D-7 [c30_TCR]


title: MII-input

city: Wuhan

first: Jing-Jing

institute: Huazhong Agricultural University

description:
Input
MII-input.bw

value: MII

tag: chip antibody


title: patient_22 C1D+1 [22_2_TCR]


title: IFN4

description: rRNA depletion RNA-seq

tag: treatment


title: MII-2


title: 22s000072_DMSO_DMSO_countsPerGene

tag: genotype

value: untreated or Trametinib treated cells with ERCC spike-ins


title: 22s000075_Trametinib_DMSO_countsPerGene


title: Con2

description: rRNA depletion RNA-seq

value: untreated


title: 22s000073_Trametinib_DMSO_countsPerGene


title: MII-1


title: patient_22 C1D-7 [22_1_TCR]


title: liver, 3e11 AAV8-scramble shRNA, chow diet, rep 3

city: San Francisco

first: Angelo

last: Pelonero

state: CA

address: 1650 Owens Street

department: Cardiovascular Disease Institute

institute: Gladstone Institutes (UCSF)

description:
PE150 (20M raw reads per library)
exp2_standardDiet_ExpMat.csv.gz
scramble_3555

data_processing:
Raw reads were QC verified with FastQC v0.11.8
aligned to mm10 genome using Rsubread v2.4.3
reads quantified with Rsubread featureCounts
Assembly: mm10
Supplementary files format and content: gene-sample read counts matrix in csv.gz (compressed comma-delimited) format

source_name: liver

extract_protocol:
Samples were collected in Invitrogen TRIzol reagent and RNA was purified using standard protocols.
1 ug of RNA was used for cDNA library construction NEBNext® Ultra Directional RNA Library Prep Kit for Illumina® (#E7420S) according to the manufacturer’s protocol. Briefly, mRNA was enriched using oligo(dT) beads followed by two rounds of purification and randomly fragmented by addition of fragmentation buffer. The first strand cDNA was synthesized using random hexamer primers, after which a second-strand synthesis buffer, dNTPs, RNase H, and DNA polymerase I were added to generate the second-strand. After terminal repair and sequencing adaptor ligation, the double-stranded cDNA library underwent size selection and PCR enrichment. The resulting 250-350 bp insert libraries were quantified using a Qubit 2.0 fluorometer and quantitative PCR. Size distribution was analyzed using an Agilent 2100 Bioanalyzer.

value: liver

value: wild type

value: chow diet, 3e11 AAV8-scramble shRNA


title: 22s000071_Trametinib_DMSO_countsPerGene


title: Con4

description: rRNA depletion RNA-seq


title: IFN3

description: rRNA depletion RNA-seq


title: Con1

description: rRNA depletion RNA-seq


title: IFN1

description: rRNA depletion RNA-seq


title: 22s000075_DMSO_DMSO_countsPerGene


title: 22s000071_DMSO_DMSO_countsPerGene


title: Con3

description: rRNA depletion RNA-seq


title: liver from a postnatal day 3 Nedd8(flox/flox; Alb-cre) mouse

city: Beijing

first: Jiyan

last: Zhang

state: China

address: 27 Taiping Road, East Building, Rm0749

institute: Institute of Basic Medical Sciences

hyb_protocol: MOA v2.1 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on MOA in the presentation of the Phalanx OneArray hybridization buffer in duplication.

scan_protocol: MOA v2.1 The arrays were scanned by Agilent Microarray Scanner (G2505C)  0.1 XDR protocol and quantify the fluoresence intensity.

data_processing: Data processing was performed and calculated by Rosetta Resolver® (Rosetta Biosoftware). The probes that ﬂag <0 in all samples were filtered out, then normalized by median scaling method between technical replicates. Pair-wise comparisons between samples were calculated by Rosetta error model and presented by log2 ratio and p-value.

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

extract_protocol: RNA extraction by Trizol Reagent (Invitrogen). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

value: Nedd8(flox/flox; Alb-cre)


title: liver from a postnatal day 3 Nedd8(flox/flox) mouse


title: 22s000070_Trametinib_DMSO_countsPerGene


title: MAB21L4-KO-sample4-KO

city: Stanford

first: Carolyn

last: Lee

address: 269 Campus Drive

institute: Stanford University School of Medicine

data_processing:
Samples were aligned using STAR (version 2.7.9) to the hg38 reference genome and RSEM (version 1.3.3) was used to generated count matrices
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files containing gene by sample count matrix

source_name: Skin

growth_protocol: Keratinocytes were seeded onto devitalized human dermis on the basement membrane side. Organoids were maintained for 3 days before harvesting.

extract_protocol:
Total RNA was then isolated from human skin organoids using QIAshredder (Qiagen) and Trizol (ThermoFisher) followed by DNA removal with the TURBO DNA-free kit (Ambion) according to the manufacturer’s instructions.
RNA-Seq libraries were prepared with the mRNA Seq Sample Prep Kit (Illumina, Inc.) as recommended by the manufacturer.

value: Human skin organoid

tag: mab21l4 genotype

value: KO

value: Skin


title: liver, 3e11 AAV8-CSDE1 shRNA, chow diet, rep 3

description:
PE150 (20M raw reads per library)
exp2_standardDiet_ExpMat.csv.gz
CSDE1_3545

value: chow diet, 3e11 AAV8-CSDE1 shRNA


title: 22s000072_Trametinib_DMSO_countsPerGene


title: 22s000070_DMSO_DMSO_countsPerGene


title: liver, 3e11 AAV8-CSDE1 shRNA, chow diet, rep 2

description:
PE150 (20M raw reads per library)
exp2_standardDiet_ExpMat.csv.gz
CSDE1_3544


title: patient_20 C1D+1 [c11_TCR]


title: liver, 3e11 AAV8-CSDE1 shRNA, chow diet, rep 1

description:
PE150 (20M raw reads per library)
exp2_standardDiet_ExpMat.csv.gz
CSDE1_3541


title: patient_21 C1D-7 [c18_TCR]


title: 22s000069_Trametinib_DMSO_countsPerGene


title: MAB21L4-KO-sample2-WT

value: WT


title: liver, 3e11 AAV8-scramble shRNA, chow diet, rep 1

description:
PE150 (20M raw reads per library)
exp2_standardDiet_ExpMat.csv.gz
scramble_3551


title: patient_17 C1D+1 [17_2_TCR]


title: patient_20 C1D-7 [c12_TCR]


title: MAB21L4-OE-sampleS5-OE

value: OE


title: patient_17 C1D-7 [17_1_TCR]

value: PBMC


title: patient_21 C1D+1 [c17_TCR]


title: 22s000068_Trametinib_DMSO_countsPerGene

value: Myelogenous leukemia cells


title: liver, 3e11 AAV8-scramble shRNA, chow diet, rep 2

description:
PE150 (20M raw reads per library)
exp2_standardDiet_ExpMat.csv.gz
scramble_3554


title: MAB21L4-KO-sample3-KO


title: patient_16 C1D+1 [c23_TCR]


title: 22s000069_DMSO_DMSO_countsPerGene

value: bcr:abl fusion gene


title: liver, 2e10 AAV8-scramble shRNA, Paigen diet, rep 2

description:
PE150 (20M raw reads per library)
exp1_paigenDiet.csv.gz
scramble_332

value: Paigen diet, 2e10 AAV8-scramble shRNA


title: patient_15 C1D+1 [15_2_TCR]


title: MAB21L4-OE-sampleS3-WT


title: liver, 2e10 AAV8-scramble shRNA, Paigen diet, rep 1

description:
PE150 (20M raw reads per library)
exp1_paigenDiet.csv.gz
scramble_331


title: patient_16 C1D-7 [c24_TCR]


title: 22s000067_Trametinib_DMSO_countsPerGene


title: MAB21L4-OE-sampleS2-WT


title: MAB21L4-OE-sampleS4-OE


title: liver, 2e10 AAV8-scramble shRNA, Paigen diet, rep 3

description:
PE150 (20M raw reads per library)
exp1_paigenDiet.csv.gz
scramble_339


title: liver, 2e10 AAV8-CSDE1 shRNA, Paigen diet, rep 3

description:
PE150 (20M raw reads per library)
exp1_paigenDiet.csv.gz
CSDE1_4085

value: Paigen diet, 2e10 AAV8-CSDE1 shRNA


title: MAB21L4-KO-sample1-WT


title: 22s000067_DMSO_DMSO_countsPerGene

value: untreated or Trametinib treated cells with ERCC spike-ins


title: patient_15 C1D-7 [15_1_TCR]


title: 22s000068_DMSO_DMSO_countsPerGene


title: 22s000066_Trametinib_DMSO_countsPerGene


title: CACYBP-KO-sampleB-KO

tag: cacybp genotype


title: 22s000066_DMSO_DMSO_countsPerGene


title: CACYBP-KO-sample2-WT


title: patient_10 C1D+1 [c27_TCR]


title: 22s000065_Trametinib_DMSO_countsPerGene


title: patient_11 C1D+1 [C5_TCR]


title: CACYBP-KO-sampleC-KO


title: liver, 2e10 AAV8-CSDE1 shRNA, Paigen diet, rep 1

description:
PE150 (20M raw reads per library)
exp1_paigenDiet.csv.gz
CSDE1_4078


title: patient_10 C1D-7 [c28_TCR]


title: 22s000064_DMSO_DMSO_countsPerGene


title: liver, 2e10 AAV8-CSDE1 shRNA, Paigen diet, rep 2

description:
PE150 (20M raw reads per library)
exp1_paigenDiet.csv.gz
CSDE1_4081


title: patient_09 C1D-7 [c10_TCR]


title: Cxcr4_minus_group_2

city: Shanghai

first: Zhenyu

last: Liao

address: No.270 Dongan Road

institute: Fudan University Shanghai Cancer Centre

data_processing:
Cutadapt software was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
We used HISAT2 software to map reads to the genome ,(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam).
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software
StringTie and ballgown were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM.
Assembly: GRCm39
Supplementary files format and content: Text files include RPKM values for each Sample

source_name: Mouse pancreatic cancer

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
RNA libraries for RNA-seq were prepared following manufacturer's protocols.

treatment_protocol: C57BL/6 mice were built for orthotopic PDAC tumor models. Mouse tumor-derived macrophages are sorted into two groups according to their expression of Cxcr4.

value: Mouse pancreatic cancer

value: macrophage cells

value: mouse pancreatic cancer model derived


title: CACYBP-KO-sampleA-KO


title: 22s000065_DMSO_DMSO_countsPerGene


title: 22s000064_Trametinib_DMSO_countsPerGene


title: Cxcr4_minus_group_3


title: HEK293 cells  Treated replicate2

city: Gothenburg

first: Subazini

last: TK

address: Medicineragatan 9A

institute: Gothenburg university

data_processing:
Sequenced reads were mapped to hg38 whole genome using hisat2 with default parameters
The reads are quantified using featureCounts from Subread package
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample analyzed

source_name: kidney; Embryo

growth_protocol: HeLa, BT-549, Caki  and HEK293 cells were routinely cultured in DMEM media supplemented with 10% FBS.

extract_protocol: RNA libraries were prepared for sequencing using TruSeq Stranded Total RNA with Ribo-Zero from Illumina (Cat # RS-122-2201). mRNA sequencing on 100PE of DNBseq platform

treatment_protocol: Cells were collected after 4 hours of FGF-2 treatment and Total RNA extraction was carried out using ReliaPrep RNA Cell Miniprep System.

tag: growth protocol

value: in vitro cultured cell line

value: kidney; Embryo

tag: disease state

value: Normal

value: Normal human epithelial cells


title: Cxcr4_add_group_2


title: 22s000063_Trametinib_DMSO_countsPerGene


title: Cxcr4_minus_group_1


title: CACYBP-KO-sample3-WT

value: Human skin organoid

value: Skin


title: patient_11 C1D-7 [C6_TCR]


title: CACYBP-KO-sample1-WT

value: WT


title: patient_08 C1D+1 [c7_TCR]


title: 22s000063_DMSO_DMSO_countsPerGene


title: Cxcr4_add_group_3


title: HEK293 cells untreated replicate1

value: control


title: 22s000062_Trametinib_DMSO_countsPerGene


title: patient_06 C1D+1 [c21_TCR]

value: PBMC


title: patient_06 C1D-7 [c22_TCR]


title: HEK293 cells untreated replicate2


title: prostate organoids - Vehicle (DMSO)

city: Los Angeles

first: Xia

last: Yang

state: California

address: 610 Charles E. Young Drive East

department: Integrative Biology and Physiology

institute: University of California, Los Angeles

data_processing:
CellRanger version 4.0 was used to demultiplex fastq files
CellRanger version 4.0 count was used for matrix generation with --expect-cells=1000 and mm10 as a reference genome
A digital gene expression matrix for each sample was generated where each row is the read count of a gene and each column is a unique single cell.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: prostate organoids

growth_protocol: Mouse prostate organoids were grown in reduced growth factor matrigel supplemented with advanced DMEM/F-12 and set of standard additives (Drost et al, Nature Protocols 2016, PMID: 26797458) and passaged every 7-10 days

extract_protocol:
Organoids were dissociated to single cells using sequential treatment with dispase followed by trypsin. Samples were counted using Countess II Automated Cell Counter (Thermo Fisher Scientific) and hemocytometer for cell concentration and viability using Trypan Blue stain 0.4% (Invitrogen). Cells were loaded to form GEMs and barcode individual cells. GEMS were treated according to manufacturer’s instructions.
Single cell gene expression libraries were created using Chromium Next GEM Single Cell 3' (v3.1 Chemistry) (10x Genomics), Chromium Next GEM Chip G Single Cell Kit (10x Genomics), and Single Index Kit T Set A (10x Genomics) according to the manufacturer’s instructions.

treatment_protocol: Organoids were treated with vehicle (DMSO) or 10uM UK5099 for 3 days

value: prostate organoids

value: Vehicle (DMSO)


title: Cxcr4_add_group_1


title: 22s000062_DMSO_DMSO_countsPerGene

department: Genome Biology

value: Myelogenous leukemia cells

value: bcr:abl fusion gene


title: HeLa cell line  Treated replicate2

source_name: Uterus; Cervix

value: HeLa

value: Uterus; Cervix

value: Adenocarcinoma

value: Cancer cells


title: prostate organoids - UK5099


title: HeLa cell line Treated replicate1

value: in vitro cultured cell line


title: M7

description:
3' nuclear RNA
snRNA_PF_EPN_Seurat.rds.gz, snRNA_PF_EPN_counts.mtx.gz, snRNA_PF_EPN_cell_barcodes.tsv.gz, snRNA_PF_EPN_features.tsv.gz, snRNA_PF_EPN_meta_data.tsv.gz

data_processing:
The Drop-seq computational pipeline (Macosko, E.Z., et al., Cell, 2015) was used to map to the human reference genome (GRCh38) via STAR alignment (version 2.6.1a), correct the cellular and molecular barcodes for sequencing errors, and build a count matrix. To account for poly-adenylated pre-mRNAs in the nucleus, we included reads that aligned to intronic regions of the genome (locus_function_list = intronic).
We removed low-quality cells, debris, and empty droplets based on the inflexion point in a plot of the number of UMIs in each droplet ranked by decreasing order of magnitude. Additionally, we plotted the number of UMIs (in log scale) against the proportion of mitochondrial genes for each droplet. For most samples, the distribution of droplets in this scatter plot was bimodal. We used a linear cut to segregate cells (high number of UMIs and low percentage of mitochondrial genes) from debris (high percentage of mitochondrial genes and low number of UMIs) in this plot.
Gene expression was log-normalized by library size in each cell and the most variable genes were selected for PCA using Seurat (version 3.2.2). We then used Harmony (version 0.1.0) with default parameters to build a consolidated representation of the 9 samples based on the top 5,000 most variable genes and 30 principal components. We clustered the data using Louvain community detection based on the top 30 dimensions of the consolidated space and used Uniform Manifold Approximation and Projection (UMAP) to construct a 2-dimensional visualization.
Assembly: GRCh38

molecule: nuclear RNA

source_name: Ependymoma biopsy, Metastasis, PFA-1

extract_protocol:
Approximately 8 mm3 of tissue was cut from each tumor. Samples were incubated at room temperature in 1 ml homogenization buffer for 3 minutes, then dissociated with 13 strokes of a tight pestle in a 2 ml glass homogenizer. Samples were then filtered with a 40 µm mesh filter followed by a 30 µm mesh filter. After brief tabletop centrifugation, the nuclei pellet was resuspended in 1 ml PBA-BSA 0.01% and counted. Nuclei were defined by shape, size, and general appearance, and diluted to 100 nuclei/µl.
Single-nucleus RNA-seq library preparation was performed as previously described in Hu, P. et al., Mol Cel, 2017  using a Drop-seq microfluidic system. The quality of the cDNA libraries was evaluated with a bioanalyzer and quantified using a KAPA Library Preparation Kit (Roche Sequencing, cat. # KK4824). Libraries were sequenced using an Illumina NextSeq 500 on high output mode with 20 bp (read 1) and 60 bp (read 2) paired end reads.

value: Ependymoma biopsy, Metastasis, PFA-1


title: patient_04 C1D-7 [c20_TCR]


title: M8

source_name: Ependymoma biopsy, Metastasis, PFA

value: Ependymoma biopsy, Metastasis, PFA


title: patient_05 C1D+1 [c25_TCR]


title: HeLa cell line untreated replicate2


title: patient_04 C1D+1 [c19_TCR]


title: Laser-induced CNV retina, cp-asiNRL treatment rep1

city: Seoul

first: Hyungwoo

address: 120-1 Neungdong-ro, Gwangjin-gu

institute: Konkuk University School of Medicine

data_processing:
Raw reads from the sequencer to remove low quality and adapter sequence before analysis and aligned the processed reads to the Mus musculus using HISAT v2.1.0.
The reference genome sequence and annotation data were downloaded from the NCBI
Transcript assembly of known transcripts was processed by featureCounts v1.6.0.
Expression abundance of transcript and gene were calculated as read count or FPKM value (Fragments Per Kilobase of exon per Million fragments mapped) per sample
Assembly: mm10
Supplementary files format and content: Excel file include FPKM for each sample

source_name: Retina

extract_protocol:
Total RNA was isolated using the following kits: Isolate RNeasy® Mini Kit (Qiagen,Cat. No. 74106) and QIAzol® Lysis Reagent (Cat. No. 79306). Total RNA concentration was calculated by Quant-IT RiboGreen (Invitrogen, #R11490).
To construct cDNA libraries with the TruSeq Stranded mRNA LT Sample Prep Kit, total RNA was used.

treatment_protocol: For all experiments, mice were randomly assigned to control or treatment groups. One microliter of 6 µg/µl cp-asiNRL or vehicle (0.5X PBS) was intravitreally injected in C57BL/6J wildtype mice and mice with laser-induced CNV, respectively.

value: Retina

value: Retinal cells

value: Intravitreal cp-asiNRL injection and laser-induced CNV


title: Laser-induced CNV retina, cp-asiNRL treatment rep3


title: patient_02 C1D+1 [c15_TCR]


title: M9


title: Laser-induced CNV retina, PBS control rep3

value: Intravitreal PBS injection and laser-induced CNV


title: HeLa cell line untreated replicate1

value: control


title: HEK293 cells Treated replicate1

value: kidney; Embryo

value: Normal

value: Normal human epithelial cells


title: patient_02 C1D-7 [c16_TCR]

value: PBMC


title: Laser-induced CNV retina, cp-asiNRL treatment rep2


title: Caki-1 cell line  Treated replicate2

source_name: Kidney

value: Kidney

value: Clear cell carcinoma


title: patient_05 C1D-7 [c26_TCR]


title: Laser-induced CNV retina, PBS control rep2


title: P6

source_name: Ependymoma biopsy, Progressive, PFA-2

value: Ependymoma biopsy, Progressive, PFA-2


title: I5

source_name: Ependymoma biopsy, Initial, PFA-1

value: Ependymoma biopsy, Initial, PFA-1


title: patient_01 C1D+1 [c13_TCR]


title: WT retina, cp-asiNRL treatment rep2

value: Intravitreal cp-asiNRL injection


title: Caki-1 cell line untreated replicate2

value: in vitro cultured cell line

value: Cancer cells


title: Laser-induced CNV retina, PBS control rep1


title: patient_01 C1D-7 [c14_TCR]


title: I4

source_name: Ependymoma biopsy, Initial, PFB

value: Ependymoma biopsy, Initial, PFB


title: patient_23 C1D+1 [c29_GEX]


title: I2

source_name: Ependymoma biopsy, Initial, PFA

value: Ependymoma biopsy, Initial, PFA


title: Caki-1 cell line Treated replicate1


title: WT retina, cp-asiNRL treatment rep3

value: Retina

value: Retinal cells


title: BT549 cell line Treated replicate2

source_name: Breast/Mammary

value: Breast/Mammary

value: Breast cancer


title: WT retina, cp-asiNRL treatment rep1


title: I3

source_name: Ependymoma biopsy, Initial, PFA-2

value: Ependymoma biopsy, Initial, PFA-2


title: I1


title: BT549 cell line Treated replicate1


title: patient_23 C1D-7 [c30_GEX]

source_name: PBMC


title: patient_22 C1D-7 [22_1_GEX]


title: WT retina, PBS control rep3

value: Intravitreal PBS injection


title: mature hiPSC co rep4

city: Madison

first: Zachary

middle: T

last: Campbell

state: WI

address: 1111 Highland Avenue

department: Anesthesiology

institute: University of Wisconsin - Madison

data_processing:
FastQ file generation was followed by quality check via FastQC 0.11.5
Adaptor sequences were trimmed and read mapping was performed using TopHat 2.1.1
Reads were mapped to their respective reference genomes and transcriptomes.
Gene abundance quantification was performed using Cufflinks 2.2.1 with option --no-length-correction
FPKM values were converted first to TPM values and then to uqTPM values.
Genome_build: mm10 and h19
Supplementary_files_format_and_content: xlsx workbook with uqTPM values for all samples
Supplementary_files_format_and_content: xlsx workbook with uqTPM values, fold changes, and p-values for all samples and their respective comparisons

source_name: hiPSC

extract_protocol:
Mouse DRGs were excised. Tissue samples were homogenized. Cultures were generated. hiPSC samples were lysed. RNA was harvested using Trizol reagent. Lexogen QuantSeq 3'mRNA-seq library kit and RiboCop rRNA depletion kit were used with 50ng-1ug total RNA.
RNA libraries were prepared for sequencing using maufacturer's protocols

value: hiPSC

tag: culture method

value: mature hiPSC astrocyte co-culture


title: patient_22 C1D+1 [22_2_GEX]

value: PBMC


title: Caki-1 cell line untreated replicate1

value: Kidney

value: Clear cell carcinoma

value: control


title: BT549 cell line untreated replicate2


title: WT retina, PBS control rep2


title: mature hiPSC co rep3


title: mature hiPSC co rep2


title: patient_21 C1D+1 [c17_GEX]


title: patient_21 C1D-7 [c18_GEX]


title: WT retina, PBS control rep1


title: mature hiPSC co rep1


title: mature hiPSC mono rep4

value: mature hiPSC monoculture


title: patient_20 C1D-7 [c12_GEX]


title: Infected d100, replicate 2, scRNAseq

city: Saint Louis

first: Shabaana

middle: Abdul

last: Khader

state: Missouri

address: 660 S Euclid Avenue, Campus Box 8230

department: Department of Molecular Microbiology

institute: Washington University in St. Louis

description: 10x Genomics

data_processing:
The raw gene expression matrices were generated by the Cell Ranger software (10x Genomics, version 3) available on the 10x website. After demultiplexing, the resulting fastq files were aligned against the mouse reference genome mm10 with cellranger count.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
Mice were euthanized with CO2 and lungs were perfused with heparin in saline. Lungs were minced and incubated in Collagenase/DNAse for 30 minutes at 37°C. Lung tissue was pushed through a 70 µm nylon screen to obtain a single-cell suspension. Red blood cells were lysed and the cells were resuspended in suitable media or buffer for further use.
Isolated total lung single-cell suspensions were enriched for live cells using dead cell depletion kit according to manufacturer’s instruction (Miltenyi Biotec) and subjected to droplet-based massively parallel single-cell RNA sequencing using Chromium Single Cell 5’ (v1) Reagent Kit as per manufacturer’s instructions (10x Genomics). Briefly, cell suspensions were loaded at 1,000 cells/µL with the aim to capture 10,000 cells/lane. The 10x Chromium Controller generated GEM droplets, where each cell was labeled with a specific barcode, and each transcript labeled with a unique molecular identifier (UMI) during reverse transcription. The barcoded cDNA underwent 16 cycles of amplification, and after SPRI bead purification, was removed from the BSL-3 space for library generation. Libraries were prepared from amplified cDNA and target enrichment products by fragmentation, end repair, A-tailing, adapter ligation, and sample index PCR as per the manufacturer’s instructions. Libraries were sequenced on a NovaSeq S4 (200 cycle) flow cell, targeting 50,000 read pairs/cell.

treatment_protocol: Mycobacterium tuberculosis W. Beijing strain, HN878 (BEI Resources) were grown to mid-log phase in Proskauer Beck medium containing 0.05% Tween 80 and frozen in at -80º C. Mice were infected with ~100 CFU Mtb HN878 via aerosol route using a Glas-Col airborne infection system.

value: Lung

value: lung cells

tag: disease stage

value: infected, 100 days post infection

tag: infection strain

value: Mtb HN878

tag: cfu delivered


title: Infected d100, replicate 3, scRNAseq

description: 10x Genomics

tag: tissue


title: mature hiPSC mono rep2


title: mature hiPSC mono rep3


title: Infected d50, replicate 1, scRNAseq

description: 10x Genomics

value: infected, 50 days post infection


title: Infected d100, replicate 1, scRNAseq

description: 10x Genomics


title: patient_16 C1D+1 [c23_GEX]


title: mature hiPSC mono rep1


title: patient_20 C1D+1 [c11_GEX]


title: patient_16 C1D-7 [c24_GEX]


title: patient_17 C1D-7 [17_1_GEX]


title: immature hiPSC rep5

value: immature hiPSC


title: immature hiPSC rep3


title: Infected d50, replicate 2, scRNAseq

description: 10x Genomics


title: patient_15 C1D-7 [15_1_GEX]


title: Uninfected, replicate 1, scRNAseq

description: 10x Genomics

value: uninfected


title: patient_15 C1D+1 [15_2_GEX]


title: Infected d50, replicate 3, scRNAseq

description: 10x Genomics


title: BT549 cell line untreated replicate1

value: in vitro cultured cell line

value: Breast/Mammary

value: Breast cancer

value: Cancer cells


title: Uninfected, replicate 2, scRNAseq

description: 10x Genomics


title: SET_C_AD3A

city: SINGAPORE

first: Chin Yan

last: Lim

address: 8A Biomedical Grove, Immunos, #06-06,

country: Singapore

institute: A*STAR Skin Research Labs

data_processing:
Sequenced data were processed using the Partek Flow genomics analysis software
Raw reads were aligned using Star 2.7.3a following pre-alignment quality check. Transcripts were quantified to mm10 mouse genome Ensemble Transcripts release 102
Raw gene counts were normalised and differential expression analysis was carried out using DESeq2 with the Benjamini Hochberg false discovery rate multiple testing.
Assembly: mm10
Supplementary files format and content: txt file including  normalised count for each sample, fold change, FDR, Log2 fold change, total counts, p values
Supplementary files format and content: txt file Raw count matrix
Supplementary files format and content: processed gene expression data file analysis details txt file

source_name: dorsal skin wounds Day 3 post wounding

growth_protocol: Young (8-12 weeks) and aged (22-26 months) C57BL/6J wild-type female mice were housed at the A*STAR Institute Biological Resource Centre (Singapore) or Biological Services Facility at the University of Manchester (Manchester, UK).

extract_protocol:
Tissues were harvested 3 days post wounding and digested using liberase TL. F4/80+ CD64+ cells were sorted out of the wounds and directly into Rneasy RLT lysis buffer and RNA was harvested
First-strand cDNA synthesis and amplification were performed using the SMART-Seq v4 ultra-low input RNA Kit for sequencing (Takara) following the supplier’s instructions. The amplified double-stranded cDNA was purified using AMPure XP beads.  For Library construction, cDNA samples were sheared using the Covaris AFA system and fragments were end-repaired, A-tailed and ligated to sequencing adaptors before PCR enrichment.  Library concentrations were quantified using a Qubit fluorometer and were diluted 2ng/µl before checking insert size on a bioanalyser. Pooled libraries were sequenced on a Novaseq6000 platform with a 150bp paired-end read length at an average depth of 50 million reads per sample.

treatment_protocol: Two 10mm full-thickness wounds were created on the dorsum of each mouse.

tag: strain

tag: age

value: aged 24 months

tag: gender

value: female


title: immature hiPSC rep2

value: hiPSC


title: immature hiPSC rep1


title: patient_11 C1D+1 [C5_GEX]

tag: subject id

tag: treatment/time point

value: PBMC


title: SET_B_AD3A


title: patient_17 C1D+1 [17_2_GEX]

tag: cell type


title: patient_11 C1D-7 [C6_GEX]


title: immature hiPSC rep4


title: SET_A_AD3A


title: SET_A_YD3A

value: young 12 weeks


title: patient_10 C1D-7 [c28_GEX]


title: SET_B_YD3A


title: patient_09 C1D-7 [c10_GEX]


title: patient_08 C1D+1 [c7_GEX]


title: patient_10 C1D+1 [c27_GEX]


title: LNCaP_R1881_24h_2_Input

city: Belfast

first: Ian

middle: G

last: Mills

address: 97 Lisburn Road

department: Centre for Cancer Research and Cell Biology

country: United Kingdom

institute: Queens University

data_processing:
Fastq files were generated with Illumina pipeline software (bcl2fastq version 2.19 using the default thresholds).
Reads were mapped to the GRCh37/hg19 reference genome using bowtie2 (version 2.2.6) and subsequently filtered to remove PCR duplicates.
Prior to peak calling, Encode curated blacklisted regions were removed from bam files.
The MACS algorithm (version 2.1.2) was used to analyse the resulting alignments and identify both transcription factor and histone binding regions.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bed files

source_name: LNCaPs

extract_protocol:
Following treatment, cells were fixed with 1% formaldehyde and chromatin prepared by sonication in Bioruptor plus. Fragmentation efficiency was analysed using fragment analyser and ChIP carried out using diagenode iDeal ChIP-seq kit for transcription factors (Cat# C01010170).
Libraries were prepared using Diagenode MicroPlex Library Preparation Kit v2 (Cat# C05010014) and purified and purified/size selected using Agencourt® AMPure® XP beads (Beckman Coulter, Cat. No. A63881).

treatment_protocol: Prostate cancer cells (LNCaPs) were cultured in RPMI media supplemented with 10% charcoal dextran stripped FBS for 72h before addition of 1nM R1881 or 0.01% ethanol for 4h and 24h.

tag: cell line

value: LNCaP

value: Prostate cancer cell line

tag: passages

tag: treatment

tag: time

tag: chip antibody


title: LNCaP_R1881_24h_1_Input


title: SC MSU rep2

city: Wenzhou

first: Yi

state: Zhejiang

address: Wenzhou Medical University

institute: Zhang Lab

data_processing:
Clean data were aligned to the mouse genome (mm39) using the hisat2 v(2.2.1).
Aligned reads were quantified using HTSeq(0.11.3) using GENCODE vM27 annotation.
Differential gene expression was estimated with DESeq2 version v1.28.1.
Genome_build: mm39
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Spinal cord

extract_protocol:
Total RNA was isolated and extracted using TRIzol Reagent (ThermoFisher). For mRNA sequencing, libraries were produced by a VAHTS Universal V6 RNA-seq Library Prep Kit for MGI based on the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MSU and 1 x PBS was injected subcutaneously in a volume of 100ul into the right ankle joint separately. 8 hours post-MSU and post-PBS mice were sacrificed.

value: Spinal cord

value: 10 weeks

value: treated with MSU for 8 hours


title: SC MSU rep1


title: SC MSU rep3


title: patient_06 C1D+1 [c21_GEX]


title: patient_06 C1D-7 [c22_GEX]


title: LNCaP_vehicle_24h_2_O-GlcNAc

value: Vehicle

value: O-GlcNAc [RL2] (Abcam, ab2739)


title: LNCaP_R1881_24h_1_O-GlcNAc


title: patient_05 C1D+1 [c25_GEX]


title: LNCaP_R1881_24h_2_O-GlcNAc


title: patient_05 C1D-7 [c26_GEX]


title: patient_04 C1D+1 [c19_GEX]


title: SC WT rep2

value: untreated


title: LNCaP_R1881_24h_2_AR

value: AR (Abcam, ab74272)


title: LNCaP_vehicle_24h_2_AR


title: LNCaP_vehicle_24h_2_Input


title: SC WT rep1


title: LNCaP_vehicle_24h_1_O-GlcNAc


title: SET_C_YD3A


title: LNCaP_vehicle_24h_1_Input


title: patient_04 C1D-7 [c20_GEX]


title: LNCaP_R1881_24h_1_AR


title: DRG MSU rep3

source_name: Dorsal root ganglia

value: Dorsal root ganglia


title: DRG MSU rep2


title: patient_02 C1D+1 [c15_GEX]


title: patient_02 C1D-7 [c16_GEX]


title: LNCaP_vehicle_24h_1_AR


title: SC WT rep3


title: DRG WT rep3


title: DRG MSU rep1


title: LNCaP_R1881_4h_1_Input


title: LNCaP_R1881_4h_2_Input


title: patient_01 C1D+1 [c13_GEX]


title: patient_01 C1D-7 [c14_GEX]


title: LNCaP_vehicle_4h_2_Input


title: DRG WT rep1


title: Hydrogren peroxide T2 N3

city: Seattle

first: E. Virginia

last: Armbrust

state: WA

address: 616 NE Northlake Place

department: Oceanography

institute: University of Washington

data_processing:
Sequence reads were trimmed using Trimmomatic 0.39,25 run in paired-end mode with cut adaptor and other Illumina-specific sequences (ILLUMINACLIP) set to TruSeq3-PE.fa:2:30:10:1:true, Leading and Trailing thresholds of 25, a sliding window trimming approach (SLIDINGWINDOW) of 4:15, an average quality level (AVGQUAL) of 20, and a minimum length (MINLEN) of 60.
Reads were mapped to the genome of T. pseudonana (Thaps3 FilteredModels2) using Hisat2-2.1.0.
We calculated the number of T. pseudonana reads that aligned to the gene models from resulting SAM alignment files with aligned sequences used in subsequent analyses.
Genome_build: Thaps3 FilteredModels2
Supplementary_files_format_and_content: csv files include TPM values for each sample,

organism: Thalassiosira pseudonana

source_name: Thalassiosira pseudonana

extract_protocol:
Total RNA was extracted from 0.2 µm membrane filters with the Zymo Direct-zol RNA MiniPrep Plus kit.
Poly-A-selection, library preparation and sequencing were performed at the Northwest Genomics Center (University of Washington) with standard Illumina NextSeq protocols

value: CCMP 1335

value: Hydrogen peroxide treated

tag: time of sampling

value: 2 h


title: LNCaP_vehicle_4h_1_Input


title: Hydrogren peroxide T2 N2


title: Ankle MSU rep3

source_name: Ankle joint

value: Ankle joint


title: Hydrogren peroxide T2 N1


title: Control for H202 T2 N3

value: Control


title: LNCaP_R1881_4h_2_O-GlcNAc


title: Barley_3dpi_1

city: Cologne

first: Jasper

middle: Robert Lisette

last: Depotter

address: Zülpicher Straße 47a

institute: University of Cologne

data_processing:
The reads were then mapped to the reference genome using Bowtie 2 (v2.3.5.1) with the first 15 nucleotides on the 5’-end of the reads being trimmed due to inferior quality
Reads were counted to the U. hordei loci using the R package Rsubread (v1.34.7). Here, multi-mapping reads were counted and the default minimum mapping quality score of 0 was used, to include reads that would have multiple best mapping locations. For the gene loci, reads were counted that were mapped to the predicted coding regions. For the LTR-RT loci, reads were only counted that mapped within LTR-RT loci, excluding the reads that mapped onto the 10% of either edge of the locus.
Assembly: GCA_022749175.1
Supplementary files format and content: tab-deliminated file including the read counts for every sample

organism: Ustilago hordei

source_name: Infected barley leaves

extract_protocol:
RNA was isolated by using the TRIzol® extraction method (Invitrogen; Karlsruhe, Germany) according to the manufacturer’s instructions. Subsequently, total RNA samples were treated with Turbo DNA-Free™ Kit (Ambion/Applied Biosystems; Darmstadt, Germany) to remove any DNA contamination according to the manufacturer’s instructions.
NEB Next® Ultra™ RNA Library Prep Kit (NEB, Ipswich, MA, USA)

value: Infected barley leaves

value: fungal + plant cells


title: Ankle MSU rep2


title: Barley_3dpi_3


title: Barley_3dpi_2


title: Axenic_YEPSlight_3

source_name: fungal tissue

value: fungal tissue

value: fungal cells


title: Ankle WT rep3


title: DRG WT rep2


title: LNCaP_vehicle_4h_1_O-GlcNAc

value: LNCaP

value: Prostate cancer cell line


title: Ankle MSU rep1

value: 10 weeks

value: treated with MSU for 8 hours


title: Axenic_YEPSlight_1


title: LNCaP_vehicle_4h_2_AR

value: Vehicle


title: Filtrate treated T120 N2

value: Bacteria filtrate treated


title: Ankle WT rep2

value: untreated


title: Filtrate treated T120 N3


title: CGc_RAW_3

city: Frederiksberg C

first: Andrew

last: Williams

state: --- Select One ---

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

data_processing:
Adaptor sequences and low quality reads removed
Mapped to Mus Muscularis (mm10) using HISAT
DEG assessed using DeSeq2
Assembly: mm10
Supplementary files format and content: excel file with count data for each sample.

organism: Mus

source_name: Macrophage

growth_protocol: RAW264.7 cells were exposed to 1 ug/mL LPS, or LPS together withh 100 uM of caffeic acid, chlorgenic acid, or the corresponding cystiene adducts

extract_protocol:
Total RNA was extracted using miRNAeasy kits (Qiagen).
Standard Illumina

treatment_protocol: 6 hours treatment prior to RNA extraction

value: Macrophage

value: LPS + chlorogenic acid-Cys


title: Control for H202 T2 N2

value: CCMP 1335