title: 5AD_ApoEsiRNA_2Months_F_C10

value: Brain (Cortex)

value: Apoe siRNA


title: AB2114

status: Public on Oct 02 2023

type: SRA

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: SPIDseq

library_source: transcriptomic single cell

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: meta_for_ncbi2.txt

molecule: total RNA

organism: Mus musculus

source_name: C57/b6 PA-GFP

growth_protocol: Tumor cells (5×105 EO771-tdTomato cells) were suspended in PBS and mixed 1:1 with Matrigel (BD Biosciences, 354230). A total of 100 µL of cell mixture was injected into the right inguinal mammary glands of 8-week-old female PA-GFP C57BL/6 mice. Tumors were resected 3 weeks following the injection, and CT imaging of lungs was performed once a week until metastases appeared. Mice were anesthetized and lung perfusion was performed. Photoactivation and imaging were performed as described previously. Following perfusion and dissection of the intact lungs, lung lobes were separated (at this stage metastatic sites were often seen by eye as distinct red dots). Tissues were viewed in the microscope to identify metastases or validate the lack of tdTomato signal in distal normal, relapse-free, or Pre-MET tissues. Because we attempted to characterize metastasis as early as possible after their first detection, in some cases only one metastatic lesion was found and therefore we were able to only label either the core or the invasive margin.

extract_protocol:
Lung tissues or primary EO771 tumors underwent mechanical and enzymatic digestion for 15 min at 37°C (gentleMACSTM C tube, Miltenyi Biotec Inc., San Diego, CA; 0.1mg/ml DNase type I (Roche), and 1mg/ml Collagenase IV (Worthington) in RPMI-1640). Lungs were dissociated with the m_lung program, and tumors with the h_tumor program. Cells were then filtered through a 100µm cell strainer, washed with cold PBS, and centrifuged (5 min, 4°C, 300g). Following tissue digestion, cells were washed and resuspended in cold FACS buffer (0.5% BSA and 2 mM EDTA in PBS), and incubated with fluorophore conjugated antibodies (CD31-PE/Cy7, Biolegend 102417 ; CD45-APC/Cy7, Biolegend 103115). Following the staining cells were filtered through a 70-µm strainer. Before sorting, cells were stained with DAPI to exclude dead/dying cells. Cell sorting was performed using a BD FACSAria Fusion flow cytometer (BD Biosciences), gating for CD31-CD45+ cells, or when isolating photoactivated cells for CD31-GFP+ (after exclusion of dead cells and doublets).
3' end mRNA libraries were prepared for sequencing using SPID-seq.

tag: strain

value: C57/b6 PA-GFP

tag: mouse id

value: BC #6

value: NO

tag: sorted cells_(gating)

tag: area

value: No-MET

tag: sample type

value: Whole lungs

tag: status

value: Relapse-free


title: HNRNPU D28 [P16902_149]

city: Solna

first: Kristiina

last: Tammimies

address: Visiongatan 4

department: Department of Women's and Children's Health

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic

data_processing:
fastq files were aligned to version GRCh37/hg19 of human reference genome, using Star aligner.
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Assembly: GRCh37/hg19 of human reference genome
Supplementary files format and content: tab-delimited text files include sequence counts per gene for each Sample

organism: Homo sapiens

source_name: iPSCs-derived NES cells differentiated for 28 days

growth_protocol: Patient-derived and previously established NES cells were seeded on 20 µg/ml poly-L-ornithine, and 1 µg/ml laminin precoated plastic surfaces in DMEM/F12 + Glutamax medium supplemented with 0.05X B-27, 1X N-2, 10 ng/ml bFGF , 10 ng/ml EGF and 10 U/ml penicillin/streptomycin, replacing media every day. Upon starting the differentiation, cells were changed to medium with an increased 0.5X B-27 concentration without bFGF and EGF.

extract_protocol:
Cells were lysed in TRIzol reagent (Invitrogen), and RNA isolated with ReliaPrep RNA Cell Miniprep kit (Promega Z6012)
Libraries were prepared using the TruSeq Stranded Total RNA Kit with Ribo-Zero Gold, except for siNTC-D28 and siHNRNPU-D28 libraries prepared with Illumina TruSeq Stranded mRNA kit due to low RNA yields. All libraries were sequenced on the NovaSeq6000 platform with a 2x151 setup using NovaSeqXp workflow in S4 mode flowcell.

tag: treatment

value: untreated


title: AB2022

description: SPIDseq


title: HNRNPU D28 [P16902_145]


title: AB2021

description: SPIDseq


title: 5AD_ApoEsiRNA_2Months_F_C8

city: Worcester

first: Samuel

last: Hildebrand

state: MA

address: 368 Plantation Street

department: RNA Therapeutics Institute

country: USA

institute: University of Massachusetts Medical School

data_processing:
FASTQ files were mapped to the mouse genome using STAR v2.7.6e with default settings. Custom .gtf files were used for each Alzheimer's mouse model.
Transcripts were quantified using RSEM v1.3.3 using default settings.
Libraries were normalized and differential expression analysis was performed using DESeq2 v1.22.2 with apeglm shrinkage and alpha=0.05
Genome_build: mm10
Supplementary_files_format_and_content: Normalized counts data from DESeq2 are provided as .csv files. Metadata files for DESeq2 analysis are provided as .csv files.

molecule: polyA RNA

source_name: Brain (Cortex)

growth_protocol: Mice were fed on a normal chow diet

extract_protocol:
RNA was extracted using the NEB Monarch Total RNA Miniprep Kit (T2010S) with the protocol to purify long as well as short RNAs
Sequencing libraries were constructed using the Illumina TruSeq Stranded mRNA Library Prep kit (Illumina cat# 20020595) according to the manufacterers protocol. Briefly, PolyA RNA was purified with oligo-dT beads. This RNA was fragmented and first and second strand cDNA was synthesized. 3' cDNA ends were adenylated, adapters were ligated, and the library PCR was performed. library quality was checked using a Bioanalyzer High Sensitivity DNA kit (Agilent cat# 5067-4626). Libraries were purified from adapter dimers by gel extraction. Final libraries were quantified using the KAPA Library Quantification kit (Roche cat# 07960140001) according to the manufacterer's protocol.

treatment_protocol: Mice were injected with either a non-targeting control siRNA or a mouse Apoe targeting siRNA

tag: tissue

tag: collection time post-treatment

value: 2 Months

tag: injection

value: Bilateral Intracerebroventricular

tag: scaffold/conjugate

value: Divalent siRNA


title: 5AD_ApoEsiRNA_2Months_F_C7


title: CTRL D28 [P16902_148]


title: HNRNPU D28 [P16902_144]


title: 5AD_ApoEsiRNA_2Months_F_C6


title: liver mitochondrial RNA, C57BL-NASH

city: Fukushima

first: Yoshimi

last: Homma

address: 1 Hikariga-oka

department: Biomolecular Research

country: Japan

institute: Fukushima Medical University School of Medicine

data_processing:
Basecalls performed using bcl2fastq v2.20.
Sequencing adaptors, low quality reads, and bases were trimmed with Trimmomatic-0.32 tool.
The sequence reads were aligned to the Mouse reference genome (mm10) using Tophat2-2.1.1 (Bowtie2-2.3.2).
The read counts allocated for each gene and transcript (Ensembl Genes 2013.4.3) were quantified using a Trimmed Mean of M-value (TMM) method using StrandNGS 3.1 software (Agilent Technologies, Santa Clara, CA).
Genome_build: mm10
Supplementary_files_format_and_content: An excel format file (XLSX) includes TMM quantification values and Ensembl gene annotations of all samples.

source_name: liver mitochondria

extract_protocol:
Total RNA was extracted using QIAGEN miRNeasy Mini Kit (Qiagen) with manufacturer's instructions.
Total RNA obtained from each sample was subjected to a sequencing library construction using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, MA) with NEBNext rRNA Depletion Kit (Human/Mouse/Rat) according to the manufacturer’s protocols.

value: liver

tag: age

value: post natal week 7

tag: genotype

value: wild type-NASH


title: liver mitochondrial RNA, C57BL-db


title: CTRL D28 [P16902_147]


title: 5AD_NTC_2Months_F_C5

value: NTC


title: CTRL D28 [P16902_146]


title: liver mitochondrial RNA, C57BL-ob


title: 5AD_ApoEsiRNA_2Months_F_C9


title: 5AD_NTC_2Months_F_C4


title: siHNRNPU D5 [P13555_215]

source_name: iPSCs-derived NES cells differentiated for 5 days

value: 0.5 microM siHNRNPU (Dharmacon E-013501-00-0010)


title: liver mitochondrial RNA, C57BL

value: wild type


title: AB2020

description: SPIDseq


title: 5AD_NTC_2Months_F_C3

value: Brain (Cortex)


title: siNTC D0 [P13555_214]

source_name: iPSCs-derived NES cells

value: 0.5 microM siNTC (Dharmacon D-001950-01-20)


title: Delta-5

city: Baltimore

first: Maria

last: Golson

state: MD

address: 5501 Hopkins Bayview Circle, Allergy and Asthma 2A.20

institute: Johns Hopkins University

description: bulk RNA-seq, NuGen Ovation and NEB Ultra

data_processing:
Gene expression values were generated for human genome release hg19 using RUM
Differential expression was assessed using EdgeR
False discovery rates were calculated fromP-values using the R function p.adjust in BH mode
Normalization was done by scaling the reads per kb values by the mean ratio for expressed genes
Assembly: hg19
Supplementary files format and content: text files contain normalized expression data for each sample
Supplementary files format and content: text files contain FPKM for each sample

source_name: Islets

growth_protocol: Cultured in Prodo Complete

extract_protocol:
Total RNA was extracted with a Recoverall Total Nucleic Acid kit (Life Technologies
Illumina RNA-Seq libraries were prepared from total RNA using the NuGen Ovation and NEB Ultra kit to produce cDNA for 10 samples (2 cell types, 5 donors). Fragmentation, blunt-ending, A-tailing and adapter ligation were then performed with the Illumina non-stranded RNA-Seq library prep kit to produced indexed libraries

value: Islets

tag: cell type

value: Delta Cell


title: 5AD_NTC_2Months_F_C2


title: Delta-4


title: 5AD_NTC_2Months_F_C1


title: Delta-3


title: siNTC D0 [P13555_213]


title: HNRNPUdel D5 [P13555_212]


title: Human Ependymoma Tissue (EPEND099P)

type: genomic

city: Nottingham

first: Timothy

middle: A

last: Ritzmann

address: Coates Road

department: Children's Brain Tumour Research Centre

country: United Kingdom

institute: University of Nottingham

hyb_protocol: Illumina Protocol

scan_protocol: Illumina Protocol

data_processing: Bioconductor (version 3.3) package minifi (version 1.18) using function preprocessIllumina. Data filtered for SNPs, sex chromosomes and probes with detection p-value>0.01.

label: biotin/dnp

molecule: genomic DNA

source_name: Human Ependymoma Tissue

label_protocol: Illumina Protocol

extract_protocol: DNA extracted from formalin fixed, paraffin embedded material using the Qiagen ALLprep kit as per protocol.

tag: disease state

value: pediatric ependymoma

tag: methylation class

tag: gender

value: Female

tag: who grade

tag: tumor location

value: PF

tag: event free survival

tag: overall survival

tag: survival status

value: Alive

tag: recurrence

value: No Recurrence

tag: 1q gain

value: no gain

tag: resection status

value: Complete


title: 5AD_ApoEsiRNA_2Weeks_M_B9

tag: tissue

tag: treatment

value: Apoe siRNA

tag: collection time post-treatment

value: 2 Weeks

value: Bilateral Intracerebroventricular

value: Divalent siRNA

tag: strain


title: Delta-2


title: CTRL D5 [P13555_210]

value: untreated


title: 5AD_ApoEsiRNA_2Weeks_M_B8

tag: injection

tag: scaffold/conjugate


title: Delta-1

tag: cell type


title: 5AD_ApoEsiRNA_2Weeks_M_B10


title: Beta-5

value: Beta Cell


title: Human Ependymoma Tissue (Epend213P)

tag: disease state

tag: methylation class

value: recurrence


title: siHNRNPU D5 [P13555_140]

value: 0.5 microM siHNRNPU (Dharmacon E-013501-00-0010)


title: Human Ependymoma Tissue (EPEND126P)

tag: gender

tag: who grade

value: Recurrence


title: Beta-4

value: Islets


title: siHNRNPU D5 [P13555_139]


title: 5AD_ApoEsiRNA_2Weeks_M_B6

value: Brain (Cortex)


title: 5AD_ApoEsiRNA_2Weeks_M_B7


title: Beta-3


title: 5AD_NTC_2Weeks_M_B5

value: NTC


title: Human Ependymoma Tissue (EPEND101P)

value: pediatric ependymoma

value: Male

tag: tumor location

value: PF

tag: event free survival

value: Death

value: Incomplete


title: siHNRNPU D5 [P13555_136]


title: Human Ependymoma Tissue (EPEND212P)

tag: overall survival

tag: survival status

value: Alive

value: No Recurrence

value: no gain

value: Complete


title: Beta-2


title: CTRL D5 [P13555_211]

value: untreated


title: Human Ependymoma Tissue (EPEND021P)

tag: recurrence

tag: 1q gain


title: Beta-1

tag: tissue

value: Beta Cell


title: Human Ependymoma Tissue (EPEND311P)

value: Female

tag: resection status


title: Human Ependymoma Tissue (EPEND173P)


title: Human Ependymoma Tissue (EPEND157P)


title: Human Ependymoma Tissue (EPEND320P)


title: Human Ependymoma Tissue (EPEND170P)


title: Human Ependymoma Tissue (EPEND219P)


title: Human Ependymoma Tissue (EPEND019P)

value: gain


title: siHNRNPU D5 [P13555_137]

tag: treatment

value: 0.5 microM siHNRNPU (Dharmacon E-013501-00-0010)


title: siHNRNPU D0 [P13555_132]


title: Human Ependymoma Tissue (EPEND036P)

value: Recurrence


title: Human Ependymoma Tissue (EPEND125P)


title: 5AD_NTC_2Weeks_M_B1

value: Brain (Cortex)

tag: collection time post-treatment

value: 2 Weeks

value: Bilateral Intracerebroventricular

value: Divalent siRNA

tag: strain


title: Human Ependymoma Tissue (EPEND143P)

value: pediatric ependymoma

value: Male

value: PF


title: 5AD_NTC_2Weeks_M_B4

value: NTC

tag: injection

tag: scaffold/conjugate


title: Control, treated with DMSO 0.1% for 4 days

city: Toronto

first: Micheal

middle: D

last: Tyers

state: Ontario

address: 555 University Avenue

country: Canada

institute: The Hospital for Sick Children

description:
Illumina HiSeq 2000
sgRNAs PCR-amplified from genomic DNA
7_days_DOX_4_days_DMSO_0.1%

library_source: genomic

data_processing:
Reads were aligned using Bowtie2.2.5 in the forward direction only (--norc option) with otherwise default parameters and total read counts per sgRNA were tabulated.
Read counts from different sequencing lanes for the same sample were summed and counts for all control samples were summed.
Assembly: For Nalm-6 screens: EKO sgRNA library (Bertomeu et al. 2017, PMID:29038160), using only the core RefSeq gene-targeting sgRNA set of of the library.
Supplementary files format and content: Tab-separated sgRNA read counts per sample

growth_protocol: Nalm-6 cells were grown in 10% FBS (v/v) (Wisent) RPMI 1640 medium (Wisent) at 5% (v/v) CO2 and 37°C.

extract_protocol:
Samples were PBS-washed and cell pellets frozen. Genomic DNA was extracted using the QIAamp DNA blood maxi kit (Qiagen).
sgRNA libraries were prepared by PCR amplification to add sequencing adapters and indices.

treatment_protocol: A Nalm-6 clone with inducible expression of Cas9 was thawed, and Cas9 expression induced with doxycycline at 2 µg/mL for 7 days (see Bertomeu et al., 2017 for details). The pooled EKO library was split in different T-75 flasks, compounds added, and propagated for 8 days. Fresh media and compound was added at each cell passage.

tag: cell line

tag: cell type

value: pre-B lymphoid cell line

value: 0.1% DMSO

tag: time

value: 4 days


title: Human Ependymoma Tissue (EPEND007P)

tag: disease state

tag: methylation class

tag: gender

tag: who grade

value: Alive

value: No Recurrence

value: Complete


title: siHNRNPU D0 [P13555_134]


title: 5AD_NTC_2Weeks_M_B2


title: Human Ependymoma Tissue (EPEND169P)

tag: tumor location

tag: event free survival

tag: overall survival

tag: survival status

value: Death

value: no gain


title: siHNRNPU D0 [P13555_135]

value: 0.5 microM siHNRNPU (Dharmacon E-013501-00-0010)


title: siHNRNPU D0 [P13555_133]


title: Human Ependymoma Tissue (EPEND210P)

tag: recurrence

tag: 1q gain

tag: resection status

value: Incomplete


title: Control, treated with DMSO 0.1% for 6 days

description:
Illumina HiSeq 2000
sgRNAs PCR-amplified from genomic DNA
7_days_DOX_6_days_DMSO_0.1%

tag: treatment

value: 6 days


title: Control, treated with DMSO 0.1% for 2 days

description:
Illumina HiSeq 2000
sgRNAs PCR-amplified from genomic DNA
7_days_DOX_2_days_DMSO_0.1%

value: 2 days


title: 5AD_ApoEsiRNA_2Week_F_A9

tag: tissue

value: Brain (Cortex)

value: Apoe siRNA

tag: collection time post-treatment

value: 2 Weeks

tag: injection

value: Bilateral Intracerebroventricular

value: Divalent siRNA

tag: strain


title: 5AD_ApoEsiRNA_2Week_F_A7

tag: scaffold/conjugate


title: Control, treated with DMSO 0.3% for 8 days

description:
Illumina HiSeq 2000
sgRNAs PCR-amplified from genomic DNA
DMSO_0.3%

tag: cell line

tag: cell type

value: pre-B lymphoid cell line

value: 0.3% DMSO

tag: time

value: 8 days


title: Human Ependymoma Tissue (EPEND086P)

tag: disease state

value: pediatric ependymoma

tag: methylation class

tag: gender

value: Male

tag: who grade

value: PF

value: Alive


title: siNTC D5 [P13555_129]

value: 0.5 microM siNTC (Dharmacon D-001950-01-20)


title: Human Ependymoma Tissue (EPEND379P)

tag: tumor location


title: siNTC D5 [P13555_130]


title: Control, untreated for 8 days

description:
Illumina HiSeq 2000
sgRNAs PCR-amplified from genomic DNA
7_days_DOX_8_days_no_treatment


title: 5AD_ApoEsiRNA_2Week_F_A6


title: 5AD_ApoEsiRNA_2Week_F_A8


title: siNTC D5 [P13555_128]


title: siHNRNPU D0 [P13555_131]

value: 0.5 microM siHNRNPU (Dharmacon E-013501-00-0010)


title: Treated with 12.5 nM BI6727 for 8 days

description:
Illumina HiSeq 2000 and Illumina NextSeq 500
sgRNAs PCR-amplified from genomic DNA
BI6727_12.5nM


title: 5AD_ApoEsiRNA_2Week_F_A5


title: Treated with 100 nM GSK461364A for 8 days

description:
Illumina HiSeq 2000 and Illumina NextSeq 500
sgRNAs PCR-amplified from genomic DNA
GSK461364A_100nM


title: Control, Cas9 induced with Doxycicline 7 days

description:
Illumina HiSeq 2000
sgRNAs PCR-amplified from genomic DNA
7_days_DOX_day_0_of_screen

value: Not applicable

value: 0 days


title: 5AD_NTC_2Week_F_A4

value: NTC


title: siNTC D5 [P13555_127]


title: Human Ependymoma Tissue (Epend371R)

value: Female

tag: event free survival

tag: overall survival

tag: survival status

tag: recurrence

value: recurrence

value: gain


title: Human Ependymoma Tissue (EPEND127P)

value: Recurrence

tag: 1q gain

value: no gain

tag: resection status

value: Incomplete


title: Treated with 4.2 nM BI2536 for 8 days

description:
Illumina HiSeq 2000 and Illumina NextSeq 500
sgRNAs PCR-amplified from genomic DNA
BI2536_4.2nM

value: pre-B lymphoid cell line

tag: treatment


title: 5AD_NTC_2Weeks_M_B3

tag: tissue

value: Brain (Cortex)

tag: collection time post-treatment

value: 2 Weeks

tag: injection

value: Bilateral Intracerebroventricular

value: Divalent siRNA

tag: strain


title: Human Ependymoma Tissue (EPEND119P)

value: pediatric ependymoma

value: PF

value: Alive

value: No Recurrence

value: Complete


title: 5AD_NTC_2Week_F_A3

value: NTC

tag: scaffold/conjugate


title: 5AD_NTC_2Week_F_A2


title: 5AD_NTC_2Week_F_A1


title: siNTC D0 [P13555_124]

value: 0.5 microM siNTC (Dharmacon D-001950-01-20)


title: siNTC D5 [P13555_126]


title: AML Pt#46, CD34+TMIGD2 negative [X46_TMnegative_19200R_02_12]

city: bronx

first: Hao

last: Wang

state: NY

address: 1300 morris park ave, Forch 405

institute: Albert Einstein College of Medicine

data_processing:
RNA-seq reads from the flow-sorted primary AML cells were aligned to the human genome (hg38) using the program STAR (version 2.6.1b)
HTSeq (version 0.6.1) was then used to count the number of RNA-seq fragments in each gene in the refSeq annotation (downloaded from the UCSC genome browser in 11/2019)
DESeq2 (version 3.11) was utilized to perform differential expression analysis and principal component analysis (PCA) on genes that had an average read count >= 1 in either of the two compared sample groups
Assembly: hg38
Supplementary files format and content: xlsx
Supplementary files format and content: output from DESeq

source_name: primary AML cells

extract_protocol:
For RNA-seq using primary AML cells, total RNA was extracted from the flow-sorted CD34+TMIGD2+ and CD34+TMIGD2- cells using RNeasy Plus Micro Kit (QIAGEN).
cDNA libraries were generated using the SMARTer Ultra Low RNA kit (Clontech) for Illumina sequencing with >= 40 million paired-end reads per sample by Admera Health.

tag: cell type

value: primary AML cells

tag: genotype

value: CD34+TMIGD2 negative


title: AML Pt#46, CD34+TMIGD2 postive [X46_TMpositive_19200R_02_11]

value: CD34+TMIGD2 postive


title: AML Pt#40, CD34+TMIGD2 postive [X40_TMpositive_19200R_02_09]


title: melatonin rep4

city: Hangzhou

first: Chen

last: Wentao

state: Zhejiang

address: No. 866 Yuhangtang Road

country: China

institute: Zhejiang University

data_processing:
FastQC software was used for quality control of the original sequencing data bases with default parameter. StringTie was used to calculated Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) value. Differential gene expression was calculated using the DESeq2 package. Genes with the corresponding q values < 0.05 and fold change > 2 were considered to be differentially expressed genes (DEGs).
Assembly: scrofa.Sscrofa11.1
Supplementary files format and content: Text file includes FPKM value for every sample

organism: Sus scrofa

source_name: Longissimus dorsi

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) . The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000.

value: Longissimus dorsi

tag: breed

value: Duroc x Landrace x Yorkshire

value: melatonin


title: siNTC D0 [P13555_123]


title: melatonin rep3


title: AML Pt#36, CD34+TMIGD2 negative [X36_TMnegative_19200R_02_08V1]


title: AML Pt#40, CD34+TMIGD2 negative [X40_TMnegative_19200R_02_10]


title: Human Ependymoma Tissue (Epend288R1)

tag: disease state

tag: methylation class

tag: gender

value: Female

tag: who grade

value: Death

value: recurrence

value: no gain


title: Human Ependymoma Tissue (Epend288P)

value: pediatric ependymoma

tag: tumor location

tag: event free survival

tag: overall survival

tag: survival status


title: siNTC D0 [P13555_122]

tag: treatment


title: HNRNPUdel D5 [P13555_119]

value: untreated


title: melatonin rep2

tag: tissue


title: HNRNPUdel D5 [P13555_120]


title: HNRNPUdel D5 [P13555_118]


title: Human Ependymoma Tissue (Epend331R)

value: PF

tag: recurrence

tag: 1q gain

tag: resection status


title: AML Pt#36, CD34+TMIGD2 postive [X36_TMpositive_19200R_02_07V1]


title: Human Ependymoma Tissue (Epend288R2)


title: HNRNPUdel D5 [P13555_116]


title: AML Pt#31, CD34+TMIGD2 negative [X31_TMnegative_19200R_02_06]


title: melatonin rep1


title: control rep4

value: saline


title: AML Pt#31, CD34+TMIGD2 postive [X31_TMpositive_19200R_02_05]


title: Human Ependymoma Tissue (Epend330R)

value: ST

value: Alive

value: gain

value: Complete


title: control rep3


title: HNRNPUdel D0 [P13555_115]


title: HNRNPUdel D0 [P13555_114]


title: AML Pt#24, CD34+TMIGD2 negative [X24_TMnegative_19200R_02_04]

value: primary AML cells

value: CD34+TMIGD2 negative


title: control rep2

value: Longissimus dorsi


title: AML Pt#24, CD34+TMIGD2 postive [X24_TMpositive_19200R_02_03]

value: CD34+TMIGD2 postive


title: HNRNPUdel D0 [P13555_113]


title: HNRNPUdel D0 [P13555_112]


title: control rep1

value: Duroc x Landrace x Yorkshire


title: Human Ependymoma Tissue (Epend203P)

value: Female

value: Incomplete


title: HNRNPUdel D0 [P13555_111]


title: AML Pt#8, CD34+TMIGD2 postive [X8_TMpositive_19200R_02_01]


title: AML Pt#8, CD34+TMIGD2 negative [X8_TMnegative_19200R_02_02]


title: CTRL D5 [P13555_110]


title: SAMPLE 6_WT

type: RNA

city: Leuven

first: Patrizia

last: Agostinis

address: Herestraat 49 - box 802

department: Cellular and Molecular Medicine

country: Belgium

institute: VIB-KU Leuven

description: Extracted RNA was processed and data was recorded using a protocol recommended by the supplier.

hyb_protocol: Recommended protocol

scan_protocol: Recommended protocol

data_processing:
The raw data was processed using nSolver 4.0 advanced platform. Fusion Analysis Details
Perform fusion analysis: No
p-value end probe threshold: 0.05
p-value junction probe threshold: 0.05. SNV Analysis Details
Perform snv analysis: No
Fold change threshold(s): 1, 2
p-value threshold(s): 0.01, 0.01
Reference samples:
NA
Use EM post processing: Yes
Use debiasing post processing: Yes. Normalization Details
Perform normalization on: mRNA
Number of normalization probes: mRNA: Dynamic. Pathway Scoring Analysis Details
Perform pathway scoring analysis: TRUE. Differential Expression Analysis Details
Perform differential expression testing: TRUE
Predictors: New.Annotation
Confounders: none
P-value adjustment: BY
Run gene set analysis TRUE
Covariates to include in plots: New.Annotation. Pathview Details
Display results using Pathview: TRUE
Color Pathview pathview plots by: Fold-change
P-value threshold: 0.05
Additional KEGG IDs: none

label: N/Ap

source_name: B16-F10 derived endothelial cells

label_protocol: Recommended protocol

growth_protocol: N/Ap

extract_protocol: Trizol with Glycogen carrier

treatment_protocol: N/Ap

tag: strain

value: WT

value: B16-F10 derived endothelial cells


title: SAMPLE 5_ATG5BECKO

tag: cell type


title: CTRL D5 [P13555_109]


title: SAMPLE 4_WT

tag: genotype


title: Human Ependymoma Tissue (Epend205R1)

value: pediatric ependymoma

value: Male

value: Death

value: recurrence

value: no gain


title: Human Ependymoma Tissue (Epend205P)

value: PF


title: Human Ependymoma Tissue (Epend205R2)


title: Human Ependymoma Tissue (Epend234R)


title: CTRL D5 [P13555_106]

value: untreated


title: CTRL D0 [P13555_105]


title: SAMPLE 3_ATG5BECKO


title: Case 9

city: Tlalpan

first: M Elizabeth

last: Tejero

state: Ciudad de MÃ©xico

address: Periferico sur 4809

country: Mexico

institute: Instituto Nacional de Medicina Genomica, Mexico City

description:
Small RNA expression data in human plasma
PlasmaMiRNA MetSyndrome

hyb_protocol: FlashTag Biotin HSR RNA labeling kit

scan_protocol: Microarrays were scanned using the Affymetrix GeneChip Command Console.

data_processing: Data were analyzed in the R/Bioconductor environment with the software Oligo, pd.mirna.3.0 and Linear Models for Microarray Analysis (LIMMA).

label: biotin

source_name: human plasma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from  ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

extract_protocol: Total RNA was isolated from 1 mL plasma using Trizol reagent following the manufacturer’s instructions

tag: diagnosis

value: Metabolic syndrome

value: Plasma


title: SAMPLE 2_ATG5BECKO


title: Control 9

value: control


title: Human Ependymoma Tissue (Epend234P)

tag: disease state

value: Complete


title: SAMPLE 1_WT


title: Case 8


title: Human Ependymoma Tissue (Epend197R)

tag: methylation class


title: CTRL D0 [P13555_104]


title: Control 8

tag: gender


title: Patient#47

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute

hyb_protocol: hybridization was performed at 65°C for 16h

scan_protocol: data were collected using nCounter Digital Analyzer at the standard resolution of 280 fields of view (fov)

data_processing: Raw counts were extracted from the nSolver analysis software 4.0 and raw RCC files were analysed using nSolver Software and Advaced Analysis Module

source_name: epithelial ovarian cancer

label_protocol: NanoString target-specific oligonucleotide probe pairs, fluorescently-labeled specific Reporter Tags, and a biotinylated universal Capture Tag were used

extract_protocol: Nanostring technology, total RNA was extracted from FFPE samples by using Maxwell RSC RNA FFPE Kit and Maxwell RSC Instrument (Promega), according to manufacturer’s instructions.

value: ovary

tag: Stage


title: CTRL D0 [P13555_103]


title: Patient#45


title: Control 7


title: CTRL D0 [P13555_102]


title: Patient#44


title: CTRL D0 [P13555_101]


title: Human Ependymoma Tissue (Epend195R)

tag: who grade

tag: tumor location

value: gain


title: Case 7

value: Female


title: Patient#43


title: Human Ependymoma Tissue (Epend196R)

tag: event free survival

tag: overall survival


title: Patient#41


title: Case 6


title: Control 6


title: MCF7 ICI R3

city: Utrecht

first: Stefan

last: Prekovic

address: Universiteitsweg 100

department: CMM

country: Netherlands

institute: UMC Utrecht

data_processing:
Sequencing data were aligned to the human reference genome hg38 using HISAT2 (v2.1.0), and the number of reads per gene was measured with HTSeq count (v0.5.3)
Assembly: hg38
Supplementary files format and content: csv files include count values for each Sample

growth_protocol: DMEM + 10% FCS + 1% Pen/Strep, cultured at 5% CO2 and 37 °C.

extract_protocol: Total RNA was extracted using RNeasy Mini kit (Qiagen, Germany) following manufacturer´s instructions.

treatment_protocol: Cells were left untreated or treated with 100nM Dexamethasone or 100nM Fuvlestrant for 16 hours.

tag: cell line

value: Breast Cancer Cells

tag: treatment

value: 100nM Fulvestrant

tag: time

value: 16 hours


title: MCF7 ICI R2

value: WT


title: Patient#42

tag: tissue


title: Human Ependymoma Tissue (Epend195P)

value: pediatric ependymoma

value: Male

tag: survival status

tag: recurrence

tag: 1q gain

tag: resection status


title: Control 4

tag: diagnosis


title: Control 5


title: Human Ependymoma Tissue (Epend256R)

tag: disease state

value: Death

value: recurrence

value: Incomplete


title: Patient#40


title: Human Ependymoma Tissue (Epend197P)

tag: methylation class

value: PF

value: no gain


title: Human Ependymoma Tissue (Epend211R)

tag: gender

value: Alive


title: Case 4

value: Metabolic syndrome

value: Plasma


title: Human Ependymoma Tissue (Epend331P)

value: Complete


title: MCF7 ICI R1

tag: cell type

tag: genotype


title: Patient#38

value: ovary

tag: Stage


title: MCF7 DEXA R3

value: 100nM Dexamethasone


title: Patient#39


title: Control 3

value: control

value: Female


title: MCF7 DEXA R2

value: Breast Cancer Cells

value: 16 hours


title: Human Ependymoma Tissue (Epend306R)

value: pediatric ependymoma

tag: who grade

tag: tumor location

value: ST

tag: event free survival


title: MCF7 DEXA R1

tag: cell line

value: WT

tag: treatment


title: Patient#37

tag: tissue


title: Case 3


title: Human Ependymoma Tissue (Epend256P)

value: Male

tag: overall survival

tag: survival status

value: Death

value: recurrence


title: Patient#36


title: Control 2


title: Human Ependymoma Tissue (Epend211P)

value: PF

tag: recurrence

tag: 1q gain

value: no gain


title: Human Ependymoma Tissue (Epend306P)

tag: resection status


title: Human Ependymoma Tissue (Epend203R)

tag: disease state

value: Alive

value: Incomplete


title: MCF7 FCS R3

value: DMSO

tag: time


title: Patient#35

value: ovary


title: MCF7 FCS R2


title: Case 2

tag: diagnosis

value: Metabolic syndrome

tag: gender

value: Plasma


title: Human Ependymoma Tissue (Epend213R)

tag: methylation class

value: Female

value: Complete


title: Patient#34

tag: Stage


title: MCF7 FCS R1

tag: cell type

value: Breast Cancer Cells

tag: genotype

value: 16 hours


title: RNA-seq siPRMT1 HEK293

city: Xiamen

first: Guosheng

last: Hu

state: Fujian

address: Xiang'an South Road, Xiang'an District

department: School of Pharmaceutical Sciences

institute: xiamen University

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Tophat version 2.1.1.
Assembly: hg19

growth_protocol: HEK293 cells were cultured in DMEM medium supplemented with 10% FBS and 1%penicillin and streptomycin

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality.
RNA library preparation was performed by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420L). Paired-end sequencing was performed with Illumina HiSeq platform.

treatment_protocol: HEK293 cells were transfected with control siRNA or siRNA specifically targeting PRMT1 and maintained in  DMEM medium supplemented with 10% FBS and 1% penncilin and streptomycin for three days.

value: Human Embryonic Kidney 293

tag: transfection


title: Human Ependymoma Tissue (Epend329P)

value: pediatric ependymoma

tag: who grade

tag: tumor location

tag: event free survival

value: gain


title: RNA-seq siCTL HEK293

tag: cell line

tag: treatment

value: siCTL


title: Patient#33

tag: tissue


title: Patient#32


title: Input3_shCtrl

city: Montpellier

first: Rosemary

last: Kiernan

address: 141 rue de la cardonille

country: France

institute: UMR9002 CNRS-UM

data_processing:
Raw reads quality control performed with Fastqc (version 0.11.5).
Reads alignment with BWA (0.7.10) on hg38 human genome version.
Bigwig files were generated using deeptools (3.2.0) bamCompare and normalized by the corresponding input using RPGC normalization.
Assembly: hg38 (GRCh38)
Supplementary files format and content: bigwig files containing ChIP-seq coverage for each sample normalized by the corresponding input.

source_name: HeLa cells

growth_protocol: HeLa cells were routinely cultured in DMEM medium (Sigma-Aldrich) supplemented with FCS 10% and penicillin/streptomycin.

extract_protocol:
ChIP experiments were performed in HeLa cells using the ChIP IP High Sensitivity (Active Motif 53040).
ChIP-seq libraries were constructed using the Next Gen DNA Library Kit (Active Motif 53216 and 53264).

treatment_protocol: Lentiviral particles allowing expression of shRNAs were added to the medium of cells for 5 days.

value: HeLa

value: shCtrl

tag: passages

tag: chip antibody


title: Input3_shZ1

value: shRNA ZFC3H1


title: PA-500 µM treated day 25 OS-HLOs, replicate 2, scRNAseq

city: Boston

first: Alan

middle: C.

last: Mullen

address: 55 Fruit St.

department: Department of Medicine

institute: Massachusetts General Hospital

description: 10x Genomics

data_processing:
Raw bcl files were converted to fastq by the command bcl2fastq --use-bases-mask Y26,I8,Y98. Demultiplexing, barcoded processing, gene counting, aggregation and alignment to the GRCh38 genome was   performed with the cellranger software version 3.0.2 or 6.0.2. Downstream analysis was performed in python (version => 3.6) with scanpy (version => 1.7.2).
Assembly: GRCh38 (human)
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Human liver organoid (HLO)

growth_protocol: HLOs were generated from hPSCs. ULA-HLOs were grown for 21 or 34 days. OS-HLOs were cultured for 20 days before undergoing 5 days of treatment.

extract_protocol:
Freshly collected human liver organoids were washed 1X with warm DPBS(-/-) and briefly dissociated by incubation with 0.05-0.25% Trypsin-EDTA for 10 minutes at 37°C.   Day 34 ULA- and day 25 OS-HLOs underwent an additional DBPS (-/-) wash and 10 minutes of trypsinization to allow complete digestion. For each replicate, full single cell dissociation was confirmed manually by light microscopy. After a final DPBS(-/-) wash, organoids were resuspended in DPBS(-/-), counted after with the TC20™ Automated Cell Counter (Trypan Blue) and transferred on ice for library preparation.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

treatment_protocol: OS-HLOs were treated for 5 days with TGF-β1 (10 ng/ml) or PA (500 µM).

value: Human liver organoid (HLO)

value: W01, WiCell

value: hPSC-derived HLOs

value: Wild-type

value: PA 500 µM

value: day 25


title: Z1_shZ1 rep2

description: ChIP-seq anti-ZFC3H1 (Bethyl A301-457A)

value: anti-ZFC3H1 (Bethyl A301-457A)


title: PA-500 µM treated day 25 OS-HLOs, replicate 1, scRNAseq

description: 10x Genomics


title: Human Ependymoma Tissue (Epend051P)

tag: disease state

value: Female

value: PF

tag: overall survival

tag: survival status

value: Death

tag: recurrence

value: recurrence

tag: 1q gain

value: no gain

tag: resection status

value: Incomplete


title: Human Ependymoma Tissue (Epend098P)

value: pediatric ependymoma

tag: methylation class

tag: gender


title: Z1_shCtrl rep2

description: ChIP-seq anti-ZFC3H1 (Bethyl A301-457A)

value: HeLa


title: Control-for-PA day 25 OS-HLOs, replicate 2, scRNAseq

description: 10x Genomics

tag: cell type

tag: genotype

value: Control-PA

tag: time


title: Input_2


title: Case 10

tag: diagnosis

value: Metabolic syndrome

value: Plasma


title: Human Ependymoma Tissue (Epend280P)

tag: who grade

tag: tumor location

value: ST

tag: event free survival

value: gain


title: Control 1

value: control

tag: tissue


title: Patient#30

value: ovary

tag: Stage


title: Patient#28


title: RBM26

description: ChIP-seq anti-RBM26 (Bethyl A301-216A)

tag: cell line

tag: treatment

tag: passages

tag: chip antibody

value: anti-RBM26 (Bethyl A301-216A)


title: Human Ependymoma Tissue (Epend305P)

tag: disease state

value: Male

tag: overall survival

tag: survival status

tag: recurrence

tag: 1q gain


title: trial number 10, Nonresponder at 24W

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

data_processing:
Sequencing fastq files were demultiplexed using Casava v1.8.2 pipeline.
Reads with adapter contaminations were trimmed using cutadapt.
The alignment of reads to the reference genome was performed using TopHat version v2.1.0;  the quantification of expression was performed using RSEM v1.17
Only genes with more than 2 counts per million in at least 2 samples were considered for statistical analysis.
Normalisation and differential expression analysis was performed using DESeq2
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: normalised expression matrix

source_name: Peripheral blood

extract_protocol:
After ficoll centrifugation of blood, mononuclear cells were subjected to red blood cell lysis and CD34+ HSPCs were immunomagnetically isolated using the Ultrapure CD34 microbead kit suing AUTOMACS. RNA was extracted using Trizol.
Briefly, the Smart-seq2 protocol was implemented with improved reverse transcription, template switching and preamplification to increase both yield and length of cDNA libraries generated from individual cells. The Illumina-compatible cDNA sequencing library was prepared with Nextera XT DNA Library Preparation Kit

value: Myeloproliferative neoplasms

tag: treatment response

value: non-responder

tag: timepoint

value: Peripheral blood

tag: cell type

value: CD34+ HSPCs


title: Patient#31


title: Human Ependymoma Tissue (Epend258P)

tag: methylation class

tag: gender

tag: who grade

value: Alive

value: recurrence

value: no gain

tag: resection status


title: Control 10

tag: diagnosis

value: Female

tag: tissue


title: Patient#29

tag: Stage


title: Control-for-PA day 25 OS-HLOs, replicate 1, scRNAseq

description: 10x Genomics

value: Human liver organoid (HLO)

tag: cell line

value: W01, WiCell

value: hPSC-derived HLOs

tag: genotype

value: Wild-type

tag: treatment

value: Control-PA

tag: time

value: day 25


title: Patient#27

value: ovary


title: Human Ependymoma Tissue (Epend305R)

tag: disease state

value: pediatric ependymoma

tag: tumor location

value: PF

tag: event free survival

tag: overall survival

tag: survival status

value: Death

value: Incomplete


title: Patient#26


title: PAPOLG

description: ChIP-seq anti-PAPgamma (Bethyl A301-427A)

value: HeLa

tag: passages

tag: chip antibody

value: anti-PAPgamma (Bethyl A301-427A)


title: trial number 06, Nonresponder at 24W

value: Myeloproliferative neoplasms

tag: treatment response

value: non-responder

tag: timepoint

value: Peripheral blood

tag: cell type

value: CD34+ HSPCs


title: Patient#25


title: trial number 01, Nonresponder at 24W

tag: diagnosis


title: Human Ependymoma Tissue (Epend230R)

tag: methylation class

tag: gender

value: Male

tag: who grade

tag: recurrence

value: recurrence

tag: 1q gain

value: no gain

tag: resection status

value: Complete


title: trial number 05, Nonresponder at 24W

tag: tissue


title: Input_1

tag: cell line

tag: treatment


title: Patient#24

tag: Stage


title: Z1 rep1

description: ChIP-seq anti-ZFC3H1 (Bethyl A301-457A)

value: anti-ZFC3H1 (Bethyl A301-457A)


title: Patient#23


title: PolII rep1

value: anti-PolII


title: Input_shZ1

description:
shZ1_input
Input

data_processing:
Raw reads quality control performed with Fastqc (version 0.11.5).
Reads alignment with BWA (0.7.10) on hg38 human genome version.
Bigwig files were generated using deeptools (3.2.0) bamCompare and normalized by the corresponding input using RPGC normalization.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: bigwig files containing ChIP-seq coverage for each sample normalized by the corresponding input.

value: shRNA ZFC3H1


title: Human Ependymoma Tissue (Epend122P)

tag: disease state

value: pediatric ependymoma

value: Female

tag: tumor location

tag: event free survival

tag: overall survival

tag: survival status

value: Alive


title: Human Ependymoma Tissue (Epend122R)

value: PF

value: Incomplete


title: trial number 03, Nonresponder at 24W

tag: treatment response

tag: timepoint

tag: cell type


title: Patient#22

value: ovary


title: Input shCtrl

description:
shCtrl_input
Input

value: HeLa

value: shCtrl

tag: passages

tag: chip antibody


title: trial number 02, Nonresponder at 24W

tag: diagnosis

value: Myeloproliferative neoplasms

value: non-responder

value: Peripheral blood


title: Human Ependymoma Tissue (Epend97R)

tag: methylation class

tag: gender

tag: who grade

tag: recurrence

value: recurrence

tag: 1q gain

value: gain


title: Patient#20

tag: tissue

tag: Stage


title: trial number 08, Responder at 24W

value: responder

value: CD34+ HSPCs


title: Human Ependymoma Tissue (Epend121P)

tag: disease state

value: Male

tag: tumor location

tag: resection status

value: Complete


title: Patient#19


title: PAPgamma_shZ1

description:
shZ1_IP_PAPGamma
ChIP-seq anti-PAPgamma (Bethyl A301-427A)

tag: cell line

tag: treatment

value: shRNA ZFC3H1

value: anti-PAPgamma (Bethyl A301-427A)


title: WT s1026 rep1 lane3 & lane4

city: Martinsried

first: Herwig

last: Baier

address: Am Klopferspitz 18

department: Genes - Circuits - Behavior

country: Germany

institute: Max Planck Institute for Biological Intelligence

data_processing:
Standard cellRanger alignment and filtering
processed data files are output files from cellranger used for analysis in single-cell sequencing pipelines
Assembly: GRCz11
Supplementary files format and content: Standard 10x genomics cellranger output

organism: Danio rerio

source_name: brain

extract_protocol:
Cell dissociation
10X genomics

value: brain

value: s1026 transgenic line

value: neurons

tag: genotype

value: WT


title: Z1_shZ1

description:
shZ1_IP_Z1
ChIP-seq anti-ZFC3H1 (Bethyl A301-457A)

value: HeLa

value: anti-ZFC3H1 (Bethyl A301-457A)


title: trial number 04, Responder at 24W

value: Myeloproliferative neoplasms

tag: treatment response

tag: timepoint

tag: cell type


title: RBM26_shZ1

description:
shZ1_IP_RBM26
ChIP-seq anti-RBM26 (Bethyl A301-216A)

tag: passages

tag: chip antibody

value: anti-RBM26 (Bethyl A301-216A)


title: Patient#18

value: ovary


title: Human Ependymoma Tissue (Epend30P)

value: pediatric ependymoma

tag: methylation class

tag: gender

value: PF

tag: event free survival

tag: overall survival

tag: survival status

value: Death

value: recurrence

value: no gain


title: Human Ependymoma Tissue (Epend207P)

value: Female

tag: who grade

tag: recurrence

tag: 1q gain

value: gain

value: Incomplete


title: trial number 25, Responder at 24W

tag: diagnosis

value: responder

tag: tissue

value: Peripheral blood

value: CD34+ HSPCs


title: lakritz HGn12C rep4 lane1 & lane2

value: brain

tag: cell line

value: HGn12C transgenic line

value: neurons

value: lakritz

tag: treatment


title: Human Ependymoma Tissue (Epend193R)

tag: disease state

value: Male

tag: tumor location

tag: resection status

value: Complete


title: Human Ependymoma Tissue (Epend03R)

value: pediatric ependymoma

value: Alive


title: Human Ependymoma Tissue (Epend85P)

value: PF


title: trial number 13, Responder at 24W

value: Myeloproliferative neoplasms

tag: treatment response

tag: timepoint

tag: cell type


title: Patient#16

value: ovary

tag: Stage


title: trial number 18, Nonresponder at baseline

value: non-responder

value: baseline


title: lakritz HGn12C rep3 lane1 & lane2

tag: genotype


title: Human Ependymoma Tissue (Epend22R)

tag: methylation class

tag: gender

tag: event free survival

tag: overall survival

value: recurrence

value: Incomplete


title: Human Ependymoma Tissue (Epend03P)

tag: who grade

tag: survival status

tag: recurrence

tag: 1q gain

value: gain


title: Patient#17

tag: tissue


title: Z1_shCtrl

description:
shCtrl_IP_Z1
ChIP-seq anti-ZFC3H1 (Bethyl A301-457A)

tag: cell line

value: HeLa

tag: treatment

value: shCtrl

tag: passages

tag: chip antibody

value: anti-ZFC3H1 (Bethyl A301-457A)


title: trial number 17, Nonresponder at baseline

tag: diagnosis

tag: treatment response

tag: timepoint

value: Peripheral blood

value: CD34+ HSPCs


title: Patient#15

tag: Stage


title: lakritz HGn12C rep2 lane1 & lane2

value: brain

value: HGn12C transgenic line

tag: cell type

value: neurons

tag: genotype

value: lakritz


title: trial number 10, Nonresponder at baseline


title: Patient#14


title: Double Knockout 2 [DL579FOR_DKO2]

city: The Bronx

first: Alexander

last: Ferrena

address: 1301 Morris Park Ave

department: Genetics

data_processing:
RNA-seq reads were mapped to the mouse reference genome (mm10) using the STAR software (v2.6.1) with default parameters.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include aligned read count values for each Sample

source_name: Osteosarcoma tumor

extract_protocol:
Mouse tumor tissues from DKO or TKO animals were harvested and processed for RNA-seq. Approximately 100 mg of fresh tumor tissue was collected and processed using the RNeasy Mini Kit (#74104 Qiagen) for RNA extraction following the manufacturer’s protocol. Samples were first quantified and then evaluated for RNA integrity, degradation, and contamination.
Next, the rRNA-depleted RNA sample was enriched using oligo(dT) beads and randomly fragmented. This was then followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) was added with dNTPs, RNase H, and E. coli polymerase I to generate the second strand by nick translation. The final cDNA library was completed following a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection, and PCR enrichment. The library concentration was quantified using a Qubit 2.0 fluorometer (Life Technologies). The insert size was checked by an Agilent 2100 Bioanalyzer and then further quantified by qPCR.
Libraries were then sequenced using an Illumina HiSeq platform . Raw data were processed by the Illumina pipeline to produce fastq reads.

value: Osteosarcoma tumor

tag: Sex

value: female


title: lakritz HGn12C rep1 lane1 & lane2


title: Patient#13

value: ovary


title: Human Ependymoma Tissue (Epend33R)

tag: disease state

value: pediatric ependymoma

tag: methylation class

tag: gender

value: Male

tag: tumor location

value: PF

tag: event free survival

tag: overall survival

value: Death

tag: resection status


title: Human Ependymoma Tissue (Epend95R)

value: Female

tag: who grade

tag: survival status

tag: recurrence

value: recurrence

tag: 1q gain

value: no gain

value: Complete


title: Human Ependymoma Tissue (Epend118P)

value: ST

value: gain

value: Incomplete


title: Related WT HGn12C rep3 lane1 & lane2

tag: tissue

value: brain

tag: cell line

value: HGn12C transgenic line

value: Related WT

tag: treatment


title: Human Ependymoma Tissue (Epend95P)


title: PAPgamma_shCtrl

description:
shCtrl_IP_PAPGamma
ChIP-seq anti-PAPgamma (Bethyl A301-427A)

value: HeLa

value: shCtrl

tag: passages

tag: chip antibody

value: anti-PAPgamma (Bethyl A301-427A)


title: Double Knockout 3 [DL608F1R_DKO3]

tag: cell type

value: Osteosarcoma tumor

tag: genotype

tag: Sex

value: female


title: Double Knockout 1 [DL761M2R_DKO1]

value: male


title: trial number 11, Nonresponder at baseline

tag: diagnosis

value: Myeloproliferative neoplasms

tag: treatment response

value: non-responder

tag: timepoint

value: baseline

value: Peripheral blood

value: CD34+ HSPCs


title: Related WT HGn12C rep2 lane1 & lane2

value: neurons


title: Triple Knockout 3 [TL744F2T_TKO3]


title: Patient#11

value: ovary

tag: Stage


title: Related WT HGn12C rep1 lane3 & lane4


title: Human Ependymoma Tissue (Epend92P)

tag: disease state

value: pediatric ependymoma

tag: methylation class

tag: gender

value: Female

tag: tumor location

value: ST

tag: event free survival

tag: overall survival

value: Alive

value: recurrence

tag: resection status

value: Incomplete


title: Triple Knockout 2 [TL30F1T_TKO2]


title: Human Ependymoma Tissue (Epend22P)

value: Male

tag: who grade

value: PF

tag: survival status

tag: recurrence


title: trial number 05, Nonresponder at baseline

tag: tissue

tag: cell type


title: Patient#10


title: Related WT HGn12C rep1 lane1  & lane2

value: brain

tag: cell line

value: HGn12C transgenic line

tag: genotype

value: Related WT

tag: treatment


title: Patient#12


title: Triple Knockout 1 [TL724M0T_TKO1]

value: Osteosarcoma tumor

tag: Sex

value: male


title: trial number 12, Nonresponder at baseline

tag: diagnosis

value: Myeloproliferative neoplasms

tag: treatment response

value: non-responder

tag: timepoint

value: baseline

value: Peripheral blood


title: Patient#8

value: ovary

tag: Stage


title: Unrelated WT HGn12C rep4 lane1 & lane2

value: neurons

value: Unrelated WT


title: Patient#9


title: trial number 02, Nonresponder at baseline

value: CD34+ HSPCs


title: Unrelated WT HGn12C rep4 lane3 & lane4


title: Patient#7


title: S_17_1811_AN2 (WT-SALT)

city: Jeddah

first: Sabiha

last: Parween

address: Thuwal

department: Hirt lab

country: Saudi Arabia

institute: KAUST

data_processing:
Read quality was checked using FastQC and low quality reads were trimmed using the Trimmomatic version 0.32
transcript structures were reconstructed usingTopHat and  Cufflinks
visualisation of differential expression was done using cummeRbund v2.14.0
Assembly: TAIR10
Supplementary files format and content: Excel, classic fpkm

organism: Arabidopsis thaliana

source_name: 14 days old seedlings

growth_protocol: Seedlings were grown for 5 days on 1/2 MS

extract_protocol:
Total RNA extractions were performed using the NucleoSpin RNA kit (Macherey-Nagel) following the manufacturer's recommendations
RNA seq libraries were prepared using Illumina kits

treatment_protocol: 5d old seedlings were transferred to 1/2 MS plates ± 100mM NaCl

tag: genetic background


title: trial number 23, Nonresponder at baseline


title: S_17_1812_BN2 (idd4-SALT)


title: Unrelated WT HGn12C rep3 lane3 & lane4


title: trial number 07, Responder at 24W

value: responder


title: S_17_1807_B2 (idd4-MOCK)


title: Patient#6


title: trial number 33, Responder at baseline


title: Unrelated WT HGn12C rep3 lane1 & lane2


title: S_17_1806_A2 (WT-MOCK)


title: trial number 08, Responder at baseline


title: Patient#5


title: trial number 03, Nonresponder at baseline


title: Unrelated WT HGn12C rep2 lane2 & lane3


title: trial number 25, Responder at baseline


title: Patient#21


title: S_17_1802_BN1 (idd4-SALT)


title: trial number 19, Responder at baseline


title: Unrelated WT HGn12C rep2 lane1


title: Patient#3


title: trial number 07, Responder at baseline


title: S_17_1797_B1 (idd4-MOCK)


title: Patient#2


title: Unrelated WT HGn12C rep1 lane2 & lane3


title: S_17_1796_A1 (WT-MOCK)


title: trial number 13, Responder at baseline


title: Unrelated WT HGn12C rep1 lane1 & rep2 lane4


title: CsubMADS1 OX_Replicate 2

status: Public on Oct 01 2023

city: Thiruvananthapuram

first: Saraswati

last: Nayar

state: Kerala

address: Thycaud Post, Poojappura

country: India

institute: Rajiv Gandhi Centre for Biotechnology

data_processing:
The raw data generated was checked for the quality using FastQC2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Pre-processing of the data is done with Trimgalore3 (https://www.encodeproject.org/software/trim_galore).
HISAT-24 which is a splice aligner (Kim et al., 2015) was used to align the high-quality reads to the reference Coccomyxa subellipsoidea C-169 genome (https://www.ncbi.nlm.nih.gov/genome/?term=Coccomyxa+subellipsoidea+C-169) downloaded from NCBI database with the default parameters.
HTSeq was used to estimate and calculate gene abundance (Anders et al., 2015). Absolute counts for each gene were identified, which were used in differential expression calculations.
Assembly: GCA_000258705.1 Coccomyxa subellipsoidae v2.0 (https://www.ncbi.nlm.nih.gov/genome/?term=Coccomyxa+subellipsoidea+C-169)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Coccomyxa subellipsoidea C-169

source_name: Algal cell culture

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen, USA) from stationary phase Coccomyxa subellipsoidea cells (WT and CsubMADS1 OX, three biological replicates each) as per the manufacturer’s protocol.
RNA sequencing libraries were prepared with Illumina-compatible NEB Next® Ultra™ II Directional RNA Library Prep Kit (New England Bio Labs, USA) following manufacturer’s instructions.

value: Algal cell culture

tag: age

value: Stationary phase

tag: time harvested

value: 3 hours before dark phase

value: Overexpressor CsubMADS1 OX


title: CsubMADS1 OX_Replicate 1


title: WT_Replicate 1

value: Wild type


title: Patient#4


title: S_17_1801_AN1 (WT-SALT)


title: WT s1026 rep1 lane1 & lane2

value: brain

value: s1026 transgenic line

value: WT


title: WT_Replicate 3


title: Unrelated WT HGn12C rep1 lane4 & lane5

value: HGn12C transgenic line


title: WT_Replicate 2


title: PH_RR_rep8

city: Brno

first: Andrea

middle: Vetešníková

last: Šimková

address: Kamenice 5

department: Department of Botany and Zoology

country: Czech Republic

institute: Masaryk University

description: Rutilus rutilus

data_processing:
A quality check of raw paired-end fastq reads was carried out by FastQC and a contamination check against human (GRCh38), mouse (GRCm38), yeast (S. cerevisiae R64-1-1), E. coli BL21(DE3) and other organisms by BioBloom tools.
The quality and Illumina adapter trimming of raw reads was performed using Trimmomatic v0.39 (options: PE CROP:250 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 ILLUMINACLIP:adapters.fa:2:30:10:3:true MINLEN:35).
Trimmed reads were aligned to the reference transcriptome using STAR v2.7.3a with options:  --runMode alignReads --sjdbOverhang 100 --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 1.0 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMatchNmin 0 --outFilterScoreMinOverLread 0.66 --outFilterMatchNminOverLread 0.66 --outSAMheaderHD @HD VN:1.4 SO:coordinate --peOverlapMMp 0.1 --chimOutJunctionFormat 1 --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimOutType Junctions SeparateSAMold --outSAMunmapped Within --outFilterType BySJout --outSAMattributes All --quantMode GeneCounts TranscriptomeSAM --sjdbScore 1 --twopassMode Basic --outMultimapperOrder Random --outSAMtype BAM SortedByCoordinate
The mapped reads were deduplicated by Picard’s MarkDuplicates v2.27.1 with options: -REMOVE_DUPLICATES False -ASSUME_SORTED true -PROGRAM_RECORD_ID null -VALIDATION_STRINGENCY LENIENT
The quantification of gene expression was performed by Subread's featureCounts v1.6.4 with options: -t exon -g gene_id  -p -P -C -s 0 -T 10 -F GTF -Q 0 -d 1 -D 25000
Differential gene expression analysis between infected and non-infected individuals for each fish line of OK experiment was performed according to gene counts produced by featureCounts, and further processed using the Bioconductor package DESeq2 v1.34.0. Genes were considered as differentially expressed only if having the adjusted p-value (FDR) smaller than 0.05 and the absolute value of the log2 expression fold-change higher than 1. The DESeq2 tool computes the normalized and shrunk log2 expression fold-change for each gene (for the results see supplemetray files called deseq2...tsv).
The functional role of significantly differentially expressed genes (i.e., enrichment analysis) was performed according to the KEGG pathway database and the Gene ontology database. For each fish line, the differentially expressed genes were used as the target set, and all of the annotated genes within the transcriptome served as a background for the statistical testing. The core of the analysis was performed by an in-house script using the R package clusterProfiler for individual fish lines separately for three sets: up-, down- and dis-regulated significantly differentially expressed genes. The Gene ontology (GO) annotation comes from the transcriptome assembly of R. rutilus using the semi-automatic annotation tool called Trinotate. From the total of 33767 predicted genes, 12590 were annotated with GO. KEGG annotation comes from the KAAS - KEGG Automatic Annotation Server using GHOSTZ on peptide sequences of predicted genes against the set of all fish genes of the KEGG database. From the total of 33767 predicted genes, 12618 were annotated with KEGG orthology identifiers (for the results see supplemetray files called GO_enrich...tsv and KEGG_enrich...tsv, respectively).
Assembly: R. rutilus transcriptome assembly
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Rutilus rutilus

source_name: head kidney

growth_protocol: Specimens of A. brama, R. rutilus, and their F1 hybrids were collected from the Hamry Reservoir (49.73724N, 15.91395E; the Czech Republic) and transported to the breeding facility. The hybrids were identified using meristic traits (i.e., the number of gill rakers, the number of scales in the lateral line, and the number of branched rays in the anal fin) and molecular markers (the cytochrome b gene and microsatellite loci). The fish were separated according to sex into two well-aerated tanks and stimulated for ovulation/spermiation by carp pituitary (females received 2 doses, 0.3 and 2.7 mg/kg, 24 h and 12 h before propagation, respectively; males received 1 mg/kg 24 h before propagation) and by subsequently increasing the water temperature to 22 °C. Oocytes of ovulating females were obtained by the dry method and sperm was sampled. Hatchery water was used for gamete activation. Artificial spawning based on individual pair mating was performed using the following parental combinations: (1) A. brama female and A. brama male (2) R. rutilus female and R. rutilus male, (3) A. brama female and R. rutilus male, (4) A. brama male and R. rutilus female, (5) F1 hybrid female (with A. brama mtDNA) and A. brama male, and (6) F1 hybrid female (with A. brama mtDNA) and R. rutilus male. As a result of artificial crosses, one R. rutilus line, one A. brama line, one F1 hybrid line with A. brama mtDNA (termed F1 A. brama x R. rutilus), one F1 hybrid line with R. rutilus mtDNA (termed F1 R. rutilus x A. brama), and two backcross lines, i.e. the backcross generation resulting from the crosses of both parents with A. brama mtDNA (F1 hybrid female with A. brama mtDNA and A. brama male, termed BC of F1 hybrid x A. brama), and the backcross generation resulting from the crosses of parents with different mtDNA (F1 hybrid female with A. brama mtDNA and R. rutilus male, termed BC of F1 hybrid x R. rutilus). All fish were reared to the age of 2 years.

extract_protocol:
Fish were investigated for the presence of parasites one month after oncomiracidia infection (or following cohabitation) by fish dissection, and parasites were counted. Head kidney was collected from individual fish including 4-5 non-infected control specimens per each fish line and at least 4 P. homoion-infected specimens per each of five fish lines (R. rutilus, A. brama, F1 generation with A. brama mtDNA, backcross generation of F1 hybrid with A. brama mtDNA and paternal A. brama, backcross generation of F1 hybrid with A. brama mtDNA and paternal R. rutilus) in the case of OK experiment, six fish lines in the case of PH experiment including F1 generation with R. rutilus mtDNA.
Total RNA was isolated from the head kidney of each fish specimen. For extraction, PureLink RNA Mini Kit (Ambion) with Trizol reagent (Thermo Fisher Scientific) and on-column PureLink DNase treatment were used according to the manufacturer´s protocol. Reagent and buffer volumes were adjusted according to the weight of tissue entering the isolation process (15.3 mg on average). The final elution was performed using 100 µl of RNAse-free water in the first step and the primal eluate in the second step. The yield and concentration of RNA isolates were checked using a QubitTM 4 fluorometer (Invitrogen by Thermo Fisher Scientific) and Qubit RNA HS Assay Kit (Thermo Fisher Scientific). The quality and integrity of RNA were analyzed using RNA 6000 Nano Kit on a 2100 Bioanalyzer instrument (Agilent Technologies).
All RNA isolates were normalized by dilution at a uniform concentration of 20 ng/µl with RNase-free water. They served as templates for DNA library preparation and for the reverse transcription of total RNA into single-stranded cDNA using High Capacity RNA-to-cDNA Kit (Applied Biosystems by Thermo Fisher Scientific) in twice the reaction volume recommended by the manufacturer.
All fish samples (RNA integrity number – RIN > 7) were used for DNA library preparation. 500 ng of total RNA was used for mRNA enrichment using the Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). Subsequently, NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®, and NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 2, New England Biolabs) were used for library preparation, with 11 PCR cycles utilized for PCR enrichment. RNA fragmentation (13 minutes at 94°C) and the size selection conditions (a bead volume of 30 µl and 15 µl for the first and second bead selections, respectively) were further modified in the protocol. The quantification of DNA libraries was performed on a QubitTM 4 fluorometer (Invitrogen by Thermo Fisher Scientific) using Qubit dsDNA HS Assay Kit, and quality and size control were performed on a 2100 Bioanalyzer with DNA 1000 Kit (Agilent Technologies). Finally, amplicons were pooled in equimolar amounts. The final concentration of each particular library in the pool was 10nM in the pool. Libraries were sequenced by Macrogen Europe B.V. (Amsterdam, Netherlands) on an Illumina NovaSeq6000 system (one line on an S4 flow cell) in a paired-end configuration producing 150 bp long reads.

treatment_protocol:
OK experiment was performed using twenty-five larval (oncomiracidia) specimens of P. homoion that were transferred into the aerated and standing tap water in each aquarium in which a single naïve fish specimen of five fish lines (R. rutilus, A. brama, F1 generation with A. brama mtDNA, backcross generation of F1 hybrid with A. brama mtDNA and paternal A. brama, backcross generation of F1 hybrid with A. brama mtDNA and paternal R. rutilus) was placed.
PH experiment was performed as cohabitation experiment. A total of eight fish specimens per each of six fish lines (A. brama, R. rutilus, F1 generation with A. brama mtDNA, F1 generation with R. rutilus mtDNA, backcross generation of F1 hybrid with A. brama mtDNA and paternal A. brama, backcross generation of F1 hybrid with A. brama mtDNA and paternal R. rutilus) were all placed in one tank with aerated water under temperature 20°C together with 25 specimens of P. homoion-infected donor fish Rhodeus ocellatus (Asian species was used in the laboratory to retain life cycle of P. homoion).

value: head kidney

value: PH


title: PH_RR_rep2

description: Rutilus rutilus


title: PH_RR_rep6

description: Rutilus rutilus


title: lakritz HGn12C rep3 lane3 & lane4

value: lakritz


title: PH_RR_rep1

description: Rutilus rutilus


title: PH_RR_rep7

description: Rutilus rutilus


title: PH_RR_rep5

description: Rutilus rutilus


title: PH_RR_rep4

description: Rutilus rutilus


title: OK_RR_rep3

description: Rutilus rutilus

value: OK


title: OK_RR_rep4

description: Rutilus rutilus


title: OK_RR_rep1

description: Rutilus rutilus


title: OK_RR_rep5

description: Rutilus rutilus


title: trial number 15, Nonresponder at baseline

value: Myeloproliferative neoplasms

value: non-responder

value: baseline

value: Peripheral blood


title: CsubMADS1 OX_Replicate 3

value: Algal cell culture


title: K_RR_rep3

description: Rutilus rutilus

value: K


title: K_RR_rep4

description: Rutilus rutilus


title: PH_F1_RRAB_rep7

description: F1 hybrid of A. brama and R. rutilus with R. rutilus mtDNA

organism: Rutilus rutilus x Abramis brama


title: Patient#1

value: ovary


title: K_RR_rep1

description: Rutilus rutilus


title: PH_F1_RRAB_rep5


title: PH_F1_RRAB_rep6


title: PH_F1_RRAB_rep4


title: PH_F1_RRAB_rep1


title: PH_F1_RRAB_rep3


title: PH_F1_RRAB_rep2


title: PH_F1_ABRR_rep8

description: F1 hybrid of A. brama and R. rutilus with A. brama mtDNA


title: K_RR_rep5

description: Rutilus rutilus


title: RBM26_shCtrl

description:
shCtrl_IP_RBM26
ChIP-seq anti-RBM26 (Bethyl A301-216A)

value: HeLa

value: shCtrl

tag: passages

tag: chip antibody

value: anti-RBM26 (Bethyl A301-216A)


title: PH_BK_RR_rep4

description: backcross generation of F1 hybrid with A. brama mtDNA and paternal R. rutilus


title: PH_BK_RR_rep6


title: PH_BK_RR_rep5


title: PH_F1_ABRR_rep1


title: PH_F1_ABRR_rep7


title: PH_BK_RR_rep2


title: PH_F1_ABRR_rep4


title: PH_F1_ABRR_rep2


title: OK_F1_ABRR_rep5


title: OK_F1_ABRR_rep4


title: PH_BK_RR_rep3


title: OK_F1_ABRR_rep3


title: PH_F1_ABRR_rep5


title: OK_BK_RR_rep5


title: OK_BK_RR_rep3


title: HEC9

city: Beijing

first: Jia

last: Yu

address: Dong Dan San Tiao 5, Dongcheng District

institute: Peking Union Medical College

data_processing:
Guppy (V3.5.2) software used for basecalling.
Sequenced reads were firstly processed with nanopack, then mapped to GENCODE (vM22) mouse genome (mm10) with minimap2 (v2.18-r1015) with default parameters
Isofrorm-level expression was quantified as counts with Salmon (version 1.1.0).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPT10K at  isoform level.

source_name: mouse embryonic cells

growth_protocol: Wildtype AECs and HECs were sorted from the E10 embryonic AGM region of C57 mice.

extract_protocol:
Morphologically deformed cells were discarded. Living single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette; 0.05 μl of 1:200,000 dilution of External RNA Controls Consortium (ERCC) RNA spike-in Mix1 (Ambion) was added to lysis buffer per reaction.
The cDNA fragments were end-repaired and added dA-tailed using Ultra II End Prep module and then tethered to 1D adaptor by using Quick Ligation Module. After that, each cDNA library was loaded into 1 FLOPRO002 flow cell and sequenced on PromethION.Beta.
PolyA enriched single-cell Nanopore Sequencing

treatment_protocol: FACS-sorted cells were kept on ice until lysed and reverse transcribed.

value: aorta-gonads-mesonephros (AGM)

value: Hematopoietic stem cells

tag: developmental stage


title: HEC6


title: HEC5


title: OK_BK_RR_rep2


title: HEC4


title: HEC3


title: HEC8


title: PH_BK_RR_rep7


title: K_F1_RRAB_rep5


title: OK_BK_RR_rep1


title: HEC2


title: PH_F1_RRAB_rep8


title: HEC24


title: HEC23


title: OK_F1_ABRR_rep1


title: HEC22


title: K_F1_RRAB_rep2


title: K_F1_RRAB_rep3


title: HEC21


title: K_F1_RRAB_rep4


title: HEC7


title: HEC20


title: HEC19


title: K_F1_ABRR_rep4


title: K_F1_RRAB_rep1


title: HEC18


title: K_F1_ABRR_rep3


title: HEC17


title: HEC1


title: K_F1_ABRR_rep1


title: HEC16


title: K_BK_RR_rep3


title: K_F1_ABRR_rep2


title: HEC15


title: K_BK_RR_rep2


title: HEC14


title: HEC13


title: K_BK_RR_rep4


title: HEC12


title: K_BK_RR_rep1


title: K_F1_ABRR_rep5


title: K_BK_RR_rep5


title: HEC11


title: HEC10


title: PH_BK_AB_rep7

description: backcross generation of F1 hybrid with A. brama mtDNA and paternal A. brama

organism: Abramis brama


title: AEC8

value: AEC


title: PH_BK_AB_rep6

value: head kidney


title: PH_BK_AB_rep4

value: PH


title: AEC7


title: PH_BK_AB_rep2


title: AEC5


title: AEC6


title: AEC9


title: PH_AB_rep5

description: Abramis brama


title: AEC3


title: PH_AB_rep4

description: Abramis brama


title: PH_AB_rep2

description: Abramis brama


title: AEC24


title: PH_AB_rep1

description: Abramis brama


title: AEC2


title: PH_BK_AB_rep8


title: PH_AB_rep3

description: Abramis brama


title: AEC23


title: OK_BK_AB_rep5


title: AEC22


title: OK_BK_AB_rep4


title: PH_BK_AB_rep5


title: OK_BK_AB_rep3


title: AEC21


title: AEC20


title: AEC1


title: OK_BK_AB_rep2


title: OK_BK_AB_rep1


title: AEC19


title: OK_AB_rep5

description: Abramis brama


title: PH_BK_AB_rep1


title: AEC18


title: AEC4


title: AEC16


title: OK_AB_rep3

description: Abramis brama


title: AEC17


title: OK_AB_rep2

description: Abramis brama


title: OK_AB_rep4

description: Abramis brama


title: AEC14


title: AEC11


title: AEC12


title: AEC10


title: OK_AB_rep1

description: Abramis brama


title: K_AB_rep4

description: Abramis brama


title: K_AB_rep5

description: Abramis brama


title: K_BK_AB_rep4


title: AEC15


title: K_BK_AB_rep2


title: K_BK_AB_rep5


title: K_AB_rep2

description: Abramis brama


title: K_AB_rep1

description: Abramis brama


title: B. cereus, MOD, Rep a

city: Hannover

first: Nadja

last: Jessberger

address: Bischofsholer Damm 15

department: Institute for Food Quality and Food Safety

institute: University of Veterinary Medicine Hannover, Foundation

data_processing:
Samples were sequenced via Illumina HiSeq. 2500 Genome Sequencer with 2 x 150 bp paired-end mode. Data analysis included mapping of the samples against a reference genome (B. cereus F837/76; CP003187) and determination of gene expression.
Mapping of reads to reference sequences was performed using BWA-MEM (version 0.7.12-r1039, http: //bio-bwa.sourceforge.net/). The reads and their associated alignment positions are provided as BAM formatted files.
Raw read counts were created using featureCounts (version 1.5.1, http://subread.sourceforge. net/, Liao et al. (2014)). Only reads overlapping "CDS" features were counted. All reads mapping to features with the same meta-feature attribute were summed. Hereby, the "META_FEATURE_ID" attribute was used as a meta-feature attribute. Please see the provided .gff file for used annotations. Only reads with unique mapping positions and a mapping quality score of at least 10 were considered for read counting. Supplememtary alignments were ignored for read counting. Paired-end reads that mapped to different chromosomes or with unexpected strandedness were ignored.
Instead of counting paired-end reads twice, they were counted only once, i.e. as single fragment. Reads mapping to multiple features were assigned to the feature that has the largest number of overlapping bases. A Trimmed Mean of M-values (TMM) normalization was performed using the edgeR package (version 3.16.5, Robinson and Oshlack, 2010. Robinson and McCarthy, 2010. http://bioconductor.org/ packages/release/bioc/html/edgeR.html).
The basic assumption of this normalization technique is that most features (e.g. genes) should not be differentially expressed between samples. Roughly, for each sample a normalization factor is calculated as the weighted mean of feature-wise log ratios between this sample and a reference sample. For this calculation, the most expressed features and the features with the largest log ratios are excluded. The counts-per-million values of the normalized read counts are provided in the *.profiling-table.txt file. Length-normalization was not performed.
Assembly: CP003187.fasta
Supplementary files format and content: tsv format

organism: Bacillus cereus

source_name: INRA C3

growth_protocol: 100 ml mMOD medium were inoculated with strain INRA C3 to OD600 = 0.1 and incubated at 37 °C for five hours under continuous agitation. The culture was centrifuged (10 min, 4,000 x g, 4 °C) and washed twice in cold mMOD-Fe. 50 ml mMOD, mMOD-Fe and mMOD with 10 mg/ml lactoferrin-based food supplement no. 1 were inoculated to OD600 = 1 and further incubated for two hours before centrifugation (2 min, 10,000 x g, 4 °C).

extract_protocol:
Total RNA preparation and on-column DNase digestion were performed using RNeasy® Mini Kit (Qiagen) according to the instructions of the manufacturer. RNA quality was tested via spectrophotometer and agarose gel electrophoresis. RNA purity was confirmed via PCR for 16 S rRNA.
Random primed cDNA libraries were constructed according to the Illumina Genome Analyzer II protocol.

tag: strain

value: INRA C3

value: mMOD minimal medium


title: B. cereus, MOD, Rep b


title: B. cereus, MOD-Fe, Rep a

value: iron depletion


title: B. cereus, LF10, Rep b

value: 10 mg/ml lactoferrin


title: B. cereus, LF10, Rep a


title: IN_A28

city: Cincinnati

first: David

last: Linz

state: Ohio

address: 26 Martin Luther King Dr W

institute: EPA

data_processing:
Reads were quality checked using FastQC v.0.11.9 and cleaned using Trimmomatic v.0.39to remove adapter sequences and perform quality trimming. Trimmomatic was run with the following parameters:, ‘ILLUMINACLIP with custom fasta files containing detected adaptor contamination’ and ‘LEADING:2 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:50’. The trimmed reads were then mapped against the Mus musculus genome (GRCm39) using STAR (v.2.7.9a) using default settings. Read counting was done for each gene using featureCounts (v2.0.1).
Assembly: mm39
Supplementary files format and content: tab-delimited text file for each treatment type (aerosol and intransal) including raw counts for each Sample.

source_name: RNAseq of mus musculus: lung tissue: 72hr post exposure: rep4: Intranasal exposure

extract_protocol:
Each dissected lung was moved separately to a 1.5 mL micro bead tube containing 600ul of buffer RLT plus from Qiagen RNeasy Mini Kit (QIAGEN, Hilden, Germany). Tissues were homogenized for one minute in a Mini-Beadbeater-16 (BioSpec Products, Inc., Bartlesville, Oklahoma, USA) and subsequently centrifuged for three minutes to reduce foaming. RNA was then extracted using the RNeasy Mini Kit following the manufacture’s protocol. Samples were further purified using TURBO DNase (Invitrogen, ThermoFisher Scientific, Waltham, WA, USA) to remove contaminating genomic DNA following manufacturer’s protocols.
Total RNA quality and quantity were assessed using a BioAnalyzer 2100 (Agilent, Santa Clara, California, USA) and determined to be of good quality. Additionally, RNA concentrations were measured with both a Qubit 2.0 (ThermoFisher Scientific, Waltham, MA, USA) and a NanoDrop spectrometer (ThermoFisher Scientific, Waltham, MA, USA) and samples were diluted to a starting amount of 1µg of total RNA. In all, 45 sequencing libraries (16 aerosol treated, 19 intranasally treated, and five controls for each) were constructed using TruSeq RNA sample prep kit v2 (Illumina, San Diego, CA, USA) following manufacturer’s instructions and reaching the final expected size of 200-500bp (average ~350bp).

tag: tissue

value: lung

value: WT

value: Legionella exposed

value: intranasal

tag: time


title: K_BK_AB_rep3

value: K


title: IN_A26

source_name: RNAseq of mus musculus: lung tissue: 72hr post exposure: rep2: Intranasal exposure


title: IN_A25

source_name: RNAseq of mus musculus: lung tissue: 72hr post exposure: rep1: Intranasal exposure


title: AEC13

tag: cell type


title: IN_A23

source_name: RNAseq of mus musculus: lung tissue: 48hr post exposure: rep5: Intranasal exposure

tag: genotype


title: B. cereus, MOD-Fe, Rep b

tag: treatment


title: K_AB_rep3

description: Abramis brama


title: IN_A19

source_name: RNAseq of mus musculus: lung tissue: 48hr post exposure: rep2: Intranasal exposure


title: IN_A17

source_name: RNAseq of mus musculus: lung tissue: 24hr post exposure: rep5: Intranasal exposure


title: IN_A21

source_name: RNAseq of mus musculus: lung tissue: 48hr post exposure: rep3: Intranasal exposure


title: IN_A18

source_name: RNAseq of mus musculus: lung tissue: 48hr post exposure: rep1: Intranasal exposure


title: K_BK_AB_rep1


title: IN_A16

source_name: RNAseq of mus musculus: lung tissue: 24hr post exposure: rep4: Intranasal exposure


title: IN_A14

source_name: RNAseq of mus musculus: lung tissue: 24hr post exposure: rep2: Intranasal exposure


title: IN_A15

source_name: RNAseq of mus musculus: lung tissue: 24hr post exposure: rep3: Intranasal exposure


title: 48hour post infection PR8+Armstrong

city: Shanghai

first: Avon

last: Taylor

address: Caolang Road No.2901

institute: Fudan University

description: Gene expression data from lung tissue without Trm at 48 hour after re-infection

hyb_protocol: Following fragmentation, 6-9 ug of cRNA were hybridized for 16 hr at 45℃ on Affymetrix clariom S mouse Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

data_processing: The data were analyzed with Transcriptome Analysis Console (version 4.0).

label_protocol:
Synthesize double strand cDNA according to the first strand master mix and second strand master mix
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (WT Terminal Labeling and Controls Kit, Affymetrix).

extract_protocol:
P14 Trm cells in lung airway were sorted. Infected lung tissues were pulverized with a mortar and pestle under liquid nitrogen
Trizol extraction of total RNA of lung tissue was performed by Direct-zol RNA MiniPrep Kit. Trizol extraction of total RNA of Trm cells was performed by RNeasy Mini Protocol.

treatment_protocol: P14  T cells were adoptively transferred to generate immune chimeras. Mice were challenged with LCMV Armstrong at d30 after PR8 or PR8-gp33 infection.

value: lung tissue without Trm

tag: infection

value: 30 days after PR8 infection

tag: re-infection

value: 48h after re-infection

tag: time after re-infection


title: 3hour post infection PR8+Armstrong

description: Gene expression data from lung tissue without Trm at 3 hour after re-infection

value: 3h after re-infection


title: 12hour post infection PR8+Armstrong

description: Gene expression data from lung tissue without Trm at 12 hour after re-infection

value: 12h after re-infection


title: 6hour post infection PR8+Armstrong

description: Gene expression data from lung tissue without Trm at 6 hour after re-infection

value: 6h after re-infection


title: 0hour post infection PR8+Armstrong

description: Gene expression data from lung tissue without Trm at 0 hour after re-infection

value: 0h after LCMV Armstrong re-infection at 30-day-infected mice


title: IN_A12

source_name: RNAseq of mus musculus: lung tissue: 24hr post exposure: rep1: Intranasal exposure


title: IN_A11

source_name: RNAseq of mus musculus: lung tissue: 1hr post exposure: rep5: Intranasal exposure


title: IN_A22

source_name: RNAseq of mus musculus: lung tissue: 48hr post exposure: rep4: Intranasal exposure


title: IN_A09

source_name: RNAseq of mus musculus: lung tissue: 1hr post exposure: rep4: Intranasal exposure


title: 6hour post infection PR8-gp33+Armstrong

description: Gene expression data from lung tissue with Trm at 6 hour after re-infection

value: lung tissue with Trm

value: 30 days after PR8-gp33 infection


title: 12hour post infection PR8-gp33+Armstrong

description: Gene expression data from lung tissue with Trm at 12 hour after re-infection


title: 3hour post infection PR8-gp33+Armstrong

description: Gene expression data from lung tissue with Trm at 3 hour after re-infection


title: IN_A08

source_name: RNAseq of mus musculus: lung tissue: 1hr post exposure: rep3: Intranasal exposure


title: 24hour post infection PR8+Armstrong

description: Gene expression data from lung tissue without Trm at 24 hour after re-infection

value: 24h after re-infection


title: 48hour post infection P14 Trm

description: Gene expression data from airway Trm cells at 48h after re-infection

value: CD3+CD8+CD45.1+CD69+CD11a- Trm cells

value: cells from lung BAL


title: BAP+IAA,Day15,Rep3

city: Uppsala

first: Ai

last: Zhang

state: Uppsala

address: Biocenter, Almas allé 5

department: Plant Biology

institute: SLU

data_processing:
The residual rRNA contamination was removed using SortMeRNA
adapter and low-quality sequences were removed using the fastp software
The cleaned reads were aligned to version 1.0 of the Norway spruce genome using STAR
The number of reads was counted using htseq
Differentially expressed genes were identified using the DESeq2
Assembly: Picea abies reference genome v1.0
Supplementary files format and content: Matrix table with raw gene counts for each gene and each sample

organism: Picea abies

source_name: cell line: FP-518 TreO G7 Söregärde

extract_protocol:
Total RNA was extracted using a modified CTAB/LiCl method(Azevedo et al., 2003). Briefly, frozen tissue was ground into a fine powder. Extraction buffer was prepared (100 mM Tris-HC1 (pH 8), 2% (w/v) CTAB, 30 mM EDTA, 2 M NaCI, 0.05% (w/v) spermidine, 2% (w/v) PVPP, 2% (v/v) 2-mercaptoethanol, proteinase K (10 mg/mL) to a final concentration of 1.5 mg/mL) and warmed for 10 min at 42℃, then added to the ground frozen tissue and incubated for at 42℃for 90 min.  Chloroform-isoamyl alcohol (24:1 [v/v]) was added to extract RNA. After vortexing and centrifuging at 15,000 g for 15 min at 4℃, the top aqueous phase was transferred to a new tube and ¼ vol of 10 M LiC1 was added, allowing overnight precipitation at 4℃. Samples were centrifuged at 15,000 g for 30 min and supernatant discarded. Finally, the pellet was washed with 2 M LiCl twice and dissolved in RNase-free water. RNA concentration was measured using Qubit 2.0. The RNA Integrity Number (RIN) was analyzed by using an Agilent 2100 Bioanalyzer with RNA 6000 Nano kit. The RINs of all samples were above 8.0.
mRNA library preparation (poly A enrichment) by Novogene

value: hypocotyl

value: middle hypocotyl region

value: BAP+IAA

value: 15 days


title: IN_A07

source_name: RNAseq of mus musculus: lung tissue: 1hr post exposure: rep2: Intranasal exposure

value: lung

value: WT

value: Legionella exposed

value: intranasal


title: IN_A06

source_name: RNAseq of mus musculus: lung tissue: 1hr post exposure: rep1: Intranasal exposure


title: 12hour post infection P14 Trm

description: Gene expression data from airway Trm cells at 12h after re-infection


title: BAP+IAA,Day15,Rep2


title: 24hour post infection P14 Trm

description: Gene expression data from airway Trm cells at 24h after re-infection


title: 0hour post infection PR8-gp33+Armstrong

description: Gene expression data from lung tissue with Trm at 0 hour after re-infection


title: 48hour post infection PR8-gp33+Armstrong

description: Gene expression data from lung tissue with Trm at 48 hour after re-infection

value: 48h after re-infection


title: IN_A05

source_name: RNAseq of mus musculus: lung tissue: control rep5: Intranasal exposure

value: untreated


title: 24hour post infection PR8-gp33+Armstrong

description: Gene expression data from lung tissue with Trm at 24 hour after re-infection


title: BAP+IAA,Day15,Rep1


title: 6hour post infection P14 Trm

description: Gene expression data from airway Trm cells at 6h after re-infection

value: 6h after re-infection


title: 3hour post infection P14 Trm

description: Gene expression data from airway Trm cells at 3h after re-infection

value: 3h after LCMV Armstrong re-infection at 30-day-infected mice


title: BAP,Day15,Rep3

value: BAP


title: BAP,Day15,Rep1


title: BAP,Day15,Rep2


title: IN_A04

source_name: RNAseq of mus musculus: lung tissue: control rep4: Intranasal exposure


title: IN_A02

source_name: RNAseq of mus musculus: lung tissue: control rep2: Intranasal exposure


title: IN_A03

source_name: RNAseq of mus musculus: lung tissue: control rep3: Intranasal exposure


title: IN_A27

source_name: RNAseq of mus musculus: lung tissue: 72hr post exposure: rep3: Intranasal exposure


title: IAA,Day15,Rep3

value: IAA


title: IN_A01

source_name: RNAseq of mus musculus: lung tissue: control rep1: Intranasal exposure


title: AERO_A21

source_name: RNAseq of mus musculus: lung tissue: 72hr post exposure: rep4: Aerosol exposure

value: aerosol


title: IAA,Day15,Rep2


title: 0hour post infection P14 Trm

description: Gene expression data from airway Trm cells at 0h after re-infection

value: CD3+CD8+CD45.1+CD69+CD11a- Trm cells

value: 30 days after PR8-gp33 infection

value: 0h after LCMV Armstrong re-infection at 30-day-infected mice


title: IAA,Day15,Rep1

value: hypocotyl

value: middle hypocotyl region


title: AERO_A20

source_name: RNAseq of mus musculus: lung tissue: 72hr post exposure: rep3: Aerosol exposure


title: AERO_A19

source_name: RNAseq of mus musculus: lung tissue: 72hr post exposure: rep2: Aerosol exposure


title: AERO_A18

source_name: RNAseq of mus musculus: lung tissue: 72hr post exposure: rep1: Aerosol exposure


title: AERO_A17

source_name: RNAseq of mus musculus: lung tissue: 48hr post exposure: rep4: Aerosol exposure


title: Mock,Day15,Rep3

value: Mock

value: 15 days


title: Mock,Day15,Rep2

value: WT


title: Mock,Day15,Rep1


title: BAP+IAA,Day10,Rep1

value: BAP+IAA

value: 10 days


title: AERO_A14

source_name: RNAseq of mus musculus: lung tissue: 48hr post exposure: rep1: Aerosol exposure

value: lung

value: Legionella exposed


title: AERO_A13

source_name: RNAseq of mus musculus: lung tissue: 24hr post exposure: rep4: Aerosol exposure


title: AERO_A12

source_name: RNAseq of mus musculus: lung tissue: 24hr post exposure: rep3: Aerosol exposure


title: AERO_A15

source_name: RNAseq of mus musculus: lung tissue: 48hr post exposure: rep2: Aerosol exposure


title: IAA,Day10,Rep2

source_name: cell line: FP-518 TreO G7 Söregärde


title: IAA,Day10,Rep3


title: AERO_A11

source_name: RNAseq of mus musculus: lung tissue: 24hr post exposure: rep2: Aerosol exposure


title: BAP,Day10,Rep1


title: BAP,Day10,Rep2


title: BAP,Day10,Rep3


title: AERO_A09

source_name: RNAseq of mus musculus: lung tissue: 1hr post exposure: rep4: Aerosol exposure


title: AERO_A10

source_name: RNAseq of mus musculus: lung tissue: 24hr post exposure: rep1: Aerosol exposure


title: AERO_A07

source_name: RNAseq of mus musculus: lung tissue: 1hr post exposure: rep2: Aerosol exposure


title: IAA,Day10,Rep1


title: BAP+IAA,Day10,Rep3


title: AERO_A06

source_name: RNAseq of mus musculus: lung tissue: 1hr post exposure: rep1: Aerosol exposure


title: AERO_A05

source_name: RNAseq of mus musculus: lung tissue: control rep5: Aerosol exposure

value: untreated


title: AERO_A04

source_name: RNAseq of mus musculus: lung tissue: control rep4: Aerosol exposure


title: AERO_A16

source_name: RNAseq of mus musculus: lung tissue: 48hr post exposure: rep3: Aerosol exposure


title: BAP+IAA,Day5,Rep3

value: 5 days


title: AERO_A02

source_name: RNAseq of mus musculus: lung tissue: control rep2: Aerosol exposure


title: BAP+IAA,Day5,Rep2


title: AERO_A03

source_name: RNAseq of mus musculus: lung tissue: control rep3: Aerosol exposure


title: Mock,Day10,Rep1


title: Mock,Day10,Rep3


title: BAP+IAA,Day10,Rep2


title: BAP+IAA,Day5,Rep1


title: AERO_A08

source_name: RNAseq of mus musculus: lung tissue: 1hr post exposure: rep3: Aerosol exposure


title: AERO_A01

source_name: RNAseq of mus musculus: lung tissue: control rep1: Aerosol exposure


title: BAP,Day5,Rep3

value: BAP


title: BAP,Day5,Rep2


title: IAA,Day5,Rep3

value: IAA


title: siZcchc8_expC_RNAseq_Rep2

city: New York

first: Robert

last: Sebra

state: New York

address: 1 Gustave L. Levy Place

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Illumina adapters were trimmed from reads using Trim Galore (v0.5.0). Reads were aligned to the GRCm38/mm10 reference genome using STAR (v2.7.5b) with the following custom parameters: --outFilterMultimapNmax 100 –winAnchorMultimapNmax 100. Gene and TE-level counts were calculated using TEcount (v2.2.1) using the Ensembl GRCm38 v102 transcript annotation and the GRCm38 RepeatMasker annotation downloaded from UCSC table browser.
Assembly: mm10
Supplementary files format and content: TSV file containing gene counts

source_name: mESC

extract_protocol:
For RNA extraction, cells were washed 3x with DPBS and lysed directly on the plate with 1mL of TRIzol reagent (Invitrogen, 15596026). Subsequently, RNA was purified using Direct-zol RNA Miniprep Plus Kits (Zymo, R2072) following manufacturer instructions. In brief, lysed cells in TRIzol were mixed 1:1 with 100% ethanol. Mixed lysates were added to the Zymo-spin columns, treated with DNase I, and washed with provided buffers. RNA was eluted with UltraPure DNase/RNase-Free Distilled Water (Invitrogen, 10977015). For DNA extraction, PureLink™ Genomic DNA Mini Kit (Invitrogen, K1820-00) was used followed manufacturer instructions. In brief, cells were washed 3x with DPBS and lysed directly on the plates using supplied Lysis/Binding buffer. Lysates were subsequently applied to the column and washed with buffers provided. DNA was eluted in PureLink Genomic Elution Buffer provided in the kit.
For complementary DNA synthesis, 100-200 µg of DNase I treated RNA was reverse transcribed using High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, 4368814). Random hexamers were used to capture total RNA.

value: mESC

tag: group

value: Experiment C


title: siZcchc8_expC_RNAseq_Rep3


title: IAA,Day5,Rep2


title: siZcchc8_expC_RNAseq_Rep1


title: Mock,Day10,Rep2


title: IAA,Day5,Rep1


title: siCpsf2_expC_RNAseq_Rep3


title: siCpsf2_expC_RNAseq_Rep2


title: siCtrl_expC_RNAseq_Rep3

value: siCtrl


title: Mock,Day5,Rep3


title: Mock,Day5,Rep2


title: siCtrl_expC_RNAseq_Rep2


title: Mock,Day5,Rep1


title: siCtrl_expC_RNAseq_Rep1


title: Grafted,Day28,Rootstock,Rep2

source_name: cell line: FP-96. Skogsgård

extract_protocol:
Total RNA was extracted using a modified CTAB/LiCl method(Azevedo et al., 2003). Briefly, frozen tissue was ground into a fine powder. Extraction buffer was prepared (100 mM Tris-HC1 (pH 8), 2% (w/v) CTAB, 30 mM EDTA, 2 M NaCI, 0.05% (w/v) spermidine, 2% (w/v) PVPP, 2% (v/v) 2-mercaptoethanol, proteinase K (10 mg/mL) to a final concentration of 1.5 mg/mL) and warmed for 10 min at 42℃, then added to the ground frozen tissue and incubated for at 42℃for 90 min.  Chloroform-isoamyl alcohol (24:1 [v/v]) was added to extract RNA. After vortexing and centrifuging at 15,000 g for 15 min at 4℃, the top aqueous phase was transferred to a new tube and ¼ vol of 10 M LiC1 was added, allowing overnight precipitation at 4℃. Samples were centrifuged at 15,000 g for 30 min and supernatant discarded. Finally, the pellet was washed with 2 M LiCl twice and dissolved in RNase-free water. RNA concentration was measured using Qubit 2.0. The RNA Integrity Number (RIN) was analyzed by using an Agilent 2100 Bioanalyzer with RNA 6000 Nano kit. The RINs of all samples were above 8.0.
1 ug total RNA per sample was used for RNA-seq library preparation. mRNA isolation was performed using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB #E7490S), followed directly by using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7760S) and NEBNext Multiplex Oligos for Illumina (NEB #E7600S) for library construction. The quality of DNA libraries was checked by with an Agilent 2100 Bioanalyzer DNA High Sensitivity Kit.

value: Rootstock

value: grafting


title: siRbm7_expB_RNAseq_Rep2

value: Experiment B


title: Grafted,Day28,Rootstock,Rep3

value: hypocotyl


title: siCtrl_expB_RNAseq_Rep2


title: siCtrl_expB_RNAseq_Rep1


title: Grafted,Day28,Scion,Rep3

value: Scion


title: Grafted,Day28,Rootstock,Rep1

value: WT


title: siRbm7_expB_RNAseq_Rep1


title: Grafted,Day28,Scion,Rep1


title: Grafted,Day28,Scion,Rep2


title: siInts11_expA_RNAseq_Rep1

value: Experiment A


title: siInts11_expA_RNAseq_Rep2


title: siCpsf2_expC_RNAseq_Rep1


title: BAP,Day5,Rep1

value: middle hypocotyl region


title: siExosc3_expA_RNAseq_Rep2


title: siExosc3_expA_RNAseq_Rep1


title: siCtrl_expA_RNAseq_Rep2


title: Grafted,Day14,Rootstock,Rep3


title: Exosc3_FKBP_12hr_Rep3

tag: timepoint


title: Exosc3_FKBP_12hr_Rep1


title: Ungrafted,Day28,Intact,Rep1

value: Intact

value: ungrafting


title: Grafted,Day14,Rootstock,Rep1


title: Exosc3_FKBP_12hr_Rep2


title: Grafted,Day14,Scion,Rep3


title: siCtrl_expA_RNAseq_Rep1


title: Grafted,Day14,Scion,Rep2


title: Exosc3_FKBP_6hr_Rep3


title: Ungrafted,Day28,Intact,Rep2


title: Grafted,Day14,Scion,Rep1


title: Ungrafted,Day14,Intact,Rep3


title: Exosc3_FKBP_6hr_Rep2


title: Exosc3_FKBP_6hr_Rep1


title: Ungrafted,Day14,Intact,Rep2


title: Ungrafted,Day28,Intact,Rep3


title: Exosc3_FKBP_0hr_Rep3


title: Ungrafted,Day14,Intact,Rep1


title: Grafted,Day7,Rootstock,Rep3


title: Exosc3_FKBP_0hr_Rep2


title: Exosc3_FKBP_0hr_Rep1


title: Grafted,Day7,Rootstock,Rep2


title: Grafted,Day14,Rootstock,Rep2


title: Grafted,Day7,Rootstock,Rep1


title: Nonagouti sample, scRNA-seq, pairs with Mc1rE

city: Bethesda

first: Dawn

last: Watkins-Chow

state: Maryland

address: 9000 Rockville Pike

institute: NIH

data_processing:
Cell Ranger (10x Genomics) was used for alignment, barcode counting, and UMI counting
Downstream processing (filtering and differential analysis) of the data was performed with Partek Flow™ Genomic Analysis Software
Assembly: mm39
Supplementary files format and content: Tab-separated values (.TSV)
Supplementary files format and content: Matrix (.mtx)

source_name: Skin

extract_protocol:
FACS-isolated melanocytes were captured in a solution of 1xPBS + 0.04% FBS. Cell viability and concentration were analyzed using a Luna-FX7 cell counter
Gel Bead-in-Emulsions were prepared by loading cells onto a Chromium Chip G and run using the Chromium controller per 10x Genomics' specififcations. cDNA libraries were generated with Chromium Single Cell 3’ GEM, Library and Gel Bead Kit V3.1.

value: Skin


title: Nonagouti_LethalYellow sample, scRNA-seq, pairs with LethalYellow


title: LethalYellow sample, scRNA-seq, pairs with Nonagouti_LethalYellow


title: Grafted,Day7,Scion,Rep2


title: Grafted,Day7,Scion,Rep1


title: Ungrafted,Day7,Intact,Rep3