title: 3621_4_MUT_POST_NOTEL

city: San Francisco

first: Alice

middle: Fitzgerald

last: Goodwin

state: CA

address: 513 Parnassus Ave, HSE1506

department: Orofacial Sciences

institute: UCSF School of Dentistry

description: processed data file: All_genes_Normalized_Counts_Goodwin.txt

data_processing:
Read counts were generated by STAR v2.7.2 using the —quantMode GeneCounts option. Only mapped reads uniquely assigned to the mouse genome were used for differential expression testing.
The expression matrix was imported into R and normalized for sequencing read depth with DESeq2.
QC plots were created from the counts generated by DESeq2’s variance Stabilizing Transformation (with blind=True).
Differential expression was performed using DESeq2 (Wald Test), and significant genes were filtered by a threshold of 0.05 false discovery rate.
Genome_build: Not provided
Supplementary_files_format_and_content: All_genes_Normalized_Counts_Goodwin.txt: Matrix of normalized counts for all 8 samples (.norm=sequencing depth normalized sample values, .stabilized=log transformed and variance stabilized values).

source_name: Posterior palatal shelf tissue

extract_protocol:
E14.5 embryos were collected, and the two (right and left), non-elevated posterior palatal shelves (posterior and medial to the molars) were excised using forceps and immediately placed in RLT buffer on ice (Qiagen 79216), and then RNA extraction was performed using the RNeasy Mini Kit (Qiagen 74104).
Sequencing libraries were generated. RNA-Seq was performed on an Illumina HiSeq 4000.

value: Yapfl/fl;Tazfl/fl;Col2Cre Mutant

tag: developmental stage

value: Posterior non-elevated palatal shelf epithelial and mesenchymal tissue


title: 3602_8_MUT_POST_NOTEL

status: Public on May 25 2020

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: genotype

tag: tissue


title: 3602_9_MUT_POST_NOTEL


title: 2057_5_MUT_POST_NOTEL


title: 2057_1_CON_POST_NOTEL

value: Yapfl/fl;Tazfl/fl Control


title: P209_B18_WT_C57BL/6J_hippocampus_rep2

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Freiburg

data_processing:
Individual Fastq files were aligned to the mouse Genome (Gencode M11 / GRCm38) using the STAR aligner version 2.5.2b with parameters STAR --runThreadN <cpu> --genomeDir <index> --genomeLoad LoadAndKeep --limitBAMsortRAM 20000000000 --readFilesIn <fastq> --readFilesCommand zcat --outFileNamePrefix <sampleID> --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate
Gene counts were obtained from BAM files using featureCounts v1.5.1 with parameters -a <Gencode_vM11.gtf> -G <GRCm38.primary_assembly.genome.fa> -o counts.txt -F GTF -R -g gene_id -t exon -T 12 --largestOverlap <bamfiles>
single cell RNAseq analysis and clustering was performed using RaceId/StemId2 (Grün, D., L. Kester, and A. van Oudenaarden. 2014. “Validation of noise models for single-cell transcriptomics.” Nat. Methods 11 (6): 637–40.). Cells with less than 500 detected genes, less than 5000 aligned reads or more than 700 000 aligned reads were discarded. Only genes with a count of 5 in at least a single cell were used for analysis.
Genome_build: Gencode M11 / GRCm38
Supplementary_files_format_and_content: comma separated (csv) file with gene counts per sample

source_name: microglia

extract_protocol:
After transcardial perfusion with PBS, brains were roughly minced and homogenized with a potter in HBSS containing 15 mM HEPES buffer and 0.54 % Glucose. Whole-brain homogenate was separated by 70/37/30 % layered Percoll gradient centrifugation at 800 g for 30 min at 4 °C (no brake). The CNS macrophages containing interphase was then collected and washed once with PBS containing 2% FCS and 10mM EDTA before staining. Cells were stained with primary antibodies directed against CD11b (M1/70, BioLegend), CD45 (30-F11, BD Biosciences), Ly6C (AL-21, BD Biosciences) and Ly6G (1A8, BD Biosciences) for 20 min, and CD206 (C068C2, BioLegend) for 45 min at 4 °C. After washing, cells were analyd using a MoFlo Astrios (Beckman Coulter). microglia were FACS-sorted from six different CNS regions of healthy and diseased brains (see gating strategy shown in supplementary Fig.2) into a 384-well plate containing a lysis buffer.
Single cell RNAseq libraries were generated following the published SmartSeq2 protocol (Picelli et al. Nature Metods 2013)

tag: strain

value: hippocampus

value: wildtype


title: P209_C10_WT_C57BL/6J_cortex_rep4

value: cortex


title: P209_B16_WT_C57BL/6J_hippocampus_rep2


title: P209_B17_WT_C57BL/6J_hippocampus_rep2


title: CD235a+ cells - Bone Marrow 3

city: Guangzhou

first: Xiangmin

last: Xu

state: Guangdong

address: 1838 Guangzhou Avenue North

department: Department of Medical Genetics

country: China

institute: School of Basic Medical Sciences

description: generated by cellranger v2.1.0

data_processing:
generate feature-barcode matrice by cellranger v2.1.0
Genome_build: hg19
Supplementary_files_format_and_content: MTX, TSV

organism: Homo sapiens

source_name: Bone Marrow 3

extract_protocol:
Chromium Single Cell 3’ Reagent Kit v3
To reliably construct scRNA-seq library, we isolated primary human terminally differentiated erythroblasts directly from adult BM and UCB samples using magnetic beads via CD34 negative selection followed by CD235a (Glycophorin A, GYPA) positive selection. Single cell sequencing libraries were constructed based on the 10× Genomics Chromium protocols and transcriptomic data was generated on Illumina ×10 platform.

tag: source

value: in vivo

value: bone marrow

tag: library type

value: Gene Expression Library


title: CD235a+ cells - Bone Marrow 4

description: generated by cellranger v2.1.0

source_name: Bone Marrow 4


title: 2057_7_CON_POST_NOTEL


title: P209_B15_WT_C57BL/6J_hippocampus_rep1


title: P209_B23_WT_C57BL/6J_hippocampus_rep4


title: P209_B3_WT_C57BL/6J_cortex_rep1


title: P209_B14_WT_C57BL/6J_hippocampus_rep1


title: CD235a+ cells - Bone Marrow 2

description: generated by cellranger v2.1.0

source_name: Bone Marrow 2


title: P209_B13_WT_C57BL/6J_hippocampus_rep1


title: 3606_5_CON_POST_NOTEL


title: DC-CCR7L

city: shanghai

first: kun

last: chen

address: No.800 Xiangyin Road, Yangpu District

institute: Zhejiang University

description: total RNA without ribosomal RNA

data_processing:
cDNA library construction and sequencing were performed by Beijing Genomics Institute using Illumina HiSeq 4000 platform.
High-quality reads were aligned to the mouse reference genome (GRCm38) using Bowtie2
The high-quality reads were aligned to publicly available NONCODE database. The expression levels for each of the genes were normalized to fragments per kilobase of exon model per million mapped reads (FPKM) by Expectation Maximization (RSEM).
Genome_build: GRCm38
Supplementary_files_format_and_content: FPKM

source_name: dendritic cells

growth_protocol: Dendritic cells are cultured in RPMI1640 medium plus GM-CSF and IL4 for 5 days and further stimulated with LPS (100 ng/ml) for 24 h to generate mature BMDCs (mDCs).

extract_protocol:
Total RNA was extracted from treated mDCs using TRIzol reagent (Invitrogen) according to manufacturer’s protocol then removed ribosomal RNAs
cDNA library construction and sequencing were performed by Beijing Genomics Institute using HiSeq 4000 platform.

treatment_protocol: mDCs were stimulated with CCR7 ligand CCL19 and CCL21 (CCR7L) for 12 h or left unstimulated (Med), and then subjected to lncRNA seq

tag: cells

value: LPS-stimulated mature DCs


title: P209_B11_WT_C57BL/6J_cortex_rep4


title: CD235a+ cells - umbilical cord blood 1

description: generated by cellranger v2.1.0

source_name: umbilical cord blood 1

value: umbilical cord blood


title: DC-Med

description: total RNA without ribosomal RNA


title: P209_B10_WT_C57BL/6J_cortex_rep4


title: 3602_1_CON_POST_NOTEL


title: P209_B1_WT_C57BL/6J_cortex_rep1


title: P209_A7_WT_C57BL/6J_cortex_rep3


title: P209_A8_WT_C57BL/6J_cortex_rep3


title: P209_A6_WT_C57BL/6J_cortex_rep2


title: P209_A9_WT_C57BL/6J_cortex_rep3


title: Gata3-_SNS_9

city: Cambridge

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

country: United Kingdom

institute: University of Cambridge

data_processing:
RNA-seq reads were aligned to mm10 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: mm10
Supplementary_files_format_and_content: HT-Seq counts(.txt)

source_name: Gata3- Sympathatic nervous system cells

extract_protocol:
cells were sorted from freshly isolated mouse embryos; dissected tissues were treated with collagenase and then stained with cell surface markers and directly sorted into lysis buffer
SmartSeq2

value: Gata3-GFP +/-

value: aorta-gonads-mesonephros (AGM)

tag: cell type

value: Gata3- Sympathatic nervous system cells


title: Gata3-_SNS_8


title: P209_A4_WT_C57BL/6J_cortex_rep2


title: CD235a+ cells - umbilical cord blood 2 and umbilical cord blood 3,UCB3

description: generated by cellranger v2.1.0

value: Gene Expression Library and Antibody Capture


title: P209_B12_WT_C57BL/6J_cortex_rep4


title: Gata3-_SNS_6


title: Gata3-_SNS_7


title: P209_A3_WT_C57BL/6J_cortex_rep1


title: P209_A24_WT_C57BL/6J_hippocampus_rep4


title: P209_A22_WT_C57BL/6J_hippocampus_rep4


title: Gata3-_SNS_4


title: P209_A23_WT_C57BL/6J_hippocampus_rep4


title: Gata3-_SNS_5


title: P209_A21_WT_C57BL/6J_hippocampus_rep3


title: P209_A20_WT_C57BL/6J_hippocampus_rep3


title: Gata3-_SNS_3


title: P209_A2_WT_C57BL/6J_cortex_rep1


title: P209_A19_WT_C57BL/6J_hippocampus_rep3


title: Gata3-_SNS_2


title: P209_A18_WT_C57BL/6J_hippocampus_rep2


title: AGS cell line treated DMSO

type: RNA

city: Incheon

first: Seungyoon

last: Nam

state: Incheon

address: Namdong-gu, Namdongdae-ro 774-21

country: South Korea

institute: Gachon University Colleage of Medicine

description: AGS cell line treated DMSO

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Human  2.0 ST Array at 45°C for 16hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix). Signal values were computed using the Affymetrix® GeneChip™ Command Console software.

data_processing:
Raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC).
The data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Expression Console™ Software (EC).

label: biotin

source_name: stomach cancer cell line

label_protocol: cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer. The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: grown in RPMI-1640 (Invitrogen) and 10% fetal calf serum (Hyclone), at 37oC, under 5% CO2. Cells (2.5 × 105) were seeded and grown to 70–80% confluence

extract_protocol: total cellular mRNA was isolated using RNeasy kits (Qiagen)

treatment_protocol: treated with DMSO, Rhosin, JK136 and JK139.

tag: cell line

value: AGS

value: stomach cancer cell line


title: AGS cell line treated JK136

description: AGS cell line treated JK136


title: SNU601 cell line treated Rhosin

description: SNU601 cell line treated Rhosin


title: SNU601 cell line treated JK136

description: SNU601 cell line treated JK136


title: SNU601 cell line treated DMSO

description: SNU601 cell line treated DMSO


title: SNU601 cell line treated JK139

description: SNU601 cell line treated JK139


title: Gata3-_SNS_20


title: P209_A15_WT_C57BL/6J_hippocampus_rep1


title: P209_A13_WT_C57BL/6J_hippocampus_rep1


title: P209_A16_WT_C57BL/6J_hippocampus_rep2


title: P209_A12_WT_C57BL/6J_cortex_rep4


title: MKN1 cell line treated JK139

description: MKN1 cell line treated JK139


title: P209_A11_WT_C57BL/6J_cortex_rep4


title: Gata3-_SNS_1


title: MKN1 cell line treated JK136

description: MKN1 cell line treated JK136


title: Gata3-_SNS_19


title: Gata3-_SNS_17


title: P211_P9_5xFAD_C57BL/6J_hippocampus_rep3


title: P209_A17_WT_C57BL/6J_hippocampus_rep2


title: MKN1 cell line treated DMSO

description: MKN1 cell line treated DMSO


title: P211_P8_5xFAD_C57BL/6J_hippocampus_rep2


title: Gata3-_SNS_16


title: MKN1 cell line treated Rhosin

description: MKN1 cell line treated Rhosin


title: AGS cell line treated Rhosin

description: AGS cell line treated Rhosin


title: Gata3-_SNS_15


title: P211_P6_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_P5_5xFAD_C57BL/6J_hippocampus_rep2


title: P209_A10_WT_C57BL/6J_cortex_rep4


title: P209_A1_WT_C57BL/6J_cortex_rep1


title: D2: SMMC-7721_Drug_rep2

city: Shanghai

first: Qianqian

last: Cai

address: No.138, Yixueyuan Road

department: Department of biochemistry and molecular biology

institute: Fudan University

description:
Biological replicate 2 of 3. SMMC-7721 cells treated with 2μM sulfatide,harvested after 24h.
We used the spiked-in control RNA as the reference sample with the Arraystar Spike-In RNA kit. The spike-in control RNA, which developed by ERCC(external RNA controls consortium, NIST, U.S.), as an internal control during the entire process. The spike-in control was used in equal amount to the sample RNA in labeling reaction, and the dilution of fresh spike-in control according to Table 1 following the manufacturer's instructions.

hyb_protocol: 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were scanned with using the Agilent DNA Microarray Scanner (part number G2505B). Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies).

label_protocol: lncRNA and mRNA was purified from 1 μg total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was  fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min.

growth_protocol: SMMC-7721 cells were cultured in Dulbecco’s Modified Eagle’s Medium (Gibco-Life Technologies) supplemented with 10% fetal bovineserum (FBS)and 5% CO2 at 37 °C

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: treated with 2 μM Galactose-cerebroside or sulfatide (Sigma, St.Louis, Missouri, USA)

value: human hepatocellular carcinoma

tag: treatment time

source_name: reference pool

tag: sample type

value: pool of all samples


title: P211_P4_5xFAD_C57BL/6J_hippocampus_rep1


title: D3: SMMC-7721_Drug_rep3

description:
Biological replicate 3 of 3. SMMC-7721 cells treated with 2μM sulfatide,harvested after 24h.
We used the spiked-in control RNA as the reference sample with the Arraystar Spike-In RNA kit. The spike-in control RNA, which developed by ERCC(external RNA controls consortium, NIST, U.S.), as an internal control during the entire process. The spike-in control was used in equal amount to the sample RNA in labeling reaction, and the dilution of fresh spike-in control according to Table 1 following the manufacturer's instructions.


title: AGS cell line treated JK139

description: AGS cell line treated JK139


title: Gata3-_SNS_13


title: P211_P3_5xFAD_C57BL/6J_hippocampus_rep1


title: Gata3-_SNS_14


title: D1: SMMC-7721_Drug_rep1

description:
Biological replicate 1 of 3. SMMC-7721 cells treated with 2μM sulfatide,harvested after 24h.
We used the spiked-in control RNA as the reference sample with the Arraystar Spike-In RNA kit. The spike-in control RNA, which developed by ERCC(external RNA controls consortium, NIST, U.S.), as an internal control during the entire process. The spike-in control was used in equal amount to the sample RNA in labeling reaction, and the dilution of fresh spike-in control according to Table 1 following the manufacturer's instructions.


title: P211_P24_blank

description: blank

value: blank


title: C3: SMMC-7721_Control_rep3

description:
Biological replicate 3 of 3. SMMC-7721 cells treated with 2μM Galactose-cerebroside,as Control , harvested after 24h.
We used the spiked-in control RNA as the reference sample with the Arraystar Spike-In RNA kit. The spike-in control RNA, which developed by ERCC(external RNA controls consortium, NIST, U.S.), as an internal control during the entire process. The spike-in control was used in equal amount to the sample RNA in labeling reaction, and the dilution of fresh spike-in control according to Table 1 following the manufacturer's instructions.


title: Gata3-_SNS_12


title: P211_P22_5xFAD_C57BL/6J_cerebellum_rep3

value: cerebellum


title: C2: SMMC-7721_Control_rep2

description:
Biological replicate 2 of 3. SMMC-7721 cells treated with 2μM Galactose-cerebroside,as Control , harvested after 24h.
We used the spiked-in control RNA as the reference sample with the Arraystar Spike-In RNA kit. The spike-in control RNA, which developed by ERCC(external RNA controls consortium, NIST, U.S.), as an internal control during the entire process. The spike-in control was used in equal amount to the sample RNA in labeling reaction, and the dilution of fresh spike-in control according to Table 1 following the manufacturer's instructions.


title: P211_P23_5xFAD_C57BL/6J_cerebellum_rep3


title: C1: SMMC-7721_Control_rep1

description:
Biological replicate 1 of 3. SMMC-7721 cells treated with 2μM Galactose-cerebroside,as Control , harvested after 24h.
We used the spiked-in control RNA as the reference sample with the Arraystar Spike-In RNA kit. The spike-in control RNA, which developed by ERCC(external RNA controls consortium, NIST, U.S.), as an internal control during the entire process. The spike-in control was used in equal amount to the sample RNA in labeling reaction, and the dilution of fresh spike-in control according to Table 1 following the manufacturer's instructions.


title: P211_P21_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_P20_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_P2_5xFAD_C57BL/6J_hippocampus_rep1

value: hippocampus


title: P211_P19_5xFAD_C57BL/6J_cerebellum_rep2


title: Gata3-_SNS_11


title: P209_A14_WT_C57BL/6J_hippocampus_rep1

value: wildtype


title: Gata3-_SNS_10


title: P211_P16_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_P7_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_P18_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_P17_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_P15_5xFAD_C57BL/6J_cerebellum_rep1


title: Gata3+_SNS_8

source_name: Gata3+ Sympathatic nervous system cells

value: Gata3+ Sympathatic nervous system cells


title: Gata3+_SNS_9


title: P211_P13_5xFAD_C57BL/6J_cerebellum_rep1


title: Gata3+_SNS_7


title: S700C_DMSO_R1_HL-60_TempO-Seq

city: Leiden

first: Tom

last: van der Wel

address: Einsteinweg 55

department: Molecular Physiology

country: Netherlands

institute: Leiden University

data_processing:
Raw data were processed by BiosSpyder technologies according to company's standard procedures. TempO-Seq sequence files were analysed using the Tempo-SeqR software package. The input for TempO-Seq data analysis is a folder of zipped FASTQ files. Each FASTQ file contains the reads and quality scores for one sample. Each FASTQ file is aligned using the STAR algorithm to a pseudo-transcriptome corresponding to the gene panel used in the assay.
Internal normalization using DESeq2.
Statistical analysis by t-test with Benjamini-Hochberg multiple comparison correction (FDR = 1%).
Differentially expressed genes were identified using following cut-offs: fold change of corrected counts of FESS700C over WT HL-60 cells < 0.5 or > 2 with q-value < 0.05.
Genome_build: hg38

source_name: HL-60 (human promyeloblast)

growth_protocol: HL-60 (human promyeloblast) cells were cultured at 37°C under 5% CO2 in HEPES-supplemented RPMI containing phenol red, stable glutamine, 10% (v/v) fetal calf serum (Biowest), penicillin and streptomycin (200 μg/mL each), unless stated otherwise. Cell density was maintained between 0.2E6 and 2.0E6 cells/mL. Cell lines were purchased at ATCC and were tested on regular basis for mycoplasma contamination. Cultures were discarded after 2-3 months of use.

extract_protocol:
Cells were washed in PBS and then lysed in BioSpyder BBN buffer (50 µL per well, 15 min, rt). Lysates were flash-frozen and shipped to BioSpyder technologies.
Library was constructed at BioSpyder technologies according to company's standard procedures. In TempO-Seq, each Detector Oligo consists of a sequence complementary to an mRNA target plus a universal (i.e. same for every targeted gene) primer binding site. They anneal in immediate juxtaposition to each other on the targeted RNA template such that they can be ligated together. Ligated detector oligos are PCR-amplified using a primer set (single-plex PCR reaction, with a single primer pair for each sample) that introduces both the adaptors required for sequencing and a sample-specific barcode. The barcode sequences flank the target sequence and are inserted appropriately into the standard Illumina adaptors to permit standard dual-index sequencing of the barcodes and deconvolution of sample-specific reads from the sequencing data using the standard Illumina software. All the PCR-amplified and barcoded samples are pooled into a single library for sequencing. Sequencing reads are demultiplexed using the standard sequencing instrument software for each sample using the barcodes to give a FASTQ file for each.

treatment_protocol: One day prior to induction of differentiation, cells were diluted to 0.4E6 cells/mL (20,000 cells per well in 96-well plate). Monocyte/macrophage differentiation was induced by addition of phorbol 12-myristate 13-acetate (PMA; 16 nM) for 48 h, during which cells attached to the plastic surface, were positive for CD11b and acquired monocyte/macrophage morphology.

value: human promyeloblast

tag: genotype/variation

value: FES_S700C mutant

tag: differentiation type

value: Macrophages (16 nM PMA, 48 h)


title: S700C_DMSO_R2_HL-60_TempO-Seq


title: S700C_DMSO_R3_HL-60_TempO-Seq


title: P211_P12_blank

description: blank


title: Gata3+_SNS_5


title: P211_P10_5xFAD_C57BL/6J_hippocampus_rep3


title: P211_P14_5xFAD_C57BL/6J_cerebellum_rep1


title: WT_DMSO_R3_HL-60_TempO-Seq

value: Wild-type


title: P211_P11_5xFAD_C57BL/6J_hippocampus_rep3


title: P211_P1_5xFAD_C57BL/6J_hippocampus_rep1


title: Gata3+_SNS_6

value: Gata3-GFP +/-


title: P211_O9_5xFAD_C57BL/6J_hippocampus_rep3


title: WT_DMSO_R1_HL-60_TempO-Seq


title: Gata3+_SNS_2

value: aorta-gonads-mesonephros (AGM)


title: WT_DMSO_R2_HL-60_TempO-Seq


title: P211_O6_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_O7_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_O5_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_O8_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_O4_5xFAD_C57BL/6J_hippocampus_rep1


title: Gata3+_SNS_4


title: Gata3+_SNS_3


title: Gata3+_SNS_20


title: Meis_IP_HL

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

description: ChIP sample

library_source: genomic

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2.
Illumina adapter contaminations were removed from reads using Cutadapt v1.3.
Processed reads were mapped against mm9 whole genome using bwa aln / bwa samse; samtools was used to generate output files in bam format.
Alignments were filtered with samtools to retain only properly mapped, non duplicate reads, with mapping quality above 0, not aligning to unlocalized or unassembled contigs, the mitochondrial genome, or chromosome Y.
ChIPSeq peaks were called against input using MACS2.
Genome_build: mm9
Supplementary_files_format_and_content: ENCODE narrow peak files (extended bed format) including coordinates, score and qvalue for ChIPSeq peaks called for each sample against input, using MACS2.

molecule: genomic DNA

source_name: Hindlimb

extract_protocol:
Around 500 E10.5 (36so) wild-type FLs and 500 E10.5 wild-type HLs were fixed according to standard procedures for ChIP experiments. For the IP, we used ChIP-IT High Sensitivity Columns (Active Motif). Two anti-Meis antibodies were used simultaneously, one recognizing Meis1a and Meis2a,c and the other recognizing all Meis1 isoforms.
ChIP-seq libraries were generated using the NEBNext Ultra DNA Library Prep Kit for Illumina and sequenced (single-end mode and length of 50 bp) on a HiSeq 2500 (Illumina)

value: Hindlimb


title: P211_O3_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_O23_5xFAD_C57BL/6J_cerebellum_rep3


title: Gata3+_SNS_19


title: Gata3+_SNS_1


title: Gata3+_SNS_18


title: Rosettes, Salt_Mannitol_Heat_3

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

institute: Heinrich-Heine-University

data_processing:
Illumina Casava-1.9software used for basecalling.
After successful quality control with the Fast QC software (v0.11.5), Illumina reads were quantified by mapping against the Arabidopsis reference transcriptome (Araport 11 representative CDS, Araport11_genes.201606.cds.fasta.gz, retrieved from www.araport.org) using Kallisto v 0.45.1 (Bray et al., 2016) in default mode with 50 times bootstrapping (option -b 50) for sleuth. Kallisto provides normalized transcript abundance as transcripts per million (tpm).
Differential transcript abundance comparing each of the treatments against the control were determined using the likelihood ratio test implemented in sleuth v0.30.0 (Pimentel et al., 2016). An alpha of 0.05 was chosen after adjusting p-values (thereafter termed ‘q-value’) for multiple hypothesis testing via Benjamini–Hochberg correction (Benjamini and Hochberg, 1995) as implemented in sleuth. The ‘b value’ supplied by sleuth was used as adapted log2-fold change (LFC) between the respective treatment and control.
Means and standard deviation of tpm of biological triplicates group were calculated.
Genome_build: Araport 11 representative CDS, Araport11_genes.201606.cds.fasta.gz, retrieved from www.araport.org
Supplementary_files_format_and_content: Excel file including Arabidopsis locus ID, brief annotation, mapman annotation, raw estimated counts (kallisto), tpm (kallisto) for each sample and mean and standard deviation of tpm for biological triplicates, sleuth results of differential gene expression comparing each  treatment against control.

organism: Arabidopsis thaliana

source_name: Rosettes

growth_protocol: Seeds of wild-type Arabidopsis thaliana ecotype Columbia-0 (Col-0; WT) were sown on soil. After stratification at 4°C for 2 days, the seeds were transferred to a long-day (16 h light/8 h dark) growth chamber using a mix of bulbs from Spectralux®Plus NL 36W/840 (Radium) and Fluora L 36W/77 (Osram) with a light intensity of approximately 100 µE m-2 s-1 and a temperature regime of 22°C day/18°C night temperatures. Two-week old seedlings were transplanted to new soil. After another 14 days of growth, plants were subjected to the stress treatments.

extract_protocol:
Rosettes were harvested and immediately frozen in liquid nitrogen. Tissue was ground into fine powder using liquid nitrogen, and then kept at -80°C until use. Total RNA was extracted using the Promega Kit (SV Total RNA Isolation System, spin protocol). The integrity of the extracted RNA was anaylsed by gel electrophoresis and its concentration was measured using a NanoDrop (ND-1000) spectrophotometer.
Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA, United States) and quantified with a Qubit 2.0 (Invitrogen, Waltham, MA, United States). Samples were multiplexed with 12 libraries per lane and sequenced in paired-end mode (Rapid Run, 100 bp read length) on an Illumina HiSeq 2500 platform.

treatment_protocol: For salt stress treatment, plants were watered with 150 mM NaCl solution 16 h before sampling. The osmotic stress treatment was applied by watering plants with 200 mM mannitol 16 h before sampling. For heat treatment, plant trays were transferred to a growth cabinet pre-adjusted at 35°C for 4 hours before sampling. To avoid the circadian clock effects that could interfere with the interactions between our treatments, we started the heat treatment after 3 h after light onset, and collected all samples at the midday where the plant metabolism is at a steady state. Double treatment of salt and mannitol was applied by watering plants with a mixed solution containing final concentration of 150 mM NaCl and 200 mM mannitol. For double treatments of heat with NaCl or mannitol, a fraction of the plants that were watered with NaCl or mannitol were moved after 12 hours to a growth cabinet pre-adjusted at 35°C for extra 4 h, making a total of 16 h before sampling. For multiple stress treatments, a patch of the plants treated with the double treatment of NaCl 150 mM and 200 mM mannitol were transferred after 12 h to a growth cabinet pre-adjusted at 35°C for extra 4 hours, making total of 16 h before sampling (Figure 1A). To apply multiple stress treatment similar to field conditions as much as possible, Arabidopsis plants were treated with salt and mannitol 1 hour before the light is off, and kept for 12 h before starting heat treatment. After 3 h of light turning on, plant trays were transferred to 35°C growth cabinet for extra 4 h making a total of 16 h treatment.

tag: stress treatment

value: Rosettes

tag: biological replicate


title: P211_O22_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_O24_blank

description: blank


title: Rosettes, Salt_Mannitol_Heat_2


title: P211_O2_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_O21_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_O19_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_O20_5xFAD_C57BL/6J_cerebellum_rep3


title: N-myc-low-B-ALL cells

first: Chiqi

last: Chen

address: 上海市黄浦区重庆南路280号

institute: Shanghai Jiao Tong University School of Medicine

description: gene expression

hyb_protocol: 1.65 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 25x fragmentation buffer and 10x blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 μl of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole mouse Genome Oligo Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for array slides (Scan Area 61x21.6 mm, Scan resolution 5 μm, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

label: cyanine 3

source_name: SoNar-low B-ALL cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 μg RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNeasy Mini Kit purification (Qiagen p/n 74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: SoNar-high and SoNar-low B-ALL were lysed by TRIzol reagent for extraction of RNA. RNA was prepared using RNasey Mini Kit(Qiagen p/n 74104) according to  the manufacturer's recommendations. After clean-up, RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored by RNA electrophoresis.

treatment_protocol: SoNar-high and SoNar-low B-ALL cells were sorted from bone marrow based on ratio F405/F488 nm.

value: bone marrow

tag: age

value: 8 weeks

value: B-cell acute lymphoblastic leukemia (B-ALL)

tag: cell population

value: SoNar-low


title: Meis_Input_HL

description: Input sample

tag: developmental stage


title: Gata3+_SNS_16

tag: genotype


title: P211_O18_5xFAD_C57BL/6J_cerebellum_rep2

tag: tissue


title: Gata3+_SNS_17


title: Rosettes, Mannitol_Heat_3


title: Rosettes, Mannitol_Heat_2


title: P211_O13_5xFAD_C57BL/6J_cerebellum_rep1

tag: strain


title: P211_O15_5xFAD_C57BL/6J_cerebellum_rep1


title: Gata3+_SNS_15


title: P211_O12_blank

description: blank

value: blank


title: Rosettes, Mannitol_Heat_1


title: Gata3+_SNS_14


title: P211_O10_5xFAD_C57BL/6J_hippocampus_rep3


title: N-myc-high-B-ALL cells

address: 上海市黄浦区重庆南路280号

description: gene expression

source_name: SoNar-high B-ALL cells

value: SoNar-high


title: Gata3+_SNS_13


title: Rosettes, Salt_Mannitol_Heat_1


title: P211_O17_5xFAD_C57BL/6J_cerebellum_rep2

value: cerebellum


title: P211_O16_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_O14_5xFAD_C57BL/6J_cerebellum_rep1


title: Gata3+_SNS_11


title: Rosettes, Salt_Heat_3


title: P209_A5_WT_C57BL/6J_cortex_rep2

value: cortex

value: wildtype


title: P211_N8_5xFAD_C57BL/6J_hippocampus_rep2

value: hippocampus


title: P211_N6_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_N5_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_N7_5xFAD_C57BL/6J_hippocampus_rep2


title: Rosettes, Salt_Heat_2


title: Gata3-_SNS_18

value: Gata3- Sympathatic nervous system cells


title: Gata3+_SNS_10

value: Gata3+ Sympathatic nervous system cells


title: P211_N4_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_O11_5xFAD_C57BL/6J_hippocampus_rep3


title: P211_N9_5xFAD_C57BL/6J_hippocampus_rep3


title: Rosettes, Salt_Heat_1


title: Rosettes, Salt_Mannitol_3


title: Gata3-_MC_9

source_name: Gata3- Mesenchymal cells

value: Gata3- Mesenchymal cells


title: P211_N3_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_N24_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_O1_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_N23_5xFAD_C57BL/6J_cerebellum_rep3


title: Gata3-_MC_8

value: Gata3-GFP +/-


title: P211_N21_5xFAD_C57BL/6J_cerebellum_rep3


title: Rosettes, Salt_Mannitol_2


title: Rosettes, Salt_Mannitol_1


title: Gata3+_SNS_12

value: aorta-gonads-mesonephros (AGM)


title: P211_N20_5xFAD_C57BL/6J_cerebellum_rep3


title: Gata3-_MC_7


title: P211_N19_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_N2_5xFAD_C57BL/6J_hippocampus_rep1


title: Rosettes, Heat_3

value: Heat


title: P211_N18_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_N16_5xFAD_C57BL/6J_cerebellum_rep2


title: Gata3-_MC_5


title: P211_N17_5xFAD_C57BL/6J_cerebellum_rep2


title: Rosettes, Heat_1

value: Rosettes


title: P211_N15_5xFAD_C57BL/6J_cerebellum_rep1


title: Gata3-_MC_4


title: Rosettes, Mannitol_3

value: Mannitol


title: P211_N12_5xFAD_C57BL/6J_cerebellum_rep1


title: P211_N11_5xFAD_C57BL/6J_hippocampus_rep3


title: Rosettes, Mannitol_2


title: Gata3-_MC_3


title: Rosettes, Heat_2


title: P211_N22_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_N14_5xFAD_C57BL/6J_cerebellum_rep1


title: Rosettes, Mannitol_1


title: P211_N13_5xFAD_C57BL/6J_cerebellum_rep1


title: P211_N1_5xFAD_C57BL/6J_hippocampus_rep1


title: Gata3-_MC_20


title: P211_M9_5xFAD_C57BL/6J_hippocampus_rep3


title: Rosettes, Salt_3

value: Salt


title: P211_N10_5xFAD_C57BL/6J_hippocampus_rep3


title: P211_M8_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_M7_5xFAD_C57BL/6J_hippocampus_rep2


title: Gata3-_MC_6


title: Gata3-_MC_1


title: P211_M6_5xFAD_C57BL/6J_hippocampus_rep2


title: Gata3-_MC_19


title: Rosettes, Salt_2


title: P211_M5_5xFAD_C57BL/6J_hippocampus_rep2


title: Rosettes, Salt_1


title: Gata3-_MC_2


title: P211_M24_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_M23_5xFAD_C57BL/6J_cerebellum_rep3


title: Rosettes, Control_3

value: Control


title: Gata3-_MC_16


title: Gata3-_MC_17


title: Rosettes, Control_2


title: P211_M21_5xFAD_C57BL/6J_cerebellum_rep3


title: Gata3-_MC_15


title: Gata3-_MC_18


title: P211_M2_5xFAD_C57BL/6J_hippocampus_rep1


title: Rosettes, Control_1


title: P211_M22_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_M19_5xFAD_C57BL/6J_cerebellum_rep2


title: S384_11_471_T_plus

data_processing:
fastq files were aligned to GRCm36 with STAR version 2.7.2a with command line   STAR --runThreadN 10 --genomeDir xxx --genomeLoad LoadAndKeep --limitBAMsortRAM 20000000000 --readFilesIn .xxx --readFilesCommand zcat --outFileNamePrefix xxx --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --seedSearchStartLmax 30 --outSAMtype BAM SortedByCoordinate --outBAMcompression 10
BAM files were used to generate a counts matrix with featureCounts 1.6.2 using Gencode M21 with command line featureCounts -a gencode.vM21.annotation.gtf -G GRCm38.p6.genome.fa -o counts.txt -F GTF -g gene_name -t exon -T 10 --largestOverlap
differential gene expression analysis was performed using the limma/voomWithQualityWeights pipeline as published in hte limma vignette.
Genome_build: Gencode M21 (GRCm38)
Supplementary_files_format_and_content: counts file, tab delimited text file

source_name: brain

extract_protocol:
Total RNA was extracted from FACS sorted microglial cells stabilized in RNAprotect buffer according to the “Purification of total RNA from animal and human cells” protocol of the RNeasy Plus Micro Kit (QIAGEN, Hilden, Germany).  In brief, cells were stored and shipped in buffer RNAprotect at 2-8 °C. After pelleting by centrifugation for 5 minutes at 5,000 x g, the RNAprotect was replaced by 350 µl buffer RLT Plus and the samples were homogenized by vortexing for 30 seconds. Genomic DNA contamination was removed by using gDNA Eliminator spin columns. Next one volume of 70 % ethanol was added and the samples were applied to RNeasy MinElute spin columns followed by several wash steps. Finally the total RNA was eluted in 12 μl of nuclease free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip reagent set (Agilent, Palo Alto, CA, USA).
The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from 500 pg total-RNA. Double stranded cDNA was amplified by LD PCR (12 cycles) and purified via magnetic bead clean-up. Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA). 150 pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step 1:5 dilutions of index 1 (i7) and index 2 (i5) primers were used. The libraries were quantified using the KAPA Library Quantification Kit - Illumina/ABI Prism User Guide (Roche Sequencing Solutions, Inc., Pleasanton, CA, USA). Equimolar amounts of each library were sequenced on a NextSeq 500 instrument controlled by the NextSeq Control Software (NCS) v2.2.0, using a 75 Cycles High Output Kit with the dual index, single-read (SR) run parameters. Image analysis and base calling were done by the Real Time Analysis Software (RTA) v2.4.11. The resulting .bcl files were converted into .fastq files with the bcl2fastq v2.18 software.    RNA extraction, library preparation and RNAseq were performed at the Genomics Core Facility “KFB - Center of Excellence for Fluorescent Bioanalytics” (University of Regensburg, Regensburg, Germany; www.kfb-regensburg.de).

value: microglia

value: brain


title: P211_M17_5xFAD_C57BL/6J_cerebellum_rep2

source_name: microglia


title: Gata3-_MC_14


title: P211_M16_5xFAD_C57BL/6J_cerebellum_rep2


title: Gata3-_MC_13


title: S384_12_472_T_T


title: P211_M14_5xFAD_C57BL/6J_cerebellum_rep1


title: Gata3-_MC_12


title: P211_M4_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_M3_5xFAD_C57BL/6J_hippocampus_rep1


title: S384_10_470_plus_plus

value: wild type


title: P211_M15_5xFAD_C57BL/6J_cerebellum_rep1

value: cerebellum


title: S384_09_469_T_plus


title: Gata3-_MC_11


title: P211_M13_5xFAD_C57BL/6J_cerebellum_rep1


title: S384_08_467_T_T


title: P211_M20_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_M10_5xFAD_C57BL/6J_hippocampus_rep3


title: Gata3-_MC_10


title: P211_M1_5xFAD_C57BL/6J_hippocampus_rep1


title: Gata3+_MC_9

source_name: Gata3+ Mesenchymal cells

value: Gata3+ Mesenchymal cells


title: P211_M18_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_M11_5xFAD_C57BL/6J_hippocampus_rep3


title: P211_L9_5xFAD_C57BL/6J_hippocampus_rep3


title: S384_07_464_plus_plus


title: S384_06_463_T_plus


title: P211_L8_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_L7_5xFAD_C57BL/6J_hippocampus_rep2


title: S384_05_462_T_T


title: P211_L6_5xFAD_C57BL/6J_hippocampus_rep2


title: Gata3+_MC_8


title: Gata3+_MC_7


title: P211_L5_5xFAD_C57BL/6J_hippocampus_rep2


title: S384_04_461_T_plus


title: S384_03_460_T_T


title: Gata3+_MC_6


title: P211_L24_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_L3_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_L23_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_L4_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_M12_5xFAD_C57BL/6J_cerebellum_rep1


title: Gata3+_MC_5


title: P211_L22_5xFAD_C57BL/6J_cerebellum_rep3


title: S384_02_458_plus_plus


title: P211_L21_5xFAD_C57BL/6J_cerebellum_rep3


title: Gata3+_MC_4


title: S384_01_457_plus_plus


title: P211_L20_5xFAD_C57BL/6J_cerebellum_rep3


title: Gata3+_MC_3


title: P211_L19_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_L18_5xFAD_C57BL/6J_cerebellum_rep2


title: Gata3+_MC_2


title: P211_L2_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_L17_5xFAD_C57BL/6J_cerebellum_rep2


title: AK7987-7KO

city: Dresden

first: Francis

last: Stewart

address: Tatzberg 47-49

institute: BIOTEChnology Center TU Dresden

data_processing:
Basecalling: bcl2fastq2 v. 2.19.1
Read alignment: GSNAP version 2019-06-10 called with args: gsnap.sse42 -D /projects/seq-work/user/pipeline/gmap -d mm10 --gunzip -A sam -t 20 --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -n 1 -m 0.6 -s EnsemblGene-98.ss.mm10.iit -N 0 --read-group-id=L47609_AK7987-7KO --read-group-name=AK7987-7KO --read-group-library=L47609 --read-group-platform=illumina --action-if-cigar-error noprint fastq/L47609_AK7987-7KO_R1.fastq.gz
Counts per feature: featureCounts v1.6.3; Command:"featureCounts" "-a" "/projects/seq-work/user/pipeline/annotation/mus_musculus/mm10/EnsemblGene-98.mm10.TR.gtf" "-s" "2" "-o" "genecount/bfx1298.mm10.e98.txt" "-Q" "1" "-T" "8" "--tmpDir" "/tmp/776544.1.all.q" "gsnap/L47608_AK7987-2KO.bam" "gsnap/L47604_AK7986-2C.bam" "gsnap/L47606_AK7987-5C.bam" "gsnap/L47607_AK7986-1KO.bam" "gsnap/L47605_AK7986-6C.bam" "gsnap/L47609_AK7987-7KO.bam"
Read count normalization: The raw read counts (absolute number of reads) were normalized with the DESeq2 R package (v. 1.24.0)(Anders and Huber, 2010)
Genome_build: mm10
Supplementary_files_format_and_content: bfx1298.mm10.e98.txt.original.csv: tab delimited file with raw readcounts per gene (rows) and sample (columns) (featureCounts output)
Supplementary_files_format_and_content: bfx1298.normalised_counts.de-expl.csv: tab delimited file with sample size normalized counts (with DESeq2) per gene (rows) and sample (columns)

source_name: lung E18.5

extract_protocol:
E18.5 lungs were dissected without aeration of the lung. Lung lobes were snapfrozen in liquid nitrogen and RNA was harvested using Trizol reagent.
mRNA was isolated from 1 ug total RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) according to the manufacturer’s instructions. Samples were eluted in 11.5ul of a mixture of NEBNext First Strand Synthesis Buffer and Random Primers, and then directly subjected to the workflow for strand-specific RNA-Seq library preparation (Ultra II Directional RNA Library Prep, NEB). For ligation custom adaptors were used (Adaptor-Oligo 1: 5'-ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT-3', Adaptor-Oligo 2: 5'-P-GAT CGG AAG AGC ACA CGT CTG AAC TCC AGT CAC-3'). After ligation, adapters were depleted by an XP bead purification (Beckman Coulter) adding the beads solution in a ratio of 1:0.9. Dual unique indexing was done during the following PCR enrichment (8 cycles, 65 °C) using custom amplification primers carrying the same sequence for i7 and i5 index (Primer 1: AAT GAT ACG GCG ACC ACC GAG ATC TAC AC NNNNNNNN ACA TCT TTC CCT ACA CGA CGC TCT TCC GAT CT, Primer 2: CAA GCA GAA GAC GGC ATA CGA GAT NNNNNNNN GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T). After two more XP bead purifications (1:0.9), libraries were quantified using the Fragment Analyzer (Agilent). For Illumina flowcell production, samples were equimolarly pooled and sequenced 75bp single read on an Illumina NextSeq 500.

value: Mll3FDC/FDC (Mll3 KO)


title: Gata3+_MC_20


title: AK7986-1KO


title: AK7987-2KO


title: P211_L15_5xFAD_C57BL/6J_cerebellum_rep1


title: AK7987-5C


title: P211_L13_5xFAD_C57BL/6J_cerebellum_rep1


title: AK7986-6C


title: P211_L12_5xFAD_C57BL/6J_cerebellum_rep1


title: Gata3+_MC_19


title: P211_L10_5xFAD_C57BL/6J_hippocampus_rep3

value: hippocampus


title: Gata3+_MC_18


title: P211_L1_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_L11_5xFAD_C57BL/6J_hippocampus_rep3


title: AK7986-2C


title: P211_K9_5xFAD_C57BL/6J_hippocampus_rep3


title: Gata3+_MC_17


title: Gata3+_MC_16


title: samhd- KOH rep4

city: Göteborg

first: Anders R.

last: Clausen

address: Box 440

country: Sweden

institute: University of Gothenburg

description: KOH treated

data_processing:
Library strategy: DNA-seq
All reads were trimmed for quality and adaptor sequence with cutadapt 1.12 (-m 15 -q 10 –match-read-wildcards). Pairs with one or both reads shorter than 15 nt were discarded. Mate 1 of the remaining pairs was aligned to an index containing the sequence of all oligos used in the preparation of these libraries with bowtie 1.2 (-m1 -v2), and all pairs with successful alignments were discarded. Pairs passing this filter were subsequently aligned to the mm10 M. musculus reference genome (-m1 -v2 –X2000). Single-end alignments were then performed with mate 1 of all unaligned pairs (-m1 -v2). Using the –m1 setting causes Bowtie to discard all reads which align to multiple places in the genome, including nuclear mitochondrial DNA segments (NUMTs). To calculate the base identity of ribonucleotides in mtDNA, the count of 5′-ends of all paired-end and single-end alignments were determined for all samples and shifted one base upstream to the location of the free 5′-end or hydrolyzed ribonucleotide.
Genome_build: UCSC (mm10)

source_name: tissue

extract_protocol:
Individual mouse tissues were incubated overnight with proteinase K (#P6556, Sigma), and total DNA (i.e. nDNA and mtDNA) was isolated according to standard protocols [27]. Individual mouse tissues were incubated overnight with proteinase K (#P6556, Sigma), and total DNA (i.e. nDNA and mtDNA) was isolated according to standard protocols [27].                  For the pure mtDNA in Fig. S1b-c, the TA muscle was minced into small pieces, washed in PBS containing 10 mM EDTA, and incubated with 0.05% trypsin in PBS with 10 mM EDTA for 90 min on ice. After centrifugation (200 x g, 5 min, 4°C), the pelleted tissue was resuspended in homogenization buffer HB (225 mM mannitol, 75 mM sucrose, 10 mM Hepes-KOH pH 7.8, 10 mM EDTA) and homogenized using 10 strokes of a Teflon-coated pestle. Nuclei and cell debris were pelleted at 800 x g for 10 min at 4°C, and the supernatant was subjected to centrifugation at 12,000 x g for 10 min at 4°C to pellet mitochondria. The mitochondria were resuspended in HB, overlaid on a sucrose gradient consisting of 1 M and 1.5 M sucrose in gradient buffer (10 mM Hepes pH 7.4 and 10 mM EDTA), and centrifuged at 40,000 x g for 1 h at 4°C. The purified mitochondria were diluted in gradient buffer, pelleted by centrifugation at 12,000 x g for 10 min at 4°C, and resuspended in HB buffer containing 100 ng/μl proteinase K and incubated for 15 min on ice. Mitochondria were pelleted (12,000 x g, 10 min, 4°C), resuspended in lysis buffer (75 mM NaCl, 50 mM EDTA, 1% SDS, 20 mM Hepes pH 7.8) containing 100 ng/μl proteinase K, and incubated on ice for 30 min. MtDNA was purified by phenol-chloroform extraction followed by ethanol precipitation.
5´-ends in mtDNA and nuclear DNA from mouse liver were mapped by 5´-End-seq by treating 1 μg total DNA with 0.3M KCl for 2 h at 55°C. RNA residues in mtDNA and nuclear DNA were mapped by HydEn-seq [30] by hydrolyzing 1 μg DNA with 0.3M KOH for 2 h at 55°C. Afterwards, the ethanol precipitated DNA fragments were treated for 3 min at 85°C, phosphorylated with 10 U of phosphatase-minus T4 polynucleotide kinase (New England BioLabs) for 30 min at 37°C, heat inactivated for 20 min at 65°C and purified with HighPrep PCR beads (MagBio). Phosphorylated products were treated for 3 min at 85°C, ligated to oligo ARC140 [30] overnight at room temperature with 10 U of T4 RNA ligase, 25% PEG 8000 and 1mM CoCl3(NH3)6, and purified with HighPrep PCR beads (Mag-Bio). Ligated products were treated for 3 min at 85°C. The ARC76±ARC77 adaptor was annealed to the fragments for 5 min at room temperature. The second strand was synthesized with 4 U of T7 DNA polymerase (New England BioLabs) and purified with HighPrep PCR beads (MagBio). Libraries were purified, quantified with a Qubit fluorometric instrument (ThermoFisher Scientific) and 75-base paired-end sequenced on an Illumina NextSeq500 instrument, to identify the location of the 5´-ends.

value: liver

value: 13 weeks


title: P211_K7_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_L16_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_K8_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_K4_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_K5_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_K6_5xFAD_C57BL/6J_hippocampus_rep2


title: Gata3+_MC_14


title: Gata3+_MC_15


title: P211_K3_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_K24_5xFAD_C57BL/6J_cerebellum_rep3


title: Gata3+_MC_1


title: Gata3+_MC_13


title: samhd- KOH rep3

description: KOH treated


title: P211_K23_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_L14_5xFAD_C57BL/6J_cerebellum_rep1


title: samhd- KCl rep3

description: KCl treated


title: Gata3+_MC_12


title: P211_K21_5xFAD_C57BL/6J_cerebellum_rep3


title: samhd- KOH rep2

description: KOH treated


title: P211_K22_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_K2_5xFAD_C57BL/6J_hippocampus_rep1


title: Gata3+_MC_11


title: P211_K20_5xFAD_C57BL/6J_cerebellum_rep3


title: samhd- KCl rep4

description: KCl treated


title: P211_K19_5xFAD_C57BL/6J_cerebellum_rep2


title: Gata3+_MC_10


title: samhd- KOH rep1

description: KOH treated


title: samhd- KCl rep1

description: KCl treated


title: P211_K18_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_K16_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_K17_5xFAD_C57BL/6J_cerebellum_rep2


title: Gata3-_HC_9

source_name: Gata3- Haematopoietic cells

value: Gata3- Haematopoietic cells


title: P211_K14_5xFAD_C57BL/6J_cerebellum_rep1


title: P211_K15_5xFAD_C57BL/6J_cerebellum_rep1


title: P211_K13_5xFAD_C57BL/6J_cerebellum_rep1


title: wild type KOH rep3

description: KOH treated


title: Gata3-_HC_7

value: Gata3-GFP +/-


title: P211_K12_5xFAD_C57BL/6J_cerebellum_rep1


title: Gata3-_HC_8

value: aorta-gonads-mesonephros (AGM)


title: wild type KOH rep2

description: KOH treated


title: wild type KCl rep3

description: KCl treated


title: samhd- KCl rep2

description: KCl treated


title: P211_K10_5xFAD_C57BL/6J_hippocampus_rep3


title: Gata3-_HC_6


title: Gata3-_HC_5


title: P211_K1_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_J9_5xFAD_C57BL/6J_hippocampus_rep3


title: P211_J8_5xFAD_C57BL/6J_hippocampus_rep2


title: wild type KCl rep2

description: KCl treated


title: wild type KOH rep1

description: KOH treated


title: Gata3-_HC_4


title: P211_J6_5xFAD_C57BL/6J_hippocampus_rep2


title: wild type KCl rep1

description: KCl treated


title: Gata3-_HC_3


title: P211_J7_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_J5_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_J4_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_J3_5xFAD_C57BL/6J_hippocampus_rep1


title: RNA_seq_siUAP56

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

institute: CABIMER, Universidad de Sevilla

data_processing:
DRIPc-seq and RNA-seq: All fastq files were trimmed with FASTQ Toolkit before mapping.
DRIPc-seq reads were aligned to the hg38 Canonical genome using Bowtie2/BWA.
DRIPc-seq peaks were called using MACS2 callpeak.
RNA-seq reads were aligned to the hg38 genome using HISAT2, counted using FeatureCounts and normalized by RPKM.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: BigWig files were generated using bedtools bamcoverage.

source_name: Erythromyeloblastoid leukemia cell line

extract_protocol:
Total RNA was extracted from K562 cells using RNeasy Mini kit (Qiagen) and further processed with the TruSeq Stranded Total RNA Illumina Kit.
Illumina TruSeq protocol.

tag: antibody


title: DRIPc_seq_siUAP56_RNH_treated

description: RNA-DNA

data_processing:
Library strategy: DRIP-seq
DRIPc-seq and RNA-seq: All fastq files were trimmed with FASTQ Toolkit before mapping.
DRIPc-seq reads were aligned to the hg38 Canonical genome using Bowtie2/BWA.
DRIPc-seq peaks were called using MACS2 callpeak.
RNA-seq reads were aligned to the hg38 genome using HISAT2, counted using FeatureCounts and normalized by RPKM.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: BigWig files were generated using bedtools bamcoverage.

extract_protocol:
Genomic DNA from K562 cells enzymatically fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI. Monoclonal S9.6 antibody was used to immunoprecipitate RNA-DNA hybrids.
Standard Illumina protocol.

value: Monoclonal S9.6

tag: treatment

value: RNase H


title: P211_K11_5xFAD_C57BL/6J_hippocampus_rep3


title: P211_J23_5xFAD_C57BL/6J_cerebellum_rep3


title: Gata3-_HC_20


title: P211_J21_5xFAD_C57BL/6J_cerebellum_rep3


title: DRIPc_seq_siC_RNH_treated

description: RNA-DNA

value: siC control


title: P211_J20_5xFAD_C57BL/6J_cerebellum_rep3


title: DMSO_D_3

city: Toronto

first: Jeff

last: Wrana

state: Ontario

address: 600 University Avenue

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

description: #DMSO treated A375 (BRAF V600E) cells in triplicate: D-3

data_processing:
Real-time base call (.bcl) files were converted to FASTQ files using Illumina bcl2fastq2 conversion software v2.17 (on CentOS 6.0 data storage and computation linux servers).
The RNAseq data was processed with an in-house pipeline running on Mac OS X 10.14.6.
The quality was inspected with FastQC (v0.11.5) and multiQC (v1.8.dev0). to verify the quality, sequence content, and length of the sequences.
The data was trimmed to remove 15 nucleotides on the 5' end of each read resulting in reads having a length of 87.
The data was mapped to the reference human genome hg19 using Tophat (version 1.4.1) (-r =  100), and bowtie (version 0.12.7) with default parameters.
The mapped read files were converted to sam format with samtools (version 0.1.18), and ambiguous reads were filtered out with an in-house script.
truRPM (transcript union Reads Per Million reads) values, which includes reads mapped to both intron and exon reads, were calculated using in-house scripts, and represent overall transcript level normalized by total mapped reads
An unrelated control sample was included in the processing pipeline to verify the integrity of the output.
Genome_build: hg19
Supplementary_files_format_and_content: rpm_matrix.txt: a text file with a matrix of normalized expression data

source_name: A375 melanoma cells

growth_protocol: cells were grown in DMEM supplemented with 10% FBS and 1X pen-strep

extract_protocol:
RNA was extracted using Ambion TRIzol Reagent following the manufacturer protocol.
RNA was accessed by Fragment Analyzer, 1 ug high quality total RNA was subjected to library preparation using the Illumina TruSeq Stranded mRNA Library Preparation Kit (Cat# 20020594) according to the manufacturer's instructions. The library fragment size was checked using an Agilent Fragment, and then quantified with BioRad ddPCR  using ddPCRª Library Quantification Kit for Illumina TruSeq (BioRad, Cat#1863040) on a QX200 Droplet Digital PCR System. Quality checked libraries were loaded onto an Illumina NextSeq 500 run with Illumina NextSeq 500/550 Hi Output Kit v2.5 (75 Cycles).

treatment_protocol: 200nM compound treatment for 20 hours

value: homozygous BRAF_V600E mutation


title: Gata3-_HC_1


title: P211_J2_5xFAD_C57BL/6J_hippocampus_rep1


title: Gata3-_HC_19


title: DMSO_D_2

description: #DMSO treated A375 (BRAF V600E) cells in triplicate: D-2


title: P211_J19_5xFAD_C57BL/6J_cerebellum_rep2


title: Gata3-_HC_18


title: P211_J17_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_J16_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_J18_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_J15_5xFAD_C57BL/6J_cerebellum_rep1


title: Gata3-_HC_17


title: P211_J14_5xFAD_C57BL/6J_cerebellum_rep1


title: DMSO_D_1

description: #DMSO treated A375 (BRAF V600E) cells in triplicate: D-1


title: Gata3-_HC_2


title: Trametinib_2

description: #Trametinib (MEK inhibitor – also in the clinic that hits the same pathway as BRAF inhibitors but different node) treated A375 (BRAF V600E) cells in triplicate: 6-2


title: P211_J24_5xFAD_C57BL/6J_cerebellum_rep3


title: Gata3-_HC_16


title: Trametinib_3

description: #Trametinib (MEK inhibitor – also in the clinic that hits the same pathway as BRAF inhibitors but different node) treated A375 (BRAF V600E) cells in triplicate: 6-3


title: Trametinib_1

description: #Trametinib (MEK inhibitor – also in the clinic that hits the same pathway as BRAF inhibitors but different node) treated A375 (BRAF V600E) cells in triplicate: 6-1


title: P211_J13_5xFAD_C57BL/6J_cerebellum_rep1


title: Gata3-_HC_15


title: P211_J22_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_J10_5xFAD_C57BL/6J_hippocampus_rep3


title: P211_J11_5xFAD_C57BL/6J_hippocampus_rep3


title: Gata3-_HC_14


title: Gata3-_HC_13


title: P211_I9_5xFAD_C57BL/6J_hippocampus_rep3


title: P211_I8_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_J1_5xFAD_C57BL/6J_hippocampus_rep1


title: Vermurafenib_3

description: #Vermurafenib (another classical BRAF inhibit similar to BI) treated A375 (BRAF V600E) cells in triplicate: 5-3


title: P211_I7_5xFAD_C57BL/6J_hippocampus_rep2


title: Gata3-_HC_12


title: Vermurafenib_2

description: #Vermurafenib (another classical BRAF inhibit similar to BI) treated A375 (BRAF V600E) cells in triplicate: 5-2


title: Vermurafenib_1

description: #Vermurafenib (another classical BRAF inhibit similar to BI) treated A375 (BRAF V600E) cells in triplicate: 5-1


title: P211_I6_5xFAD_C57BL/6J_hippocampus_rep2


title: Gata3-_HC_11


title: P211_I4_5xFAD_C57BL/6J_hippocampus_rep1


title: Dabrafenib_3

description: #8736 Dab (Dabrafenib  - classical BRAF inhibitor similar to BI) treated A375 (BRAF V600E) cells in triplicate: 4-3


title: P211_I5_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_I24_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_I23_5xFAD_C57BL/6J_cerebellum_rep3


title: Dabrafenib_1

description: #8736 Dab (Dabrafenib  - classical BRAF inhibitor similar to BI) treated A375 (BRAF V600E) cells in triplicate: 4-1


title: Gata3-_HC_10


title: P211_J12_5xFAD_C57BL/6J_cerebellum_rep1


title: Gata3+_HC_9

source_name: Gata3+ Haematopoietic cells

value: Gata3+ Haematopoietic cells


title: P211_I21_5xFAD_C57BL/6J_cerebellum_rep3


title: Dabrafenib_2

description: #8736 Dab (Dabrafenib  - classical BRAF inhibitor similar to BI) treated A375 (BRAF V600E) cells in triplicate: 4-2


title: P211_I3_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_I20_5xFAD_C57BL/6J_cerebellum_rep3


title: P4B_me_2

description: #18876 (aka P4Bme. Methylated version of P4B PROTAC that does not bind E3 ligase) treated A375 (BRAF V600E) cells in triplicate: 3-2


title: P4B_me_3

description: #18876 (aka P4Bme. Methylated version of P4B PROTAC that does not bind E3 ligase) treated A375 (BRAF V600E) cells in triplicate: 3-3


title: Gata3+_HC_6


title: P211_I18_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_I17_5xFAD_C57BL/6J_cerebellum_rep2


title: Gata3+_HC_8


title: P211_I19_5xFAD_C57BL/6J_cerebellum_rep2


title: Gata3+_HC_5


title: P211_I16_5xFAD_C57BL/6J_cerebellum_rep2


title: P4B_me_1

description: #18876 (aka P4Bme. Methylated version of P4B PROTAC that does not bind E3 ligase) treated A375 (BRAF V600E) cells in triplicate: 3-1


title: P211_I2_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_I15_5xFAD_C57BL/6J_cerebellum_rep1


title: BI882370_3

description: #BI (BRAF binding moiety only used to make P4B) treated A375 (BRAF V600E) cells in triplicate: 2-3


title: P211_I14_5xFAD_C57BL/6J_cerebellum_rep1


title: BI882370_2

description: #BI (BRAF binding moiety only used to make P4B) treated A375 (BRAF V600E) cells in triplicate: 2-2


title: P211_I13_5xFAD_C57BL/6J_cerebellum_rep1


title: Gata3+_HC_3


title: P211_I11_5xFAD_C57BL/6J_hippocampus_rep3


title: P211_I12_5xFAD_C57BL/6J_cerebellum_rep1


title: Gata3+_HC_7


title: BI882370_1

description: #BI (BRAF binding moiety only used to make P4B) treated A375 (BRAF V600E) cells in triplicate: 2-1


title: Gata3+_HC_2


title: P211_I10_5xFAD_C57BL/6J_hippocampus_rep3


title: P4B_1_3

description: #P4B (ie BRAF PROTAC) treated A375 (BRAF V600E) cells in triplicate: 1-3


title: P211_I1_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_H9_5xFAD_C57BL/6J_hippocampus_rep3


title: Gata3+_HC_20


title: P4B_1_2

description: #P4B (ie BRAF PROTAC) treated A375 (BRAF V600E) cells in triplicate: 1-2


title: P211_H8_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_H7_5xFAD_C57BL/6J_hippocampus_rep2


title: Gata3+_HC_1


title: P211_H6_5xFAD_C57BL/6J_hippocampus_rep2


title: Gata3+_HC_19


title: P4B_1_1

description: #P4B (ie BRAF PROTAC) treated A375 (BRAF V600E) cells in triplicate: 1-1


title: P211_H3_5xFAD_C57BL/6J_hippocampus_rep1


title: Gata3+_HC_4


title: P211_H24_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_H4_5xFAD_C57BL/6J_hippocampus_rep1


title: Gata3+_HC_17


title: P211_H23_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_H21_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_H20_5xFAD_C57BL/6J_cerebellum_rep3


title: Gata3+_HC_16


title: CD8_T_Cells_Neonate_3_CD3CD28IL12_RNA-seq

city: Cuernavaca

first: Darely

middle: Yarazeth

last: Gutiérrez Reyna

state: Morelos

address: Av. Universidad 1001, Col. Chamilpa

department: Centro de Investigación en Dinámica Celular

country: Mexico

institute: Universidad Autónoma del Estado de Morelos

data_processing:
The quality of the data was evaluated with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).  Adapters and low-quality sequences were trimmed or discarded using Trimmomatic. Quality check using FastQC was performed again on the trimmed sequences.
Reads were aligned to the human reference genome GRCh38/hg38 to generate the Binary Alignment Map (BAM) files with STAR (v2.4.2a).
Transcripts discovery was performed using Cufflinks (v2.2.1) with the “library-type” argument set to fr-firstrand, and a GTF file obtained from GENCODE (“Comprehensive gene annotation”, vM1) provided as the genomic annotation. GTF files were produced by Cufflinks, and combined using Cuffmerge. Only de novo transcripts with counts greater than 0 in at least one RNA-seq sample were kept for subsequent analyses. These de novo transcripts were combined with the GENCODE GTF file to produce the final genomic annotation used with FeatureCounts (v1.4.6-p4) for quantification.
DESeq2 (v1.6.3) was used to screen differentially expressed genes and normalization of the count data.
Genome_build: hg38
Supplementary_files_format_and_content: fastq

source_name: CD8+ T cells

extract_protocol:
Total RNA from CD8+ T cells was extracted using TRIZOL® Reagent, following the manufacturer’s protocol.
RNA-seq libraries were constructed at the Transcriptomic & Genomic Platform Marseille Luminy (Aix-Marseille University, TAGC) using the TruSeq RNA Library Prep Kit v2 (Illumina; California, USA). Libraries were paired end sequenced on an Illumina NextSeq 500 sequencer.

treatment_protocol: CD8+T cells were cultured in RPMI 1640 medium supplemented with 2 mM glutamine, commercial antibiotics (50 U/mL penicillin,50lg/mL streptomycin) and 5% fetal coalf serum. Cells were activated with 1µg/mL anti-CD3 (OKT3; TONBO Bio-sciences) and 1µg/mL anti-CD28 (CD28.2;TONBO Biosciences) and recombinant protein IL-12p70 (10ng/ml, TONBO Bio-sciences), cross-linked with 1ug/mL goat anti-mouseIgG (Jackson ImmunoResearch) and incubated for 36 h under 5% CO2 at 37°C

value: Cord Blood

value: CD8+ T cells

tag: number biological replicate

value: replicate 3

tag: stimulus


title: CD8_T_Cells_Neonate_1_CD3CD28IL12_RNA-seq

tag: cell type

value: replicate 1


title: Gata3+_HC_15


title: P211_I22_5xFAD_C57BL/6J_cerebellum_rep3

data_processing:
Individual Fastq files were aligned to the mouse Genome (Gencode M11 / GRCm38) using the STAR aligner version 2.5.2b with parameters STAR --runThreadN <cpu> --genomeDir <index> --genomeLoad LoadAndKeep --limitBAMsortRAM 20000000000 --readFilesIn <fastq> --readFilesCommand zcat --outFileNamePrefix <sampleID> --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate
Gene counts were obtained from BAM files using featureCounts v1.5.1 with parameters -a <Gencode_vM11.gtf> -G <GRCm38.primary_assembly.genome.fa> -o counts.txt -F GTF -R -g gene_id -t exon -T 12 --largestOverlap <bamfiles>
single cell RNAseq analysis and clustering was performed using RaceId/StemId2 (Grün, D., L. Kester, and A. van Oudenaarden. 2014. “Validation of noise models for single-cell transcriptomics.” Nat. Methods 11 (6): 637–40.). Cells with less than 500 detected genes, less than 5000 aligned reads or more than 700 000 aligned reads were discarded. Only genes with a count of 5 in at least a single cell were used for analysis.
Genome_build: Gencode M11 / GRCm38
Supplementary_files_format_and_content: comma separated (csv) file with gene counts per sample

extract_protocol:
After transcardial perfusion with PBS, brains were roughly minced and homogenized with a potter in HBSS containing 15 mM HEPES buffer and 0.54 % Glucose. Whole-brain homogenate was separated by 70/37/30 % layered Percoll gradient centrifugation at 800 g for 30 min at 4 °C (no brake). The CNS macrophages containing interphase was then collected and washed once with PBS containing 2% FCS and 10mM EDTA before staining. Cells were stained with primary antibodies directed against CD11b (M1/70, BioLegend), CD45 (30-F11, BD Biosciences), Ly6C (AL-21, BD Biosciences) and Ly6G (1A8, BD Biosciences) for 20 min, and CD206 (C068C2, BioLegend) for 45 min at 4 °C. After washing, cells were analyd using a MoFlo Astrios (Beckman Coulter). microglia were FACS-sorted from six different CNS regions of healthy and diseased brains (see gating strategy shown in supplementary Fig.2) into a 384-well plate containing a lysis buffer.
Single cell RNAseq libraries were generated following the published SmartSeq2 protocol (Picelli et al. Nature Metods 2013)

value: cerebellum


title: CD8_T_Cells_Neonate_3_CD3CD28_RNA-seq


title: P211_H5_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_H2_5xFAD_C57BL/6J_hippocampus_rep1


title: Day14 Ventral hto library

city: Copenhagen

first: Gaurav

middle: Singh

last: Rathore

address: Department of Neuroscience Faculty of Health and Medical Sciences Blegdamsvej 3B, Building 7, 4th floor

department: Department of Neuroscience

country: Denmark

institute: University of Copenhagen

data_processing:
Read alignment: The Cellranger 2.0 pipeline (10x Genomics, USA) was used to align reads, quantify unique molecular identifiers (UMI) and generate feature-barcode expression matrices. Index read number is 8 base pairs. Read 1 (26 base pairs) consists of the 10x barcode and UMIs and Read 2 comprises of 56 base pairs. The reads were mapped to hg19 transcriptome a reference package provided by 10X genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references).
Genome_build: hg19
Supplementary_files_format_and_content: Format: barcodes.tsv for detected cellular barcodes obtained through cell ranger pipeline. genes.tsv contains the list of detected genes mapped on reference transcriptome. matrix.mtx files are sparse matrices which contains numbers of UMIs associated with genes and barcodes (https://kb.10xgenomics.com/hc/en-us/articles/115000794686-How-is-the-MEX-format-used-for-the-gene-barcode-matrices).

source_name: MiSTR tissue

growth_protocol: Human embryonic stem cells (H9 cells) differentiated using neural patterning media: 1:1 mix of DMEM/F12 and NeuroMedium, plus N2 supplement (1:200) and Neuro-Brew 21 without vitamin A (1:100); supplemented from day 1 to 9 with: 10uM SB431542 and 100ng/ml of rh-Noggin and a 0-2uM gradient of CHIR99021. Ventralized samples were further supplemented from day 1 to 9 with SHH-C24II (200ng/ml) and Purmorphamine (0.5uM).

extract_protocol:
MiSTR tissue was divided into two halves along the gradient, one side used to collect the five A-E samples for mRNA analysis. The other side was dissociated into a single-cell suspension using Accutase (Thermofisher), for day 0, day 1 and day 2 samples, or with Neural dissociation kit (P) on a GentleMACS dissociator (both from Miltenyi Biotec) for day 14 samples. The cells were then frozen in CS10 CryoStor (Stemcell Technologies) and stored at -150oC until needed. In the meantime, each sample underwent mRNA analysis for quality control selection for scRNA-seq. Cryopreserved cells, quality control cleared, were thawed, counted and mixed in equal numbers into a final single-cell suspension of 350 to 500 cells/ml solution in 0.01% BSA in PBS. For 0 to 48h tissues, cells from 3 biological MiSTR tissue replicates were pooled prior to sequencing. For day 14 tissues, the sequenced samples contained a mix of cells from regions A to E (n=1-3 biological replicates per region). A total of 9000-17000 cells were loaded per lane onto the 10X Chromium (10X Genomics) . For day14 ventral Cells from region A-E were hashed with hashtagging antibodies and then loaded on 10X chromium to generate hashing and cDNA libraries simultaneously.
Chromium Single Cell 3' Reagent Kits (v2 Chemistry).

tag: cell type of origin

value: H9 human embryonic stem cells

tag: day of differentiation

value: day 14 hto

tag: location


title: Gata3+_HC_18


title: P211_H19_5xFAD_C57BL/6J_cerebellum_rep2


title: CD8_T_Cells_Neonate_2_CD3CD28_RNA-seq

value: replicate 2


title: Gata3+_HC_12


title: CD8_T_Cells_Neonate_2_CD3CD28IL12_RNA-seq


title: P211_H15_5xFAD_C57BL/6J_cerebellum_rep1


title: P211_H13_5xFAD_C57BL/6J_cerebellum_rep1


title: CD8_T_Cells_Neonate_3_Basal_RNA-seq

value: BASAL


title: P211_H17_5xFAD_C57BL/6J_cerebellum_rep2


title: CD8_T_Cells_Neonate_1_CD3CD28_RNA-seq


title: P211_H14_5xFAD_C57BL/6J_cerebellum_rep1


title: CD8_T_Cells_Neonate_2_Basal_RNA-seq


title: Gata3+_HC_11


title: P211_H22_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_H1_5xFAD_C57BL/6J_hippocampus_rep1

value: hippocampus


title: P211_H10_5xFAD_C57BL/6J_hippocampus_rep3


title: Gata3+_HC_10

value: Gata3-GFP +/-


title: P211_H11_5xFAD_C57BL/6J_hippocampus_rep3


title: Gata3-_EC_9

source_name: Gata3- Endothelial cells

value: aorta-gonads-mesonephros (AGM)

value: Gata3- Endothelial cells


title: Gata3+_HC_14


title: P211_H18_5xFAD_C57BL/6J_cerebellum_rep2


title: CD8_T_Cells_Neonate_1_Basal_RNA-seq


title: Gata3+_HC_13


title: CD8_T_Cells_Adult_3_CD3CD28IL12_RNA-seq

value: Venous Blood


title: P211_G8_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_G9_5xFAD_C57BL/6J_hippocampus_rep3


title: P211_H16_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_G7_5xFAD_C57BL/6J_hippocampus_rep2


title: CD8_T_Cells_Adult_2_CD3CD28IL12_RNA-seq


title: Gata3-_EC_8


title: P211_G6_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_H12_5xFAD_C57BL/6J_cerebellum_rep1


title: Gata3-_EC_7


title: CD8_T_Cells_Adult_1_CD3CD28IL12_RNA-seq


title: P211_G3_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_G5_5xFAD_C57BL/6J_hippocampus_rep2


title: Gata3-_EC_5


title: P211_G4_5xFAD_C57BL/6J_hippocampus_rep1


title: Gata3-_EC_6


title: P211_G22_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_G24_5xFAD_C57BL/6J_cerebellum_rep3


title: CD8_T_Cells_Adult_2_CD3CD28_RNA-seq


title: P211_G23_5xFAD_C57BL/6J_cerebellum_rep3


title: Gata3-_EC_3


title: P211_G20_5xFAD_C57BL/6J_cerebellum_rep3


title: CD8_T_Cells_Adult_1_CD3CD28_RNA-seq


title: Gata3-_EC_4


title: P211_G2_5xFAD_C57BL/6J_hippocampus_rep1


title: CD8_T_Cells_Adult_3_Basal_RNA-seq


title: Gata3-_EC_2


title: P211_G19_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_G18_5xFAD_C57BL/6J_cerebellum_rep2


title: Gata3-_EC_20


title: P211_G14_5xFAD_C57BL/6J_cerebellum_rep1


title: P211_G15_5xFAD_C57BL/6J_cerebellum_rep1


title: CD8_T_Cells_Adult_2_Basal_RNA-seq


title: Gata3-_EC_1


title: CD8_T_Cells_Adult_1_Basal_RNA-seq


title: CD8_T_Cells_Adult_3_CD3CD28_RNA-seq


title: P211_G12_5xFAD_C57BL/6J_cerebellum_rep1


title: Gata3-_EC_19


title: P211_G13_5xFAD_C57BL/6J_cerebellum_rep1


title: Gata3-_EC_18


title: siNXF1_8hr_4sU_cyt_rep2_2

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

data_processing:
Library strategy: SLAM-seq
Quantification using RSEM
Alignment to the hg19 human genome using STAR
Preparation of bigWig files using wigToBigWIg
Genome_build: hg19
Supplementary_files_format_and_content: RSEM quantification files and bigWig read coverage, summary files for half-lives estimated for SLAM-seq and UMI count for MPRA data

source_name: SLAM-seq, siNXF1, 8hr, rep2 additional sequencing

growth_protocol: MCF7 cells (ATCC) were grown in DMEM (Gibco) containing 10% fetal bovine serum and Penicillin-Streptomycin mixture (1%) at 37°C in a humidified incubator with 5% CO2. For export factor knockdown, cells were transfected with 10nM siRNA pool targeting indicated genes or with a control pool (Dharmacon) using Lipofectamin 3000 reagent (L3000001, Thermo Fisher). For double knockdowns, 5nM of each pool were used for a total mix of 10nM. Cells were collected for cytosolic and nuclear fractionation 72h post-transfection for all export factor depletion assays, except for siNXF1 and siALY+UAP56, where we collected the cells 48h post-transfection.

extract_protocol:
Cells were washed in cold PBS and detached from plates by 10mM EDTA, a fraction was transferred to a new tube and RNA was extracted with TRIREAGENT (MRC) to obtain WCE. Remaining cells were washed in cold PBS, resuspended in 180µl RLN buffer (50mM Tris•Cl pH8, 140mM NaCl, 1.5mM MgCl2, 10mM EDTA, 1mM DTT, 0.5% NP-40, 10U/ml RNAse inhibitor), and incubated on ice for 5 min. The extract was centrifuged for 5min at 300g in a cold centrifuge, the supernatant was transferred to a new tube and centrifuged again for 1min at 500g in a cold centrifuge. The supernatant (cytoplasmic fraction) was transferred to a new tube and RNA was extracted using TRIREAGENT. The nuclear pellet was washed once in 180µl RLN buffer, resuspended in 1ml of buffer S1 (250mM Sucrose, 10mM MgCl2, 10U/ml RNAse inhibitor), layered over 3ml of buffer S3 (880mM Sucrose, 0.5mM MgCl2, 10U/ml RNAse inhibitor), and centrifuged for 10min at 2800g in a cold centrifuge. The supernatant was removed and RNA was extracted from the nuclear pellet using TRIREAGENT.
Lexogen SENSE mRNA-seq kit

value: MCF-7 cell line


title: siNXF1_8hr_4sU_cyt_rep2

source_name: SLAM-seq, siNXF1, 8hr, rep2


title: siNXF1_8hr_4sU_cyt_rep1

source_name: SLAM-seq, siNXF1, 8hr, rep1


title: P211_G11_5xFAD_C57BL/6J_hippocampus_rep3

first: Ori

last: Staszewski

institute: University Medical Center Freiburg


title: Gata3-_EC_17

data_processing:
RNA-seq reads were aligned to mm10 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: mm10
Supplementary_files_format_and_content: HT-Seq counts(.txt)

extract_protocol:
cells were sorted from freshly isolated mouse embryos; dissected tissues were treated with collagenase and then stained with cell surface markers and directly sorted into lysis buffer
SmartSeq2


title: P211_G1_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_G10_5xFAD_C57BL/6J_hippocampus_rep3


title: siNXF1_4hr_4sU_cyt_rep2

source_name: SLAM-seq, siNXF1, 4hr, rep2


title: P211_F8_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_G21_5xFAD_C57BL/6J_cerebellum_rep3


title: Gata3-_EC_16


title: P211_G17_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_G16_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_F6_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_F7_5xFAD_C57BL/6J_hippocampus_rep2


title: siNXF1_4hr_4sU_cyt_rep1

source_name: SLAM-seq, siNXF1, 4hr, rep1


title: siNXF1_2hr_4sU_cyt_rep2

source_name: SLAM-seq, siNXF1, 2hr, rep2


title: P211_F4_5xFAD_C57BL/6J_hippocampus_rep1

source_name: microglia


title: P211_F24_5xFAD_C57BL/6J_cerebellum_rep3


title: Gata3-_EC_14


title: Gata3-_EC_13


title: P211_F5_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_F3_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_F22_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_F23_5xFAD_C57BL/6J_cerebellum_rep3


title: siNXF1_0hr_no4sU_cyt_rep2

source_name: SLAM-seq, siNXF1, 0hr, rep2


title: Gata3-_EC_12


title: P211_F9_5xFAD_C57BL/6J_hippocampus_rep3


title: P211_F21_5xFAD_C57BL/6J_cerebellum_rep3


title: siNXF1_0hr_no4sU_cyt_rep1

source_name: SLAM-seq, siNXF1, 0hr, rep1


title: Gata3-_EC_11


title: siNT_8hr_4sU_cyt_rep2_2

source_name: SLAM-seq, siNT, 8hr, rep2 additional sequencing


title: Gata3-_EC_10


title: P211_F19_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_F18_5xFAD_C57BL/6J_cerebellum_rep2


title: siNT_8hr_4sU_cyt_rep2

source_name: SLAM-seq, siNT, 8hr, rep2


title: P211_F2_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_F17_5xFAD_C57BL/6J_cerebellum_rep2


title: Gata3-_EC_15


title: Gata3+_EC_9

source_name: Gata3+ Endothelial cells

value: Gata3+ Endothelial cells


title: P211_F16_5xFAD_C57BL/6J_cerebellum_rep2


title: siNT_8hr_4sU_cyt_rep1

source_name: SLAM-seq, siNT, 8hr, rep1


title: P211_F15_5xFAD_C57BL/6J_cerebellum_rep1


title: Gata3+_EC_8


title: siNXF1_2hr_4sU_cyt_rep1

source_name: SLAM-seq, siNXF1, 2hr, rep1


title: siNT_4hr_4sU_cyt_rep2

source_name: SLAM-seq, siNT, 4hr, rep2


title: P211_F14_5xFAD_C57BL/6J_cerebellum_rep1


title: P211_F13_5xFAD_C57BL/6J_cerebellum_rep1


title: Gata3+_EC_7


title: P211_F12_5xFAD_C57BL/6J_cerebellum_rep1


title: Gata3+_EC_6


title: P211_F11_5xFAD_C57BL/6J_hippocampus_rep3


title: P211_F10_5xFAD_C57BL/6J_hippocampus_rep3


title: P211_F20_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_F1_5xFAD_C57BL/6J_hippocampus_rep1


title: siNT_2hr_4sU_cyt_rep2

source_name: SLAM-seq, siNT, 2hr, rep2


title: Gata3+_EC_5


title: P211_E9_5xFAD_C57BL/6J_hippocampus_rep3


title: P211_E8_5xFAD_C57BL/6J_hippocampus_rep2


title: Gata3+_EC_4


title: P211_E7_5xFAD_C57BL/6J_hippocampus_rep2


title: siNT_2hr_4sU_cyt_rep1

source_name: SLAM-seq, siNT, 2hr, rep1


title: siNT_0hr_no4sU_cyt_rep2

source_name: SLAM-seq, siNT, 0hr, rep2


title: siNT_0hr_no4sU_cyt_rep1

source_name: SLAM-seq, siNT, 0hr, rep1


title: P211_E6_5xFAD_C57BL/6J_hippocampus_rep2


title: Gata3+_EC_3


title: Gata3+_EC_2


title: P211_E4_5xFAD_C57BL/6J_hippocampus_rep1


title: K562_lib_siNXF1_tot_rep3

source_name: Splicing library, siNXF1, WCE, rep3

value: K562 cell line


title: P211_E5_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_E23_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_E24_5xFAD_C57BL/6J_cerebellum_rep3


title: siNT_4hr_4sU_cyt_rep1

source_name: SLAM-seq, siNT, 4hr, rep1


title: P211_E21_5xFAD_C57BL/6J_cerebellum_rep3


title: Gata3+_EC_20


title: K562_lib_siNXF1_tot_rep1

source_name: Splicing library, siNXF1, WCE, rep1


title: P211_E3_5xFAD_C57BL/6J_hippocampus_rep1


title: Gata3+_EC_19


title: K562_lib_siNXF1_nuc_rep1

source_name: Splicing library, siNXF1, nuclear fraction, rep1


title: K562_lib_siNXF1_nuc_rep3

source_name: Splicing library, siNXF1, nuclear fraction, rep3


title: Gata3+_EC_18


title: P211_E22_5xFAD_C57BL/6J_cerebellum_rep3

source_name: microglia


title: P211_E18_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_E20_5xFAD_C57BL/6J_cerebellum_rep3


title: Gata3+_EC_1


title: Gata3+_EC_17


title: K562_lib_siNXF1_cyt_rep1

source_name: Splicing library, siNXF1, cytoplasmic fraction, rep1


title: K562_lib_siNXF1_cyt_rep3

source_name: Splicing library, siNXF1, cytoplasmic fraction, rep3


title: P211_E15_5xFAD_C57BL/6J_cerebellum_rep1


title: P211_E16_5xFAD_C57BL/6J_cerebellum_rep2


title: Gata3+_EC_16


title: Gata3+_EC_15


title: P211_E13_5xFAD_C57BL/6J_cerebellum_rep1


title: P211_E11_5xFAD_C57BL/6J_hippocampus_rep3


title: P211_E14_5xFAD_C57BL/6J_cerebellum_rep1


title: P211_E12_5xFAD_C57BL/6J_cerebellum_rep1


title: Gata3+_EC_14


title: P211_E10_5xFAD_C57BL/6J_hippocampus_rep3


title: Gata3+_EC_13


title: P211_E1_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_E2_5xFAD_C57BL/6J_hippocampus_rep1


title: K562_lib_siNT_nuc_rep3

source_name: Splicing library, siNT, nuclear fraction, rep3


title: K562_lib_siNT_tot_rep3

source_name: Splicing library, siNT, WCE, rep3


title: P211_E19_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_D9_5xFAD_C57BL/6J_hippocampus_rep3


title: P211_E17_5xFAD_C57BL/6J_cerebellum_rep2


title: K562_lib_siNT_nuc_rep1

source_name: Splicing library, siNT, nuclear fraction, rep1


title: K562_lib_siNT_cyt_rep3

source_name: Splicing library, siNT, cytoplasmic fraction, rep3


title: Gata3+_EC_12

source_name: Gata3+ Endothelial cells


title: P211_D6_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_D7_5xFAD_C57BL/6J_hippocampus_rep2


title: Gata3+_EC_11


title: P211_D8_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_D5_5xFAD_C57BL/6J_hippocampus_rep2


title: Gata3+_EC_10


title: P211_D4_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_D3_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_D24_5xFAD_C57BL/6J_cerebellum_rep3


title: K562_lib_siNT_tot_rep1

source_name: Splicing library, siNT, WCE, rep1


title: S348_08_T-T_microglia

source_name: brain

extract_protocol:
Total RNA was extracted from cells stabilized in RNAprotect buffer according to the “Purification of total RNA from animal and human cells” protocol of the RNeasy Plus Micro Kit (QIAGEN, Hilden, Germany).  In brief, cells were stored and shipped in RNAprotect buffer at 2-8 °C. After pelleting, the RNAprotect buffer was replaced by RLT Plus and the samples were homogenized by vortexing for 30 sec. Genomic DNA contamination was removed using gDNA Eliminator spin columns. Next ethanol was added and the samples were applied to RNeasy MinElute spin columns followed by several wash steps. Finally total RNA was eluted in 12 μl of nuclease free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip reagent set (Agilent, Palo Alto, CA, USA).
The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from 500 pg total-RNA. Double stranded cDNA was amplified by LD PCR (12 cycles) and purified via magnetic bead clean-up. Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA). 150 pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step 1:5 dilutions of index 1 (i7) and index 2 (i5) primers were used. The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems, Inc., Woburn, MA, USA). Equimolar amounts of each library were pooled, and the pools were used for cluster generation on the cBot with the Illumina TruSeq SR Cluster Kit v3. The sequencing run was performed on an HiSeq 1000 instrument using the indexed, 50 cycles single-read (SR) protocol and the TruSeq SBS v3 Reagents according to the Illumina HiSeq 1000 System User Guide. Image analysis and base calling resulted in .bcl files, which were converted into .fastq files with the bcl2fastq v2.18 software.  RNA extraction, library preparation and RNAseq were performed at the Genomics Core Facility “KFB - Center of Excellence for Fluorescent Bioanalytics” (University of Regensburg, Regensburg, Germany; www.kfb-regensburg.de).

value: microglia

value: brain

value: Hexb-tdTomato/tdTomato


title: NXF9_total

data_processing:
Library strategy: MPRA
Quantification using RSEM
Alignment to the hg19 human genome using STAR
Preparation of bigWig files using wigToBigWIg
Genome_build: hg19
Supplementary_files_format_and_content: RSEM quantification files and bigWig read coverage, summary files for half-lives estimated for SLAM-seq and UMI count for MPRA data

source_name: CytoLib, siNXF1 WCE, rep5

extract_protocol:
Cells were washed in cold PBS and detached from plates by 10mM EDTA, a fraction was transferred to a new tube and RNA was extracted with TRIREAGENT (MRC) to obtain WCE. Remaining cells were washed in cold PBS, resuspended in 180µl RLN buffer (50mM Tris•Cl pH8, 140mM NaCl, 1.5mM MgCl2, 10mM EDTA, 1mM DTT, 0.5% NP-40, 10U/ml RNAse inhibitor), and incubated on ice for 5 min. The extract was centrifuged for 5min at 300g in a cold centrifuge, the supernatant was transferred to a new tube and centrifuged again for 1min at 500g in a cold centrifuge. The supernatant (cytoplasmic fraction) was transferred to a new tube and RNA was extracted using TRIREAGENT. The nuclear pellet was washed once in 180µl RLN buffer, resuspended in 1ml of buffer S1 (250mM Sucrose, 10mM MgCl2, 10U/ml RNAse inhibitor), layered over 3ml of buffer S3 (880mM Sucrose, 0.5mM MgCl2, 10U/ml RNAse inhibitor), and centrifuged for 10min at 2800g in a cold centrifuge. The supernatant was removed and RNA was extracted from the nuclear pellet using TRIREAGENT.
One microgram of RNA was used for cDNA production using the qScript Flex cDNA synthesis kit (95049, Quanta) and a gene specific primer containing part of the Illumina RD2 region. The entire cDNA reaction was diluted into 100 μl second strand reaction with a primer containing a unique molecular identifier (UMI) and part of the Illumina RD1 region. The second strand reaction was carried for a single cycle using Phusion Hot Start Flex DNA Polymerase (NEB, M0535), purified using AMpure beads at a 1.2:1 beads:sample ratio and eluted in 20μl ddH2O. 20µl of the second strand reaction was used for amplification with barcoded primers, and the amplified libraries were purified by two-sided AMpure purification;  First with a 0.5:1 beads:sample ratio followed by a 0.7:1 ratio.


title: P211_D23_5xFAD_C57BL/6J_cerebellum_rep3


title: S348_07_T-T_microglia


title: NXF9_nuc

source_name: CytoLib, siNXF1 nuclear fraction, rep5


title: P211_D22_5xFAD_C57BL/6J_cerebellum_rep3


title: NXF9_cyto

source_name: CytoLib, siNXF1 cytoplasmic fraction, rep5


title: P211_D20_5xFAD_C57BL/6J_cerebellum_rep3


title: S348_06_T-T_microglia


title: P211_D2_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_D19_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_D21_5xFAD_C57BL/6J_cerebellum_rep3


title: NXF8_total

source_name: CytoLib, siNXF1 WCE, rep4


title: P211_D18_5xFAD_C57BL/6J_cerebellum_rep2


title: K562_lib_siNT_cyt_rep1

source_name: Splicing library, siNT, cytoplasmic fraction, rep1


title: P211_D16_5xFAD_C57BL/6J_cerebellum_rep2


title: S348_04_microglia

value: wild type


title: S348_03_microglia


title: S348_05_T-T_microglia


title: P211_D14_5xFAD_C57BL/6J_cerebellum_rep1

value: cerebellum


title: P211_D15_5xFAD_C57BL/6J_cerebellum_rep1


title: NXF8_nuc

source_name: CytoLib, siNXF1 nuclear fraction, rep4


title: NXF8_cyto

source_name: CytoLib, siNXF1 cytoplasmic fraction, rep4


title: P211_D13_5xFAD_C57BL/6J_cerebellum_rep1

source_name: microglia


title: P211_D17_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_D12_5xFAD_C57BL/6J_cerebellum_rep1


title: NXF7_total

source_name: CytoLib, siNXF1 WCE, rep3


title: NXF7_nuc

source_name: CytoLib, siNXF1 nuclear fraction, rep3


title: P211_D11_5xFAD_C57BL/6J_hippocampus_rep3


title: S348_01_microglia


title: NXF7_cyto

source_name: CytoLib, siNXF1 cytoplasmic fraction, rep3


title: S302_12_Tomato-4

value: Hexb-tdTomato/wt


title: P211_D1_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_C8_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_C7_5xFAD_C57BL/6J_hippocampus_rep2


title: S302_11_Tomato-3


title: NXF2_nuc

source_name: CytoLib, siNXF1 nuclear fraction, rep2


title: NXF2_total

source_name: CytoLib, siNXF1 WCE, rep2


title: P211_C6_5xFAD_C57BL/6J_hippocampus_rep2


title: NXF2_cyto

source_name: CytoLib, siNXF1 cytoplasmic fraction, rep2


title: S302_09_Tomato-1


title: S302_10_Tomato-2


title: P211_C5_5xFAD_C57BL/6J_hippocampus_rep2


title: P211_C23_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_C4_5xFAD_C57BL/6J_hippocampus_rep1


title: S348_02_microglia


title: S302_03_Con-3


title: S302_04_Con-4


title: NXF1_nuc

source_name: CytoLib, siNXF1 nuclear fraction, rep1


title: P211_C24_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_C21_5xFAD_C57BL/6J_cerebellum_rep3


title: NXF1_total

source_name: CytoLib, siNXF1 WCE, rep1


title: P211_C20_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_C9_5xFAD_C57BL/6J_hippocampus_rep3


title: P211_C2_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_C3_5xFAD_C57BL/6J_hippocampus_rep1


title: NXF1_cyto

source_name: CytoLib, siNXF1 cytoplasmic fraction, rep1


title: S302_02_Con-2

source_name: brain


title: S302_01_Con-1


title: NT9_total

source_name: CytoLib, siNT WCE, rep5


title: P211_D10_5xFAD_C57BL/6J_hippocampus_rep3


title: P211_C19_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_C18_5xFAD_C57BL/6J_cerebellum_rep2


title: NT9_nuc

source_name: CytoLib, siNT nuclear fraction, rep5


title: P211_C22_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_C17_5xFAD_C57BL/6J_cerebellum_rep2


title: S295_12_Het

value: Hexb-KO/wt


title: P211_C15_5xFAD_C57BL/6J_cerebellum_rep1


title: NT9_cyto

source_name: CytoLib, siNT cytoplasmic fraction, rep5


title: S295_11_Het


title: P211_C16_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_C13_5xFAD_C57BL/6J_cerebellum_rep1


title: S295_10_KO

value: Hexb-KO/KO


title: P211_C11_5xFAD_C57BL/6J_hippocampus_rep3


title: P211_C10_5xFAD_C57BL/6J_hippocampus_rep3


title: NT8_nuc

source_name: CytoLib, siNT nuclear fraction, rep4


title: P211_C1_5xFAD_C57BL/6J_hippocampus_rep1


title: NT8_cyto

source_name: CytoLib, siNT cytoplasmic fraction, rep4


title: P211_C12_5xFAD_C57BL/6J_cerebellum_rep1


title: NT8_total

source_name: CytoLib, siNT WCE, rep4


title: S295_09_Het


title: P211_B7_5xFAD_C57BL/6J_hippocampus_rep2

source_name: microglia


title: P211_B9_5xFAD_C57BL/6J_hippocampus_rep3


title: P211_B6_5xFAD_C57BL/6J_hippocampus_rep2


title: NT7_total

source_name: CytoLib, siNT WCE, rep3


title: S295_07_KO


title: P211_B8_5xFAD_C57BL/6J_hippocampus_rep2


title: WT3-CB

city: Montréal

first: Marc

last: Therrien

state: Québec

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

data_processing:
Basecalls performed using Illumina RTA 1.17.21.3
Samples demultiplexed using Illumina Casava 1.8.2 and masked for sequencing adapters with N characters.
Sequenced reads were trimmed for masked adapters and low quality extremities using Trimmomatic 0.35 and then mapped to the reference genome using STAR version 2.7.1a, guided by transcript annotations from Ensembl release 99.
Expression values for stranded samples were computed using RSEM version 1.2.28.
Genome_build: BDGP6.28
Supplementary_files_format_and_content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output (first line identifies the columns)

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Whole lymph glands

growth_protocol: 25˚C, semi-defined medium from BDSC

extract_protocol:
Qiagen Rneasy column purification
KAPA RNA Stranded PolyA

tag: background strain

value: BL-30140 crossed to w1118

tag: experimenter

value: Experiement done by C. Baril

tag: Stage

value: Third instar larval stage

value: wild-type


title: NT7_nuc

source_name: CytoLib, siNT nuclear fraction, rep3


title: P211_C14_5xFAD_C57BL/6J_cerebellum_rep1

city: Freiburg

address: Breisacher Str. 64


title: P211_B5_5xFAD_C57BL/6J_hippocampus_rep2

value: hippocampus


title: NT7_cyto

source_name: CytoLib, siNT cytoplasmic fraction, rep3


title: P211_B4_5xFAD_C57BL/6J_hippocampus_rep1


title: WT2-CB


title: P211_B3_5xFAD_C57BL/6J_hippocampus_rep1


title: S295_08_KO


title: P211_B24_5xFAD_C57BL/6J_cerebellum_rep3


title: WT3-GG

value: Experiement done by G. Gavory


title: P211_B23_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_B20_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_B2_5xFAD_C57BL/6J_hippocampus_rep1


title: WT1-CB


title: NT2_cyto

source_name: CytoLib, siNT cytoplasmic fraction, rep2

value: MCF-7 cell line


title: P211_B19_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_B22_5xFAD_C57BL/6J_cerebellum_rep3


title: WT2-GG


title: NT1_total

source_name: CytoLib, siNT WCE, rep1


title: WT1-GG


title: P211_B18_5xFAD_C57BL/6J_cerebellum_rep2


title: NT2_total

source_name: CytoLib, siNT WCE, rep2


title: NT1_nuc

source_name: CytoLib, siNT nuclear fraction, rep1


title: P211_B17_5xFAD_C57BL/6J_cerebellum_rep2


title: NT1_cyto

source_name: CytoLib, siNT cytoplasmic fraction, rep1


title: P211_B16_5xFAD_C57BL/6J_cerebellum_rep2


title: P211_B13_5xFAD_C57BL/6J_cerebellum_rep1


title: NT2_nuc

source_name: CytoLib, siNT nuclear fraction, rep2


title: P211_B21_5xFAD_C57BL/6J_cerebellum_rep3


title: P211_B15_5xFAD_C57BL/6J_cerebellum_rep1


title: EBOV_S_26

city: Créteil

first: cecile

last: lefebvre

address: 51 Avenue du Marechal De Lattre de Tassigny

country: France

institute: INSERM U955_VRI

data_processing:
Base calls were performed using Illumina CASAVA 1.8.2
Sequenced reads were trimmed for low-quality sequence, then mapped to hg19 whole genome using Star 2.5.3 with performed using Partek® Flow® software, Copyright ©; 2019 Partek Inc.
Aligned reads were quantified to annotation model hg19 - GENCODE Genes - release 19, with Partek E/M and counts normalized by the counts per million (CPM + 0.0001) method with performed using Partek® Flow® software, Copyright ©; 2019 Partek Inc.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized_counts CPM+0.0001 59 samples.txt

source_name: Blood

extract_protocol:
Total RNA was purified from whole blood with the Tempus™ Spin RNA Isolation Kit (Invitrogen) and globine mRNA depletion carried out with GLOBINclear™ Kit
mRNA libraries were prepared with the Illumina TruSeq® Stranded mRNA kit. Single read of 101 bp sequencing was performed on the Illumina HiSeq 2500 at VRI genomic Platform

value: Blood

tag: status

value: Ebola virus disease survivors


title: siU2AF_tot_rep3

data_processing:
Quantification using RSEM
Alignment to the hg19 human genome using STAR
Preparation of bigWig files using wigToBigWIg
Genome_build: hg19
Supplementary_files_format_and_content: RSEM quantification files and bigWig read coverage, summary files for half-lives estimated for SLAM-seq and UMI count for MPRA data

source_name: WCE, siU2AF2 cells, rep3


title: EBOV_S_24


title: EBOV_S_25


title: P211_B14_5xFAD_C57BL/6J_cerebellum_rep1


title: P211_B12_5xFAD_C57BL/6J_cerebellum_rep1


title: siU2AF_tot_rep4

source_name: WCE, siU2AF2 cells, rep4


title: P211_B10_5xFAD_C57BL/6J_hippocampus_rep3


title: EBOV_S_23


title: siU2AF_tot_rep1

source_name: WCE, siU2AF2 cells, rep1


title: P211_B11_5xFAD_C57BL/6J_hippocampus_rep3


title: siU2AF_nuc_rep4

source_name: Nuclear fraction, siU2AF2 cells, rep4


title: P211_A9_5xFAD_C57BL/6J_hippocampus_rep3


title: EBOV_S_21


title: P211_A7_5xFAD_C57BL/6J_hippocampus_rep2


title: EBOV_S_20


title: P211_A6_5xFAD_C57BL/6J_hippocampus_rep2


title: siU2AF_nuc_rep3

source_name: Nuclear fraction, siU2AF2 cells, rep3


title: P211_A5_5xFAD_C57BL/6J_hippocampus_rep2

source_name: microglia


title: P211_A8_5xFAD_C57BL/6J_hippocampus_rep2


title: siU2AF_nuc_rep1

source_name: Nuclear fraction, siU2AF2 cells, rep1


title: P211_A4_5xFAD_C57BL/6J_hippocampus_rep1


title: P211_A3_5xFAD_C57BL/6J_hippocampus_rep1


title: EBOV_S_22


title: EBOV_S_18


title: P211_B1_5xFAD_C57BL/6J_hippocampus_rep1


title: EBOV_S_17


title: P211_A23_5xFAD_C57BL/6J_cerebellum_rep3


title: siU2AF_cyt_rep3

source_name: Cytoplasmic fraction, siU2AF2 cells, rep3


title: siU2AF_cyt_rep1

source_name: Cytoplasmic fraction, siU2AF2 cells, rep1


title: EBOV_S_16


title: EBOV_S_15