title: DLE2_E12_DFL

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL

description: E12 Distal forelimb DLE2 viewpoint

data_processing:
Library strategy: 4C-seq
Multiplexed libraries were sequenced on Illumina HiSeq 2500 to obtain 100 bp single-end reads.
De-multiplexing, mapping and 4C-analysis were performed as described in David F et al, 2014. Reads were mapped to the mm10 (GRCm38) mouse genome assembly with bowtie2 version 2.2.1 (Langmead B et al, 2012) with parameters “--end-to-end --sensitive -k 20”. The segtofrag files were obtained after mapping the 4C data.
4C figures were made using a running mean algorithm with a window size of eleven fragments. Normalisation is done by dividing the fragment scores by the mean of fragments scores falling into a region defined as +/-5Mb around the centre of the bait coordinates, such as to see only changes in contact distribution and to minimize PCR complexity bias in each sample).
When multiple independent biological replicates were available, average 4Cseq profiles were calculated
all scripts are available at  at https://github.com/lldelisle/scriptsForBeccariEtAl2021
Genome_build: mm10
Supplementary_files_format_and_content: Smoothed/normalized data (bedGraph), when multiple biological replicates were done, the average was done.

source_name: E12 Distal forelimb

growth_protocol: Twelve pairs of embryonic distal and/ or proximal forelimbs were dissected in cold PBS from E12,5 wild-type mouse embryos for each biological replicate and pooled together.

extract_protocol:
Cells were lysed with 10 mM Tris pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EDTA, 1x Protease inhibitor cocktail to isolate nuclei and stored at -80°C. Nuclei from pools of at least 10 distal or proximal limbs were digested with DpnII (New England Biolabs) and ligated with T4 DNA ligase HC (Promega) in diluted conditions to promote intramolecular ligation. Samples were digested again with NlaIII (New England Biolabs) and ligated with T4 DNA ligase HC (Promega) in diluted conditions.
These templates were amplified using Expand long template (Roche) and inversed PCR primers flanked with adaptors allowing multiplexing (Table III). Barcodes (4bp) were added between the Illumina adaptor and the specific DpnII primers. Libraries were prepared by means of 8–10 independent PCR reactions using 70–100 ng of DNA per reaction. PCR products were pooled and purified using the PCR purification kit (Qiagen).  The illumina adaptors used were 5'-AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCT-3' for the inverse-forward primers located at the DpnII site and 5'-CAAGCAGAAGACGGCATACGA-3' for the inverse-reverse primers located at the DpnII site. Barcodes (4bp) were added between the illumina adaptor and the specific DpnII primers when the same viewpoints were multiplexed in the same run. Specific primer information for each viewpoint is displayed in the related publication (Beccari L et al, 2021). Undigested and self-ligated (and for Ano6 identified off-targets) fragments were discarded according to the sequences provided as an associated file named "4C-seq_filtered_out_sequences.txt". Multiplexed libraries were sequenced on Illumina HiSeq 2500 to obtain 100 bp single-end reads.

treatment_protocol: The tissues were dissociated with collagenase (Sigma Aldrich/Fluka) and filtered through a 35 micron mesh to isolate single cells. Cells were fixed with 2% formaldehyde (in PBS/10%FBS) for 10 min at room temperature and the reaction was quenched on ice with glycine. After washing three times with cold PBS, the material was stored at -80C for subsequent processing.

value: Distal forelimb

value: wild-type

tag: experiment

value: DLE2 viewpoint


title: WT-6_E15 embryo cortex total RNA

status: Public on Jan 23 2021

type: SRA

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

molecule: total RNA

organism: Mus musculus

source_name: cerebral cortex

extract_protocol: Total mRNA profiles of E15 wild type (WT) and Serpina3/+;Nestin-Cre mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500.

tag: genotype

value: Wildtype

tag: strain


title: 40LB_IgE#3

city: Yokohama

first: Kosuke

last: Miyauchi

state: Kanagawa

address: 1-7-22 Suehiro-sho

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole mouse genome using STAR 2.7.0c (command --runThreadN 60 --outSAMtype BAM SortedByCoordinate) Genome: mm10 GRCm38.p6 ENSEMBL GTF: GRCm38.97 ENSEMBL
featurecounts v1.6.0 (command: -M -O -t exon -g gene_id -a) GTF: GRCm38.97 ENSEMBL
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for genes

growth_protocol: B cells were cultured on the CD154+  fibroblast cell line expressing CD40L and BAFF, NB21.2D9 feeder cells in the presence of recombinant murine IL-4, or IL-21 and/or IL-13

extract_protocol:
IgG+ B cells and IgE reporter (Venus) positive B  cells were sorted by flow cytometer, and RNA was harvested using Trizol reagent. Lexogen 3'mRNA-seq library prep kit (Cat#015) was used with 10 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Lexogen 3'QuantSeq protocols

tag: tissue

value: spleen

tag: age

value: 8 weeks

tag: agent

value: IgE

value: Verigem KI/+


title: L12KO-rep01

city: La Jolla

first: Shenghong

last: Ma

state: CA

address: 2880 TORREY PINES SCENIC DR, Sanford Consortium

country: USA

institute: UCSD

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Homo sapiens

growth_protocol: DMEM with 10% FBS

extract_protocol:
RNA were isolated and purified with standard Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: cell type

value: breast cancer cell line

tag: passage

tag: origin tissue

value: breast

tag: genotype/variation

value: LATS1/2 knockout


title: 40LB+IL-4_IgE#3


title: WT-rep03

value: wild type


title: 40LB+IL-4_IgE#2


title: 40LB+IL-4_IgG#2


title: 40LB+IL-4_IgG#3


title: WT-rep02


title: 40LB_IgG#1

value: IgG


title: T106c_5month_Lead_F_Heart

city: Ann Arbor

first: Siyu

last: Liu

state: MI

address: 100 Washtenaw avenue

department: Bioinformatics

institute: University of Michigan

library_source: genomic

data_processing:
The sample quality was first assessed with FastQC (v0.11.3), then Trim Galore! (v0.4.5) was used for adapter and quality trimming. More specifically, low-quality bases (quality score lower than 20), adapter sequences (required overlap of 6bp), and end-repair bases from the 3’ end of reads were trimmed, and all reads shorter than 20bp after trimming were discarded.
Bismark was used for alignment and methylation calling, where reads were aligned to mm10 genome using Bowtie2 and methylation calls were reported for all nucleotides with a read depth of at least 5.
Genome_build: mm10
Supplementary_files_format_and_content: bismark coverage files including the percentage of methylation at each position, the number of C bases that are methylated and the number of C bases that are unmethylated

molecule: genomic DNA

source_name: heart

extract_protocol:
Upon euthanasia at 5 months of age, heart were collected. Briefly, blood was removed by cardiac puncture (to be used in another study) and organs were perfused with PBS. Heart tissue was snap frozen in liquid nitrogen and stored at -80 deg C. Heart DNA extraction was performed using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen #80224).
A total of 50 ng of genomic DNA was digested using restriction enzyme Mspl, and the digested DNA was then purified using phenol:chloroform extraction and ethanol precipitation in the presence of glycogen, before blunt-ending and phosphorylation. A single adenine nucleotide was next added to the 3′ end of the fragments in preparation for the ligation of the adapter duplex with a thymine overhang. The ligated fragments were cleaned, then processed for size selection on agarose gel. Selected fragments were treated with sodium bisulfite to convert unmethylated cytosines to uracils, which are then replaced with thymines during PCR amplification. These libraries were next cleaned up with AMPure XP beads (Product #A63880; Beckman Coulter), quantified using the Agilent TapeStation genomic DNA kit (Catalog #G2991AA; Agilent) and Qubit High Sensitivity dsDNA (Catalog #Q32850; Invitrogen).

value: heart

tag: Sex

value: Female

value: 5 months

tag: treatment

value: Lead


title: WT-3_E15 embryo cortex total RNA


title: 40LB_IgG#2


title: NEU PBS2

data_processing:
Sample1-25; Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole mouse genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Sample1-25; featurecounts v1.6.0 (command: -M -O -t exon -g gene_id -a) GTF: mm9 ENSEMBL release 67
Sample26-43; Read alignment: TopHat2 v2.0.8 with default settings
Sample26-43; expression level: Cufflinks v2.1.1 with default settings
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include read counts for genes

source_name: neutrophils

extract_protocol:
Lung were removed from influenza virus infected mice (3 day post infection) and digested with collagenase D and DNase I in HBSS for 30 min at 37C, then cells were stained with anti-, CC10, CD103, CD11c, FceR1, Siglec-F, Gr-1, CD11b, or F4/80 antibodies, and were sorted using flow cytometer. Total RNA was harvested using Trizol reagent.  NEB Next Ultra RNA Library Prep Kit (Cat#E7530) for Sample1-25 or Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) for 26-43 was used with 10 ng or 1 ug of total RNA, respectively.
RNA libraries were prepared for sequencing using standard NEB Ultra protocols or Illumina TruSeq RNA Sample Prep Kit  protocols

value: lung

value: WT


title: NEU PBS1


title: T112d_5month_Lead_M_Heart

value: Male


title: T103c_5month_Lead_F_Heart


title: Dbx2_E12_PFL_rep3

description: E12 Proximal forelimb Dbx2 promoter viewpoint replicate 3

source_name: E12 Proximal forelimb

value: Proximal forelimb

value: wild-type

value: Dbx2 promoter viewpoint


title: Ano6_E12_DFL

description: E12 Distal forelimb Ano6 promoter viewpoint

value: Distal forelimb

value: Ano6 promoter viewpoint


title: NEU Flu2

source_name: neutrophils  from flu infected mouse's lung

value: 8 weeks


title: NEU Flu1


title: T107d_5month_Lead_M_Heart


title: Nell2_E12_DFL

description: E12 Distal forelimb Nell2 promoter viewpoint

value: Nell2 promoter viewpoint


title: T116d_5month_Lead_M_Heart


title: IM PBS3

source_name: infiltrated macrophage


title: DLE1_E12_DFL

description: E12 Distal forelimb DLE1 viewpoint

value: DLE1 viewpoint


title: T106d_5month_Lead_M_Heart


title: IM Flu1

source_name: infiltrated macrophage  from flu infected mouse's lung


title: IM PBS1


title: T116c_5month_Lead_F_Heart


title: IM Flu2


title: EOS Flu2

source_name: Eosinophils  from flu infected mouse's lung


title: Dbx2_E12_PFL_rep2

description: E12 Proximal forelimb Dbx2 promoter viewpoint replicate 2


title: Dbx2_E12_PFL_rep1

description: E12 Proximal forelimb Dbx2 promoter viewpoint replicate 1


title: 40LB_IgE#2

value: spleen

value: IgE

value: Verigem KI/+


title: IM PBS2


title: T103d_5month_Lead_M_Heart

value: heart


title: EOS PBS1

source_name: Eosinophils


title: Dbx2_E12_DFL_rep3

description: E12 Distal forelimb Dbx2 promoter viewpoint replicate 3


title: T105d_5month_Lead_M_Heart

value: 5 months


title: NEU Flu3


title: Dbx2_E12_DFL_rep2

description: E12 Distal forelimb Dbx2 promoter viewpoint replicate 2


title: T112c_5month_Lead_F_Heart

value: Female

value: Lead


title: ASXL2LysM OC 3

city: St Louis

first: nidhi

last: rohatgi

state: MO

address: 660 S Euclid Ave

department: pathology and immunology

institute: washington university in st. louis

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with custom demultipler written in python
Technical replicate fastq files were combined and aligned with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and annotated with Ensembl Biomart
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text format

source_name: Osteoclast

growth_protocol: Primary bone marrow cells were isolated from ASXL2flox or LysM cre mice and cultured on petridishes for 5 days in alpha MEM  + 10% FBS

extract_protocol:
Total RNA was extracted using RNA easy kit (Qiagen). RNA was also treated with DNAse1 to remove any contaminating genomic DNA
oligo-dT

treatment_protocol: After 5 days, cells were trypsinized and replated on culture dishes. Media was supplemented with 2% MCSF with or without RANKL (50ng/ml) for 2 days.

value: osteoclast

value: LysM Cre positive (KO)

value: MCSF + RankL (50ng/ml)


title: Dbx2_E12_DFL_rep1

description: E12 Distal forelimb Dbx2 promoter viewpoint replicate 1

value: wild-type


title: T102c_5month_Lead_F_Heart


title: EOS PBS2

value: lung

value: WT


title: T105c_5month_Lead_F_Heart


title: 40LB_IgE#1


title: ASXL2LysM OC 2


title: EOS Flu1


title: ASXl2flox OC 2

value: Flox


title: ASXL2LysM OC 1


title: Male PVAT Mesenteric HFD G76#1 [G76MHF1]

city: East Lansing

first: G. Andres

last: Contreras

address: 736 Wilson Road Room D202, Michigan State University

department: Large Animal Clinical Sciences

institute: Michigan State University

data_processing:
Samples were transcriptomic sequenced via Illumina platform by Novogene (Sacramento, CA, USA). After quality control, the paired-end clean reads were mapped onto reference genome using STAR (v2.5)
HTSeq (v 0.6.1) was used to count the read numbers of each gene. The gene read counts matrix was fed into DESeq2 (v 1.24.0) to identify the differentially expressed genes (DEGs).
To identify the outliers in the samples, principal component analysis was done with 10 principal components and the rotation matrix was used to calculate the mahalanobis distance among the samples.
For data analysis in R, tidyverse (v 1.3.0) and Rattus.norvegicus (v 1.3.1) libraries were used.
Genome_build: rn v 1.3.1
Supplementary_files_format_and_content: FPKM values

organism: Rattus norvegicus

source_name: Male PVAT Mesenteric HFD

extract_protocol:
RNA was extracted using Zymo Research kit Quick RNA MiniPrep kit (Cat# R1054)
For data analysis in R, tidyverse (v 1.3.0) and Rattus.norvegicus (v 1.3.1) libraries were used.

treatment_protocol: Control or High Fat Diet were fed for24 weeks. At 24weeks rats fed High Fat Diet were hypertensive while those on control diet remained normotensive

value: Dahl S

value: Control

value: PVAT mesenteric resistance artery

value: Adipocytes, Stromal Vascular Cells


title: AM PBS3

source_name: Alveolar macrophage

value: 8 weeks


title: Male PVAT Mesenteric Control G76#4 [G76MC4]

source_name: Male PVAT Mesenteric control


title: Male PVAT Mesenteric HFD G76#2 [G76MHF2]


title: AM PBS2


title: ASXl2flox OC 3


title: 9982865056_F: STO cells treated with miR-550a-3p

type: RNA

city: Milano

first: Stefano

last: Percio

state: Milano

address: Via Amadeo 42

department: DRAST

country: Italy

institute: Fondazione IRCCS - Istituto Nazionale dei Tumori

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Array data export processing and analysis was performed using Illumina BeadStudio v4. Raw expression data were log2-transformed and normalized using the robust spline normalization method.

label: Biotin

source_name: STO cells treated with miR-550a-3p

label_protocol: Biotinylated cRNA were prepared with Illumina RNA TotalPrep amplification kit (Ambion)

growth_protocol: 5 x 104 cells/ml of STO cells in 2 ml of DMEM/F-12 10% FBS medium per well (in a 6-well plate) so that they were 40% confluent at the time of transfection

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up treatment with QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: STO cells were transfected with 20 pM of mimic pre-miR-550a-3p or mimic negative control (Neg), using Lipofectamine® RNAiMAX Transfection Reagent and resuspended in a total of 500ml of Opti-MEM I Medium (amounts per well)

value: STO

value: diffuse malignant peritoneal mesothelioma


title: CMT93 cells CA 2

city: Frederiksberg C

first: Andrew

last: Williams

state: --- Select One ---

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: Affymetrix

label: biotin

source_name: CMT93 cells

label_protocol: Affymetrix

growth_protocol: Mice were given CA for 21 days in drinking water.

extract_protocol: Total RNA extracted with Qiagen RNAeasy kits.

treatment_protocol: Infection with Hp was for 14 days (200 larvae). Cells were exposed to CA (5 µg/mL) for 5 hours

tag: diet

value: cinnamaldehyde (CA)


title: 9982865056_D: STO cells treated with miR-550a-3p


title: AM PBS1


title: ASXL2LysM BMM 2

source_name: Bone Marrow Macrophages

value: Bone Marrow Macrophages

value: MCSF


title: 9982865056_E: STO cells treated with miR-550a-3p


title: AM Flu3

source_name: Alveolar macrophage  from flu infected mouse's lung


title: 9982865056_C: STO cells treated with negative control

source_name: STO cells treated with negative control


title: 9982865056_B: STO cells treated with negative control


title: AM Flu2


title: ASXl2flox OC 1

value: osteoclast


title: Male PVAT Mesenteric Control G76#3 [G76MC3]

value: Male


title: Male PVAT Mesenteric Control G76#5 [G76MC5]

value: Female


title: AEC PBS3

source_name: AEC


title: ASXL2LysM BMM 3

value: LysM Cre positive (KO)


title: ASXl2flox BMM 3


title: AM Flu1

value: lung


title: AEC PBS2

value: WT


title: Female PVAT Mesenteric HFD G75#5 [G75FHF5]

source_name: Female PVAT Mesenteric HFD

value: High Fat Diet


title: Female PVAT Mesenteric HFD G75#1 [G75FHF1]

value: Dahl S


title: ASXl2flox BMM 1

value: Flox


title: AEC PBS1


title: AEC Flu2

source_name: AEC  from flu infected mouse's lung


title: Male PVAT Mesenteric HFD G74#3 [G74MHF3]

value: PVAT mesenteric resistance artery


title: ASXL2LysM BMM 1


title: AEC Flu1


title: ASXl2flox BMM 2


title: Hp infected, CA fed mice 5

source_name: Mouse jejunum

tag: infection

value: Heligmosomoides polygyrus


title: CMT93 cells control 1

value: control


title: CMT93 cells CA 1


title: CMT93 cells control 2


title: 9982865056_A: STO cells treated with negative control

value: STO


title: CC10_PB33

source_name: Clara cells

value: 8 weeks


title: Hp infected, CA fed mice 2

value: cinnamaldehyde (CA)


title: Hp infected, CA fed mice 4


title: Female PVAT Mesenteric Control G73#5 [G75FC5]

source_name: Female PVAT Mesenteric control

value: Adipocytes, Stromal Vascular Cells


title: CC10_PBS2


title: Female PVAT Mesenteric Control G75#4 [G75FC4]


title: Male PVAT Mesenteric Control G74#5 [G74MC5]

value: Control


title: Female PVAT Mesenteric HFD G73#2 [G73FHF2]


title: HPAP Healthy rep 1

city: Aurora

first: Dale

middle: R

last: Brown

state: Colorado

address: 12700 East 19th Avenue

institute: University of Colorado Anschutz Medical Campus

data_processing:
Quality control of sequencing runs with NGS tool, CLCBio Genomics Workbench (Qiagen).  Average 70% mapped reads, 31 Million mapped reads per sample
Data normalization and transformation with PROC MIX procedure of SAS to transform the expression data from negative binomial distribution to normal distribution
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated
Genome_build: ENSEMBL bovine reference genome UMD 3.1, release 77.
Supplementary_files_format_and_content: RPKM, threshold abundance RPKM > 0.2

organism: Bos taurus

source_name: heart right ventricle

growth_protocol: Male calves were born and raised on grass-hay forage with grain supplement at 7120 ft/2170 m, weaned and castrated at age 6-8 mos, slaughtered at age 13-15 mos.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Chronic environmental hypoxia in montane field environment

tag: animal id

tag: breed

value: Angus

tag: phenotype

value: High PAP - Healthy

value: Heart


title: HPAP Heart Failure rep 3

value: High PAP - Heart Failure

tag: genotype


title: HPAP Heart Failure rep 2


title: HPAP Heart Failure rep 1


title: CA fed mice 5

tag: strain


title: Hp infected, CA fed mice 3


title: CC10_Flu1

source_name: Clara  from flu infected mouse's lung

tag: tissue

value: lung


title: CC10_PBS1

tag: age

value: WT


title: LPAP rep 5

value: Hypoxia-tolerant Low PAP


title: HPAP Healthy rep 3


title: CA fed mice 4


title: Hp infected, CA fed mice 1


title: CA fed mice 1


title: Male PVAT Mesenteric Control G74#4 [G74MC4]

value: Dahl S

value: Male


title: Hp infected mice 5


title: HPAP Healthy rep 2


title: Female PVAT Mesenteric HFD G75#3 [G73FHF3]

value: High Fat Diet

value: PVAT mesenteric resistance artery


title: CA fed mice 3


title: CC10_Flu3

source_name: Clara cells  from flu infected mouse's lung


title: LPAP rep 4


title: CD11b+ cDC Flu2

source_name: CD11b+ cDC from flu infected mouse's lung


title: CC10_Flu2


title: Male PVAT Mesenteric HFD G74#2 [G74MHF2]

source_name: Male PVAT Mesenteric HFD


title: Female PVAT Mesenteric Control G73#3 [G73FC3]


title: LPAP rep 6


title: Female PVAT Mesenteric HFD G73#1 [G73FHF1]


title: CA fed mice 2


title: Female PVAT Mesenteric Control G73#4 [G73FC4]


title: CD11b+ cDC PBS2

source_name: CD11b+ cDC


title: 10/21/19 Sequencing Run #2

city: Baltimore

first: Suraj

last: Kannan

state: MD

address: 720 Rutland Avenue Ross 954

department: Cardiology

institute: Johns Hopkins University

description: Please see our code at https://github.com/skannan4/wls for demultiplexing of the Multiseq barcodes. Mapping was done in Kallisto|Bustools using 10xv3 custom setting (-x 10xv3). Note that for this sample, we didn’t demultiplex the indithe 10x run was demultiplexed by i7 tag. However, we mapped in one shot using Kallisto|Bustools.

data_processing:
Mapping of the data was done with kallisto|bustools (0.46.1), using an index generated from the CellRanger mouse reference.
Genome_build: GRCm38_r92
Supplementary_files_format_and_content: Please see our code at https://github.com/skannan4/wls for the full approach used to demultiplex the Multiseq barcode tags. Likewise, the code there contains our entire strategy for clustering and labeling cells; additional files may be found there. The processed files provided here are the UMI tables for all the runs combined (combined_data.txt) as well as the metadata for these cells (combined_pheno.txt). UMI counts are also provided in sparse format.

source_name: Mesp1+ cells (Wls fl/+ and Wls fl/fl)

growth_protocol: The following mice were used to generate the appropriate samples for this experiment: Mesp1-Cre (Saga et al., 1999), Ai9 (stock no. 007909, Jackson Laboratory, (Madisen et al., 2010)), and Wntless flox (stock no. 027484, Jackson Laboratory, (Fu et al., 2011)).

extract_protocol:
Embryos were dissected, staged, and stored on ice in cold PBS -/-. Embryos were dissociated and barcoded using MULTI-seq anchor and primers , before FACS on Mesp1+/tdTomato cells using Sony SH800. Cells were then captured for 10x library prep and single cell RNA sequencing.
We performed cell capture and library construction using 10x Chromium v3. For the experiments sequenced on 10/21/19, sequencing of the endogenous transcripts was done on a NextSeq500 high output lane using a 28/8/91 bp design for R1/i7/R2. Sequencing of the barcodes was done a NextSeq500 mid output lane using a 28/8/8 design for R1/i7/R2. For the experiments sequenced on 03/04/20, sequencing for both endogenous and barcode transcripts was done on a NovaSeq6000 S1 flow cell, using a 28/8/91 bp design; the barcode transcripts were subsequently trimmed using the BBMap/BBTools suite.

tag: strain/background

value: Mesp1-Cre; Ai9; Wlsfl/+ and Wlsfl/f

value: Mesp1+ cells


title: Hp infected mice 2

value: Heligmosomoides polygyrus

value: control


title: Hp infected mice 4


title: CD11b+ cDC Flu3

value: 8 weeks


title: CD11b+ cDC PBS1


title: Lenalidomide treated donor 2

city: Erlangen

first: Heiko

last: Bruns

address: Hartmannstraße 24

country: Germany

institute: University Hospital Erlangen

data_processing:
Raw reads in fastq format were trimmed to 50 bp using FASTX (v0.0.13) before mapping to the annotated human genome GRCh38 (Gencode v23) using STAR (v2.4.2a) with the following parameters: --outBAMsortingThreadN 6   --outSAMtype BAM SortedByCoordinate  --quantMode GeneCounts   --outWigType bedGraph   --outWigStrand Unstranded  --outFilterIntronMotifs RemoveNoncanonicalUnannotated  --outSAMstrandField intronMotif  --outReadsUnmapped Fastq  --outFilterType BySJout  --outFilterMultimapNmax 20  --alignSJoverhangMin 8   --alignSJDBoverhangMin 1   --alignIntronMin 20   --alignIntronMax 1000000.
Read Count Tables (unstranded) were generated using STAR and assembled in R.

source_name: Macrophage

growth_protocol: PBMC were isolated by density gradient centrifugation of buffy coat preparations from the peripheral blood of healthy donors. Monocytes were isolated by adherence on plastic and cultured in the presence of  M-CSF (50 ng/ml) to obtain M2 macrophages. Macrophages were detached with EDTA after 6d of culture.

extract_protocol:
RNA was isolated from the cells using an RNeasy mini kit (Qiagen) according to the manufacturer’s recommended protocol. 100 ng RNA of each total RNA sample was used as template.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Macrophages were incubated with or without lenalidomide for 3 days at a concentration of 1μM.

value: macrophage

value: Lenalidomide treated

tag: donor


title: LPAP rep 3

value: Angus


title: Lenalidomide treated donor 5

tag: cell type


title: Hp infected mice 3


title: CD11b+ cDC Flu1


title: LPAP rep 2

value: Heart


title: Lenalidomide treated donor 4


title: CD11b+ cDC PBS3


title: LPAP rep 1


title: Lenalidomide treated donor 3


title: HNRNPU KD K562 nuclear RNA [Nc_RNPU]

city: Sha Tin

first: Yile

last: Huang

state: Hong Kong

address: Room 503, Li Ka Shing Health and Science Buiding, Prince of Wales Hospital, Sha Tin

department: Chemical Pathology

institute: The Chinese University of HongKong

data_processing:
Base-calling performed by CASAVA
The raw RNA-seq reads were evaluated by FastQC and preprocessed by Illumina universal adapter trimming and low-quality reads filtering with our in-house scripts
All clean paired-end reads were mapped to the mouse genome (mm9) using Tophat version 2.0.13
The novel lncRNAs were predicted by iSeeRNA program
Abundance of each lncRNA in nuclear or cytosolic fraction was quantified and compared by Cuffdiff (version 2.2.1) and nucleus-enriched lncRNAs (nuc-lncRNAs) were defined when ratio of transcript abundances in the nucleus over the cytosol >1.5
Genome_build: hg19
Supplementary_files_format_and_content: Abundance measurements

source_name: HNRNPU KD K562

growth_protocol: K562 (CCL-243) cells were obtained from ATCC and maintained in RPMI 1640 with 2mM L-glutamine supplemented with 10% fetal bovine serum, 100 U/mL penicillin, 100 μg/mL streptomycin and in a 5% CO2 humidified incubator at 37 °C.

extract_protocol:
RNAs were extracted from the total, cytoplasmic or nuclear fractions using TRIzol reagent (Invitogen) and then delivered to BGI HK for rRNA depletion. Total RNAs were extracted from K562 cells using TRIzol reagent (Invitogen) following the manufacturer’s instructions
For total RNA-seq, RNAs were submitted to Novogene, Beijing. The libraries were prepared following strand specific RNA-seq library preparation procedures and sequenced on the Illumina HiSeq X-10 platform.

treatment_protocol: K562 cells were transfected with 300 nM siRNA targeting hnRNPU or with control oligos

tag: cell line

value: chronic myelogenous leukemia (CML) cell line

tag: tissue source

value: bone marrow

value: transfected with siRNA targeting hnRNPU


title: Hp infected mice 1


title: Lenalidomide treated donor 1


title: HNRNPU KD K562 cytosolic RNA [Cy_RNPU]


title: CD103+ cDC Flu3

source_name: CD103+ cDC from flu infected mouse's lung

value: lung

value: WT


title: CD103+ cDC PBS2

source_name: CD103+ cDC


title: Control mice 3


title: CD103+ cDC Flu2


title: RNA-Seq-siPRMT5-HEK293

city: Xiamen

first: Guosheng

last: Hu

state: Fujian

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

department: School of Pharmaceutical Sciences

institute: xiamen University

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

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

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

treatment_protocol: HEK293 cells were transfected with control siRNA or siRNA specifically targeting PRMT4, PRMT5 or PRMT7 and maintained in  DMEM medium supplemented with 10% FBS and 1% penncilin and streptomycin for three days.

value: Human Embryonic Kidney


title: Control K562 nuclear RNA [Nc_NC]

source_name: Control K562

value: transfected with siRNA control oligos


title: Control mice 5


title: RNA-Seq-siPRMT4-HEK293


title: Control donor 4

value: untreated


title: CD103+ cDC Flu1


title: HNRNPU KD K562 whole cell RNA [To_RNPU]


title: Control mice 2


title: Control donor 5


title: RNA-Seq-siPRMT7-HEK293


title: Control mice 4


title: 10/21/19 Sequencing Run #1

value: Mesp1-Cre; Ai9; Wlsfl/+ and Wlsfl/f


title: RNA-Seq-siCTL-HEK293


title: Control donor 3


title: CD103+ cDC PBS3


title: Control K562 cytosolic RNA [Cy_NC]


title: Control donor 2


title: CD103+ cDC PBS1


title: Control donor 1


title: 4-hour Transmigrated neutrophils from healthy donor 6 (HD6_4H)

status: Public on Jan 22 2021

city: Atlanta

first: Diego

last: Moncada

state: Georgia

address: 201 Dowman Dr

department: Pediatrics

institute: Emory University

data_processing:
Hisat2 was used to align next-generation sequencing reads to the reference genome
SAMtools was used to sort BAM files.
FeatureCounts from the  Subread package was used to generate read counts expressed per gene
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Blood

growth_protocol: we used Alvetex (Reprocell) 200 μm-thick inert 3D scaffolds with >90% porosity (pore sizes of 36–40 μm, with interconnects of 12–14 μm). In brief, inserts were activated with 70% ethanol, coated overnight at 37ºC with rat-tail collagen I (3 mg/mL, Sigma) and seeded with H441 cells at 2.5×105 cells per 12-well insert. Cells were first grown in submerged cultures with DMEM/F12 supplemented with 10% heat-inactivated serum, penicillin, and streptomycin. After 2 days, cells were supplemented basally with serum-free DMEM/F12 with 10% Ultroser G (Pall Life Sciences) to establish ALI. Cultures were grown for 2 weeks at ALI and supplemented basally with fresh medium every 48 hours. For TM experiments, the ALI cultures were placed with the apical compartment exposed to RPMI, leukotriene B4 (LTB4, 100 nM) or airway supernatant (ASN) from CF patiens Sputum. then. 0.5–1 ×106  blood neutrophils were loaded onto the 200 μm-thick basal compartment of the Alvetex scaffold (situated upside), and allowed to migrate at 37°C at 5% CO2 through the collagen and epithelial layers into the apical compartment (situated downside, and bathed with either control medium with chemoattractant, or ASN) doi: 10.1002/JLB.5HI1117-454RR. Finally,Using the in vitro model, airway neutrophils (transmigrated neutrophiuls)were collected after 1, 2, 4 and 6 hour of transmigration towards CFASN.

extract_protocol:
RNA was isolated from purified (blood >98% purity) and transmigrated (LTB4 or CFASN, >98% purity) neutrophils using the Nucleospin RNA isolation kit (Clontech, Takara Bio) following manufacturer protocol. RNA quality and concentration were quantified using a Bioanalyzer (Agilent technologies, Inc.) and only samples with RIN>8.0 were used for sequencing.
Libraries were prepared using the TruSeq RNA Single Indexes Set B kit (Illumina) and AmPure beads (Beckman) and sequenced as paired end (100bp) by high seq rapid run (Illumina) with an aim of ~20 million reads per sample

treatment_protocol: In this model, naïve blood neutrophils are migrated through a small airway epithelium grown at air-liquid interface toward CF airway fluid supernatant (CFASN, which corresponds to sputum sequentially centrifuged to remove cells and bacteria) or leukotriene B4 (LTB4, transmigration control), placed apically

value: Blood

value: airway neutrophils


title: 6-hour Transmigrated neutrophils from healthy donor 6 (HD6_6H)


title: Control K562 whole cell RNA [To_NC]


title: 2-hour Transmigrated neutrophils from healthy donor 2 (HD2_2H)


title: 6-hour Transmigrated neutrophils from healthy donor 2 (HD2_6H)


title: 4-hour Transmigrated neutrophils from healthy donor 2 (HD2_4H)


title: 4-hour Transmigrated neutrophils from healthy donor 1 (HD1_4H)


title: 1-hour Transmigrated neutrophils from healthy donor 1 (HD1_1H)


title: 1-hour Transmigrated neutrophils from healthy donor 2 (HD2_1H)


title: 1-hour Transmigrated neutrophils from healthy donor 6 (HD6_1H)


title: 2-hour Transmigrated neutrophils from healthy donor 1 (HD1_2H)


title: Blood neutrophils from healthy donor 3 (HD3)


title: 2-hour Transmigrated neutrophils from healthy donor 6 (HD6_2H)


title: Control mice 1

value: control


title: Linehan-7

city: Bethesda

first: Mayank

last: Tandon

address: 41 CENTER DR, BG 41 RM B620

institute: CCR Collaborative Bioinformatics Resource

data_processing:
The sequencing quality of the reads was assessed using FastQC (version 0.11.5), Preseq (version 2.0.3), Picard tools (version 1.119), and RSeQC (version 2.6.4). Reads were trimmed using Trimmomatic (version 0.33) to remove sequencing adapters, prior to mapping to the human reference genome, hg38, using STAR (version 2.5.2b) in two-pass mode.
Expression levels were quantified using RSEM version 1.3.0 with GENCODE annotation version 21.
The RSEM counts were then normalized using the variance stabilization transformation (VST) from the DESeq2 R package (version 1.24.0).
Genome_build: hg38
Supplementary_files_format_and_content: Raw gene counts from RSEM for all genes and all samples
Supplementary_files_format_and_content: VST-Normalized expression values for all genes and all samples

molecule: polyA RNA

source_name: kidney

extract_protocol:
Total RNA was extracted from cell lines or cryo-pulverized tumor/normal tissues using Trizol Reagent (Invitrogen) following the manufacturer’s protocol and stored at -80 °C. RNA concentrations and purities were measured using a NanoDrop 2000 UV-Vis Spectrophotometer (Thermo Fisher Scientific) and 5μg of total RNA was sent to ACGT, Inc. (Germantown, MD, USA) for RNAseq analysis.
All samples were processed with the TruSeq mRNA kit using oligo-dT beads to capture polyA tails, sequenced on a single flowcell of an Illumina HiSeq 2500 instrument, and data were delivered as a Multiplex Fast-Q file with adaptors trimmed.

tag: tissue type

value: Primary Tumor

tag: tissue type details

value: HLRCC Tumor


title: Linehan-9

value: Adjacent Normal

value: Renal Cortex


title: 6-hour Transmigrated neutrophils from healthy donor 1 (HD1_6H)


title: Linehan-8

value: Metastasis

value: HLRCC Metastasis


title: Linehan-41


title: Linehan-5


title: Linehan-6


title: Blood neutrophils from healthy donor 2 (HD2)


title: Linehan-3


title: Linehan-4


title: Linehan-25


title: Linehan-26


title: NHEK1-Ado

city: Chapel Hill

first: David

last: Corcoran

state: NC

address: 125 Mason Farm Rd

department: Genetics

institute: University of North Carolina at Chapel Hill

description: total RNA ng/ul: 29.58; 260/280:2.00

hyb_protocol: Hybridization targets were prepared from total RNA using a MessageAmp Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX, USA), hybridized to GeneChip™ Human U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA, USA) in an Affymetrix GeneChip hybridization Oven 645, washed in Affymetrix GeneChip Fluidics Station 450, and scanned with Affymetrix GeneChip Scanner 7G according to standard Affymetrix GeneChip hybridization, wash, and stain protocols.

scan_protocol: Affymetrix scanning protocol according to manufacturer, Affymetrix GeneChip Command Console Scan Control 3.2.3.1515 and Expression Console version 1.2.0.20

data_processing: Data was RMA normalized using the Affy Bioconductor package in the R statistical programming environment.

source_name: Normal human epidermal keratinocytes (NHEK)

label_protocol: Ambion MessageAmp Premier labeling

growth_protocol: Normal human epidermal keratinocytes (NHEKs) were cultured in serum-free EpiLife cell culture medium containing 0.06 mM Ca2+, EpiLife Defined Growth Supplement, 50 U/ml penicillin and 50 mg/ml streptomycin, maintained for up to five passages, and used at approximately 75-80% confluence for experiments.

extract_protocol: RNAeasy mini kit for RNA isolation; Total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies,Santa Clara, CA)) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE). Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA, hybridized to GeneChip® ____________ arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450 and scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA).

treatment_protocol: To determine the effect of eADO on keratinocyte gene expression, we stimulated keratinocytes with either vehicle or 10 µM adenosine

tag: stimulation

value: adenosine


title: Linehan-21


title: Linehan-22


title: NHEK2-Ado

description: total RNA ng/ul: 31.23; 260/280: 2.00

value: Normal human epidermal keratinocytes (NHEK)


title: Linehan-42


title: Blood neutrophils from healthy donor 1 (HD1)


title: Linehan-19


title: Linehan-20


title: Linehan-2


title: Linehan-14


title: Linehan-13


title: Linehan-11


title: Linehan-12


title: NHEK2-control

description: total RNA ng/ul: 22.78; 260/280: 2.12


title: Linehan-10


title: Linehan-24


title: Linehan-1


title: Linehan-23


title: Linehan-15


title: Linehan-17


title: treatment-20

city: 成都市

first: 一

last: 王

state: 四川省

address: 一环路西一段132号

institute: 四川省骨科医院

description: Gene expression in  human blood

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°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 (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

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.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Peripheral Blood

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

extract_protocol: Ten millilitres of fasting WB was collected from the left median cubital vein of each participant between 7:00 and 7:30 AM. All WB samples were incubated in a PAXgene Blood RNA tube (BD, USA) for less than 72 h at -20°C and then submitted to Shanghai Bohao Biotechnology Co., Ltd (Shanghai, China) for gene chip hybridization screening.

value: whole blood

tag: diagnosis

value: intervertebral disc degeneration

tag: treatment

value: Traditional Chinese Medicine


title: treatment-24

description: Gene expression in  human blood


title: treatment-12

description: Gene expression in  human blood


title: treatment-18

description: Gene expression in  human blood


title: treatment-14

description: Gene expression in  human blood


title: treatment-16

description: Gene expression in  human blood


title: NHEK1-control

description: total RNA ng/ul: 30.52; 260/280: 2.01


title: treatment-25

description: Gene expression in  human blood


title: treatment-22

description: Gene expression in  human blood


title: treatment-10

description: Gene expression in  human blood


title: treatment-8

description: Gene expression in  human blood


title: treatment-21

description: Gene expression in  human blood


title: treatment-6

description: Gene expression in  human blood


title: treatment-7

description: Gene expression in  human blood


title: treatment-23

description: Gene expression in  human blood


title: treatment-19

description: Gene expression in  human blood


title: treatment-17

description: Gene expression in  human blood


title: treatment-5

description: Gene expression in  human blood


title: treatment-13

description: Gene expression in  human blood


title: treatment-15

description: Gene expression in  human blood


title: treatment-11

description: Gene expression in  human blood


title: patient-23

description: Gene expression in  human blood


title: treatment-4

description: Gene expression in  human blood


title: treatment-3

description: Gene expression in  human blood


title: patient-25

description: Gene expression in  human blood


title: patient-19

description: Gene expression in  human blood


title: patient-20

description: Gene expression in  human blood


title: patient-18

description: Gene expression in  human blood


title: patient-22

description: Gene expression in  human blood


title: treatment-9

description: Gene expression in  human blood


title: treatment-1

description: Gene expression in  human blood


title: patient-17

description: Gene expression in  human blood


title: patient-24

description: Gene expression in  human blood


title: patient-11

description: Gene expression in  human blood


title: patient-10

description: Gene expression in  human blood


title: volunteer-25

description: Gene expression in  human blood

value: healthy control


title: Xmoo1 line, ctrl, replicate 2, for FLAM-seq

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

description:
NR_AR_ORG_HSV1_2_gene_polyA_length.csv.gz
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
NR_AR_ORG_HSV1_2
FLAMseq (Legnini et al. 2019)

data_processing:
For bulk RNA-sequencing, Illumina base calling, demultiplexing and FASTQ conversion with bcl2fastq v2.20.0 (Illumina)
alignment to GRCh38 genome using STAR v2.7.1a (https://github.com/alexdobin/STAR)
reads counted on GENCODE 27 gene models with htseq-count 0.9.1 (https://htseq.readthedocs.io/)
The HSV1 genome was extended from strain 17 (genbank entry NC_001806) with the GFP and loxP sequences, error-corrected based on the total RNA-sequencing data, and terminal repeats removed to avoid multi-mapping reads
Provided here are the resulting HSV-1 fasta and gtf file used in the data analysis
For FLAM-seq, the CCS reads were then used as input to the FLAManalysis pipeline (https://github.com/rajewsky-lab/FLAMAnalysis), that outputs gene assignment and poly(A) tail length and sequence for each read.
For single-cell RNA-sequencing, data was processed using the pigx pipeline version 1.1.4 (http://bioinformatics.mdc-berlin.de/pigx/, Wurmus et al. 2018 doi: 10.1093/gigascience/giy123) using a combined human/HSV1 genome
Genome_build: Homo sapiens hg38
Genome_build: HSV-1 GFP truncated corrected
Supplementary_files_format_and_content: fasta file
Supplementary_files_format_and_content: gtf file
Supplementary_files_format_and_content: comma-separated values

organism:
Homo sapiens
Human alphaherpesvirus 1

source_name: Brain organoid

growth_protocol: Cerebral organoids were generated according to modified Lancaster protocol (Lancaster et al., 2013, doi: 10.1038/nature12517),

extract_protocol:
For isolation of bulk RNA, organoids were dissolved in Trizol. Ribosomal RNA was depleted using Rnase H (Epicentre)
Total bulk RNA-seq libraries were generated using the TruSeq Stranded Total LT Sample Prep Kit (Illumina). FLAMseq libraries were constructed as previously described (Legnini et al. 2019, doi: 10.1038/s41592-019-0503-y)

treatment_protocol: Organoids were infected using Herpes simplex virus 1, strain 17 containing a GFP gene controlled by an MCMV promoter (Snijder et al. 2012, doi: 10.1038/msb.2012.9)

value: Brain organoid

tag: hsv-1 infection status

value: yes

tag: sampling timepoint

tag: rna population

value: polyA+ RNA


title: patient-21

description: Gene expression in  human blood


title: volunteer-23

description: Gene expression in  human blood


title: patient-13

description: Gene expression in  human blood


title: volunteer-16

description: Gene expression in  human blood


title: volunteer-22

description: Gene expression in  human blood


title: volunteer-19

description: Gene expression in  human blood


title: patient-16

description: Gene expression in  human blood


title: patient-14

description: Gene expression in  human blood


title: patient-9

description: Gene expression in  human blood


title: volunteer-18

description: Gene expression in  human blood


title: volunteer-12

description: Gene expression in  human blood


title: patient-15

description: Gene expression in  human blood


title: patient-12

description: Gene expression in  human blood


title: volunteer-20

description: Gene expression in  human blood


title: volunteer-17

description: Gene expression in  human blood


title: Xmoo1 line, ctrl, replicate 1, for FLAM-seq

description:
NR_AR_ORG_HSV1_1_gene_polyA_length.csv.gz
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
NR_AR_ORG_HSV1_1
FLAMseq (Legnini et al. 2019)


title: Xmoo1 line, 3dpi, replicate 2, for single-cell RNA-seq

description:
hg38HSV1GFPtc.Seurat.500.RDS.gz
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
NP2-60d-3dpi-Rep2
Dropseq including second strand synthesis

data_processing:
For bulk RNA-sequencing, Illumina base calling, demultiplexing and FASTQ conversion with bcl2fastq v2.20.0 (Illumina)
alignment to GRCh38 genome using STAR v2.7.1a (https://github.com/alexdobin/STAR)
reads counted on GENCODE 27 gene models with htseq-count 0.9.1 (https://htseq.readthedocs.io/)
The HSV1 genome was extended from strain 17 (genbank entry NC_001806) with the GFP and loxP sequences, error-corrected based on the total RNA-sequencing data, and terminal repeats removed to avoid multi-mapping reads
Provided here are the resulting HSV-1 fasta and gtf file used in the data analysis
For FLAM-seq, the CCS reads were then used as input to the FLAManalysis pipeline (https://github.com/rajewsky-lab/FLAMAnalysis), that outputs gene assignment and poly(A) tail length and sequence for each read.
For single-cell RNA-sequencing, data was processed using the pigx pipeline version 1.1.4 (http://bioinformatics.mdc-berlin.de/pigx/, Wurmus et al. 2018 doi: 10.1093/gigascience/giy123) using a combined human/HSV1 genome
Genome_build: Homo sapiens hg38
Genome_build: HSV-1 GFP truncated corrected
Supplementary_files_format_and_content: fasta file
Supplementary_files_format_and_content: gtf file
Supplementary_files_format_and_content: Seurat R object

extract_protocol:
For single-cell RNA-sequencing, single cell suspensions were generated by enzymatic digestion of organoids, and then fixed using methanol (Alles et al. 2017, doi: 10.1186/s12915-017-0383-5)
Single-cell RNA-seq libraries were generated using an extended Dropseq protocol containing a second-strand synthesis step (Wyler et al. 2020, doi: 10.1101/2020.05.05.079194)


title: Xmoo1 line, 3dpi, replicate 1, for FLAM-seq

description:
NR_AR_ORG_HSV1_4_gene_polyA_length.csv.gz
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
NR_AR_ORG_HSV1_4
FLAMseq (Legnini et al. 2019)


title: Neuron control_rep2 [3-2.mock]

city: Tianjin

first: Huan

last: Jian

address: NO.22 Qixiangtai Road

institute: Tianjin medical university

data_processing:
Basecalls performed using CASAVA version 1.8
Paired-end reads were quality controlled by Q30, and low-quality reads were removed after 3’ adaptor trimming by Cutadapt software (v1.9.3)
STAR software was used to match clean reads of the input library to the reference genome (version mm10) , and meRanGh software (a component of meRanTK) was used to align the clean reads of the bisulfite-treated library to the reference genome
Genome_build: mm10
Supplementary_files_format_and_content: Processed gene methylation site information
Supplementary_files_format_and_content: Matrix table with raw gene counts and methylation site information for every gene and every sample

source_name: Neuron control

growth_protocol: Neurons were isolated from the cortex of the embryonic mice, single cells were resuspended in DMEM-HG containing 10% fetal bovine serum and 1% penicillin/streptomycin. After four hours, the medium was replaced with neurobasal medium. The neurobasal medium were changed every 3 days.

extract_protocol:
TRIzol reagent (Invitrogen Corporation, CA, USA) was used to extract RNA from the primary cultured neurons following the manufacturer's protocol, and the NEBNext® rRNA Depletion Kit was used to reduce the rRNA content.
RNA was bisulfite-converted and purified using the EZ RNA Methylation Kit,TruSeq Stranded Total RNA Library Prep Kit (Illumina) was used to construct the RNA libraries

treatment_protocol: Neuronal medium was removed, and neuron cells were cultured in glucose-free DMEM. Then, neurons were placed in hypoxic conditions (37°C, 94% N2, 21% O2, 5% CO2) for 1.5 and 3 hours. Then, the glucose-free DMEM was changed to normal neuronal culture medium, and neurons were incubated under normal incubatory conditions (37°C, 5% CO2) for 24 hours.

value: day 18 fetal mouse after pregnancy

value: untreated

value: Cerebral cortex

value: Neuron


title: AD17 skin scRNA-seq

city: Vienna

first: Katharina

last: Rindler

address: Waehringer Guertel 18-20

department: Dermatology

country: Austria

institute: Medical University of Vienna

description: Atopic Dermatitis

data_processing:
Raw sequencing data were demultiplexed, aligned to a reference genome (GrCh38) and counted using Cell Ranger (version 3.0.2; 10x Genomics).
Genome_build: refdatacellranger-  GRCh38-3.0.0’
Supplementary_files_format_and_content: mtx (count matrix in sparse matrix format), barcodes.tsv (barcode ids),  features.tsv: (gene ids)

source_name: Skin Suction blister

extract_protocol:
Skin suction blisters were formed using a low pressure device from Electronic Diversities (Ridge Road, Finksburg, Md) by mounting 2 sterile 5-hole (5-mm diameter per hole) skin suction plates onto each antecubital fossa. Negative pressure (150-200 mm Hg) was applied over 1 to 2 hours, and blister fluid obtained was centrifuged to clear the fluid from cells and debris. The blister roof (constituting an epidermal sheet) was collected using standard surgical instruments and processed using 0.25% trypsin/EDTA (10 minutes at 37°C; Invitrogen, San Diego, Calif) to obtain a single-cell suspension. Cells from blister fluid and from the epidermis (blister roof) were enriched for CD45+ cells using fluorescence-activated cell sorting ([FACS]; FACSAria III, BD Biosciences, Franklin Lakes, NJ) and pooled within each donor sample. CD45− cells from the blister fluid and the epidermis were added to obtain a total number of 15,000 cells per scRNA-seq sample. Immediately after sorting, cells were subjected to scRNA-seq processing (10x Genomics, Pleasanton, Calif).
Single-cell libraries were generated using the Chromium Controller and Single Cell 3− Library & Gel Bead Kit version 3 (10x Genomics) according to the manufacturer’s protocol.

value: Skin cell

value: Dupilumab (16 weeks)

tag: easi score (reduction)

tag: chemistry

value: Single Cell 3' v3


title: Neuron control_rep3 [3-3.m5c]

tag: strain

tag: tissue


title: Neuron control_rep1 [3-1.mock]

tag: age


title: Xmoo1 line, ctrl, replicate 3, for FLAM-seq

description:
NR_AR_ORG_HSV1_3_gene_polyA_length.csv.gz
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
NR_AR_ORG_HSV1_3
FLAMseq (Legnini et al. 2019)


title: volunteer-24

description: Gene expression in  human blood


title: volunteer-9

description: Gene expression in  human blood


title: HeLa_G1_replicate1

city: Birmingham

first: John

last: Halsall

address: Medical School, Vincent Drive

department: Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

description: This sample is of Hela cells in G1.  It is the first of three biological replicates in this experiment, each from separate cultures

hyb_protocol: Hybridization was performed by the Functional Genomics  Laboratory, University of Birmingham, Birmingham, UK following the standard Nimblegen operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by the Functional Genomics  Laboratory, University of Birmingham, Birmingham, UK following the standard Nimblegen operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: HeLa cells

label_protocol: Labeling was performed by the Functional Genomics  Laboratory, University of Birmingham, Birmingham, UK following the standard Nimblegen operating protocol. See www.nimblegen.com.

growth_protocol: Immortalized, EBV-transformed lymphoblastoid cell lines (LCL) from healthy, karyotypically normal individuals were established in house and maintained at  37oC, 5% CO2 in RPMI 1640 medium, 10% foetal bovine serum, supplemented with L-glutamine (2mM, Life Technologies) and penicillin/streptomycin (Life Technologies). HeLa cells were cultured in DMEM medium supplemented with 10% foetal bovine serum (Sigma), supplemented with L-glutamine (2mM) and penicillin/streptomycin.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

treatment_protocol: LCL cells were seeded at 1x106 cells/ml, cultured for 24 hours and harvested in log phase. HeLa cells were shaken off in mitosis, replated and grown for a further 4 hours (mid G1) before harvesting by trypsinisation.

tag: cell cycle phase


title: volunteer-14

description: Gene expression in  human blood


title: treatment-2

description: Gene expression in  human blood


title: HeLa_G1_replicate3

description: This sample is of Hela cells in G1.  It is the third of three biological replicates in this experiment, each from separate cultures


title: volunteer-21

description: Gene expression in  human blood


title: Neuron control_rep1 [3-1.m5c]

tag: cell type


title: volunteer-10

description: Gene expression in  human blood


title: LCL_untreated_replicate2

description: This sample is of untreated lymphoblastoid cell cell line.  It is the second of three biological replicates in this experiment, each from separate cultures

source_name: Lymphoblastoid cell line

value: Asynchronous


title: volunteer-13

description: Gene expression in  human blood


title: Xmoo1 line, 6dpi, replicate 2, for single-cell RNA-seq

description:
hg38HSV1GFPtc.Seurat.500.RDS.gz
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
NP2-60d-6dpi-Rep2
Dropseq including second strand synthesis


title: volunteer-15

description: Gene expression in  human blood


title: Neuron control_rep3 [3-3.mock]


title: Xmoo1 line, 6dpi, replicate 1, for single-cell RNA-seq

description:
hg38HSV1GFPtc.Seurat.500.RDS.gz
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
NP2-60d-6dpi-Rep1
Dropseq including second strand synthesis


title: LCL_untreated_replicate3

description: This sample is of untreated lymphoblastoid cell cell line.  It is the third of three biological replicates in this experiment, each from separate cultures


title: volunteer-11

description: Gene expression in  human blood


title: Xmoo1 line, 3dpi, replicate 1, for single-cell RNA-seq

description:
hg38HSV1GFPtc.Seurat.500.RDS.gz
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
NP2-60d-3dpi-Rep1
Dropseq including second strand synthesis


title: AD19 skin scRNA-seq

description: Atopic Dermatitis

value: Dupilumab (1 year)


title: AD18 skin scRNA-seq

description: Atopic Dermatitis


title: AD16 skin scRNA-seq

description: Atopic Dermatitis


title: Neuron OGD/R1.5h_rep3 [2-3.mock]

source_name: Neuron OGD/R1.5h

value: OGD/R 1.5h


title: Neuron OGD/R1.5h_rep3 [2-3.m5c]


title: AD15 skin scRNA-seq

description: Atopic Dermatitis


title: AD14 skin scRNA-seq

description: Atopic Dermatitis


title: Neuron control_rep2 [3-2.m5c]


title: AD13 skin scRNA-seq

description: Atopic Dermatitis


title: HeLa_G1_replicate2

description: This sample is of Hela cells in G1.  It is the second of three biological replicates in this experiment, each from separate cultures


title: Neuron OGD/R1.5h_rep2 [2-2.m5c]


title: AD12 skin scRNA-seq

description: Atopic Dermatitis


title: Neuron OGD/R1.5h_rep1 [2-1.mock]


title: AD11 skin scRNA-seq

description: Atopic Dermatitis


title: Neuron OGD/R1.5h_rep2 [2-2.mock]


title: AD10 skin scRNA-seq

description: Atopic Dermatitis


title: Neuron OGD/R1.5h_rep1 [2-1.m5c]


title: Neuron OGD/R3h_rep3 [1-3.m5c]

source_name: Neuron OGD/R3h

value: OGD/R 3h


title: Neuron OGD/R3h_rep2 [1-2.mock]


title: Neuron OGD/R3h_rep1 [1-1.m5c]


title: Neuron OGD/R3h_rep3 [1-3.mock]


title: Female Fru Minus R2 [RNA-Seq]

city: Ann Arbor

first: Eleanor

middle: Josephine

last: Clowney

address: 1105 North University, 4218

department: MCDB

institute: University of Michigan

data_processing:
reads were trimmed with trim galore! For universal adaptors using default settings (Galaxy Version 0.6.3)
reads were further trimmed with trimmomatic in paired-end mode using sliding window (4 base average, 20 average quality) followed by dropping reads below length 20. Only paired reads were output
paired reads were aligned to dm6 using HISAT2 in unstranded mode with default parameters (Galaxy Version 2.1.0+galaxy5)
aligned reads below MAPQ30 were discareded using JSON Filter ((Galaxy Version 2.4.1)
uniquely aligned reads were selected using Picard MarkDuplicates (Galaxy Version 2.18.2.2)
Genome_build: dm6
Supplementary_files_format_and_content: bigwig files were generated with deeptools bamCoverage
Supplementary_files_format_and_content: text files were generated with StringTie (Galaxy Version 2.1.1) using default parameters

organism: Drosophila melanogaster

source_name: Female Fru Minus

growth_protocol: Flies were raised on standard cornmeal-agarose with molasses at 25C on a 12 hour light/dark cycle

extract_protocol:
Cells were sorted into Trizol-LS and stored at -80C until RNA isolation. For RNA extraction, we followed the standard Trizol-LS protocol until the aqueous phase was isolated. We then passed the aqueous phase over Arcturus Picopure columns, including a DNAse treatment on the column.
Samples were subject to quality control on an RNA TapeStation. Total starting RNA was around 1 ng per sample. Library preparation was performed using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina, with amplification cycles calibrated to the amount of total RNA. Unstranded, poly-A selected libraries were sequenced on an Illumina NovaSeq using 150bp paired end reads to a depth of ~30 million reads per library.

treatment_protocol: Male and female brains were dissected separately, optic lobes removed, and subjected to dissociation and flow cytometry.

value: central brain neuron

value: 2-7 day adult

tag: genotype

value: UAS-mCD8-GFP/MB247-Gal80; Fru-GAL4/+


title: Male Fru Minus R2 [RNA-Seq]

source_name: Male Fru Minus


title: Neuron OGD/R3h_rep2 [1-2.m5c]


title: LCL_untreated_replicate1

description: This sample is of untreated lymphoblastoid cell cell line.  It is the first of three biological replicates in this experiment, each from separate cultures


title: Female Fru Minus R1 [RNA-Seq]


title: Female Fru Plus R1 [RNA-Seq]

source_name: Female Fru Plus


title: Male Fru Plus R1 [RNA-Seq]

source_name: Male Fru Plus


title: Female Fru Minus R2

description:
ATAC_FemaleFruMinus_Rep2_March2018
Profile of open chromatin

data_processing:
reads were trimmed with cutadapt using the following parameters:  --minimum-length 18
alignment to dm6 using bowtie2 with the following parameters: -X 1000
Aligned reads were processed with samtools to create a bam file, Picard MarkDuplicates was used to mark duplicates and samtools was used to generate a final bam file with de-duplicated reads passing a q30 quality filter
Genome_build: dm6
Supplementary_files_format_and_content: bigwig files were generated with deeptools bamCoverage
Supplementary_files_format_and_content: peak calls were generated with MACS2 by pooling replicate bam files using -nomodel -shift -0 -ext -1 -fdr 0.001.

extract_protocol:
Nuclear isolation and Tn5 transposition were performed as in Buenrostro J et al., 2015 with modifications made for small numbers of cells as described in Monahan K et al. 2017.
Transposed DNA was amplified with barcoded primers in NEBNext High Fidelity 2X PCR Master Mix (NEB) and purified with Ampure XP beads (Beckman Coulter) at a ratio of 1.6uL beads per 1uL library. Purified library was eluted in 30uL of 10mM Tris-HCl pH8, 0.1mM EDTA. The quality of prepared libraries was verified with a Bioanalyzer 2100 using a high sensitivity DNA kit (Agilent). Libraries were quantified using KAPA qPCR assay (KAPA Biosystems), and multiplexed and sequenced on a NextSeq Illumina machine with 75 base pair, paired-end reads.

value: UAS-mCD8-GFP/MB247-Gal80; Fru-GAL4/TM2 or TM6B


title: Male Fru Plus R2 [RNA-Seq]


title: RNA-Seq HPCLSK_BCRABLp210_CDK6_KO, replicate 3

first: Markus

last: Zojer

address: Josef-Baumanngasse

department: Institute for Pharmakology and Toxokology

institute: University of Veterinary Medicine

description: BSF_0671_HCKT3BBXY_*_HPCLSK_CDK6_KO_140119_A_plus_p210_SCF_S56731

data_processing:
Samples which were split onto multiple lanes during sequencing were merged into one bam file prior to analysis
Alignment to genome version GRCm38 using STAR (RNA-Seq)
Adapter trimming and removing of low quality bases was performed using Trimmomatic
Counting of reads was done using featureCounts
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: raw count file (tab delimited)

source_name: RNA-Seq HPCLSK_BCRABLp210_CDK6_KO

growth_protocol: HPCLSK cells were plated in IMDM culture media supplemented with 12.5 ng/ml IL-6, 2% SCF on the agarose plates. HPCLSK_BCRABLp210 were cultured cytokine independent (-SCF/-IL-6)

extract_protocol:
QIAGEN RNeasy extraction kit
RNA-seq: SENSE mRNA-Seq Library Prep kit, 50 bp single-end

tag: strain background

value: Haematopoetic stem/Progenitor cells

tag: genotype/variation

value: CDK6 KO

value: BCRABLp210 transformed


title: RNA-Seq HPCLSK_BCRABLp210_CDK6_KO, replicate 4

description:
BSF_0671_HCKT3BBXY_*_HPCLSK_CDK6_KO_140119_B_plus_p210_SCF_S56730
BSF_0681_HF3YKBBXY_4_HPCLSK_CDK6_KO_140119_B_plus_p210_SCF_S57520


title: Male Fru Minus R1 [RNA-Seq]


title: RNA-Seq HPCLSK_BCRABLp210_CDK6_KO, replicate 1

description: BSF_0671_HCKT3BBXY_*_HPCLSK_CDK6_KO_080219_A_plus_p210_SCF_S56720


title: Female Fru Minus R1

description:
ATAC_FemFruMinus_Rep1_March2018
Profile of open chromatin


title: RNA-Seq HPCLSK_BCRABLp210_CDK6_KO, replicate 2

description:
BSF_0671_HCKT3BBXY_*_HPCLSK_CDK6_KO_080219_B_plus_p210_SCF_S56727
BSF_0681_HF3YKBBXY_4_HPCLSK_CDK6_KO_080219_B_plus_p210_SCF_S57518


title: RNA-Seq HPCLSK_BCRABLp210_CDK6_WT, replicate 3

description: BSF_0671_HCKT3BBXY_*_HPCLSK_WT_140119_A_plus_p210_SCF_S56724

source_name: RNA-Seq HPCLSK_BCRABLp210_CDK6_WT

value: CDK6 WT


title: Male Fru Minus R2

description:
ATAC_FemaleFruPlus_Rep2_March2018
Profile of open chromatin


title: Male Fru Minus R1

description:
ATAC_FemFruPlus_Rep1_March2018
Profile of open chromatin


title: RNA-Seq HPCLSK_BCRABLp210_CDK6_WT, replicate 2

description: BSF_0671_HCKT3BBXY_*_HPCLSK_WT_080219_B_plus_p210_SCF_S56722


title: RNA-Seq HPCLSK_BCRABLp210_CDK6_WT, replicate 1

description: BSF_0671_HCKT3BBXY_*_HPCLSK_WT_080219_A_plus_p210_SCF_S56723


title: Female Fru Plus R2

description:
ATAC_MaleFruMinus_Rep2_March2018
Profile of open chromatin


title: RNA-Seq HPCLSK-CDK6_KO, replicate 3

description:
BSF_0671_HCKT3BBXY_*_HPCLSK_CDK6_KO_140119_B_S56743
BSF_0681_HF3YKBBXY_4_HPCLSK_CDK6_KO_140119_B_S57522

source_name: RNA-Seq HPCLSK-CDK6_KO

value: untransformed


title: Neuron OGD/R3h_rep1 [1-1.mock]

value: day 18 fetal mouse after pregnancy

value: Cerebral cortex

value: Neuron


title: Female Fru Plus R2 [RNA-Seq]


title: Female Fru Plus R1

description:
ATAC_MaleFruMinus_Rep1_March2018
Profile of open chromatin


title: RNA-Seq HPCLSK-CDK6_KO, replicate 1

description: BSF_0671_HCKT3BBXY_*_HPCLSK_CDK6_KO_080219_A_S56732


title: Male Fru Plus R2

description:
ATAC_MaleFruPlus_Rep2_March2018
Profile of open chromatin


title: RNA-Seq HPCLSK-CDK6_KO, replicate 2

description: BSF_0671_HCKT3BBXY_*_HPCLSK_CDK6_KO_080219_B_S56733


title: RNA-Seq HPCLSK-CDK6_WT, replicate 4

description:
BSF_0671_HCKT3BBXY_*_HPCLSK_WT_140119_B_S56737
BSF_0681_HF3YKBBXY_4_HPCLSK_WT_140119_B_S57524

source_name: RNA-Seq HPCLSK-CDK6_WT


title: Male Fru Plus R1

description:
ATAC_MaleFruPlus_Rep1_March2018
Profile of open chromatin


title: RNA-Seq HPCLSK-CDK6_WT, replicate 1

description: BSF_0671_HCKT3BBXY_*_HPCLSK_WT_080219_A_S56734


title: RNA-Seq HPCLSK-CDK6_WT, replicate 3

description:
BSF_0671_HCKT3BBXY_*_HPCLSK_WT_140119_A_S56736
BSF_0681_HF3YKBBXY_4_HPCLSK_WT_140119_A_S57525


title: RNA-Seq HPCLSK-CDK6_WT, replicate 2

description:
BSF_0671_HCKT3BBXY_*_HPCLSK_WT_080219_B_S56735
BSF_0681_HF3YKBBXY_4_HPCLSK_WT_080219_B_S57521


title: pTotal RNA30_Total RNA

city: Chicago

first: Yoav

last: GiladLi

state: IL

address: 920 e 58th St

department: Section of Genetic Medicine

institute: University of Chicago

description:
Total RNA
Chimpanzee individuals

data_processing:
Map 3' seq libraries to respective genome with STAR 3.30.1. Remove reads mapping to genomic regions with 6 A's in a row or 7 A's in the 10 bases upstream of read.
Merge all libraries and call PAS with in house scripts (available on github https://brimittleman.github.io/Comparative_APA/)
Use ucsc-liftover 377 to reciprocally lift PAS then assigned orthologous PAS to Refseq hg38 gene annotations.
Remove PAS used on average <5% in both human and chimpanzee nuclear libraries. Also remove PAS in genes with expession  < 2 log2CPM in 8 individuals
bed files with hg39 and Pantro 6 genomic locations scores column is the mean usage of the PAS in the respective species Nuclear data, txt file with meta data for each PAS including column for PAS name (as used in bed file), gene, and genic location
Genome_build: human hg38, chimp Pantro6
Supplementary_files_format_and_content: PAS_doublefilter_either_ChimpCoordChimpUsage.sort.bed, bed file with Pantro6 coordinates and average chimpanzee usage
Supplementary_files_format_and_content: PAS_doublefilter_either_HumanCoordHummanUsage.sort.bed, bed file with hg38 coordinates and average human usage
Supplementary_files_format_and_content: PAS_GeneLocation.txt, text file with PAS name, gene, and genic location
Supplementary_files_format_and_content: Supplemental_table1 - meta data for 3' sequencing libraries, column name explanations in second sheet
Supplementary_files_format_and_content: Supplemental_table2 - meta data for RNA sequencing libraries, column name explanations in second sheet

organism: Pan troglodytes

source_name: Imortalized Lymphoblastoid cell line

growth_protocol: LCLs were grown in 20% FBS containing RPMI at 37 and 5% CO2. They were passagd 3 times, maintained at 8 X 10^5, and collected at concentration of 1 X 10^6.

extract_protocol:
The nuclear RNA was extracted using the first part of the nuclear isolation protocl from Mayer and Churchman. Once the sampes were pelleted in the nuclear wash buffer we resuspended in 700 ul of quizol lysis reagent and RNA isolation was complted using an miRNAEasy kit (Quiagen).
For each cell line we sampled both the total RNA in the cell, and the nucear RNA fraction through the ioslated nucleus.
3' RNA seq using Lexogen Rev. QuantSeq & RNA seq using Illumina TruSeq

treatment_protocol: Cells were collected and pelleted at 200 g for 5 min at 4C, washed with cold PBS, then spun again the same way.

value: Imortalized Lymphocyte

tag: Sex

value: M


title: pTotal RNA30_Nuclear RNA

description:
Nuclear RNA
Chimpanzee individuals


title: 3659_Nuclear RNA

description:
Nuclear RNA
Chimpanzee individuals

value: F


title: 3659_Total RNA

description:
Total RNA
Chimpanzee individuals


title: 4973_Total RNA

description:
Total RNA
Chimpanzee individuals


title: pTotal RNA91_Nuclear RNA

description:
Nuclear RNA
Chimpanzee individuals


title: pTotal RNA91_Total RNA

description:
Total RNA
Chimpanzee individuals


title: 4973_Nuclear RNA

description:
Nuclear RNA
Chimpanzee individuals


title: Hippo_Bb-1

city: Grand Forks

first: Danielle

last: Perley

state: North Dakota

address: 1301 N Columbia Rd

institute: University of North Dakota Genomics Core

data_processing:
Adapter sequences were removed using Trimmomatic v0.32 with the paramaters  ILLUMINACLIP:/TruSeq3-SE.fa:2:30:10 LEADING:2 TRAILING:2 SLIDINGWINDOW:4:2 MINLEN:25
RNA-seq reads were mapped to the mouse genome assembly mm10 using STAR aligner v2.7.1a with 2-pass mapping and default parameters. Gene counts were quantified using the subread package featureCounts v1.6.4
Differential expression analysis was performed using DESeq2 v1.24.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include regularized log-transformed (rlog) gene counts for each sample as determined using DESeq2

source_name: Hippocampus

extract_protocol:
Isolated tissues were flash frozen and ground under liquid nitrogen. RNA was extracted using Trizol reagent and Zymo Research Direct-zol RNA minikit (Cat#R2052) using manufacturer's instructions.
NEBNext Ultra II RNA library prep kit (Cat#E7770S) with Poly(A) mRNA magnetic isolation module (Cat#E7490S)was used with ~250ng of total RNA for the construction of sequencing libraries using standard protocols.

value: Hippocampus

value: 7 day B. burgdorrferi infection


title: Hippo_Bb-3


title: Hippo_Bb-4


title: Hippo_Bb-2


title: 3622_Total RNA

description:
Total RNA
Chimpanzee individuals


title: Hippo_UI-4

value: Mock infect


title: Hippo_UI-2


title: Hippo_UI-3


title: 3622_Nuclear RNA

description:
Nuclear RNA
Chimpanzee individuals


title: 18358_Total RNA

description:
Total RNA
Chimpanzee individuals


title: Hippo_UI-1


title: 18358_Nuclear RNA

description:
Nuclear RNA
Chimpanzee individuals


title: Cortex_Bb-4

source_name: Cerebral cortex


title: cerebellum_P8

city: Cambridge

first: Evan

last: Macosko

state: MA

address: 75 Ames St, Broad Institute

institute: Broad Institute

description:
single-nuclei gene expression data
cb_dev_ints.mtx.gz
cb_dev_ints_barcodes.txt
cb_dev_ints_genes.txt
golgi_joint.mtx.gz
golgi_joint_barcodes.txt
golgi_joint_genes.txt
granule_joint.mtx.gz
granule_joint_barcodes.txt
granule_joint_genes.txt
interneuron_joint.mtx.gz
interneuron_joint_barcodes.txt
interneuron_joint_genes.txt
ubc_joint.mtx.gz
ubc_joint_barcodes.txt
ubc_joint_genes.txt

data_processing:
Sequencing performed on Illumina NovaSeq6000
Mouse sequencing reads were demultiplexed and aligned using 10x Cell Ranger software (Ver. 3.0.2) to the mouse reference genome (ENSEMBL Release 78/GRCm38.p3) for each sample individually. Genome_build: mm10
Mouse Digital gene expression matrices (with gene expression counts) were generated by Cell Ranger software (v3.0.2)
Human sequencing reads were demultiplexed and aligned using drop-seq tools to the human reference genome (ENSEMBL Release 78/GRCh37) for each sample individually. The drop-seq pipeline was run using exonic and intronic data as UMIs. The human gene expression matrices were also generated using drop-seq tools (2020-06-17)
Digital gene expression matrices were aggregated and analyzed with Seurat v2.3.4 and liger v0.4.2.
Genome_build: mouse samples: mm10_premrna
Genome_build: human samples: hg19
Supplementary_files_format_and_content: digital gene expression matrix (sparse format): matrix market format, rows = genes/transcripts, columns = barcodes/cells. All files for each set of libraries were included in a tar archive available on the series record.
Supplementary_files_format_and_content: barcodes.txt: names of barcodes/cells for corresponding DGE matrix file
Supplementary_files_format_and_content: genes.txt: names of transcripts/genes for corresponding DGE matrix file
In processed data, human data dropseq tools pipeline used exonic and intronic as UMIS
Developmental mouse cerebellum libraries were aggregated into cb_dev_ints.mtx.gz
Adult mouse cerebellum libraries were aggregated into cb_adult_mouse.mtx.gz.
The file cb_processed_initial.mtx.gz includes all adult mouse cerebellum libraries. Purkinje cell enriched libraries Purk_F004, Purk_F0S1 were removed from cb_processed_initial.mtx.gz (due to batch effects) to create cb_adult_mouse.mtx.gz which was used in subsequent analysis.
Human cerebellum libraries were aggregated into human_combined.mtx.gz
The mouse (adult and developmental) libraries were combined with the human libraries and separated into golgi_joint.mtx.gz (Golgi cells), granule_joint.mtx.gz (Granule Cells), interneuron_joint.mtx.gz (Interneuron cells), and ubc_joint.mtx.gz (Unipolar Brush cells) matrices

source_name: P8 Cerebellum

extract_protocol:
Please see https://www.protocols.io/view/frozen-tissue-nuclei-extraction-for-10xv3-snseq-bi62khge
10X Chromium Single Cell 3' (V3) (manufacturer's protocol)

value: Female

tag: 10x version

tag: genome build


title: Cortex_Bb-3

tag: treatment


title: cerebellum_P4

source_name: P4 Cerebellum


title: cerebellum_P16_2

source_name: P16 Cerebellum


title: Cortex_Bb-1


title: Cortex_Bb-2


title: RH.Tz.B

first: Benedikt

middle: M

last: Markus

address: 455 Main Street

institute: Whitehead Institute

data_processing:
(1) Low-quality reads, and reads aligning to rRNA were filtered using TagDust2 v.2.33 and a curated reference FASTA file containing all rRNA sequences annotated in the ME49 genome assembly (v.45) (-t 4 -dust 97 -fe 3 -1 R:N).
(2) Filtered reads were mapped onto the ME49 genome assembly (v.45) using STAR v.2.7.1a (--runMode alignReads --alignIntronMax 6000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --readMatesLengthsIn NotEqual --alignMatesGapMax 1000 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.04 --outSAMprimaryFlag AllBestScore --clip5pNbases 0 15 --outSAMtype BAM SortedByCoordinate --outSAMorder Paired).
(3) PCR duplicates were flagged within the BAM file using STAR v.2.7.1a (--bamRemoveDuplicatesType UniqueIdentical --runMode inputAlignmentsFromBAM --bamRemoveDuplicatesMate2basesN 15).
(4) Flagged duplicates were removed with SAMtools v.1.10 (samtools view -b -F 0x400).
(5) BedGraph files of 5′ tags were generated from BAM files using STAR v.2.7.1a (--runMode inputAlignmentsFromBAM --outWigType bedGraph read1_5p --outWigNorm None).
(6) Positions of 5′-tag counts in the bedGraph files were shifted 5′ by 4 nt to account for the five chemistry-only cycles at the beginning of the Illumina sequencing.
(7) Absolute 5′-tag counts in the bedGraph files were normalized by dividing counts by the total number of counts per sample, and multiplying by 1,000,000 to generate counts per million.
Genome_build: ToxoDB-45_TgondiiME49
Supplementary_files_format_and_content: bedGraphs of 5′-collapsed read coverage

organism: Toxoplasma gondii

source_name: RH tachyzoites

growth_protocol: Parasites were cultured at 37 °C in human foreskin fibroblasts (HFFs, ATCC SCRC-1041). Tachyzoites from the strains RH and ME49 were maintained at 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM; Gibco) supplemented with 3% or 10% heat-inactivated fetal bovine serum (IFS) and 10 µg/ml gentamicin (Thermo Fisher Scientific), referred to as standard medium. For bradyzoite differentiation, ME49 parasites were grown in HFFs and standard medium, before changing to alkaline-stress medium (RPMI 1640 (Sigma), supplemented with 1% IFS and 10 μg/mL gentamicin, and buffered with 50 mM HEPES, adjusted to pH 8.1 with 10 N NaOH) at 24 h post-infection. Cells were grown for an additional 48 h at 37 °C at ambient CO2 to allow for stage conversion.

extract_protocol:
RH tachyzoites were allowed to egress naturally, while ME49 tachyzoites were mechanically released by passing through a 27-gauge needle. ME49 bradyzoites were mechanically released by serially passing through 27- and 30-gauge needles. Extracellular parasites were passed through a polycarbonate filter with a 3 µm pore size (Whatman). Cell pellets were intermittently stored in TRIzol (Ambion) at -80 ˚C. Total RNA was extracted using MaXtract High Density tubes (Qiagen), following the manufacturer’s instructions. Genomic DNA contamination was removed using the TURBO DNA-free Kit (Invitrogen), following the manufacturer’s protocol (routine DNase treatment).
Libraries were constructed largely following the modifications to the original RAMPAGE protocol (Batut and Gingeras, 2013) as reported in (Adiconis et al., 2018), as detailed in the methods of the accompanying paper.

value: RH

tag: developmental stage

value: tachyzoites

tag: molecule subtype

value: capped mRNA


title: Cortex_UI-4


title: cerebellum_P16_1


title: Cortex_UI-3


title: RH.Tz.A


title: Cortex_UI-2


title: Dura_Bb-4

source_name: Dura mater

value: Dura mater


title: cerebellum_P12_1

source_name: P12 Cerebellum

value: Male


title: cerebellum_P12_2


title: ME49.Tz.A

source_name: ME49 tachyzoites


title: Dura_Bb-2


title: Dura_Bb-1


title: Dura_Bb-3


title: Dura_UI-4


title: ME49.Bz.B

value: bradyzoites


title: ME49.Tz.B


title: cerebellum_E18

source_name: E18 Cerebellum


title: cerebellum_P0

source_name: P0 Cerebellum


title: Dura_UI-3


title: Female1_Xb

description:
single-nuclei gene expression data
cb_adult_mouse.mtx.gz
cb_adult_mouse_barcodes.txt
cb_adult_mouse_genes.txt
golgi_joint.mtx.gz
golgi_joint_barcodes.txt
golgi_joint_genes.txt
granule_joint.mtx.gz
granule_joint_barcodes.txt
granule_joint_genes.txt
interneuron_joint.mtx.gz
interneuron_joint_barcodes.txt
interneuron_joint_genes.txt
ubc_joint.mtx.gz
ubc_joint_barcodes.txt
ubc_joint_genes.txt

source_name: P60 Cerebellum


title: Dura_UI-2


title: Dura_UI-1


title: ME49.Bz.A


title: Male6_Xa


title: YTHDF_NP3_Df_3Whead_rep4

city: New York

first: Brian

last: Joseph

state: New York

address: 430 E 67th St

department: Department of Developmental Biology

institute: Sloan-Kettering Institute

description: w;YTHDF[NP3]/DF, 3week,female head, n=4

data_processing:
miCLIP-seq: Adapters and low quality reads were trimmed using flexbar v2.5. FASTQ files were de-multiplexed using the pyBarcodeFilter.py script from the pyCRAC suite. Random barcodes were removed from sequencing reads and appended to sequence IDs using an awk script and PCR duplicates were removed using the pyCRAC pyDuplicateRemover.py script. Paired end reads were merged and mapped to the Drosophila reference genome sequence (BDGP Release 6/dm6) using Novoalign (Novocraft) with parameters –t 85 and -l 16. Mutations were called using the CIMS software package (Zhang and Darnell, 2011). To identify putative m6A sites, C-to-T transitions with preceding A nucleotides were extracted and filtered such that the number of mutations that support the mismatch (m) > 1 and 0.01 < m/k < 0.5, where k is the number of unique tags that span the mismatch position. Peaks were called by adapting the Model-based Analysis for ChIP-Seq (MACS) algorithm (Zhang et al., 2008). Mettl3-dependent peaks for head libraries were determined using miCLIP versus input, comparing wild type and mettl3 libraries and the MACS2 differential binding events program (bdgdiff) with parameters -g 20 and -l 120. Lastly, peaks were split using PeakSplitter (version 1.0, http://www.ebi.ac.uk/research/bertone/software).
RNA-seq: RNA sequencing libraries were mapped to the Drosophila reference genome sequence (BDGP Release 6/dm6) using HISAT2 (Kim et al., 2015) under the default settings. Gene counts were obtained by assigning and counting reads to the Ensembl transcript models for BDGP6.94 using Rsubread (Liao et al., 2013). Differential gene expression analysis was performed with comparisons as listed in Supplementary Table 5 using the R package DESeq2 (Love et al., 2014) and applying a strict adjusted p-value cutoff of 0.05.
Genome_build: BDGP Release 6/dm6
Supplementary_files_format_and_content: bigwig files

source_name: female head

extract_protocol:
Briefly, total RNA was collected from <1 week old w1118 (wild type) and mettl3[null] (mutant) female heads using TRIzol RNA extraction.
miCLIP: Poly(A)+ RNA was enriched using two rounds of selection.RNAs were fragmented, incubated with the α-m6A (202 003 Synaptic Systems) and crosslinked twice in a Stratalinker 2400 (Stratagene) using 150 mJ per cm2. Crosslinked RNAs were immunoprecipitated using Protein A/G magnetic beads (Thermo) and washed under high salt conditions to reduce non-specific binding. Samples were radiolabeled with T4 PNK (NEB), ligated to a 3' adaptor using T4 RNA Ligase I (NEB), and purified using SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and nitrocellulose membrane transfer. RNA fragments containing crosslinked antibody peptides were recovered from the membrane using proteinase K (Invitrogen) digestion. Recovered fragments were subjected to library preparation. First-strand cDNA synthesis was performed using SuperScript III (Life Technologies) and iCLIP-barcoded primers, which contain complementarity to the 3' adaptor on the RNA. cDNAs were purified using denaturing PAGE purification, circularized using CircLigase II (EpiCentre), annealed to the iCLIP Cut Oligo, and digested using BamHI (Thermo). To generate libraries for sequencing, the resulting linear cDNAs were amplified using Accuprime SuperMix I (Invitrogen) and P5 and P3 Solexa primers, and purified using Agencourt AMPure XP beads (Beckman Coulter). For input libraries, poly(A)+ RNAs were fragmented and directly subjected to radiolabelling and 3' adaptor ligation. All subsequent steps are as listed above. Libraries were paired-end sequenced on an Illumina HiSeq2500 instrument at the New York Genome Center (NYGC). RNA-seq: Sequencing libraries were prepared using the TruSeq Stranded Total RNA Sequencing Kit (Illumina) following the manufacturer’s protocol
miCLIP-seq and RNA-seq

value: head

value: 3 week


title: YTHDF_NP3_Df_3Whead_rep3

description: w;YTHDF[NP3]/DF, 3week,female head, n=3


title: Female1_Xa


title: Cortex_UI-1

value: Cerebral cortex


title: YTHDF_NP3_Df_3Whead_rep2

description: YTHDF[NP3]/Df, 3 week, n=2


title: YTHDF_Df_het_3Whead_rep3

description: w;YTHDF-DF/+, 3week,female head,n=3


title: Male1_X


title: YTHDF_NP3_Df_3Whead_rep1

description: YTHDF[NP3]/Df, 3 week, n=1


title: Male2_VIe


title: Male6_VIc


title: YTHDF_Df_het_3Whead_rep2

description: w;YTHDF-DF/+, 3week,female head,n=2


title: YTHDF_Df_het_3Whead_rep1

description: w;YTHDF-DF/+, 3week,female head, n=1


title: P3Srg170dcKOhGFAPCortexWT_4

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

institute: German Center for Neurodegenerative Diseases (DZNE)

description: P3Srg170dcKOhGFAPCortexWT_mm_rna_sr_kerimogluc_C_4_S41_L007

data_processing:
Base calling and fastq conversion were performed using Illumina pipeline scripts.
Reads were mapped to mouse genome mm10.
The reads were counted using FeaturesCount.
Genome_build: mm10
Supplementary_files_format_and_content: Count files

source_name: P3 cortex_control

extract_protocol:
RNA was isolated using TRIZOL.
Libraries were prepared using Illumina TruSeq RNA Sample Preparation v2 Kit.

value: Control

tag: age/tissue

value: P3 cortex


title: Male2_VId


title: P3Srg170dcKOhGFAPCortexWT_3

description: P3Srg170dcKOhGFAPCortexWT_mm_rna_sr_kerimogluc_C_3_S37_L006


title: YTHDF_NP3_Df_1Whead_rep2

description: YTHDF[NP3]/Df, 1 week, n=2

value: 1 week


title: P3Srg170dcKOhGFAPCortexWT_2

description: P3Srg170dcKOhGFAPCortexWT_mm_rna_sr_kerimogluc_C_2_S33_L005


title: Male2_VIc


title: YTHDF_NP3_Df_1Whead_rep1

description: YTHDF[NP3]/Df, 1 week, n=1


title: YTHDF_Df_het_1Whead_rep1

description: YTHDF-Df/+, 1 week, n=1


title: YTHDF_Df_het_1Whead_rep3

description: YTHDF-Df/+, 1 week, n=3


title: P3Srg170dcKOhGFAPCortexWT_1

description: P3Srg170dcKOhGFAPCortexWT_mm_rna_sr_kerimogluc_C_1_S29_L005


title: w_Ime4_null_dCat_Fem_Head_3W_rep3

description: w;mettl3[null]/mettl3[cat], 3week,female head,n=3


title: w_Ime4_null_dCat_Fem_Head_3W_rep2

description: w;mettl3[null]/mettl3[cat], 3week,female head,n=2


title: 9485T1_Liver tumor_Trp53-/-

type: genomic

city: Ulm

first: André

last: Lechel

address: Albert-Einstein-Allee 23

department: Department of Internal Medicine I

institute: University hospital Ulm

hyb_protocol: Labeled DNA Samples were hybridized for 24 hours at 67°C and 20 rpm rotation speed according to manufacturer´s protocol (Agilent Technologies, Santa Clara, CA, USA).

scan_protocol: Microarray slides were scanned using a G2565CA microarray scanner (Agilent Technologies, Santa Clara, CA, USA).

data_processing: The scanned images were analyzed with the Feature Extraction Software 10.7.3.1 (Agilent).

source_name: liver tumor

label_protocol: 1µg of the isolated genomic DNA was digested and labeled by random primer with Cyanine 5-UTP (liver tumor) or Cyanine 3-UTP (reference: liver) using the Agilent Genomic DNA Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer´s protocol.

growth_protocol: The animals were maintained in a specific pathogen-free environment with food and water ad libitum. Mice were housed in individually ventilated cages with a 12 hour day/night cycle.

extract_protocol: Genomic DNA was isolated from liver and liver tumor tissue according to standard phenol-chloroform extraction protocol.

treatment_protocol: non treated mice

tag: gender

value: male

value: liver tumor

source_name: spleen

value: spleen


title: P3Srg170dcKOhGFAPCortexMUT_4

description: P3Srg170dcKOhGFAPCortexMUT_mm_rna_sr_kerimogluc_M_4_S42_L007

source_name: P3 cortex_BAF cKO

value: BAF cKO


title: 297T1_Liver tumor_Trp53-/-


title: Male2_VIb


title: w_Ime4_null_dCat_Fem_Head_3W_rep1

description: w;mettl3[null]/mettl3[cat], 3week,female head,n=1


title: P3Srg170dcKOhGFAPCortexMUT_3

description: P3Srg170dcKOhGFAPCortexMUT_mm_rna_sr_kerimogluc_M_3_S38_L006


title: YTHDF_NP3_Df_1Whead_rep3

description: YTHDF[NP3]/Df, 1 week, n=3


title: w_Ime4_null_het_Fem_Head_3W_rep3

description: w;mettl3[null]/+, 3week,female head,n=3


title: w_Ime4_null_het_Fem_Head_3W_rep2

description: w;mettl3[null]/+, 3week,female head, n=2


title: YTHDF_Df_het_1Whead_rep2

description: YTHDF-Df/+, 1 week, n=2


title: 9849T11_Liver tumor_Trp53-/-


title: 987T5_Liver tumor_Trp53-/-


title: Male6_VIa


title: Male2_VIa


title: w_Ime4_null_dCat_Fem_Head_1W_rep3

description: w;mettl3[null]/mettl3[cat], 1week,female head, n=3


title: w_Ime4_null_dCat_Fem_Head_1W_rep2

description: w;mettl3[null]/mettl3[cat], 1week,female head, n=2


title: Male6_VIb


title: Male6_VI


title: w_Ime4_null_dCat_Fem_Head_1W_rep1

description: w;mettl3[null]/mettl3[cat], 1week,female head, n=1


title: w_Ime4_null_het_Fem_Head_1W_rep2

description: w;mettl3[null]/+, 1week,female head, n=2


title: Female1_VI

value: Female


title: LC3-IR3-3

city: Suzhou

first: Qiu

last: Chen

address: 199 Renai Road

institute: Soochow University

data_processing:
3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3)
 aligned to the reference genome (UCSC MM10) with hisat2 software (v2.0.4)
Cuff links calculates the reads matched to each gene and standardizes the count using the length of each gene. The commonly used fpkm (fragments per kilobase of transcript per million mapped fragments) ensures that the expression levels of different genes can be compared. The expressions in two or more samples were calculated using the cuff diff software (part of the cuff links software).
Genome_build: UCSC MM10
Supplementary_files_format_and_content: FPKM ,counts

source_name: lung

extract_protocol:
lungs were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Total RNA (1 μg) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) for the construction of sequencing libraries.
RNA libraries were constructed with TruSeq Stranded Total RNA Library Prep Kit.
10 pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer.

treatment_protocol: NC:sham irradiation; IR1:whole brain X-ray 10Gy(2Gy/min) ;IR3:whole brain X-ray 10Gy(2Gy/min) *3 times, once a week, for 3 weeks

value: whole brain 10Gy *3, once a week, for 3 weeks

value: lung


title: LC3-IR3-2


title: WT head input

description: wt head input

value: adult <1 week old

tag: m6a antibody


title: mettl3 head miCLIP

description: mettl3 head miclip

value: α-m6A (202 003 Synaptic Systems)


title: Male2_VIId

tag: strain

value: Male


title: P3Srg170dcKOhGFAPCortexMUT_2

description: P3Srg170dcKOhGFAPCortexMUT_mm_rna_sr_kerimogluc_M_2_S34_L005


title: w_Ime4_null_het_Fem_Head_1W_rep1

description: w;mettl3[null]/+, 1week,female head, n=1

tag: tissue


title: WT head miCLIP

description: wt head miclip


title: LC3-IR3-1


title: Male2_VIIc

description:
single-nuclei gene expression data
cb_adult_mouse.mtx.gz
cb_adult_mouse_barcodes.txt
cb_adult_mouse_genes.txt
golgi_joint.mtx.gz
golgi_joint_barcodes.txt
golgi_joint_genes.txt
granule_joint.mtx.gz
granule_joint_barcodes.txt
granule_joint_genes.txt
interneuron_joint.mtx.gz
interneuron_joint_barcodes.txt
interneuron_joint_genes.txt
ubc_joint.mtx.gz
ubc_joint_barcodes.txt
ubc_joint_genes.txt

tag: age


title: LC3-IR1-3

value: whole brain 10Gy


title: mettl3 head input

description: mettl3 head input

value: head


title: Male6_VIIb


title: HuT78VR, SHC030

city: Singapore

first: Kizhakeyil

last: Atish

state: Singapore

address: Mandalay road 11

country: Singapore

institute: Nanyang Technological University

data_processing:
Sequenced reads were trimmed using Cutadapt to remove low quality sequence
Trimmed reads were mapped onto hg38 using STAR package
Number of reads per annotated gene was determined using featurecounts
DESeq2 was performed to determine the differential gene expression (q-value<0.05 & abs(log2FC)>1.5)
Gene Ontology & Gene Set Enrichment Analysis was executed to draw biological conclusion
Genome_build: hg38
Supplementary_files_format_and_content: counts

source_name: Cutaneous T cell Lymphoma cells from ATCC

growth_protocol: HuT78 were grown in RPMI medium supplemented with sodium pyruvate (100mM) and were maintained in cell T75 cm2 flask(1X10^6 cells/mL). HuT78VR were grown in RPMI medium supplemented with sodium pyruvate (100mM) and were maintained in cell T75 cm2 flask(1X10^6 cells/mL). The HuT78VR cells were passaged and grown under selective pressure of vorinostat (5 µM ).

extract_protocol:
Total RNA was isolated from the cells using RNeasy Plus Mini Kit (catalougue number 74134) according to manufacturers instructions.
Libraries were prepared according to illumina Stranded mRNA-Seq.

treatment_protocol: HuT78 and HuT78VR (1X 10^6), seeded on 6 well plates and were subjected to cell lysis for total RNA extraction after 48 hrs. HuT78 (1X 10^6) cells were seeded in 6 well plate and were treated with 2 µM vorinostat for a period of 48 hours and total RNA was extracted.

value: Cutaneous T cell Lymphoma

tag: cell line

value: The HuT78VR cells were grown in media containing vorinostat (5 µM)


title: HuT78, SHC032

tag: cell type

value: The HuT78 cells were treated with vorinostat (2 µM) for 48 hours


title: HuT78VR, SHC033


title: w_Ime4_null_het_Fem_Head_1W_rep3

description: w;mettl3[null]/+, 1week,female head, n=3


title: P3Srg170dcKOhGFAPCortexMUT_1

description: P3Srg170dcKOhGFAPCortexMUT_mm_rna_sr_kerimogluc_M_1_S30_L005

value: P3 cortex


title: HuT78, SHC029


title: HuT78, SHC031

value: Control


title: LC3-IR1-2


title: HuT78, SHC028


title: Female2_VIIb


title: LC3-NC-3

value: sham IR


title: LC3-NC-2


title: ProteinE_1_i2

city: Shenzhen

first: Ruilin

last: Tian

address: 1088 Xueyuan Avenue

institute: SUSTech

description:
ProteinE_1_S96_L005
Quant-seq

data_processing:
Raw sequencing reads from QuantSeq were trimmed using Trimmomatic (v0.39)
Salmon v1.3.0 was used to obtain transcript abundance counts
Gene-level count estimates were obtained using tximport  (v1.18.0) with default settings
differential gene-expression analyses were performed using the glmQLFTest method implemented in the edgeR package(v3.28.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data files are in "CSV(Comma-separated values)" format. Each row is a gene and each column is a sample. Values are normalzied counts

source_name: Calu-3_ProteinE overexpression

extract_protocol:
RNA was extracted from cells using the Quick-RNA Miniprep Kit (Zymo; Cat. No. R1054)
Libraries were generated according to the Quantseq protocol

value: ProteinE overexpression

tag: sequencing run


title: ProteinE_2_i1

description:
ProteinE_2_S104_L005
Quant-seq


title: ProteinE_2_i2

description:
ProteinE_2_S13
Quant-seq


title: Male6_VIIa


title: Male2_VIIa


title: LC3-NC-1


title: Female2_VIIa


title: Female2_VIIId


title: Female2_VIIIc


title: Male2_VIIb


title: LC3-IR1-1


title: Male1_VIIIb


title: Female2_VIIIb


title: Female2_VIIIa


title: Human_Cerebellum_Donor_5556

description:
single-nuclei gene expression data
human_combined.mtx.gz
human_barcodes.txt
human_genes.txt
golgi_joint.mtx.gz
golgi_joint_barcodes.txt
golgi_joint_genes.txt
granule_joint.mtx.gz
granule_joint_barcodes.txt
granule_joint_genes.txt
interneuron_joint.mtx.gz
interneuron_joint_barcodes.txt
interneuron_joint_genes.txt
ubc_joint.mtx.gz
ubc_joint_barcodes.txt
ubc_joint_genes.txt

source_name: Human Cerebellum


title: Male6_VI2c


title: Human_Cerebellum_Donor_4862