title: wt_YPD_TrAEL-seq

first: Felix

last: Krueger

address: Granta Park

institute: Altos Labs

description: other_yeast_samples_reverse_read_percentage_in_1kb_windows.txt

data_processing:
Sequencing data was processed with a custom script (location available from the manuscript) to transfer the first 8bp of a each sequence to the readID of the FastQ file (UMI, unique molecular identifier). In addition, up to and including 3 T bases were removed from the 5'-end following the UMI transfer. The resulting FastQ files were trimmed with Trim Galore (v0.6.5) to remove read-through contamination with the Illumina standard adapter as well as poor base call qualities (cutoff: Phred 20). Trimmed reads were then aligned to the relevant genomes using Bowtie2 (v2.4.1) in --local mode. Following the alignments, reads were de-duplicated taking UMIs as well as mapping position into account, using UmiBam (v0.2.0; https://github.com/FelixKrueger/Umi-Grinder).
Samples were imported into Seqmonk v1.47, truncated to a single base and quantified in windows: for dmc1 total read counts in 20bp windows, for hESC %reverse reads in 250kb windows every 10kb, for SfiI digests total read counts at 13bp cleavage sites, for other samples %reverse reads in 1kb windows
Genome_build: S. cerevisiae R64-1-1 or GRCh38

extract_protocol:
For yeast: Cells in ethanol (1-3x107 per plug) were pelleted in round bottom 2 ml tubes by centrifuging 30 s 20,000 g, washed once in 1 ml PFGE wash buffer (10 mM Tris HCl pH 7.5, 50 mM EDTA) and resuspended in 60 µl same with 1 µl lyticase (17 U/ µl in 10 mM KPO4 pH7, 50% glycerol, Merck >2000 U/mg L2524). Samples were heated to 50°C for 1-10 min before addition of 40 µl molten CleanCut agarose (Bio-Rad 1703594), vortexing vigorously for 5 s before pipetting in plug mould (Bio-Rad 1703713) and solidifying 15-30 min at 4°C. Each plug was transferred to a 2 ml tube containing 500 µl PFGE was buffer containing 10 µl 17 U/µl lyticase and incubated 1 hour at 37°. Solution was replaced with 500 µl PK buffer (100 mM EDTA pH 8, 0.2% sodium deoxycholate, 1% sodium N-lauroyl sarcosine, 1 mg/ml Proteinase K) and incubated overnight at 50°. Plugs were rinsed with 1 ml TE, then washed three times with 1 ml TE for 1-2 hours at room temperature with rocking, 10 mM PMSF was added to the second and third washes from 100 mM stock (Merck 93482). Plugs were then digested 1 h at 37°C with 1 µl 1000 U/ml RNase T1 (Thermo EN0541) in 200 µl TE. RNase A was not used as it binds strongly to single stranded DNA [76]. For hESC: 1x106 cells were washed once in 5 ml L buffer (10 mM Tris HCl pH 7.5, 100 mM EDTA, 20 mM NaCl) and resuspended in 60 µl L buffer in a 2 ml tube. Samples were heated to 50°C for 2-3 min before addition of 40 µl molten CleanCut agarose (Bio-Rad 1703594), vortexing vigorously for 5 s before pipetting in plug mould (Bio-Rad 1703713) and solidifying 15-30 min at 4°C. Each plug was transferred to a 2 ml tube containing 500 µl digestion buffer (10 mM Tris HCl pH 7.5, 100 mM EDTA, 20 mM NaCl, 1% sodium N-lauroyl sarcosine, 0.1 mg/ml Proteinase K) and incubated overnight at 50°. Washing as for yeast.
TrAEL-seq: ½ an agarose plug of cells was equilibrated once in 100 µl 1x TdT buffer (NEB) for 30 min at room temperature, then incubated for 2 h at 37°C in 100 µl 1x TdT buffer containing 4 µl 10 mM ATP and 2 µl Terminal Transferase (NEB M0315L). Plugs were rinsed with 1 ml tris buffer (10 mM Tris HCl pH 8.0), equilibrated in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000 for 1 hour at room temperature then incubated overnight at 25°C in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000, 1 µl 10 pM/µl TrAEL-seq adaptor 1 ([App]NNNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTUGCGCAGGCCATTGGCC[BtndT]GCGCUACACTCTTTCCCTACACGACGCT) and 1 µl T4 RNA ligase 2 truncated KQ (NEB M0373L). Plugs were then rinsed with 1 ml tris buffer, transferred to 15 ml tubes and washed three times in 10 ml tris buffer with rocking at room temperature for 1-2 hours each, then washed again overnight under the same conditions. Plugs were equilibrated for 15 min with 1 ml agarase buffer (10 mM Bis-Tris-HCl, 1 mM EDTA pH 6.5), then the supernatant removed and 50 µl agarase buffer added. Plugs were melted for 20 min at 65°C, transferred for 5 min to a heating block pre-heated to 42°C, 1 µl β-agarase (NEB M0392S) was added and mixed by flicking without allowing sample to cool, and incubation continued at 42°C for 1 h. DNA was ethanol precipitated with 25 µl 10 M NH4OAc, 1 µl GlycoBlue, 330 µl of ethanol and resuspended in 10 µl 0.1xTE. 40 µl reaction mix containing 5µl Isothermal amplification buffer (NEB), 3 µl 100 mM MgSO4, 2µl 10 mM dNTPs and 1µl Bst 2 WarmStart DNA polymerase (NEB M0538S) was added and sample incubated 30 min at 65°C before precipitation with 12.5 µl 10 M NH4OAc, 1 µl GlycoBlue, 160 µl ethanol and re-dissolving pellet in 130 µl 1xTE.  END-seq: ½ an agarose plug of cells was equilibrated for 1 h at room temperature in 100µl NEBuffer 2 with 0.1mM dNTPs, then overnight at 37°C with 100 µl NEBuffer 2 with 0.1 mM dNTPs and 1 µl Klenow (NEB M0210S). Note that this is not the same blunting regimen used in END-seq [11] as Klenow performed best for SfiI-digested yeast genomic DNA in our hands. After rinsing twice with 1 ml tris buffer, plug was transferred to a 15 ml tube and washed three times for 15 min each with 10 ml tris buffer on rocker at room temperature before transfer to a new 2 ml tube. The plug was equilibrated with 100 µl CutSmart buffer containing 5 mM DTT and 1 mM dATP for 1 hour at room temperature before incubation for 2 h at 37°C in another 100 µl of the same buffer containing 1 µl Klenow exo- (NEB M0212S) and 1 µl T4 PNK (NEB M0201S). Plug was rinsed twice with 1 ml tris buffer then washed once with 10 ml of tris buffer for 15 min as above then returned to a 2 ml tube. The plug was equilibrated for 1 h at room temperature in 100 µl 1x Quick Ligation buffer (NEB B6058S) containing 2.7 µl END-seq adaptor 1 ([Phos]GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGUU[BtndT]U[BtndT]UUACACTCTTTCCCTACACGACGCTCTTCCGATC∗T), then overnight at 25°C with another 100 µl of the same buffer containing  2.7 µl END-seq adaptor 1 and 1 µl high concentration T4 DNA Ligase (NEB M0202M). After rinsing twice with 1 ml tris buffer, plug was transferred to a 15 ml tube and washed three times for 1-2 h each with 10 ml tris buffer on rocker at room temperature, then again overnight.  The plug was transferred to a 1.5 ml tube and equilibrated 15 min with 1 ml agarase buffer (10 mM Bis-Tris-HCl, 1 mM EDTA pH 6.5), then the supernatant removed and 50 µl agarase buffer added to the plug. Plug was melted 20 min at 65°C then transferred for 5 min to a heating block pre-heated to 42°C, 1 µl beta-agarase (NEB M0392S) was added and mixed by flicking without allowing sample to cool, and incubation continued at 42°C for 1 h. DNA was ethanol precipitated with 25 µl 10 M NH4OAc, 1 µl GlycoBlue, 330 µl of ethanol and resuspended in 130 µl 1x TE, 15 min at 65°C.
The DNA was transferred to an AFA microTUBE (Covaris 520045) and fragmented in a Covaris E220 using duty factor 10, PIP 175, Cycles 200, Temp 11, then transferred to a 1.5 ml tube containing 8 µl pre-washed Dynabeads MyOne streptavidin C1 beads (Thermo, 65001) re-suspended in 300 µl 2xTN (10 mM Tris pH 8, 2 M NaCl) along with 170 µl water (total volume 600 µl) and incubated 30 min at room temperature on a rotating wheel. Beads were washed once with 500 µl 5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl, 5 min on wheel and once with 500 µl 0.1x TE, 5 min on wheel before re-suspension in 25 µl 0.1x TE. 3.5 μl NEBNext Ultra II End Prep buffer, 1 µl 1 ng/µl sonicated salmon sperm DNA (this is added as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. After cooling, 1.25 µl 10 pM/µl TrAEL-seq adaptor 2 ([Phos]GATCGGAAGAGCACACGTCTGAACTCCAGTCUUUUGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T ) or END-seq adaptor 2c ([Phos]GATCGGAAGAGCTATTATTTAAATTTTAATTUGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T), 0.5 µl NEBNext ligation enhancer and 15 µl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature. The reaction mix was removed and discarded and beads were rinsed with 500 µl wash buffer (5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl) then washed twice with 1 ml wash buffer for 10 min on wheel at room temperature and once for 10 min with 1 ml 0.1x TE. Libraries were eluted from beads with 11 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°C, then again with 10.5 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°, and the two eluates combined. An initial test amplification was used to determine the optimal cycle number for each library. For this, 1.25 μl library was amplified in 10 µl total volume with 0.4 µl each of the NEBNext Universal and any NEBNext Index primers with 5 µl NEBNext Ultra II Q5 PCR master mix. Cycling program: 98°C 30s then 18 cycles of [98°C 10 s, 65°C 75 s], 65°C 5 min. Test PCR was cleaned with 8 µl AMPure XP beads (Beckman A63881) and eluted with 2.5 µl 0.1x TE, of which 1 µl was examines on a Bioanalyser high sensitivity DNA

tag: growth and treatment

value: YPD

tag: fix and post-processing

value: 70% ethanol


title: in_R3c: Input RNA Clean air control

status: Public on Jul 27 2020

type: SRA

city: Austin

first: Lydia

middle: M

last: Contreras

state: TX

address: 200 E. Dean Keeton St Stop C0400

department: McKetta Department of Chemical Engineering

country: USA

institute: University of Texas at Austin

library_source: transcriptomic

data_processing:
Illumina HiSeq 4000 Real-Time Analysis (RTA v2) basecalling
Sequence reads were trimmed for adaptor sequence using Trimmomatic 0.36, followed by quality check using FastQC
Reads were aligned to Ensembl comprehensive human genome annotation (GENCODE 26, GRCh38.p10) using STAR 2.5.3a, allowing novel splice junctions and using a two-pass mapping approach. Alignment was performed using parameters recommended in the STAR manual for ENCODE standards
RSEM was used to estimate transcript abundances and then differential expression and 8-oxoG enrichment  were performed using DESeq2 in R version 3.4.0.
Transcripts were annotated using biomaRt in R.
Genome_build: GRCh38.p10

molecule: total RNA

organism: Homo sapiens

source_name: BEAS-2B cells

growth_protocol: Cell cultures for exposures (passage 3 from parent stock) were initiated from T75 cultures incubated for 4 days in complete Bronchial Epithelial Cell Growth medium (BEGM, Lonza, Walkersville, MD) with a 70-80% confluency. Cells were passaged to collagen-coated inserts (30 mm diameter, hydrophilic PTFE with pore size of 0.4 µm, EMD Millipore, Burlington, MA) housed in 6-well plates (Corning Costar Clear Multiple Well Plates, Corning, NY) with a seeding density of 200,000 cells and incubated for 24 hours with 0.8 ml and 1.1 ml of medium in the apical and basolateral side, respectively. Cell culture inserts were coated with 1 ml of 57 µg/ml of Bovine Collagen Type I (Advanced BioMatrix, Carlsbad, CA) in BEGM at least 24 h before seeding. Two hours before exposure, the medium from the apical cell surface was completely removed, and the medium from the basolateral cell surface was renewed with fresh complete medium.

extract_protocol:
Following exposure, each insert membrane was treated with 1 ml of TRIzol in the apical side and gently mixed to ensure thorough lysis. The whole lysate was collected and frozen until the day of the extraction. TRIzol RNA extraction was conducted following TRIzol’s manufacturer instructions. To prevent artificial oxidation of RNA by dissolved oxygen in solutions, ethanol (200 Proof, OmniPur, EMD Millipore, Burlington, MA), isopropanol (molecular biology grade, IBI Scientific, Dubuque, IA) and nuclease-free water (Ambion, Austin, TX) used in the downstream steps after TRIzol were purged with ultra-high purity N2 for 30 min.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells adhered to membrane inserts housed in 6-well plates (with lid off) were exposed in a modular cell exposure chamber (MIC-101 Billups-Rothenberg, San Diego, CA) to an air pollution mixture (generated from the reaction of 790 ppb acrolein, 670 ppb methacrolein, and 4 ppm ozone) for 1.5 hours. Before the cell exposure chamber, 1.52 LPM (litters per minute) of the air pollution mixture was mixed with 0.08 LPM CO2 (5% final concentration).

tag: cell type

value: BEAS-2B cells (ATCC CRL-9609)

tag: tissue

value: Lung, bronchus

tag: disease

value: Normal

tag: rip antibody

tag: passages


title: SeViPS(HU)-derived vascular endothelial cells lot #1

type: RNA

city: Shinjuku-ku

first: Kumiko

last: Saeki

state: Tokyo

address: 1-21-1 Toyama

department: Department of disease control

country: Japan

institute: National Center for Global Health and Medicine

hyb_protocol: Cy3-labelled RNA was fragmented at 100oC for 5 minutes in a reaction volume of 45 ul containing Hyb Spike In and Agilent blocking agent following the manufacturers instructions. 28 ul of Agilent hybridization buffer was added to 17 uL of total RNA solution and hybridized to Agilent Human miRNA Microarray (8x60K) Rel19.0 (G4872A) for 17 hours at 55oC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 046064_D_F_20141006) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: lot 1 of vascular endothelial cells generated from human iPS line that was produced from HUVEC by using a Sendai virus vector

label_protocol: Cyanine-3 (Cy3) labeled total RNA was prepared from 0.1 ug RNA using the One-Color MicroArray-Based miRNA Analysis(miRNA Complete Labeling Reagent and Hyb Kit). 0.1 ng of total RNA samples was dephosphorylated, labeled with Cy3-pCp, purified on Micro Bio-Spin columns, dried.

growth_protocol: Primary cultured human vascular endothelial cells (VECs) were cultured on 0.1% gelatin-coated plates using EGM®-2 BulletKit (Lonza Group Ltd. Basel, Switzerland) and human embryonic stem (ES)/iPS-derived VECs were cultured on 0.1% gelatin-coated plates using VEC-differentiation medium (Nakahara M et al., Cloning Stem Cells 11: 509-522, 2009). Cells were subcultured at split ratios of 1:2 ~ 1:3 twice a week.

extract_protocol: Total RNAs were isolated by using miRNeasy Mini Kit (Cat# 217004, Qiagen, Hilden, Germany) following the manufacturer's protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: sample group

value: Type-II VECs

value: SeViPS(BJ)-derived vascular endothelial cells


title: KhES1-derived vascular endothelial cells at early passages

description: young ES(KhES1)dEC

hyb_protocol: Cy3-labelled RNA was fragmented at 100oC for 5 minutes in a reaction volume of 45 ul containing Hyb Spike In and Agilent blocking agent following the manufacturers instructions. 28 ul of Agilent hybridization buffer was added to 17 uL of total RNA solution and hybridized to Agilent Human miRNA Microarray (8x60K) Rel21.0 (G4872A) for 17 hours at 55oC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 070156_D_F_20141006) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: human ES cell (KhES-1)-derived vascular endothelial cells (at passage 2)


title: KhES3-derived vascular endothelial cells at later passages

description: aged ES(KhES3)dEC

source_name: human ES cell (KhES-3)-derived vascular endothelial cells (at passage 3)

value: Type-I VECs


title: SS 6 h rep1

city: Shenzhen

first: Xuemei

last: Mao

address: Baishi Road

department: IAS

country: China

institute: Shenzhen University

data_processing:
Zebra process software (version 0.5.0.13875) was used for basecalling.
Data was filtered by software SOAPnuke (version v1.5.2, parameters -l 15 -q 0.5 -n 0.1) to remove reads with adaptors, unknown bases (more than 10%), and low quality reads.
HISAT (version v2.0.4) was used to do the genome mapping, and clean reads were mapped to reference genes using Bowtie2 (version v2.2.5).
Gene expression level (FPKM) was calculated with RSEM software (version v1.2.12)
Genome_build: Chromochloris zofingiensis v5.2.3.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

organism: Chromochloris zofingiensis

source_name: microalgae

growth_protocol: Chromochloris zofingiensis  were grown in 250 ml columns of photoreactor with 80 μE m-2 s-1 continuous illumination and 1.5% CO2 enriched air.

extract_protocol:
Total RNA was extracted  using the plant RNA extraction kit (TaKaRa, Japan) and poly-A  mRNA was purified using poly-T oligo-attached magnetic beads.
The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers, which was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then had the addition of a single 'A' base and subsequent ligation of the adapter. The products were purified and enriched with PCR amplification. The PCR yield was quantified by Qubit, and samples were pooled together to make a single strand DNA circle (ssDNA circle), which gave the final library.

tag: strain

tag: time point


title: BC04,192h

city: Beijing

first: pinjiao

last: jin

address: No. 2 Yuanmingyuan West Road

department: Institute of Plant Protection

institute: Chinese Academy of Agricultural Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
Genomic localization analysis of sequence using Bowtie 2.2.3
Expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were estimation of gene expression level (Trapnell, Cole, et al., 2010)
Genome_build: GCF_000092385.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Streptomyces bingchenggensis

source_name: Soil

extract_protocol:
The mycelia were collected,flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: High-yielding strain


title: KhES1-derived vascular endothelial cells at later passages

description: aged ES(KhES1)dEC

source_name: human ES cell (KhES-1)-derived vascular endothelial cells (at passage 5)


title: SeViPS(HU)-derived vascular endothelial cells lot #3

source_name: lot 3 of vascular endothelial cells generated from human iPS line that was produced from HUVEC by using a Sendai virus vector


title: Human brain microvascular endothelial cells

description: HBVEC


title: mCherry - 2

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Illumina bcl2fastq2 v2.19 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human hg19 reference genome using STAR v2.5.2b.
Raw reads counts were extracted using htseq-count v0.6.1.
Differential expression analysis was performed by using DESeq2 package v1.6.3.
Genome_build: hg19
Supplementary_files_format_and_content: excel file including gene name, Ensembl gene id, normalized read counts (log scale) for each gene in each sample

source_name: brown adipocyte

growth_protocol: UCP1::mCherry H1 hES cells were differentiated according to a published protocol (Ahfeldt et al., 2012). Briefly, reporter cells were placed into suspension culture to form embryoid bodies for 7 days, after which embryoid bodies were plated onto 0.1% gelatin coated dishes with DMEM supplemented with 10% FBS and 10 µg/mL bFGF to promote mesenchymal cell outgrowth. After reaching 90% confluency, cells were trypsinized and passaged for 4-5 rounds prior to plating for infection with doxycycline inducible PPARγ, CEBPβ, and PRDM16 lentiviral constructs. These cells were placed into adipogenic medium containing KOSR, dexamethasone, insulin, and rosiglitazone, along 700 ng/mL doxycycline for 14 days. Finally, doxycycline was removed and the cells were allowed to mature for another 6 days or longer as experiments required.

extract_protocol:
For isolation of mCherry positive and negative cells for RNA-seq, differentiated cells were digested with 0.25% trypsin for 15 minutes until cells detached from plates. Cells were then digested with Liberase TM (Sigma, #5401119001) at 0.04 µg/mL in 2% BSA/DPBS on a rocking shaker at 37 degrees for 1 hour. Cell suspension was then filtered through a 70 μm mesh strainer and stained with DAPI prior to cell sorting. Cells were sorted on a BD Influx cell sorter equipped with 488 nm laser as the FSC/SSC source, a 355 nm laser for excitation of DAPI, and a 561 nm laser for excitation of mCherry. Cells were sorted directly into 750 µL lysis buffer using the Agilent Absolutely RNA Microprep kit (Cat#400805).
cDNA libraries were generated using the Illumina TruSeq stranded mRNA Sample Preparation kit and sequenced on HiSeq4000 sequencer.

value: H1 hES derived

tag: cell subtype

value: mCherry -


title: rad52_YPD_TrAEL-seq

city: Cambridge

department: Bioinformatics

country: United Kingdom

library_source: genomic

molecule: genomic DNA

organism: Saccharomyces cerevisiae


title: SeViPS(BJ)-derived vascular endothelial cells lot #1

source_name: lot 1 of vascular endothelial cells generated from human iPS line that was produced from BJ fibroblast by using a Sendai virus vector


title: BC04,144h


title: in_R5c: Input RNA Clean air control


title: fob1_YPD_TrAEL-seq

source_name: BY4741 fob1

value: BY4741 fob1


title: BC04,96h


title: Human microvascular endothelial cells

description: HMVEC

source_name: Human microvascular endothelial cells

value: Human microvascular endothelial cells


title: in_R4c: Input RNA Clean air control


title: Human coronary arterial endothelial cells

description: HCAEC


title: mCherry + 2

value: mCherry +


title: BC04,72h


title: Ctrl_DRGO_2

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
FASTQ reads were aligned to the GRCh38 human reference genome with cellranger count (10x Genomics) with default parameters, and human Gencode v33 annotations.
Gene count matrix log-normalization (10,000 scale factor), gene clustering, dimension reduction analysis (UMAP), differential gene expression analysis, and plotting were performed with Seurat within the R environment.
Functional enrichment of gene ontology biological processes datasets was performed with DAVID.
Genome_build: hg38
Supplementary_files_format_and_content: mtx

extract_protocol:
DRGOs were treated with Trypsine-EDTA 0.25% (Gibco) and DNaseI 200ug/ml (Sigma) for 30 minutes at 37°C. Then they were gentle triturated pipetting up and down, washed with PBS and counted with Trypan Blue (Invitrogen). Libraries were sequenced with a depth of 50K reads/cell.
Single cell RNA sequencing was performed through the Chromium platform (10X Genomics). Cells were separated into droplet emulsion using the Chromium Single Cell 3’ Solution (V3.0) and Single-cell RNA-seq libraries were prepared according to the Single Cell 3' Reagent Kits User Guide (V3.0).

tag: group

value: Ctrl DRGO


title: mCherry + 1


title: BC04,48h


title: Human retinal microvascular endothelial cells

description: HRMVEC


title: F. trinervia_4weeksLowCO2

city: shanghai

first: Ming

middle: Ju

last: Lu

state: shanghai

address: 320 Yueyang Road, Xuhui Area, Shanghai, China

department: Partner Institute for Computational Biology, Shanghai Institutes for Biologic Sciences, CAS

institute: Shanghai Institutes for Biological Sciences, CAS

description:
L-tri
mRNA-seq
processed data file: combine_tpm_fourweeks-lowco2-experiment.txt

data_processing:
PacBio subreads were trimmed using next-generation RNA-seq data applying proovread (Hackl et al., 2014). Corrected PacBio reads were then subjected to conduct transcript assembly applying IDP-denovo.
Transcript de novo assembly using Trinity.
Functional annotation of transcripts by searching ortholog in F. ramosissima gene reference.
Mapping RNA-seq reads to assemble transcripts to quantify the abundance of transcript using RSEM.
Call differentially expressed genes between ctrl and low CO2 conditions using edgeR package.
Genome_build: Fram_combine_HLcontig_pacbio_cds_34041_index.fasta
Supplementary_files_format_and_content: combine_tpm_fourweeks-lowco2-experiment.txt: Tab-delimited text file contains the transcript abundance (TPM) of annotated genes for each replicate.

organism: Flaveria trinervia

source_name: newly expanded mature leaf

growth_protocol: For low CO2 experiment, plants were grown in growth chamber with light intensity to be 200 μmol m-2 s-1 and temperature to be 22oC, 16h/8h light/ dark duration, 70% humidity. Plants were watered twice a week and fertilized weekly.

extract_protocol:
Total RNA was isolated following the protocol of the PureLInkTM RNA Mini (ThermoFisher Scientific).
Next-generation RNA-seq was performed in the Illumina platform in the pair-ended mode with read length 150 bp.

treatment_protocol: The CO2 concentration of low CO2 condition is 100 μmol m-2 s-1, and that of control is 380 μmol m-2 s-1.

tag: photosynthetic type

value: Newly expanded mature leaf

tag: condition

value: Low CO2 4 weeks


title: SfiI_TrAEL-seq

value: YPD

value: 70% ethanol, SfiI digested


title: F.ramosissima_PacBio_seq

description: mRNA-seq

organism: Flaveria ramosissima

source_name: flower, leaf, stem and root

value: Type I C3-C4

value: Flower, leaf, stem and root

value: Control CO2


title: Ctrl_DRGO_1


title: F. trinervia_ctrl [low C02]

description:
N-tri
mRNA-seq
processed data file: combine_tpm_fourweeks-lowco2-experiment.txt


title: bulkRNA-Seq of siRNA KD

city: Solna

first: Martin

last: Becker

address: Akademiska stråket 1

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

country: Sweden

institute: Karolinska Institutet

description: processed data file Coulmns labeled by siRNA condition: NoTarget, SMART_CASK

data_processing:
Bulk RNA-Seq Samples were sequenced on NovaSeq6000 (NovaSeq Control Software 1.4.0/RTA v3.3.3) with a 2x151 setup using 'S1' flow cell mode. The Bcl to FastQ conversion was performed using bcl2fastq_v2.19.1.403 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+. The NGI-RNASeq pipeline was used to trim reads (TrimGalore), align to reference genome GRCh38/hg38 (STAR), perform quality control (FastQC, RSeQC, dupRadar, MultiQC) and count gene reads (featureCounts).
SMART-Seq2 samples were sequenced on Illumina HiSeq2000.The samples were analyzed by first demultiplexing the fastq files using  deindexer (https://github.com/ws6/deindexer) using the nextera index adapters and the 384 well  layout. Individual fastq files were then mapped to the hg38 genome assembly using the STAR  aligner (Dobin et al. Bioinformatics 2013) using 2-pass alignment to have improved performance of de novo splice junction reads, filtered for only uniquely mapping reads that are saved in the BAM file. The count matrix shows the individual counts aligning to each gene per cell.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text files include raw sequence counts per gene

source_name: in vitro neurons

growth_protocol: NES cells were seeded on plastic surface, pre-coated with 20 ug/ml poly-ornithine (Sigma Aldrich) and 1 ug/ml laminin (Sigma Aldrich) in DEMEM/F12+glutamax medium (Gibco) supplemented with 0.5X B-27 (Gibco), 1X N-2 (Gibco) and 10 U/ml Penicillin/Streptomycin (Gibco). Cells were maintained in a 5% CO2 atmosphere at 37°C. Two third of the medium was changed every second day of differentiation with 0.4 ug/ml laminin added.

extract_protocol:
For bulk RNA-Seq, cells were lysed in TRIzol reagent (Invitrogen), and RNA was isolated using the ReliaPrep RNA Cell Miniprep (Promega #A1222). For SMART-Seq2, cells were dissociated from culture surface with 2 min trypsin incubation and subsequent trypsin inhibition. After 3 minutes centrifugation at 300 rcf the cells were resuspended in cold Dulbecco’s PBS and single cells sorted by size into lysis-buffer using BD FACS Aria III.
Bulk RNA libraries were prepared using Tru-Seq at NGI Sweden, Stockholm. Smart-Seq2 library preparation and sequencing were done with the Eukaryotic Single Cell Genomics (ESCG) facility in the SciLifeLab, Stockholm according to published protocols (Picelli et al., 2013).

treatment_protocol: For siRNA-KD experiments, cells were seeded for differentiation and transfected the next day with 0.5µM Accell SMARTpool siRNA targeting CASK mRNA (Dharmacon #E-005311-00-0010) or 0.5µM Accell Green Non-targeting siRNA (Dharmacon #D-001950-01-20) according to standard protocol.

tag: days differentiation

tag: source

value: iPSC derived NES cells


title: F. ramosissima_4weeksLowCO2

description:
L-ram
mRNA-seq
processed data file: combine_tpm_fourweeks-lowco2-experiment.txt

value: Type II C3-C4


title: F. ramosissima_ctrl [low C02]

description:
N-ram
mRNA-seq
processed data file: combine_tpm_fourweeks-lowco2-experiment.txt


title: mCherry - 1


title: BC-101-4,144h

value: wild type


title: SS 0 h rep2


title: TP53 BOB UD UT 48h Rep 1

first: Alastair

last: Crisp

address: Francis Crick Avenue

institute: MRC Laboratory of Molecular Biology

data_processing:
Adaptors were removed and reads quality trimmed using TrimGalore v0.4.4 (https://github.com/FelixKrueger/TrimGalore) with default settings
Read were aligned to the Human genome version GRCh38.87 using TopHat v2.1.0 (https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-4-r36)
Reads were quantified per genomic region and differential expression was calculated using Cufflinks v2.2.1 (https://www.nature.com/articles/nbt.2450)
Genome_build: human GRCh38.87
Supplementary_files_format_and_content: Cufflinks tab-delimited expression values

source_name: BOBSC hiSPCs

growth_protocol: Essential 8 Flex Medium or Endoderm differentiation medium was used for Undifferentiated (UD) samples and Endoderm differentiated (ENDO) samples respectively. Cells were treated to differentiate as described in Yiangou et al Stem Cell Reports 2019.

extract_protocol:
RNA was extracted using the Rneasy Qiagen Extraction Mini Kit
NEBnext Ultra II

treatment_protocol: MMS treated cells were treated with 5ppm MMS at 24 hours.

value: hiPSC

tag: passage

value: TP53 KO


title: F. sonorensis_4weeksLowCO2

description:
L-son
mRNA-seq
processed data file: combine_tpm_fourweeks-lowco2-experiment.txt

organism: Flaveria sonorensis


title: in vitro12w-2 [12]

city: Matsumoto

first: Shin

last: Kadota

address: 3-1-1 Asahi

department: Regenerative Science and Medicine

institute: Shinshu University

data_processing:
Sequenced reads were trimmed by Trimmomatic (v0.39) with parameters of SLIDINGWINDOW:10:30. All samples were separated human and rat reads using Xenome (v1.0.0). Reads classified as human were mapped to the hg38 reference with STAR (v2.7.2a) and gene count matrix was generated with featureCounts (v1.6.4).
Differential expression analysis was performed using the edgeR package, with trimmed mean of M values (TMM) normalization.  PCA plots were performed using PCAtools package, with transcripts per million (TPM) normalization.
Genome_build: hg38
Supplementary_files_format_and_content: featurecounts_3-12-23-28Enid2 contains raw counts and tpm-normalized_counts.csv contains TPM normalized data.

source_name: human embryonic cell-derived cardiomyocyte

growth_protocol: Undifferentiated human embryonic stem cells reached 90% confluency, E8 medium was supplied with 1 uM of Wnt activator CHIR99201 (Sigma-Aldrich). The next day (day 0), E8 medium was changed to the cardiac differentiation medium (RPMI 1640 with B27 supplement minus insulin (Gibco) plus L-glutamine adding activin A (100 ng/mL, R&D) and Matrigel. On day1, bone morphologic protein 4 (BMP4; 10 ng/mL, R&D) and CHIR99201, followed by addition of Wnt inhibitor XAV939 (1 uM Sigma-Aldrich) on day 3-4. After day 7, medium was changed to RPMI 1640 with B27 supplement (Gibco) every other day. The cells were heat-shocked at 43ºC for 30 minutes and cryopreserved on day 20.

extract_protocol:
For collection of in vitro samples, total RNA was extracted by ISOGEN (Nippon Gene), phenol and chloroform. For in vivo samples, rat hearts of each time points were collected and immediately embedded in an OCT-embedding compound and kept in -80℃. Tissues were sectioned at a thickness of 10 µm using a cryostat (Leica). The graft areas were captured using laser microdissection system (Leica) from unstained unfixed specimens attached on the membrane coated slides (Leica 11600289). Total RNA was extracted by Arcturus PicoPure RNA Isolation Kit (Thermo).
cDNA was synthesized by SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (TaKaRa). Library preparations were conducted using Nextera DNA Library Prep Kit

treatment_protocol: 2 x 10^7 human embryonic stem cell-derived cardiomyocytes were directly injected to rat hearts (in vivo samples)

tag: cell line

tag: tissue/cell type

value: Cardiomyocytes

tag: developmental/differentiation stage

value: differentiation day 104


title: BC04,18h

value: High-yielding strain


title: BC-101-4,96h


title: MSC of HD 4

city: Essen

first: Theresa

last: Hack

address: Hufelandstraße 55

department: Children's clinic 3

country: Germany

institute: University Hospital Essen

description: Gene expression profiles of cultured MSC

hyb_protocol: Hybridisation was performed according to the WT PlusKit (ThermoFisher) on the GeneChip™ 3000 instrument system

scan_protocol: GeneChips were scanned using the GeneChip™ Scanner 3000 with G7 update

data_processing: Image analysis of CEL files and signal summarization by the RMA method and statistical methods by ANOVA were performed with the PartekGS software

label: biotin

source_name: cultured MSC of HD 4

label_protocol: Biotinylated cRNA were prepared according to the WT PlusKit (ThermoFisher) from 200 ng of total RNA on the GeneChip™ 3000 instrument system

growth_protocol: MSC were cultured until a density of 80-90%

extract_protocol: total RNA extraction with DNase digestion was performed with RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions

tag: tissue

value: Mesenchymal stromal cells from bone marrow

tag: genotype/variation

value: healthy donor (HD)


title: MSC of HD 5

source_name: cultured MSC of HD 5


title: F. robusta_ctrl [low C02]

description:
N-rob
mRNA-seq
processed data file: combine_tpm_fourweeks-lowco2-experiment.txt

organism: Flaveria robusta

value: Newly expanded mature leaf


title: bulkRNA-Seq of cases and controls

description: processed data file columns labeled by cell line: MaleControl, FemaleControl, ASD_CASK_SS, MICPCH_CASK_dup


title: dmc1_TrAEL-seq

source_name: SK1 dmc1

value: SK1 dmc1

tag: growth and treatment

value: Sporulation for 7 hours

tag: fix and post-processing

value: 70% ethanol


title: in vitro12w-1 [11]


title: in vitro 2w-2 [8]

value: differentiation day 34


title: in vitro 4w-2 [10]

value: differentiation day 48


title: BC-101-4,48h

tag: strain


title: 2set-2(zr2012)_3

city: København

first: Steffen

last: Abay-Nørgaard

state: København

address: Ole Maaløes Vej 5

department: BRIC

country: Denmark

institute: Copenhagen University

description:
replica 3 mutant
2set-2(zr2012)_3

data_processing:
Galaxy v19.05 was used for analysis
Trimmomatic(v0.36.0) Illumina clip performed - Standard TruSeq3 single end(2,30,10) - SLIDINGWINDOW (4,2) - CROP (73)
RNA star(v2.6.0b-2) use built in index, reference genome ce10 - length of genomic sequence 100
htseq-count(v0.9.1) mode union - stranded no - alignment quality 10
Deseq2(v2.1.8.3) was used to identify DE genes from count tables
Genome_build: ce10
Supplementary_files_format_and_content: tabular files contain the raw count data from each sample

organism: Caenorhabditis elegans

source_name: embryo

growth_protocol: 20 degrees

extract_protocol:
Arcturus picopure RNA extraction kit
Illumina Truseq V2

treatment_protocol: Young adult were bleached to obtain eggs from which RNA was extracted after 4 hours

tag: developmental stage

value: midembryonic cells


title: F. robusta_4weeksLowCO2

description:
L-rob
mRNA-seq
processed data file: combine_tpm_fourweeks-lowco2-experiment.txt

value: Low CO2 4 weeks


title: MSC of HD 1

source_name: cultured MSC of HD 1


title: 2set-2(zr2012)_2

description:
replica 2 mutant
2set-2(zr2012)_2


title: MSC of HD 3

source_name: cultured MSC of HD 3


title: in vitro 4w-1 [9]


title: MSC of AMKL patient 5

source_name: cultured MSC of AMKL patient 5

value: acute megakaryoblastic leukemia (AMKL)


title: BC-101-4,72h

source_name: Soil

tag: genotype

value: wild type


title: in vitro 2w-1 [7]


title: BC-101-4,18h


title: BC-101-4,192h


title: F. sonorensis_ctrl [low C02]

description:
N-son
mRNA-seq
processed data file: combine_tpm_fourweeks-lowco2-experiment.txt

value: Type I C3-C4

value: Control CO2


title: 0w-2 [6]

value: Cardiomyocytes

value: differentiation day 20


title: 2set-2(zr2012)_1

description:
replica 1 mutant
2set-2(zr2012)_1


title: PVULG_JaloEEP558-TAL18H-W2-1

city: Beaucouze

first: Nicolas

address: 42 rue Georges Morel

country: France

institute: IRHS

data_processing:
RTA2.7.3 and bcl2fastQ V2.17.1.14 softwares used for basecalling.
glint V1.0 was used for mapping and counting
Genome_build: JAAIFG000000000 (BAT93) or JAAIFH000000000 (JaloEEP58).
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample (one file per genotype)

organism: Phaseolus vulgaris

source_name: leaves

growth_protocol: 12 days with following conditions: 16h day at 23°C, 8h night at 20°C; then 24h acclimatization with the following conditions: 100% hygrometry, 16h day at 28°C, 8h night at 25°C

extract_protocol:
TRIzol Plus RNA Purification Kit (Thermo Fisher Scientific)
PolyA-mRNA / TruSeq Stranded mRNA LT (Illumina) / TruSeq SBS HiSeq3000 (Illumina)

treatment_protocol: Treatment H2O: Vacuum infiltration of detached trifoliate leaves, then maintained 48h in agar-agar medium. Treatment CFBP6546R: Vacuum infiltration of detached trifoliate leaves, then maintained 48h in agar-agar medium.

tag: taxid

tag: treatment description

value: Treatment CFBP6546R


title: PVULG_JaloEEP558-TAL18H-W2-3


title: MSC of AMKL patient 3

source_name: cultured MSC of AMKL patient 3

value: Mesenchymal stromal cells from bone marrow


title: MSC of HD 2

source_name: cultured MSC of HD 2

value: healthy donor (HD)


title: PVULG_JaloEEP558-TAL18H-H2-3

value: Treatment H2O


title: PVULG_JaloEEP558-TAL18H-W2-2


title: 0w-1 [5]


title: Adult heart [4]

source_name: Heart

value: Heart

tag: catalog #

value: Clontech 636532

value: adult heart


title: 2N2_3

description:
replica 2.3 wild type
2N2_3


title: 2N2_2

description:
replica 2.2 wild type
2N2_2


title: MSC of AMKL patient 4

source_name: cultured MSC of AMKL patient 4


title: PVULG_JaloEEP558-TAL18H-H2-2


title: Fetal heart [3]

value: Clontech 636583

value: fetal heart


title: 2N2_1

description:
replica 2.1 wild type
2N2_1

value: midembryonic cells


title: MSC of AMKL patient 2

source_name: cultured MSC of AMKL patient 2


title: MSC of AMKL patient 1

source_name: cultured MSC of AMKL patient 1


title: set-2(tm1630)_3

description:
replica 3 mutant
set-2(tm1630)_1


title: MSC of ML-DS patient 8

source_name: cultured MSC of ML-DS patient 8

value: myeloid leukemia in Down syndrome (ML-DS)


title: miR-30e-replicate1

city: Bhopal

first: Himanshu

last: Kumar

state: MADHYA PRADESH

address: Indore bypass road

department: Biological Sciences

country: India

institute: IISER Bhopal

data_processing:
FastQC was used to assess the quality of reads.
Trimmomatic was used for filtering and trimming of bad quality reads and sequences.
HISAT2 was used to map reads to human genome (hg38).
StringTie was used for transcript assembly and generation of abundance files.
DESeq2 R package was used for Differential Expression analysis and various R packages were used for generation of different plots and heat maps.
Genome_build: GRCh38
Supplementary_files_format_and_content: txt files containg not normalized (raw) read counts for each gene.

growth_protocol: A549 cells were cultured in DMEM media supplemented with 10% FBS in 100 mm cell culture dishes. For transfection and infection cells were cultures in a 6 well cell culture plate.

extract_protocol:
Total RNA was isolated with the help of Trizol reagent (Invitrogen)
Library was constructed with the help of Illumina TruSeq library preparation kit v2.

treatment_protocol:
Transfection: Cells were transfected with miR-NC1 or miR-30e mimic using Lipofectamine 2000 reagent.
Infection: Cell monolayer were washed with PBS and infected with 5 MOI of NDV virus for 1 hour in serum free DMEM. Cells were washed again with PBS and cultured in DMEM supplemented with 1% FBS after infection.

tag: transfection

tag: infection

value: Newcastle Disease Virus (NDV)


title: PVULG_BAT93-TAL18H-W2-2


title: set-2(tm1630)_2

description:
replica 2 mutant
set-2(tm1630)_2


title: PVULG_BAT93-TAL18H-W2-3


title: miR-30e-replicate2


title: miR-NC1-replicate2


title: PVULG_BAT93-TAL18H-W2-1


title: miR-NC1-replicate1


title: MSC of ML-DS patient 6

source_name: cultured MSC of ML-DS patient 6


title: set-2(tm1630)_1

description:
replica 1 mutant
set-2(tm1630)_1


title: N2_3

description:
replica 3 wild type
N2_3


title: Mock-replicate2

value: Mock


title: PVULG_BAT93-TAL18H-H2-3


title: MSC of ML-DS patient 7

source_name: cultured MSC of ML-DS patient 7


title: Mock-replicate1


title: N2_2

description:
replica 2 wild type
N2_2


title: N2_1

description:
replica 1 wild type
N2_1


title: MSC of ML-DS patient 5

source_name: cultured MSC of ML-DS patient 5


title: PVULG_JaloEEP558-TAL18H-H2-1


title: PVULG_BAT93-TAL18H-H2-1


title: MSC of ML-DS patient 4

source_name: cultured MSC of ML-DS patient 4


title: MSC of ML-DS patient 2

source_name: cultured MSC of ML-DS patient 2


title: MSC of ML-DS patient 1

source_name: cultured MSC of ML-DS patient 1


title: PVULG_BAT93-TAL18H-H2-2


title: HBBko 48hr rep 1

status: Public on Jul 26 2020

city: ZURICH

first: Jacob

middle: Corn

last: Lab

state: zURICH

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

data_processing:
Paired-end 150bp reads were generated on a HiSeq4000.
Reads for all eighteen samples (three replicates of HBBko and three WT HUDEP-2 samples at three time-points) were quantified using kallisto (Bray et al., 2016) and the hg38 index to assign reads to transcripts.
Differential analysis of transcript abundance and consolidation of individual transcripts to gene-level abundance was calculated using sleuth (Pimentel et al., 2017)
Genome_build: hg38
Supplementary_files_format_and_content: .txt format of log2 fold change comparing WT and HBBko at different time points

source_name: erythroid progenitor cells

growth_protocol: WT-HUDEP-2 and HBBko cells were cultured and differentiated in triplicates.

extract_protocol:
Cells were harvested and RNA was extracted using the RNeasy Mini kit 74104, Rnase-Free DnaseI Kit 79254 and Qiashredder 79654. RNA concentrations were quantified using Qubit™ RNA BR Assay (ThermoFisher) and 500ng were used for library preparation.
RNA-seq library was made using Illumina TruSeq RNA Library Prep Kit v2 and following manufacturer’s instructions.

tag: cell type

value: umbilical cord derived erythroid progenitor cells

value: HBBko

tag: Stage

value: 48 hour differentiated


title: HBBko undiff rep3

treatment_protocol: WT-HUDEP-2 and HBBko cells were cultured and differentiated in triplicates.

tag: cell line

value: undifferentiated


title: WT 48 hr rep 3

value: WT


title: WT 5d rep 2

value: 5 day differentiated


title: WT 5d rep 3


title: WT 48 hr rep 2


title: HBBko 48hr rep 3


title: WT undiff rep 2


title: WT undiff rep 3


title: WT 48 hr rep 1


title: HBBko undiff rep1


title: HBBko 5d rep 1


title: HBBko 48hr rep 2


title: WT undiff rep 1


title: HBBko undiff rep2


title: MSC of ML-DS patient 3

source_name: cultured MSC of ML-DS patient 3

value: Mesenchymal stromal cells from bone marrow


title: HBBko 5d rep 3


title: HiChIP Control Superior and Middle Temporal Gyri 1

city: Boston

first: Sundari

last: Chetty

state: MA

address: 185 Cambridge Street

department: Harvard Medical School

institute: Massachusetts General Hospital, Harvard University

data_processing:
Library strategy: HiChIP
The ENCODE DCC ATAC-seq pipeline (doi:10.5281/zenodo.211733) (V1.1.7) was used to  process bulk ATAC-seq samples, starting from fastq files. The pipeline was executed with IDR  enabled and the IDR threshold set to 0.05. The GRCh38 reference genome assembly was used,  keeping only the primary chromosomes chr1 - chr22, chrX, chrY, chrM. The pipeline was executed  with ATAQC enabled, using GENCODE version 29 TSS annotations. Biological replicates were  analyzed individually, with the two technical replicates for each bio-rep provided as inputs to the  “atac.bams” argument of the pipeline. Other arguments to the pipeline were kept at their defaults.
For scATAC-seq peak calling from clusters or manually defined cell types, all single cells belonging to the given group were pooled together. These pooled fragment files were converted to the paired-end tagAlign format and processed with version 1.4.2 of the ENCODE DCC ATAC-seq pipeline. The conversion to tagAlign was performed as follows. For fragments on the positive strand, the read start coordinate was the fragment start coordinate, zero-indexed. The read end coordinate was the fragment start coordinate plus the read length (99 bp). For fragments on the negative strand, the read start coordinate was the fragment end coordinate, zero-indexed. The read start coordinate was the fragment end coordinate minus the read length (99 bp). Then, these tagAlign files were used as input to the DCC ATAC-seq pipeline. IDR optimal peak sets with an IDR threshold of 0.05 were determined for each cluster by the pipeline, using pseudo-bulk replicate tagAligns for the cluster. Other pipeline parameters were the same as for bulk ATAC-seq data
HiChIP paired-end sequencing data was processed using HiC-Pro85 version 2.11.0 with a minimum mapping quality of 10. FitHiChIP86 was used to identify “peak-to-all” interactions using  peaks called from the one-dimensional HiChIP data. A lower distance threshold of 20 kb and an  upper distance threshold of 2 Mb were used. Bias correction was performed using coverage specific bias.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig, overlap narrowPeaks, and IDR narrowPeaks were generated by the ENCODE ATAC-seq pipeline with default parameters (v1.1.7) https://github.com/ENCODE-DCC/atac-seq-pipeline. the Pval bigwig and FC bigwig signal tracks were generated by the MACS2 algorithm. Replicate overlap and IDR were applied to MACS2 called peaks.

source_name: Primary brain samples acquired post-mortem, Superior and Middle Temporal Gyri

extract_protocol:
Nuclei were isolated from frozen tissue  in accordance with protocol dx.doi.org/10.17504/protocols.io.6t8herw. After isolation, nuclei were  cryopreserved in BAM Banker (Wako Chemicals) and stored at -80°C for use in other assays such  as scATAC-seq and HiChIP.
HiChIP library generation was performed as described previously (Mumbach, M. R. et al. HiChIP: efficient and sensitive analysis of protein-directed genome   architecture. Nat. Methods 13, 919–922 (2016). ) One million cryopreserved nuclei were used per experiment. Enzyme MboI was used for restriction digest. Sonication was performed on a Covaris E220 instrument using the following settings: duty cycle 5, peak incident power 140, cycles per burst 200, time 4 minutes. All HiChIP was performed using H3K27ac as the target (Abcam ab4729).
Nuclei were isolated from frozen tissue  in accordance with protocol dx.doi.org/10.17504/protocols.io.6t8herw. After isolation, nuclei were  cryopreserved in BAM Banker (Wako Chemicals) and stored at -80°C for use in other assays such  as scATAC-seq and HiChIP.

treatment_protocol: Primary brain samples were acquired post-mortem with IRB-approved informed consent. Human donor sample sizes were chosen to provide sufficient confidence to validate methodological  conclusions. Human brain samples were collected with an average post-mortem interval of 3.9  hours (range 2.0 – 6.9 hours). Macrodissected brain regions were flash frozen in liquid nitrogen.  Some samples were embedded in Optimal Cutting Temperature (OCT) compound. All samples  were stored at -80°C until use.

value: brain

tag: brain region

value: Superior and Middle Temporal Gyri


title: HiChIP Control Superior and Middle Temporal Gyri 2


title: HiChIP Control Hippocampus 2

description: HiChIP Control Hippocampus 2

source_name: Primary brain samples acquired post-mortem, Hippocampus

value: Hippocampus


title: HiChIP Control Hippocampus 1

description: HiChIP Control Hippocampus 1


title: HiChIP Control Parietal Lobe 2

description: HiChIP Control Parietal Lobe 2

source_name: Primary brain samples acquired post-mortem, Parietal Lobe

value: Parietal Lobe


title: WT 5d rep 1


title: HiChIP Control Caudate 1

description: HiChIP Control Caudate 1

source_name: Primary brain samples acquired post-mortem, Caudate

value: Caudate


title: HiChIP Control Middle Frontal Gyrus 2

description: HiChIP Control Middle Frontal Gyrus 2

source_name: Primary brain samples acquired post-mortem, Middle Frontal Gyrus

value: Middle Frontal Gyrus


title: HiChIP Control Substantia Nigra 2

description: HiChIP Control Substantia Nigra 2

source_name: Primary brain samples acquired post-mortem, Substantia Nigra

value: Substantia Nigra


title: HBBko 5d rep 2


title: HiChIP Control Parietal Lobe 1

description: HiChIP Control Parietal Lobe 1


title: HiChIP Control Substantia Nigra 1

description: HiChIP Control Substantia Nigra 1


title: HiChIP Control Middle Frontal Gyrus 1

description: HiChIP Control Middle Frontal Gyrus 1


title: BulkATAC Control Superior and Middle Temporal Gyri 7

data_processing:
The ENCODE DCC ATAC-seq pipeline (doi:10.5281/zenodo.211733) (V1.1.7) was used to  process bulk ATAC-seq samples, starting from fastq files. The pipeline was executed with IDR  enabled and the IDR threshold set to 0.05. The GRCh38 reference genome assembly was used,  keeping only the primary chromosomes chr1 - chr22, chrX, chrY, chrM. The pipeline was executed  with ATAQC enabled, using GENCODE version 29 TSS annotations. Biological replicates were  analyzed individually, with the two technical replicates for each bio-rep provided as inputs to the  “atac.bams” argument of the pipeline. Other arguments to the pipeline were kept at their defaults.
For scATAC-seq peak calling from clusters or manually defined cell types, all single cells belonging to the given group were pooled together. These pooled fragment files were converted to the paired-end tagAlign format and processed with version 1.4.2 of the ENCODE DCC ATAC-seq pipeline. The conversion to tagAlign was performed as follows. For fragments on the positive strand, the read start coordinate was the fragment start coordinate, zero-indexed. The read end coordinate was the fragment start coordinate plus the read length (99 bp). For fragments on the negative strand, the read start coordinate was the fragment end coordinate, zero-indexed. The read start coordinate was the fragment end coordinate minus the read length (99 bp). Then, these tagAlign files were used as input to the DCC ATAC-seq pipeline. IDR optimal peak sets with an IDR threshold of 0.05 were determined for each cluster by the pipeline, using pseudo-bulk replicate tagAligns for the cluster. Other pipeline parameters were the same as for bulk ATAC-seq data
HiChIP paired-end sequencing data was processed using HiC-Pro85 version 2.11.0 with a minimum mapping quality of 10. FitHiChIP86 was used to identify “peak-to-all” interactions using  peaks called from the one-dimensional HiChIP data. A lower distance threshold of 20 kb and an  upper distance threshold of 2 Mb were used. Bias correction was performed using coverage specific bias.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig, overlap narrowPeaks, and IDR narrowPeaks were generated by the ENCODE ATAC-seq pipeline with default parameters (v1.1.7) https://github.com/ENCODE-DCC/atac-seq-pipeline. the Pval bigwig and FC bigwig signal tracks were generated by the MACS2 algorithm. Replicate overlap and IDR were applied to MACS2 called peaks.

source_name: Primary brain samples acquired post-mortem, Superior Temporal Gyri

extract_protocol:
Nuclei were isolated from frozen tissue  in accordance with protocol dx.doi.org/10.17504/protocols.io.6t8herw. After isolation, nuclei were  cryopreserved in BAM Banker (Wako Chemicals) and stored at -80°C for use in other assays such  as scATAC-seq and HiChIP.
Transposed fragments were purified and amplified as described previously (Buenrostro et al., Nature Methods 2015) with slight modification. Briefly, transposed fragments were pre-amplified for 3 cycles. Concentration of pre-amplified fragments was determined by qPCR and this concentration was used to estimate the total number of cycles required to obtain 160 femtomoles of fragments. A second PCR was performed to amplify the pre-amplified fragments for the desired number of cycles. Final libraries were again purified. Prior to sequencing, libraries were pooled and run on a 6% PAGE gel and excess primers and primer dimers below 125 bp were removed.
Nuclei were isolated from frozen tissue  in accordance with protocol dx.doi.org/10.17504/protocols.io.6t8herw. After isolation, nuclei were  cryopreserved in BAM Banker (Wako Chemicals) and stored at -80°C for use in other assays such  as scATAC-seq and HiChIP.

value: Superior Temporal Gyri


title: BulkATAC Control Superior and Middle Temporal Gyri 6


title: BulkATAC Control Superior and Middle Temporal Gyri 8


title: BulkATAC Control Superior and Middle Temporal Gyri 9


title: BulkATAC Control Superior and Middle Temporal Gyri 5


title: BulkATAC Control Superior and Middle Temporal Gyri 3


title: BulkATAC Control Superior and Middle Temporal Gyri 4


title: BulkATAC Control Superior and Middle Temporal Gyri 18


title: BulkATAC Control Superior and Middle Temporal Gyri 17


title: BulkATAC Control Superior and Middle Temporal Gyri 16


title: BulkATAC Control Substantia Nigra 8


title: BulkATAC Control Substantia Nigra 7


title: BulkATAC Control Superior and Middle Temporal Gyri 1


title: BulkATAC Control Substantia Nigra 9


title: BulkATAC Control Superior and Middle Temporal Gyri 12


title: BulkATAC Control Superior and Middle Temporal Gyri 11


title: BulkATAC Control Superior and Middle Temporal Gyri 10


title: BulkATAC Control Superior and Middle Temporal Gyri 14


title: BulkATAC Control Superior and Middle Temporal Gyri 19


title: BulkATAC Control Substantia Nigra 6


title: BulkATAC Control Superior and Middle Temporal Gyri 13


title: BulkATAC Control Substantia Nigra 3


title: BulkATAC Control Substantia Nigra 5


title: BulkATAC Control Substantia Nigra 4


title: BulkATAC Control Superior and Middle Temporal Gyri 2


title: BulkATAC Control Superior and Middle Temporal Gyri 15


title: BulkATAC Control Substantia Nigra 2


title: BulkATAC Control Substantia Nigra 14


title: BulkATAC Control Substantia Nigra 11


title: BulkATAC Control Substantia Nigra 10


title: BulkATAC Control Substantia Nigra 1


title: BulkATAC Control Putamen 8

source_name: Primary brain samples acquired post-mortem, Putamen

value: Putamen


title: BulkATAC Control Substantia Nigra 12


title: BulkATAC Control Putamen 7


title: BulkATAC Control Putamen 9


title: BulkATAC Control Substantia Nigra 13


title: BulkATAC Control Putamen 6


title: BulkATAC Control Putamen 3


title: BulkATAC Control Putamen 4


title: BulkATAC Control Parietal Lobe 6


title: BulkATAC Control Parietal Lobe 7


title: BulkATAC Control Putamen 2


title: BulkATAC Control Putamen 10


title: BulkATAC Control Putamen 1


title: BulkATAC Control Parietal Lobe 5


title: BulkATAC Control Parietal Lobe 2


title: BulkATAC Control Putamen 5


title: BulkATAC Control Parietal Lobe 9


title: BulkATAC Control Parietal Lobe 18


title: BulkATAC Control Parietal Lobe 4


title: BulkATAC Control Putamen 11


title: BulkATAC Control Parietal Lobe 17


title: BulkATAC Control Parietal Lobe 3


title: BulkATAC Control Parietal Lobe 15


title: BulkATAC Control Parietal Lobe 14


title: BulkATAC Control Parietal Lobe 16


title: BulkATAC Control Parietal Lobe 12


title: BulkATAC Control Parietal Lobe 11


title: BulkATAC Control Middle Temporal Gyri 9

source_name: Primary brain samples acquired post-mortem, Middle Temporal Gyri

value: Middle Temporal Gyri


title: BulkATAC Control Parietal Lobe 8


title: BulkATAC Control Parietal Lobe 10


title: BulkATAC Control Middle Temporal Gyri 7


title: BulkATAC Control Middle Temporal Gyri 8


title: BulkATAC Control Parietal Lobe 13


title: BulkATAC Control Parietal Lobe 1


title: BulkATAC Control Middle Temporal Gyri 4


title: BulkATAC Control Middle Temporal Gyri 6


title: BulkATAC Control Middle Temporal Gyri 5


title: BulkATAC Control Middle Temporal Gyri 10


title: BulkATAC Control Middle Temporal Gyri 11


title: BulkATAC Control Middle Temporal Gyri 12


title: BulkATAC Control Middle Temporal Gyri 1


title: BulkATAC Control Middle Temporal Gyri 3


title: BulkATAC Control Middle Frontal Gyrus 8


title: BulkATAC Control Middle Frontal Gyrus 4


title: BulkATAC Control Middle Frontal Gyrus 7


title: BulkATAC Control Middle Frontal Gyrus 5


title: BulkATAC Control Middle Frontal Gyrus 9


title: BulkATAC Control Middle Frontal Gyrus 2


title: BulkATAC Control Middle Frontal Gyrus 3


title: BulkATAC Control Middle Temporal Gyri 2


title: BulkATAC Control Hippocampus 6


title: BulkATAC Control Middle Frontal Gyrus 6


title: BulkATAC Control Hippocampus 5


title: BulkATAC Control Hippocampus 4


title: BulkATAC Control Middle Frontal Gyrus 1


title: BulkATAC Control Hippocampus 8


title: BulkATAC Control Hippocampus 9


title: BulkATAC Control Middle Frontal Gyrus 10


title: BulkATAC Control Middle Frontal Gyrus 11


title: BulkATAC Control Middle Frontal Gyrus 12


title: BulkATAC Control Hippocampus 7


title: BulkATAC Control Hippocampus 3


title: BulkATAC Control Hippocampus 22


title: BulkATAC Control Hippocampus 21


title: BulkATAC Control Hippocampus 19


title: BulkATAC Control Hippocampus 2


title: BulkATAC Control Hippocampus 20


title: BulkATAC Control Hippocampus 16


title: BulkATAC Control Hippocampus 18


title: BulkATAC Control Hippocampus 17


title: BulkATAC Control Hippocampus 12


title: BulkATAC Control Hippocampus 13


title: BulkATAC Control Hippocampus 11


title: BulkATAC Control Hippocampus 10


title: BulkATAC Control Hippocampus 14


title: BulkATAC Control Caudate 9


title: BulkATAC Control Hippocampus 1


title: BulkATAC Control Hippocampus 15


title: BulkATAC Control Caudate 8


title: HiChIP Control Caudate 2

description: HiChIP Control Caudate 2


title: BulkATAC Control Caudate 5


title: BulkATAC Control Caudate 6


title: BulkATAC Control Caudate 3


title: BulkATAC Control Caudate 30


title: BulkATAC Control Caudate 29


title: BulkATAC Control Caudate 32


title: BulkATAC Control Caudate 28


title: BulkATAC Control Caudate 7


title: BulkATAC Control Caudate 4


title: BulkATAC Control Caudate 31


title: BulkATAC Control Caudate 24


title: BulkATAC Control Caudate 27


title: BulkATAC Control Caudate 26


title: BulkATAC Control Caudate 23


title: BulkATAC Control Caudate 25


title: GATA6-AS1-KD_rep2

city: WuHan

first: Jie

last: Yang

state: Hubei Province

address: Donghu Road, No. 115

department: Medical Research Insitiute

institute: WuHan university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, the clean data were mapped to GRC38 whole genome using HISAT2 version 2.1.0 with parameters -p 64 --dta --rna-strandness RF -x.
Raw reads were performed with FeatureCounts using GRCh38.84 human gene annotation.
Raw counts were normalized to Transcripts Per Million (TPM).
Gene expression difference was analyzed by Bioconductor R package DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: TPM

source_name: differentiated GATA6-AS1-knockdown endoderm cells

growth_protocol: hESCs (HuES8) were treated with DMEM-F12 as basal medium, supplemented with 0.2% BSA, 1% Penicillin-Streptomycin. 100ng/mL Activin A and 2.5μM CHIR were added at day 1, followed by 100ng/mL Activin A only for the next two days.

extract_protocol:
RNA was extracted with HiPure Total RNA Mini Kit (Magen, Cat#R4111-03).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: GATA6-AS1 knockdown


title: BulkATAC Control Caudate 21


title: BulkATAC Control Caudate 20


title: DE_rep3

source_name: differentiated endoderm cells

value: wildtype


title: DE_rep2


title: BulkATAC Control Caudate 2


title: BulkATAC Control Caudate 18


title: DE_rep1


title: GATA6-AS1-KD_rep1


title: BulkATAC Control Caudate 17


title: GATA6-AS1-KD_rep3

source_name: differentiated GATA6-AS14-knockdown endoderm cells


title: BulkATAC Control Caudate 19


title: BulkATAC Control Caudate 22


title: IgG CHIP HUDEP2 diff

data_processing:
FastQC was used for initial quality control of reads. All samples, WT diff and undiff, HBBko diff and undiff, HSPC diff and undiff, ATF4ΔN diff, ATF4KO3, and IgG and HSPC IgG diff and undiff, were processed according to ENCODE guidelines for unreplicated transcription factor ChIP-seq analysis
raw reads were aligned against GRCh38 using bowtie2. Duplicate reads were marked using Picard’s MarkDuplicates and multimapping, low quality, duplicated and non-properly paired reads were removed. Library complexity measures and flagstats were generated for each BAM file.
BAM files were converted to tagAlign format and two subsampled pseudoreplicates were generated for each sample with half the total reads. Peak calling, fold change and p-value signal tracks were generated using MACS2
Irreproducible Discovery Rate (IDR) analysis was performed using self-pseudoreplicates and the main samples to obtain self-consistent sets of peaks. Final peak calls were filtered by ENCODE blacklist (Amemiya et al., 2019) and an IDR of 2% and a signal value > 30.
Sets of peaks for each comparison were analysed and associated to genes using the R package ChIPseeker (Yu et al., 2015) and Bioconductor hg38 TxDb (Team BC, Maintainer BP (2019). TxDb.Hsapiens.UCSC.hg38.knownGene: Annotation package for TxDb object(s). R package version 3.4.6.).
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files

extract_protocol:
10 million cells per sample were harvested and cross-linked in 1% Formaldehyde. Cross-linking was quenched with the addition of 1.5M glycine. Samples were then lysed for 10 minutes at 4C in 50 mM Hepes–KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA; 10% glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100. Cells were then centrifuged at 1500g for 3 minutes and the supernatant was discarded. The pellet was resuspended in 10 mM Tris–HCl, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA and incubated for 5 minutes at 4C. The cells were then centrifuged at 1500g for 3 minutes and the supernatant was discarded. The pellet was resuspended in 10 mM Tris–HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na–Deoxycholate; 0.5% N-lauroylsarcosine and sonicated using the Covaris S220 following manufacturer’s instructions. Protein A beads (ThermoFisher) were complexed with antibody and the antibody-bead complexes were incubated with cell lysates at 4C overnight with rotation. The antibodies used were rabbit anti-ATF4 (CST 11815S) and rabbit IgG (Novus Biologicals NBP2-24891). The beads were retrieved using a magnetic stand and rinsed with RIPA buffer. Elution buffer containing 50 mM Tris–HCl, pH 8; 10 mM EDTA; 1% SDS was added to the beads for reverse crosslinking at 65C overnight with shaking. After reverse crosslinking, the beads were removed. The eluted DNA was treated with RNaseA and Proteinase K and then purified using Qiagen MinElute PCR Purification Kit, following the manufacturer’s instructions.
Sequencing library was prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (E7647) and NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) following manufacturer’s instructions.  Paired-end 150bp reads were generated on an Illumina NextSeq500 at the Functional Genomics Center Zürich (FGCZ) and demultiplexed.

value: umbilical cord derived erythroid progenitor cells

tag: antibody

value: Differentiated


title: ATF4 CHIP HSPC early erythroblasts

value: HSPC derived erythroid progenitor cells

value: HSPC

value: rabbit anti-ATF4 (CST 11815S)

value: Early erythroblasts


title: BulkATAC Control Caudate 14

tag: tissue

value: brain


title: ATF4 CHIP HSPC late erythroblasts

value: Late erythroblasts


title: BulkATAC Control Caudate 16


title: IgG CHIP HSPC early erythroblasts

value: rabbit IgG (Novus Biologicals NBP2-24891)


title: BulkATAC Control Caudate 13

value: Caudate


title: ATF4 CHIP HUDEP2 diff


title: BulkATAC Control Caudate 12


title: IgG CHIP HSPC late erythroblasts


title: ATF4 CHIP ATF4DN diff


title: BulkATAC Control Caudate 15


title: ATF4 CHIP WT undiff

tag: genotype/variation

value: WT

value: Undifferentiated


title: ATF4 CHIP WT diff


title: BulkATAC Control Caudate 11


title: IgG CHIP WT diff


title: BulkATAC Control Caudate 10


title: BulkATAC Control Caudate 1


title: Mutator MEF cells - replicate 5

city: Biberach

first: Meshal

last: Ansari

address: Birkendorfer Straße 65

institute: Boehringer Ingelheim

data_processing:
The STAR aligner (v 2.4.2a) with modified parameter settings (--twopassMode=Basic) was used for split-read alignment against the mouse genome assembly mm10 and UCSC known gene annotation.
To quantify the number of reads mapping to annotated genes we used HTseq-count° (v0.6.0) (Anders et al., 2015). FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) values were calculated using custom scripts.
Genome_build: mm10

organism: Mus musculus

source_name: Mouse embryonic fibroblasts

growth_protocol: 300.000 cells from one representative WT and mutator MEF cell line were seeded in 6 well plates. Cells for 5 technical replicates per cell line were plated. After 48 h cells were harvested.

extract_protocol:
Strand specific, polyA-enriched RNA sequencing was performed as described earlier (Haack et al., 2013). Briefly, RNA was isolated from whole-cell lysates using the Total RNA kit (Peqlab, VWR) and RNA integrity number (RIN) was determined with the Agilent 2100 BioAnalyzer (RNA 6.000 Nano Kit, Agilent).
For library preparation, 1 μg of RNA was poly(A) selected, fragmented, and reverse transcribed with the Elute, Prime, Fragment Mix (Illumina). A-tailing, adaptor ligation, and library enrichment were performed as described in the TruSeq Stranded mRNA Sample Prep Guide (Illumina). RNA libraries were assessed for quality and quantity with the Agilent 2100 BioAnalyzer and the Quant-iT PicoGreen dsDNA Assay Kit (Life Technologies). RNA libraries were sequenced as 150 bp paired-end runs on an Illumina HiSeq4000 platform.

treatment_protocol: no treatment

value: Mouse embryonic fibroblasts

value: mutator


title: Mutator MEF cells - replicate 3


title: Mutator MEF cells - replicate 4


title: ATF4 CHIP HBBko undiff

value: HBBko


title: ATF4 CHIP HBBko diff


title: ATF4 CHIP ATF4 KO undiff

value: ATF4 KO


title: EC12group2-3

city: Hangzhou

first: Xiang

last: Zhou

state: Zhejiang

address: No. 666 Wusu

institute: Zhejiang Agricultural and Forestry University

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 the genome of Bursaphelenchus xylophilus (GCA_000231135.1) using Tophat2 (TopHat v2.1.1) with the deault parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: Bursaphelenchus xylophilus GCA_000231135.1
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample

organism: Bursaphelenchus xylophilus

source_name: EC agent treatment for 12 h

growth_protocol: the nematodes were fed on 7-d-cultivated Botrytis cinerea Pers. using potato dextrose agar plates at 25 °C

extract_protocol:
The Baermann funnel method was used to separate nematodes from PDA plates, and nematode sampleswere collected by centrifugation (4000 rpm) for 4 min
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: the nematode adults (200 nematodes/sample) were collected after being immersed in 0.1 mg/L EB for 12 h and 24 h at 25 °C (EB12 and EB24 treatments);The samples treated with equal adjuvant concentration of octylphenol polyoxyethylene-10 and n-butyl alcohol for 12 h and 24 h (ON12 and ON24 treatments)

tag: material

value: adult stage

value: adult


title: Mutator MEF cells - replicate 1


title: MET-C-019-C2

type: genomic

city: Toronto

first: Ankur

last: Chakravarthy

state: Ontario

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Center

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina infinium MethylationEPIC bead chip using standard Illumina protocol

scan_protocol: Arrays were imaged using using Illumina's  iScan using standard Illumina scanner settings

data_processing: Data processing was performed using genomestudio version 2011.1; IDAT files for Illumina EPIC beadchip data were processed using minfi R-package.

label: Cy3 and Cy5

source_name: Tumor biopsy

label_protocol: Standard Illumina protocol

growth_protocol: Not Applicable

extract_protocol: RNA and DNA were isolated from this frozen material using the AllPrep DNA/RNA Mini Kit (Qiagen, catalog No. 80204), allowing for simultaneous extraction of DNA and RNA from PBMCs or tumor biopsies

treatment_protocol: Not Applicable

tag: disease state

value: Colorectal cancer

value: Tumor biopsy

tag: timepoint

value: Post

tag: regimen

value: DNMTi + Vitamin C


title: XMIN_027_2_

city: London

first: Shaun

last: May

address: William Harvey Research Institute

department: TMT

institute: William Harvey Research Institute

description: microRNA

data_processing:
Illumina 1.9 used for base calling
Reads were alligned to miRbase and Genome GRCh37 using Bowtie 2.2.6
Genome_build: GRCh37
Supplementary_files_format_and_content: excel spreadsheet; raw counts,tpm, FDR, summary read counts

source_name: patient after non-cardiac surgery

extract_protocol:
MicroRNA was extracted using Exiqon Services proprietary extraction protocol optimized for biofluids samples to be analyzed by NGS.
NEBNext Multiplex Small RNA Library Prep Set for Illumina

value: exosome

tag: pmi

value: POSITIVE


title: MET-O-004-ST

value: Ovarian cancer

value: Pre


title: MET-B-009-C2T

value: Breast cancer


title: MET-O-005-S-T


title: MET-O-004-C2D12-T


title: MET-C-022-C1-D2


title: Mutator MEF cells - replicate 2


title: MET-C-020-C2-T


title: WT MEF cells - replicate 4

value: wild type


title: MET-C-013-C2T


title: XMIN_046_2_

description: microRNA

value: NEGATIVE


title: MET-C-011-C2T


title: MET-B-004-ST

value: DNMTi


title: MET-C-013-ST


title: scATAC Control Substantia Nigra 2

extract_protocol:
Nuclei were isolated from frozen tissue  in accordance with protocol dx.doi.org/10.17504/protocols.io.6t8herw. After isolation, nuclei were  cryopreserved in BAM Banker (Wako Chemicals) and stored at -80°C for use in other assays such  as scATAC-seq and HiChIP.
scATAC-seq library construction: Cryopreserved nuclei were thawed on ice and 65,000 nuclei were transferred to a tube containing  1 ml of RSB-T [10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween]. Nuclei were author/funder. All rights reserved. No reuse allowed without permission. bioRxiv preprint doi: https://doi.org/10.1101/2020.01.06.896159. The copyright holder for this preprint (which was not peer-reviewed) is the pelleted at 500 RCF for 5 minutes at 4°C in a fixed angle rotor. The supernatant was fully removed  using two pipetting steps (p1000 to remove down to the last 100 ul, then p200 to remove all  remaining supernatant). This pellet was then gently resuspended in 12 ul of 1x Nuclei Buffer (10x 1424 Genomics). To transpose, 5 ul of this nuclei suspension (containing 27,000 nuclei) was transferred  to a tube containing 10 ul of transposition mix (10x Genomics). This reaction mixture was 1426 incubated at 37°C for 1 hour to transpose. The remainder of library generation was completed as  described in the 10x Genomics Single Cell ATAC Regent Kits User Guide (v1 Chemistry).
Nuclei were isolated from frozen tissue  in accordance with protocol dx.doi.org/10.17504/protocols.io.6t8herw. After isolation, nuclei were  cryopreserved in BAM Banker (Wako Chemicals) and stored at -80°C for use in other assays such  as scATAC-seq and HiChIP.

value: brain

value: Substantia Nigra


title: MET-B-011-ST


title: MET-C-015-ST


title: MET--011-C2D12


title: MET-B-008-C2-T


title: MET-C-019-ST


title: scATAC Control Superior and Middle Temporal Gyri 1

value: Superior Temporal Gyri


title: XMIN_035_2_

description: microRNA


title: MET-O-005-C2D12T


title: EB12group3-3

source_name: EB agent treatment for 12 h

tag: strain

value: adult stage

tag: developmental stage


title: EC12group2-1

value: adult


title: XMIN_055_2_

description: microRNA


title: WT MEF cells - replicate 1

value: Mouse embryonic fibroblasts


title: EB12group3-2


title: scATAC Control Parietal Lobe 1

value: Parietal Lobe


title: MET-B-009-AT

value: Tumor biopsy


title: MET-B-004-C2-T

value: Post


title: scATAC Control Middle Frontal Gyrus 1

value: Middle Frontal Gyrus


title: MET-B-008-ST


title: XMIN_059_2_

description: microRNA

value: exosome


title: EC24-3

source_name: EC agent treatment for 24 h


title: EB12group3-1


title: scATAC Control Substantia Nigra 1


title: EC24-2


title: MET-C-020-ST

value: Colorectal cancer

value: DNMTi + Vitamin C


title: scATAC Control Hippocampus 2

source_name: Primary brain samples acquired post-mortem, Hippocampus

value: Hippocampus


title: XMIN_029_2_

description: microRNA


title: WT MEF cells - replicate 2

value: wild type


title: scATAC Control Hippocampus 1


title: XMIN_050_2_

description: microRNA

value: POSITIVE


title: MET-C-011-AT

value: Pre

value: DNMTi


title: XMIN_039_2_

description: microRNA


title: scATAC Control Caudate 3

value: brain

value: Caudate


title: MET-B-001-C2-T

value: Breast cancer


title: MET-C-015-AT


title: EC24-1

value: adult stage

value: adult


title: MET-C-015-C2-T


title: EB24-3

source_name: EB agent treatment for 24 h


title: XMIN_004_2_

description: microRNA


title: EB24-2


title: scATAC Control Caudate 2

source_name: Primary brain samples acquired post-mortem, Caudate


title: Control non-calcified aortic valve 3

city: Beijing

first: Dong

last: Han

address: 28 Fuxing street

institute: China PLA general hospital

description: RNA was extracted from valve leaflets and gene expression evaluated using the Agilent-078298 human ceRNA array V1.0 4X180K.

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 12.0 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: Control non-calcified aortic valve 3

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

value: non-calcified

value: aortic valve


title: Calcified aortic valve 2

source_name: Calcified aortic valve 2

value: Calcified


title: EC12group2-2


title: XMIN_018_2_

description: microRNA

value: NEGATIVE


title: XMIN_023_2_

description: microRNA

value: exosome


title: MET-C-022-ST

value: Colorectal cancer

value: Tumor biopsy


title: Control non-calcified aortic valve 2

source_name: Control non-calcified aortic valve 2


title: scATAC Control Caudate 1


title: Control non-calcified aortic valve 1

source_name: Control non-calcified aortic valve 1


title: EB24-1


title: 1wk_Ab_TBI_rep4

status: Public on Jul 25 2020

city: Charlottesville

first: Ashley

middle: Catherine

last: Bolte

state: Virginia

address: 409 Lane Road MR4

department: Neuroscience

institute: University of Virginia

data_processing:
All analysis code available at 'https://github.com/arun-b-dutta/RNA-seq-Analysis'.
The raw sequencing reads (FASTQ files) were aligned to the UCSC mm10 mouse genome build using the splice-aware read aligner HISAT2.
Samtools was used for quality control filtering/ PCR duplicate removal.
Reads were sorted into features with HTSeq, produing the processed .txt files.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample- 24hr post TBI.  Matrix table with raw gene counts for every gene and every sample- 1wk post TBI.

source_name: brain

extract_protocol:
Brains were removed, flash frozen on dry ice, and homogenized. RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing by GENEWIZ

value: brain-right hemisphere (olfactory bulbs and cerebellum removed)

tag: age

value: 10 wk old males, 1 wk post TBI

tag: treatment

value: Ablation + TBI


title: Calcified aortic valve 1

source_name: Calcified aortic valve 1


title: 1wk_Ab_Sham_rep2

value: Ablation + Sham


title: 1wk_Ab_Sham_rep3


title: MET-B-005-AT

value: Pre

value: DNMTi


title: 1wk_Ab_TBI_rep3


title: KLM1_shSNAI2_1

city: Kyoto

first: Kenji

last: Masuo

address: 54 Shogoinkawahara-cho

department: Graduate School of Medicine

institute: Kyoto university

hyb_protocol: 0.6 μμg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μμl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μμl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: cell line, 70-90% confluence, replicate1

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μμg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was extracted using the NucleoSpin RNA Plus (MACHEREY-NAGEL, Germany) following the manufacturer’s instructions.

value: human pancreatic cancer


title: 1wk_noAb_TBI_rep2

value: No Ablation + TBI


title: 1wk_noAb_TBI_rep3


title: 1wk_Ab_TBI_rep2


title: Sph_control_1

source_name: spheroid, 3D culture, day7, replicate1


title: 1wk_noAb_Sham_rep3

value: No Ablation + Sham


title: KLM1_control_1


title: 1wk_Ab_TBI_rep1


title: Sph_control_2

source_name: spheroid, 3D culture, day7, replicate2


title: 1wk_noAb_TBI_rep4


title: 1wk_Ab_Sham_rep1


title: 1wk_noAb_Sham_rep4


title: Sph_shSNAI2_2


title: Sph_shSNAI2_1


title: KLM1_control_2

source_name: cell line, 70-90% confluence, replicate2


title: 24hr_Ab_TBI_rep3

value: 10 wk old males, 24 hr post TBI


title: 24hr_Ab_TBI_rep4


title: 1wk_noAb_TBI_rep1


title: 1wk_noAb_Sham_rep2


title: KLM1_shSNAI2_2


title: 24hr_Ab_TBI_rep2


title: 1wk_Ab_Sham_rep4


title: 1wk_noAb_Sham_rep1


title: MET-B-001-ST

source_name: Tumor biopsy

value: Breast cancer


title: Calcified aortic valve 3

source_name: Calcified aortic valve 3

value: aortic valve


title: 24hr_Ab_TBI_rep1


title: 24hr_Ab_Sham_rep2


title: 24hr_Ab_Sham_rep4


title: 24hr_Ab_Sham_rep3


title: 24hr_Ab_Sham_rep1


title: 24hr_noAb_TBI_rep3


title: 24hr_noAb_TBI_rep2


title: 24hr_noAb_Sham_rep4


title: 24hr_noAb_TBI_rep4


title: 24hr_noAb_TBI_rep1


title: 24hr_noAb_Sham_rep2


title: 24hr_noAb_Sham_rep3


title: 24hr_noAb_Sham_rep1


title: WT MEF cells - replicate 3

source_name: Mouse embryonic fibroblasts

value: Mouse embryonic fibroblasts

value: wild type


title: Thoracic aorta of GK rat [M07]

city: Chengdu

first: chan

last: yang

address: No 39 Shi-er-qiao Road

institute: Hospital of Chengdu University of Traditional Chinese Medicine

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
Fragments  Per Kilobase of exon per Megabase of library size (FPKM) 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: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Thoracic aorta of GK rat

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Cat#74106, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: GK

value: Thoracic aorta

value: 7-8 Weeks

tag: group

value: Diabetic Macroangiopathy


title: Thoracic aorta of control rat [C09]

value: Wistar

value: control


title: Thoracic aorta of GK rat [M10]


title: Thoracic aorta of control rat [C10]


title: Thoracic aorta of GK rat [M08]


title: Thoracic aorta of control rat [C08]


title: Thoracic aorta of control rat [C07]


title: Thoracic aorta of GK rat [M09]


title: NW41

city: Pittsburgh

first: Mark

middle: Jay

last: Shlomchik

state: PA

address: W1052 Biomedical Science Tower 200 Lothrop St

department: Department of Immunology

institute: University of Pittsburgh

data_processing:
RNA-Seq reads were aligned to hg19 with STAR with default parameters
HTSeq was used to obtain gene read counts.
DESeq2 was used to normalize the read counts for library size difference correction.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include read counts for each sample

source_name: blood

growth_protocol: Human tissues were obtained from deceased organ donors at the time of organ acquisition for clinical transplantation as previously described, and through an approved research protocol and MTA with LiveOnNY, the organ procurement organization for the New York metropolitan area. The information on donors used in this study is presented in Supplemental Table 1. All donors were previously healthy, were free of cancer, and were serologically negative for Hepatitis B, C, and HIV. Isolation of tissues from organ donors does not qualify as "human subjects" research, as confirmed by the Columbia University IRB.

extract_protocol:
CD19+ CD27+ memory B cells (MBC) were sorted into 4 subsets defined by CD45RB and CD69 from spleen of four individual donors (D193 (D1), D256 (D2), D260 (D3), and D305 (D4), see Table S1). RNA was isolated from cell pellets using the RNeasy Mini or Micro Kit (Qiagen), and RNA concentration and quality was assessed using an Agileumnt 2100 Bioanalyzer instrument (Agileumnt Technologies).
Libraries were prepared using the Illumina TruSeq Total RNA kit with ribosomal depletion or the SMART-Seq v4 Ultra Low Input RNA Kit for sequencing and Illumina Nextera XT DNA Library preparation kit following the manufacturer's protocol

treatment_protocol: Tissue samples were maintained in cold saline and brought to the laboratory within 2-4hrs of organ procurement. Spleen and intestinal samples were processed using enzymatic and mechanical digestion resulting in high yields of live lymphocytes. Lymphocytes from blood samples were isolated by using centrifugation through a lymphopure gradient (BioLegend).

tag: b cell type

value: MBC

tag: cd69 status

tag: cd45rb  status

tag: labels

tag: donor

value: blood


title: NW35

source_name: ileum

value: naive

tag: tissue

value: ileum


title: NW33

source_name: spleen

value: spleen


title: NW31


title: NW40


title: NW39


title: NW30


title: NW27


title: NW26


title: NW29


title: NW24


title: SNARE -DsRed_3

city: Wageningen

first: Hieng-Ming

last: Ting

state: Gelderland

address: Droevendaalsesteeg 1

department: Laboratory of Plant Physiology

country: Netherlands

institute: Wageningen University

data_processing:
RNA libraries were sequenced via Illumina HiSeq 2000
The reads were assembled by using the available N. benthamiana genome sequence as template , which was carried out using the SOAPaligner/SOAP2 program with the default settings (Li et al., 2009).
The gene expression level was calculated using the RPKM method (Reads Per kb per Million reads) (Mortazavi et al., 2008).
Genome_build: N. benthamiana genome sequence (Bombarely et al., 2012)
Supplementary_files_format_and_content: Result is presented in txt table, which included the coverage of each gene, expression of gene(RPKM), total number of reads that aligned to gene, the description of gene. There are 5 columns in each xls file and meanings of each column as follows: GeneID                 GeneID        Uniq_reads_num(****)   number of reads which aligned to just one position of gene, the total uniq_reads show in the Parentheses of the front rank                               PS:Here we refer to all genes. we don't refer to the transcriptome.One gene can correspond to several transcript. The uniq_reads number result in                                 MapStatistics refer to the reads aligned to just one position of transciript        Length                 length of gene        Coverage               the coverage of gene, calculate method:the base number of all Uniq_reads in the gene/the base number of gene        RPKM                   expression, see the algorithm in help documentation of Analysis Report

organism: Nicotiana benthamiana

source_name: agroinfiltrated leaf

growth_protocol: N. benthamiana plants were grown in the greenhouse

extract_protocol:
RNA was extracted using the RNeasy® Plant Mini kit with on-column RNase-Free DNase digestion
RNA libraries were prepared for sequencing using standard Illumina protocols, performed by BGI, China

value: leaf

tag: development stage

value: 5-week-old plant

tag: harvest time

value: seven days post agroinfiltration

tag: contain agrobaterium


title: NW23


title: SNARE -DsRed_2


title: NW22


title: SNARE -DsRed_1


title: phyB-RL rep1

city: Shanghai

first: weiwei

last: Qi

address: No 99 Shangda Road

institute: Shanghai  University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR 10 whole genome using bowtie0.12.5  with parameters default
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al,Nature methods 2008.Replicate sample's reads were merged to count.
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Seeds were germinated on 1/2 MS plates plus 1% sucrose and placed at 4°C for 4 days and then tranferred to white light for 12 h before placed in red light for another 4 days

extract_protocol:
RNA was extracted with RNAprep plant kit from TIANGEN, followed by DNase I (Takara) treatment. Quality control was performed with Agilent Bioanalyser. mRNA was purifed with Dynabeads® Oligo (dT)25（Life).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ecotype

tag: genotype

value: phyB mutant

tag: light condition

value: 60 μmol/m2/s red light

tag: growth time

value: 4.5 days


title: pBin-DsRed_ 2

value: pBin+DsRed-RNAi


title: Col-RL reanalysis rep2

value: WT


title: pBin-DsRed_3


title: NW34


title: phyB-RL rep2


title: pBin-DsRed_1


title: Infected leaf, 24 hpi, replicate 1

city: Poznan

first: Agnieszka

last: Zmienko

address: Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry PAS

description: Biological replicate 1 of 2.

hyb_protocol: Microarrays were hybridized in HybArray 12 workstation (PerkinElmer) in 2x SSC and 0.08% SDS at 55 degrees for 12 h, then washed with 2x SSC, 0.5% SDS @ 55 deg, 0.5x SSC @ RT, 0.05x SSC @ RT, 5 min each and dried by blowing with nitrogen.

scan_protocol: Arrays were scanned with ScanArray Express scanner (PerkinElmer) at 100% laser intensity and variable PMT settings.

data_processing: Images were analyzed with GenePix 6.1 software (Molecular Devices) using morphological opening background subtraction method with default parameters. Data were further analyzed in R/Bioconductor environment, using limma package (Smyth and Speed 2003; Smyth 2004; Ritchie et al. 2007). Foreground and background intensities were read in with “genepix.custom” function. After background subtraction, printtip-loess normalization within arrays was applied, followed by scaling the log-ratios to have the same median-absolute-deviation (MAD) across arrays.

organism: Brassica oleracea var. capitata

source_name: leaf, infected with fungus, 24 hpi

label_protocol: 15 µg of RNA was reverse-transcribed using SuperScript Indirect cDNA Labeling System (Invitrogen) and coupled with 5 μl of Cy3 or Cy5 ester dye (Amersham Pharmacia).

growth_protocol: The seeds of Brassica oleracea var. capitata f. alba (white cabbage) cultivar 'Glory of Einkhuizen' were grown in soil: perlite mixture (15:1) in a plant growth room under fluorescent light (Super TLD Philips 865) at 100 µmol m-2 s-1, 16 h day/8 h night photoperiod, at temperature 22°C ± 1°C and relative humidity of approximately 65%. The wild type strain of A. brassicicola (ATTC 96836) was grown on potato dextrose agar plates (PDA, Difco) for 7-10 days under the same conditions as plants, but in the dark.

extract_protocol: Total RNA was extracted with RNeasy Plant Mini Kit (QIAGEN) and samples were DNase-digested with TURBO DNA-free kit (Ambion

treatment_protocol: The second leaves of four-leaf mature B. oleracea plants were inoculated with the A. brassicicola conidial suspension at concentration of 5 x 105 conidia per ml of distilled water or distilled water in case of control plants by putting one or two 10 µl drops per leaf or spraying the leaves using a Nalgene aerosol spray bottle (Sigma-Aldrich). In all experiments, plants were inoculated 4-6 hours after switching on the light (about 10.00-12.00 a.m. local time). The inoculated plants were incubated in transparent plastic boxes to maintain high humidity.

tag: forma

value: alba

tag: infection

value: infected with fungus

tag: time

value: 24 hpi

source_name: pooled control

value: mock


title: NW21


title: CST- SNARE_2


title: NW20


title: Infected leaf, 48 hpi, replicate 2

description: Biological replicate 2 of 2.

source_name: leaf, infected with fungus, 48 hpi

value: 48 hpi


title: Infected leaf, 48 hpi, replicate 1

description: Biological replicate 1 of 2.


title: CST- SNARE_3


title: Infected leaf, 12 hpi, replicate 2

description: Biological replicate 2 of 2.

source_name: leaf, infected with fungus, 12 hpi

value: 12 hpi


title: Col-RL reanalysis rep1


title: Infected leaf, 24 hpi, replicate 2

description: Biological replicate 2 of 2.


title: Infected leaf, 0 hpi, replicate 2

description: Biological replicate 2 of 2.

source_name: leaf, infected with fungus, 0 hpi

value: 0 hpi


title: Infected leaf, 12 hpi, replicate 1

description: Biological replicate 1 of 2.


title: CST- SNARE_1


title: Infected leaf, 0 hpi, replicate 1

description: Biological replicate 1 of 2.


title: CST-DsRed_3

value: CST+DsRed-RNAi


title: Col-RL rep2

growth_protocol: Seeds were germinated on 1/2 MS plates plus 1% sucrose and placed at 4°C for 4 days and then tranferred to white light for 12 h before placed in darkness or red light for another 4 days


title: NW18

value: MBC

value: spleen


title: Col-D rep2

value: Dark


title: Col-RL rep1


title: NW17


title: NW16

value: ileum


title: T-cells Donor 7

city: Zuerich

first: Yannik

last: Severin

state: ZH

address: Otto-Stern-Weg 3

department: Biology

data_processing:
Basecalls performed using CASAVA version 1.8
Illumina adapters and sequences of poor quality were removed using TrimGalore v.0.6.0 with options --nextera.  polyA and polyT sequences were removed with cutadapt v.2.0 using the parameters -b A{10} -b T{10}.
Reads were aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a with default parameters and the --quantMode GeneCounts flag to obtain read counts per gene.
Reads per gene were obtained using the --quantMode GeneCounts option in STAR. Ambiguous reads (spanning multiple genes) were not counted.
Genome_build: GRCh38, v.93

source_name: Immune cells

extract_protocol:
T-cells were isolated from healthy PMBCs via a column based extraction method (Miltenyi Biotec). RNA extraction of the isolated cells was performed with a Quick-RNA MiniPrep Kit by Zymo.
cDNA libraries were obtained according to protocols published by Picelli et al, 2014. Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample).

value: Blood

tag: cell type

value: T-cells

tag: disease state

value: Healthy


title: T-cells Donor 8


title: T-cells Donor 10


title: T-cells Donor 9


title: NW15

tag: b cell type

value: naive

tag: cd69 status


title: T-cells Donor 4


title: NW13

tag: cd45rb  status

tag: labels


title: NW9

tag: donor

tag: tissue


title: NW19


title: T-cells Donor 2


title: NW10


title: NW11


title: NW14


title: T-cells Donor 1


title: NW8


title: NW12


title: T-cells Donor 6


title: CST-DsRed_1

value: leaf

tag: development stage

value: 5-week-old plant

tag: harvest time

value: seven days post agroinfiltration


title: T-cells Donor 3