title: day 10 anti PD-1 + muGITR-L bispecific mouse 5 tumor

city: Redwood City

first: Kyle

last: Halliwill

address: 1500 Seaport Blvd

institute: Abbvie Inc

description: group 5 50 tumor

hyb_protocol: Samples processed as per NanoStringTM protocols.

scan_protocol: NanoStringTM nCounter.

data_processing: Normalization method NanoStringTM nSolver 4.0 advanced analysis, normalised to standards on NanoStringTM panel per their protocol.

source_name: tumor

label_protocol: Labeled as to group, mouse number and tissue.

growth_protocol: The adherent colorectal carcinoma cell line CT26 (cat. # CRL-2638, ATCC, Manassas, VA) and mammary gland adenocarcinoma cell line JC (cat. # CRL-2116, ATCC, Manassas, VA) were expanded and maintained in RPMI-1640 (Roswell Park Memorial Institute medium cat. # SH30021.02 GE Healthcare Life Sciences) supplemented with 10% FBS (cat. # F442-500 Sigma-Aldrich).

extract_protocol: Total RNA processed from formalin fixed paraffin embedded (FFPE) blocks as per NanoStringTM protocols.

treatment_protocol: FFPE blocks prepared.

value: CT26 tumor

value: anti-PD-1 + muGITR-L bispecific

tag: time point

value: day 10


title: day 10 anti PD-1 + muGITR-L bispecific mouse 4 tumor

status: Public on Dec 20 2021

type: RNA

state: California

country: USA

description: group 5 49 tumor

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue

tag: treatment


title: day 10 anti PD-1 + muGITR-L bispecific mouse 1 tumor

description: group 5 46 tumor


title: day 10 anti PD-1 + muGITR-L bispecific mouse 3 tumor

description: group 5 48 tumor


title: day 10 anti PD-1 + muGITR-L bispecific mouse 2 tumor

description: group 5 47 tumor


title: day 10 anti PD-1 + isotype-GITR-L mouse 5 tumor

description: group 4 45 tumor

value: anti-PD-1 + isotype-GITR-L


title: day 10 anti PD-1 + isotype-GITR-L mouse 4 tumor

description: group 4 44 tumor


title: Control-PL12-3

type: SRA

city: Barcelona

first: Mireia

last: Bundó

state: Barcelona

address: C/ de la vall moronta, edifici CRAG, campus UAB

country: Spain

institute: CRAG-Centre for research in agricultural genomics

library_source: transcriptomic

data_processing:
Base calling and demultiplexing. Processing raw data for both format conversion and demultiplexing by Bcl2Fastq 2.20 version of the Illumina pipeline.
Adapters masking. Adapter sequences are masked with Cutadapt v1.11 from raw fastq data using the following parameters: --anywhere (on both adapter sequences) --overlap 5 --times 2 --minimum-length 35 --mask-adapter
Quality check was performed on the raw sequencing data, removing low quality portions while preserving the longest high quality part of NGS reads. The minimum length was set to 35 bp and the quality score to 25. The software BBDuk was used for this scope.
The high quality reads were aligned against the Oryza sativa Japonica Group (IRGSP-1.0/Ensembl release 42) and the Oryza sativa Indica Group (ASM465v1/Ensembl release 42)with STAR aligner (version 2.5.2b).
FeatureCounts (version 1.5.1) was used to calculate gene expression values as raw fragment counts. Normalization was applied to the raw fragment counts by using the Trimmed Mean of M -values (TMM) normalization and Fragments Per Kilobase Million (FPKM) normalization
Statistical analysis of read counts was performed with R, with the HTSFilter package to remove low-expressed genes and the edge R package.
Genome_build: IRGSP-1.0
Genome_build: ASM465v1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with FPKM for every gene and every sample

organism: Oryza sativa

source_name: Leaves

growth_protocol: Rice seeds were pregerminated in water for 7 days and then transferred to hydroponic tanks with modified Yoshida solution for 7 days. Plants were grown at 28/26ºC day/night with a 14h/10h light/dark cycle.

extract_protocol:
Total RNA was extracted using the Maxwell RSC Plant RNA Kit (Promega).
TruSeq Stranded mRNA kit (Illumina, San Diego, CA) has been used for library preparation following the manufacturer’s instructions (library type: fr-firstrand).

treatment_protocol: Salt treatment was applied by supplementing the nutrient solution with 80 mM NaCl for 24 h. Control plants were not supplemented with NaCl. Leaves from salt-treated plants (80 mM NaCl, 24h of treatment) and untreated control plants were harvested (3 replicates per genotype and condition, 4 plants per replicate).

value: Control

tag: line

value: Leaves


title: ksb015_WT flu

city: Iowa City

first: Damian

middle: J

last: Krysan

state: IA

address: 25 South Grand, 2040 ML

department: Division of Pediatrics & Infectious Disease

institute: University of Iowa Hospitals and Clinics

data_processing:
Read quality was confirmed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).  Reads were mapped to the Candida glabrata CBS138 genome using HISAT2 in paired-end read mode. Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype, Nat Biotechnol 37, 907–915 (2019). Sorted and indexed bam files of mapped reads were prepared using Samtools (https://www.htslib.org). Mapped reads were assembled onto annotated CBS138 genes with Stringtie using the -eB parameter and raw gene count tables were generated using the prepDE.py script that is provided with Stringtie. Pertea M., Kim D., Pertea G.M., Leek J.T., Salzberg S.L. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown, Nature Protocols 11, 1650-1667 (2016). Differential expression and statistical analysis were done from raw counts using the DESeq2 R package. The default negative binomial general linear model and Wald test were used. Correction for multiple hypothesis tests was done using the default Benjamini and Hochberg method. Love M.I., Huber W., Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15, 550 (2014).
Genome_build: s03-m01-r23 from Candida Genome Database on 2021 July 11
Supplementary_files_format_and_content: matrix table with relative abundance measurements to wild type

organism: Nakaseomyces glabratus

source_name: Exponential phase growth yeast cells with subsequent fluconazole treatment for 4 hours

growth_protocol: Growth in YPD to exponential phase with subsequent fluconazole treatment for 4 hours

extract_protocol:
Cells were collected via centrifugation from growth medium and RNA harvested according to manufacturer protocol for MasterPure Yeast RNA Purification Kit
Libraries were prepared with paired end adapters using Illumina chemistries per manufacturer’s instructions, and sequencing of libraries were performed with read lengths of approximately 150bp with at least 50 million reads per sample.

tag: genotype

value: wild-type


title: TRV-NbDMLs/TYLCCNV-IR-Bisulfite-seq_rep3

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

country: China

institute: Tsinghua University

library_source: genomic

data_processing:
PCR duplicated reads were removed and the unique reads with read counts above 5 were retained for cytosine methylation analysis
Genome_build: TYLCCNV(AJ319675.1);BSCTV(U02311.1)
Supplementary_files_format_and_content: the processed data files contain the unique sequence and their counts

molecule: genomic DNA

organism: Nicotiana benthamiana

source_name: leaves

growth_protocol: N. benthamiana plants were grown in a controlled growth chamber at 25°C under a 16 h light/8 h dark photoperiod and A. thaliana plants were grown in a growth room under long photoperiod conditions (16 h light, 22°C/8 h dark, 18°C).

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5019), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)67. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).

treatment_protocol: For TYLCCNV inoculation following VIGS, A. tumefaciens cultures carrying pCambia1300, pTRV1 plus pTRV2-GUS (TRV-GUS) or pTRV1 plus pTRV2-NbDMLs (TRV-NbDMLs) at an OD600 = 0.2 were inoculated into N. benthamiana plants at the eight-leaf stage. One week later, A. tumefaciens cultures harboring pBinPLUS (mock) or infectious clones of TYLCCNV or TYLCCNV plus TYLCCNB (TYLCCNV+B) at an OD600 = 1.0 were inoculated into pCambia1300-, TRV-GUS- or TRV-NbDMLs-infiltrated plants. For other TYLCCNV inoculation, N. benthamiana plants at the eight-leaf stage were directly agroinoculated with infectious clones of TYLCCNV, TYLCCNV+B or TYLCCNV+BV17A. Four-week-old A. thaliana were used for BSCTV inoculation as described before27. Symmetrically infected leaves were harvested at 10 days post inoculation.

value: Wild-type

tag: infection

value: TYLCCNV


title: ksb014_WT flu


title: ksb016_upc2A∆ flu


title: day 10 anti PD-1 + isotype-GITR-L mouse 3 tumor

description: group 4 43 tumor


title: C3ci

city: Stanford

first: Terence

last: Theisen

address: Fairchild Science Building D305

institute: Stanford Univeristy

data_processing:
alignment with HT-SEQ and STAR against concatenated human and Toxoplasma genomes
filtered aligned reads to only include Toxoplasma reads
spreading data from different samples into one matrix
C0 data was renamed to C4 for the paper
Genome_build: Human (GRCh38.p13) and Toxoplasma ME49 (ToxoDB v51)
Supplementary_files_format_and_content: counts, rows are different toxoplasma genes (by gene 6id) and columns are the samples

organism: Toxoplasma gondii

extract_protocol:
Samples in TRIzol were thawed on ice and all RNA was extracted using a standard chloroform/isopropanol RNA purification, per the manufacturer’s instructions. Following the final ethanol wash, pellets were resuspended in 4 μL of Pre-RT buffer (RNase-free water (ThermoFisher 10977023), dNTPs (ThermoFisher R0194; 2.5 mM), and RNA inhibitor (TaKaRa 2313; 10 units/reaction), Oligo-dT (IDT; 2.5 μM)) except for sample C3c, which was resuspended in 8 uL of Pre-RT buffer and divided into two aliquots. For reverse transcription, 6 μL of Reverse Transcriptase Buffer (5x First strand buffer (TaKaRa 639538), Betaine (Sigma B0300; 1 M), DTT - Dithiothreitol  (TaKaRa 639538; 1.66 mM), TSO - Template Switch Olgio (IDT; 1 μM), MgCl2 (ThermoFisher AM9530G; 7 mM), and SmartScribe Reverse Transcriptase (TaKaRa 639538; 100 units/reaction)) were added to each of the samples (28). Per the instructions for the reverse transcriptase kit, the samples were run on a thermocycler with the following steps: 1) 42°C for 90 minutes; 2) 50°C for 2 minutes; 3) 42°C for 2 minutes; 4) repeat steps 2 and 3 (10x); 5) 70°C for 15 minutes. Next, cDNA was amplified using HiFi Hotstart Ready Mix (ThermoFisher 50-196-5217) with ISPCR (IDT; 0.1 μM) and Lambda Exo (New England BioLabs MO262S; 1 units/reaction) for 12 or 14 total cycles.
Amplified cDNA was purified using AMPure XP beads (Beckman Coulter A63881) and concentration was determined by Qubit 4.0 using the 1x dsDNA HS kit (ThermoFisher Q33230). Nextera XT indices were used to generate libraries from 1 ng of cDNA material for each sample following the instructions provided by Illumina (Illumina FC-131-1096 and FC-131-2001). Library preparations were purified using AMPure XP beads and checked for quality using the Agilent Bioanalyzer at Stanford Functional Genomics Facility (SFGF). A sequencing pilot was done with libraries pooled in equal amount and run on one NextSeq500 lane with high output, 1x75 sequencing. Using the results from this sequencing a second library was prepared based on the fraction of unique Toxoplasma reads to total reads for a library in an attempt to generate approximately the same number of Toxoplasma reads per sample. The second library was run over two lanes NextSeq500 lanes with high output, 1x75 sequencing at the SFGF. Results from the different lanes for each clone or subclone were pooled prior to alignment.

value: RH

tag: developmental stage

value: tachyzoite

value: wildtype

tag: clone

value: derived from Clone 3, split RNA sample


title: day 10 anti PD-1 + isotype-GITR-L mouse 2 tumor

description: group 4 42 tumor


title: Control-PL12-1


title: Control-PL12-2


title: day 10 anti PD-1 + isotype-GITR-L mouse 1 tumor

description: group 4 41 tumor


title: ksb012_upc2A∆ rox1∆

source_name: Exponential phase growth yeast cells

growth_protocol: Growth in YPD to exponential phase

value: upc2A_delta rox1_delta


title: C2c

value: derived from Clone 2


title: Control-IL22-1


title: ksb011_upc2A∆ rox1∆


title: rpb1-T,FSP3, MNase-seq

city: Salt Lake City

first: Tim

last: Formosa

state: UT

address: 15 N Medical Dr East RM 4100

department: Biochemistry

institute: University of Utah School of Medicine

description:
MNase resistant fraction
rpb1-T-FSP.normal.bw
rpb1-T-FSP.skinny.bw
rpb1-T-FSP.subnuc.bw

data_processing:
Reads were aligned to the yeast genome version SacCer3 using Novocraft novoalign version 3.7.1, with adapter trimming, allowing one random multi-mapping alignment.
Duplicate alignments were randomly sub-sampled to a level of 40% relative to non-duplicate reads using bam_partial_dedup, version 1.7, https://github.com/tjparnell/HCI-Scripts/tree/master/BamFile.
Fragment coverage was generated using bam2wig version 1.52 (https://github.com/tjparnell/biotoolbox) with an extension of 150 bp, skipping chrMito and high-copy number features including telomeric and rDNA loci, depth normalized to Reads Per Million, averaging between replicates, and converting to bigWig format.
Genome_build: SacCer3
Supplementary_files_format_and_content: bigWig files representing the nucleosomal fragment coverage (140-170 bp) or subnucleosomal fragments (90-120 bp), normalized to Reads Per Million, and averaged between replicates were generated.

organism: Saccharomyces cerevisiae

source_name: Whole yeast cells

growth_protocol: Cultures were grown to logarithmic phase in rich medium at 30° C, treated with 1% formaldehyde for 20 minutes, then harvested by centrigugation.

extract_protocol:
Glycine (final 0.2 M) was added to quench crosslinking and cells were washed with 1X Tris-buffered saline. Cell walls were removed with 500 U lyticase, 37° 20 minutes, or until >90% of cells were spheroplasted and collected by centrifugation. Cells were lysed in MNase digestion buffer and 10 U MNase, then incubated at 37° for 15 minutes, and the reaction stopped, diluted, and crosslinks reversed by incubating 5 hours at 65°. DNA was precipitated with ethanol, then treated with RNase A, followed by Proteinase K digestion and purification on Qiagen Qiaquick columns.
Sequencing libraries were constructed using NEBNext® Multiplex Oligos (Index Primers Set 1 and Set 2) and NEBNext® ChIP-seq Library Prep Reagent Set for Illumina. Ligated samples were subjected to 50 bp paired-end sequencing in an Illumina NovaSeq 6000 sequencer.

tag: growth protocol

value: Rich medium, 30°, log phase

tag: sample


title: rpb1-T,FSP1, MNase-seq


title: C3a

value: derived from Clone 3


title: rpb1-T,FSP2, MNase-seq


title: day 10 isotype-GITR-L mouse 5 tumor

description: group 3 40 tumor

value: CT26 tumor

value: isotype-GITR-L


title: ksb010_upc2A∆ rox1∆


title: day 10 isotype-GITR-L mouse 3 tumor

description: group 3 38 tumor

value: day 10


title: ksb009_rox1∆


title: WT2, MNase-seq

description:
MNase resistant fraction
WT.normal.bw
WT.skinny.bw
WT.subnuc.bw


title: C1c

value: derived from Clone 1


title: ksb008_rox1∆


title: WT3, MNase-seq


title: C2a


title: C3b


title: C2b


title: C1b


title: day 10 isotype-GITR-L mouse 2 tumor

description: group 3 37 tumor


title: day 10 isotype-GITR-L mouse 4 tumor

description: group 3 39 tumor


title: ksb013_WT flu


title: ksb007_rox1∆


title: C1a


title: day 10 anti PD-1 mouse 5 tumor

description: group 2 35 tumor


title: day 10 isotype-GITR-L mouse 1 tumor

description: group 3 36 tumor


title: ksb006_upc2A∆


title: rpb1-TPY,FSP3

description:
9998-1-3 #3
16000X27_190517_A00421_0067_BH7JKMDRXX_S27

data_processing:
Fastq reads from each lane were first concatenated, then trimmed of adapters with Cutadapt (version 1.16) with sequences AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT, allowing for a minimum adapter sequence overlap of 6 bp (option -O) and minimum trimmed read length of 20 bp (option -m).
Trimmed reads were aligned to the genome using STAR (version 2.6.1b), using the SacCer3 genome (version R64) and Ensembl annotation (release 94) to build the index. Alignments were made using a basic two-pass mode, allowing for an alignment intron maximum of 1100 bp and alignment mates gap maximum of 2000 bp.
Alignment counts were collected over gene annotation using Subread featureCounts (version 1.6.3) in paired mode, using reverse strand (option -s 2) and counting competing features with the largest overlap (option --largestOverlap). A custom annotation file lacking dubious genes and including estimated UTRs was used.
Depth-normalized, replicate-mean, stranded coverage tracks for visualization were generated using BioToolBox bam2wig application (version 1.68) with options --smartcov --rpm --bw --mean --strand --flip --nosecondary. An exclusion list was provided for excluding high copy number intervals (rDNA, telomeres).
Alignments were counted over the middle 70% of known transcripts with the application BioToolBox get_datasets (version 1.68), using the options --feature transcript --fstart 0.15 --fstop 0.85 --method ncount --strand antisense. Custom annotation representing transcripts with UTRs and lacking dubious genes was used.
Differential expression analysis was performed using DESeq2 (v1.22.2) and the hciR package (https://github.com/HuntsmanCancerInstitute/hciR) to simplify the R code.
Genome_build: SacCer3
Supplementary_files_format_and_content: Depth-normalized, replicate-mean, stranded coverage tracks; DESeq2 output

source_name: whole yeast cells_rpb1-TPY,FSP

growth_protocol: Cultures were grown to logarithmic phase in rich medium at 30° C and harvested by centrigugation.

extract_protocol:
RNA was extracted from cell pellets using an acid phenol procedure followed by pelleting in CsCl2, resuspension, ethanol precipitation, and purification by Qiagen Rneasy mini kit.
Total RNA samples (100-500 ng) were hybridized with Ribo-Zero Gold to substantially deplete cytoplasmic and mitochondrial rRNA from the samples.  Stranded RNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded Total RNA Library Prep Gold kit (20020598) with TruSeq RNA UD Indexes (20022371).  Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 1.30 nM in preparation for Illumina sequence analysis. Each library was sequenced on two lanes of an Illumina SP Flow Cell on a Novaseq 6000 instrument as 2 x 50 bp reads.

tag: growth condition

tag: genotype/variation


title: WT1, MNase-seq


title: rpb1-TPY,FSP2

description:
9998-1-3 #2
16000X26_190517_A00421_0067_BH7JKMDRXX_S26


title: C4

value: collected from Clone 4


title: ksb005_S81_upc2A∆


title: day 10 anti PD-1 mouse 4 tumor

description: group 2 34 tumor


title: rpb1-TPY,FSP1

description:
9998-1-3 #1
16000X25_190517_A00421_0067_BH7JKMDRXX_S25


title: C3cii


title: ksb005_S1_upc2A∆


title: day 10 anti PD-1 mouse 3 tumor

description: group 2 33 tumor


title: day 10 anti PD-1 mouse 1 tumor

description: group 2 31 tumor


title: ksb004_upc2A∆


title: rpb1-FSP3

description:
9800-8-4 #3
16000X24_190517_A00421_0067_BH7JKMDRXX_S24

source_name: whole yeast cells_rpb1-FSP


title: rpb1-FSP1

description:
9800-8-4 #1
16000X22_190517_A00421_0067_BH7JKMDRXX_S22


title: ksb002_WT YPD


title: day 10 Isotype control mouse 5 tumor

description: group 1 30 tumor

value: Isotype control


title: ksb003_WT YPD

value: wild-type


title: rpb1-TPY3

description:
9992-1-3 #3
16000X21_190517_A00421_0067_BH7JKMDRXX_S21

source_name: whole yeast cells_rpb1-TPY


title: day 10 Isotype control mouse 4 tumor

description: group 1 29 tumor


title: ksb001_WT YPD


title: day 10 Isotype control mouse 3 tumor

description: group 1 28 tumor


title: rpb1-TPY2

description:
9992-1-3 #2
16000X20_190517_A00421_0067_BH7JKMDRXX_S20


title: PR_rep3

city: Zhoushan

first: Jianhua

last: Liu

address: 1 Zheda Road, Lin-cheng street

institute: Ocean College, Zhejiang University

data_processing:
Using FastQC v0.11.2 to check the qualities of sequenced reads
Sequenced Reads were removed adaptor-like sequences of 12-nts at the 5’-end and low quality nucleotide with different length at the 3’-end using Trimmomatic v0.32
De novo assembly using Trinity v2.2.0 with processed reads (ALL biosamples) (--CPU 8  --KMER_SIZE 25)
Transcriptome were annotated by running BLASTX to 6 algal genomes (evalue < 1e-7) (-max_target_seqs 1 -outfmt 6 -evalue 1e-7)
Expression levels of EST were determined using Trinity-bundled perl script align_and_estimate_abundance.pl which utilizes RSEM to calculate TPM values (--est_method RSEM --aln_method bowtie2 --trinity_mode)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Nannochloropsis sp.

source_name: microalgae

growth_protocol: All the algal cells were grown in f/2 medium in glass flask with orbital shaking at 100 rpm, 25°C, under continuous illumination of 50 μM photon m-2 s-1.

extract_protocol:
Total RNA was extracted from sample cells using TRIzol Plus RNA Purification System (Invitrogen-Life Technologies Co., Carlsbad, CA, USA) according to manufacturer’s protocol, ribosomal RNA were removed prior to library construction.
RNA libraries were prepared for sequencing using standard Hiseq x-ten protocols

treatment_protocol: Cells at log phase were subjected to medium shift to f/2 without phosphorus and with phosphorus. Cells three days after medium shift were collected for RNA-seq analysis. Cells that grown in f/2 without phosphorus were shifted to f/2 with phosphorus replenishment, and then after three days collected for RNA-seq analysis.

value: PJ12 strain

tag: growth phase

value: log phase

tag: culture medium

value: f/2 medium

value: three days after medium shift to f/2 with phosphorus


title: PR_rep1


title: day 10 anti PD-1 mouse 2 tumor

description: group 2 32 tumor


title: day 10 Isotype control mouse 1 tumor

description: group 1 26 tumor


title: rpb1-FSP2

description:
9800-8-4 #2
16000X23_190517_A00421_0067_BH7JKMDRXX_S23


title: day 10 Isotype control mouse 2 tumor

description: group 1 27 tumor


title: PD-PR_rep3

value: three days after medium shift to f/2 with phosphorus replenishment


title: day 8 anti PD-1 + muGITR-L bispecific mouse 5 tumor

description: group 5 25 tumor

value: anti-PD-1 + muGITR-L bispecific

value: day 8


title: day 8 anti PD-1 + muGITR-L bispecific mouse 4 tumor

description: group 5 24 tumor


title: PD-PR_rep2


title: PR_rep2


title: spt6-R,KK2

description:
9910-1-4 #2
16000X17_190517_A00421_0067_BH7JKMDRXX_S17

source_name: whole yeast cells_spt6-R,KK


title: spt6-R,KK3

description:
9910-1-4 #3
16000X18_190517_A00421_0067_BH7JKMDRXX_S18


title: rpb1-TPY1

description:
9992-1-3 #1
16000X19_190517_A00421_0067_BH7JKMDRXX_S19


title: day 8 anti PD-1 + muGITR-L bispecific mouse 3 tumor

description: group 5 23 tumor


title: day 8 anti PD-1 + muGITR-L bispecific mouse 2 tumor

description: group 5 22 tumor


title: spt6-KK2

description:
9859-2-2K #2
16000X14_190517_A00421_0067_BH7JKMDRXX_S14

source_name: whole yeast cells_spt6-KK


title: spt6-R,KK1

description:
9910-1-4 #1
16000X16_190517_A00421_0067_BH7JKMDRXX_S16


title: spt6-KK1

description:
9859-2-2K #1
16000X13_190517_A00421_0067_BH7JKMDRXX_S13


title: spt6-KK3

description:
9859-2-2K #3
16000X15_190517_A00421_0067_BH7JKMDRXX_S15


title: PD-PR_rep1


title: day 8 anti PD-1 + isotype-GITR-L mouse 5 tumor

description: group 4 20 tumor

value: anti-PD-1 + isotype-GITR-L


title: BC-2

city: Philadelphia

first: Chunjie

state: PENNSYLVANIA

address: Colket Translational Research Building, 3501 Civic Center BLVD

department: Center for Computational and Genomic Medicine

institute: Children's Hospital of Philadelphia

data_processing:
Raw data (raw reads) of fastq format were processed with Fastp (v 0.23.0), an ultra-fast FASTQ preprocessor with useful quality.
The clean reads were mapped to the mus musculus genome (mm10) using the HISAT2 software (v 2.1.0).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: brain

extract_protocol:
The mouse brain and skull tissue contains ischemic and peri-ischemic regions were harvested for RNA sequencing. Total RNA was extracted using TRIzol Reagent (Thermo Fisher Scientific Inc.) and further treated with DNase to remove genomic DNA contamination. The mRNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA), and was then used for RNA-sequencing library preparation with the NEBNext Ultra II mRNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA). The library was performed using Illumina sequencing with the paired-end 2 x 150 sequencing mode.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BALB/c

value: brain cortex

value: control for brain


title: BC-1


title: BC-3


title: BD2-2

value: 2 day of ischemic injury in brain


title: day 8 anti PD-1 + isotype-GITR-L mouse 4 tumor

description: group 4 19 tumor

value: CT26 tumor


title: STAT5 ChIP-seq for CD127high monocytes

city: Beijing

first: Bin

last: Zhang

address: Zheng Yutong Building room D311

description: ChIP-seq

data_processing:
ChIP-seq paired-end reads were collected. The first-end reads were used for analyses and trimmed to 50 bp, and adapter sequences were further trimmed from the ends of reads by Cutadapt (v1.14), and the reads that failed to pass the quality control (Q > 10) were discarded.
Trimmed ChIP-seq reads in fastq files were aligned to human genome (UCSC hg38) using Bowtie (v1.1.2) to generate alignment file of uniquely mapped reads with maximum allowed mismatch of 2 (-m 1 -n 2) for each alignment seed.
The STAT5 ChIP-seq alignment file was used to call peaks for significantly STAT5 enriched regions using MACS2 (v2.1.1) (FDR < 0.05).
Genome_build: hg38
Supplementary_files_format_and_content: STAT5_4H_peaks.txt file contains the genomic geographic information for STAT5 ChIP-seq peaks called by MACS2.

organism: Homo sapiens

source_name: Buffy coat

extract_protocol: Buffy coat from healthy blood donor was diluted by PBS, and PBMC were isolated by Ficol gradient. CD14+ monocytes were isolated from PBMC with anti-CD14 magnetic beads (Miltenyi Biotec). CD14+ monocytes were treated with LPS for 6 h. Stimulated cells were firstly stained for surface CD127 and then fixed in 1% methanol-free formaldehyde. Then, cells were collected for FACS-based sorting of CD127high monocytes. Sorted cells were used to perform anti-STAT5 ChIP experiment by using the SimpleChIP enzymatic ChIP kit (Cell Signaling Technology) according to the manufacturer’s instructions. ChIP-seq library construction with NEBNext® Ultra™ II DNA Library Prep kit (NEB, E7103S). Constructed DNA library was sent out for sequencing on an Illumina Hiseq X-ten platform for an average of 20 million unique reads per sample.

tag: cell type

value: Human CD14+ monocytes

tag: disease state

value: Healthy

tag: cell subtype

tag: chip antibody

value: STAT5 antibody (9363S, Cell Signaling Technology)


title: spt6-R3

description:
8662-2-2K #3
16000X12_190517_A00421_0067_BH7JKMDRXX_S12

source_name: whole yeast cells_spt6-R

value: Rich medium, 30°, log phase


title: spt6-R2

description:
8662-2-2K #2
16000X11_190517_A00421_0067_BH7JKMDRXX_S11


title: PD_rep1

tag: strain

value: PJ12 strain

value: f/2 medium-P

value: three days after medium shift to f/2 without phosphorus


title: PD_rep3

value: log phase

tag: treatment


title: PD_rep2


title: spt6-R1

description:
8662-2-2K #1
16000X10_190517_A00421_0067_BH7JKMDRXX_S10


title: day 8 anti PD-1 + muGITR-L bispecific mouse 1 tumor

description: group 5 21 tumor

tag: tissue

tag: time point


title: BD2-1


title: BD2-3


title: day 8 anti PD-1 + isotype-GITR-L mouse 3 tumor

description: group 4 18 tumor


title: WT 3

description:
8127-7-4 #3
16000X3_190517_A00421_0067_BH7JKMDRXX_S3

source_name: whole yeast cells_WT

value: WT


title: WT_rep2

city: Seoul

first: Woo-Jeong

last: Shon

address: 103 Daehak-ro, Jongno-gu,

department: College of Medicine

country: South Korea

institute: Seoul National University

description:
replicate 2
9482914090_E

hyb_protocol: Amplified cRNA (1.5 Pg) was hybridized on Mouse WG-6 v.2 Expression BeadChip arrays (Illumina, San Diego, CA, USA), containing more than 45,281 well-annotated Ref transcripts.

scan_protocol: The array chips were scanned on a BeadArray reader (BeadStation 500G; Illumina)

data_processing: The raw microarray data were pre-processed through three steps: i) background correction was performed, and ii) the data were log-transformed to log2 scale and ჰ) normalized by the quantile normalization method implemented in Genome Studio software (Illumina).

label: biotin

source_name: splenic Gr-1+ cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Gr-1+ (Ly6G+) cells were MACS-purified from splenocytes on day 7 after allogeneic (or syngeneic) BMT. Cells were used for RNA extraction when the purity was higher than 97%. For microarray hybridization, total RNA was isolated and purified using a DNA-free RNA isolation kit (RNAqueous-4PCR kit; Ambion, Austin, TX, USA).

value: splenic Gr-1+ cells


title: KO_rep3

description:
replicate 3
9482914106_F

value: B6.129-Ido1tm1Alm/J (IDO KO)


title: WT 2

description:
8127-7-4 #2
16000X2_190517_A00421_0067_BH7JKMDRXX_S2


title: WT 1

description:
8127-7-4 #1
16000X1_190517_A00421_0067_BH7JKMDRXX_S1


title: KO_rep2

description:
replicate 2
9482914106_E


title: day 8 anti PD-1 + isotype-GITR-L mouse 1 tumor

description: group 4 16 tumor

source_name: tumor

value: anti-PD-1 + isotype-GITR-L

value: day 8


title: WT_rep3

description:
replicate 3
9482914090_F


title: day 8 isotype-GITR-L mouse 5 tumor

description: group 3 15 tumor

value: isotype-GITR-L


title: KO_rep1

description:
replicate 1
9482914106_D


title: syngeneic non-GVHD_rep2

description:
replicate 2
9482914090_B


title: WT_rep1

description:
replicate 1
9482914090_D


title: day 8 isotype-GITR-L mouse 4 tumor

description: group 3 14 tumor


title: BD6-1

value: BALB/c

value: brain cortex

value: 6 day of ischemic injury in brain


title: BD6-3


title: SC-3

source_name: skull

value: Interparietal bone

value: control for skull


title: syngeneic non-GVHD_rep3

description:
replicate 3
9482914090_C


title: Gns_4

first: Zhiqiang

last: Yan

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

data_processing:
Illumina bcl2fastq version 2.19 were used to the basecalling.
Sequenced reads with low quality bases, adapters and artificial sequences introduced during the experimental processes were trimmed by in house scripts.
The trimmed clean reads were aligned to the Ensembl human GRCh37 reference using Tophat2 (v2.1.0) with default settings (Trapnell et al., 2009).
Cufflinks (v2.2.1) with defualt settings was used to quantify transcription levels of annotated genes (Trapnell et al., 2010), and FPKM were calculated
Genome_build: Ensembl GRCh37
Supplementary_files_format_and_content: Tab-delimited text file includes FPKMs for each sample

source_name: pre-ovulatory follicle from Gns-stimulated patients

extract_protocol:
Isolated granulosa cells were transferred into lysis buffer. The reverse transcription reaction was performed on the whole-cell lysate and terminal deoxynucleotidyl transferase was used to add a poly A tail to the 3′ end of the first-strand cDNAs, and then 20 cycles of PCR were performed to amplify the single-cell cDNA
RNA libraries were prepared according to instructions of Kappa Hyper Prep Kit (Kappa Biosystems).

tag: subject status

value: Gns-stimulated patient

value: granulosa cells from pre-ovulatory follicle

tag: gonadotropins

value: Yes


title: BD6-2


title: CHA732A2

city: Sydney

first: Ruby

middle: CY

last: Lin

state: NSW

address: 176 Hawkesbury Road, Westmead

country: Australia

institute: The Westmead Institute for Medical Research

description: Gene expression from islets from 16-week C57BL/KsJ db/db mice.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix Mouse Gene ST 2.0 or Affymetrix Mouse Gene ST 2.1 GeneChips. They were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Interrogating probes were imported, RMA normalized and RMA background corrected, Quantile normalization, Log probes using base 2 and Probeset summarization is Median Polish (Partek Genome Suite v6.6 (6.151022).

source_name: islet

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were taken from the Garvan Institute breeding colonies. Animals were kept under conventional conditions with free access to food and water.

extract_protocol: Total RNA from islets was extracted using RNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: Islets of C57BL/KsJ db/db and C57BL/6J ob/ob mice, and their age-matched lean control mice were isolated for RNA extraction.

value: C57BL/KsJ db/db

value: Pancreatic islets

tag: age

value: 16 weeks


title: syngeneic non-GVHD_rep1

description:
replicate 1
9482914090_A


title: M249  Vemurafenib and Selumetinib resistant through double minutes

type: genomic

city: Foster City

first: Kai

last: Song

state: CA

address: 333 Lakeside Dr

institute: Gilead Sciences, Inc

hyb_protocol: Purified labeled DNA samples were prepared for hybridization, which took place on Agilent 8x60K CGH microarray slides at 67 oC for 6 hours.

scan_protocol: The slides were scanned using the Agilent SureScan Microarray Scanner (Agilent).

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

source_name: M249 melanoma cell line resistant to Vemurafenib and Selumetinib (2µM) through BRAF amplification in double minute format

label_protocol: Sample DNA and reference DNA (Agilent, Santa Clara, CA) were differentially labeled with cyanine-3 (CY3) and cyanine-5 (Cy5) dyes using the GenetiSure Amplification and Labeling Kit (Agilent) according to the manufacturer’s protocol.

growth_protocol: All cells were cultured in RPMI 1640 with L-glutamine , 10% (v/v) fetal bovine serum, and 1% (v/v) streptomycin. All cells were maintained in a humidified 5% CO2 incubator.

extract_protocol: genomic DNA was extracted using Qiagen DNeasy Blood & Tissue Kits following manufacturer's instructions.

treatment_protocol: VSR cell lines were generated by exposing cells to step-wise increasing doses of Vemurafenib and Selumetinib until 2µM.

tag: gender

value: female

tag: cell line

tag: phenotype

value: Vemurafenib and Selumetinib resistant

source_name: commercially available genomic DNA

tag: sample type

value: control


title: SC-2


title: day 8 isotype-GITR-L mouse 3 tumor

description: group 3 13 tumor

value: CT26 tumor


title: Gns_3


title: M249 Parental

source_name: M249 melanoma cell line

value: parental


title: day 8 anti PD-1 + isotype-GITR-L mouse 2 tumor

description: group 4 17 tumor

value: anti-PD-1 + isotype-GITR-L

value: day 8


title: SC-1

value: BALB/c


title: High dose bispecific treated TILs replicate 2

data_processing:
The  sequencing  data  was  processed  using  CellRanger  pipeline  (version  3.0.2,  10X Genomics) for demultiplexing, barcode assignment, single cell gene counting  and cluster analysis. The reference genome, mm10(GRCm38.93), was provided by 10x Genomics. The cells with greater than 500 unique molecule identifiers  (UMI)  were  recovered,  and  their  gene  expression  data  were  used  for  downstream  analysis.
Genome_build: refdata-cellranger-mm10-3.0.0 downloaded from 10x Genomics website(10X Genomics, Pleasanton, CA)
Supplementary_files_format_and_content: bam files; matrix of cell bacodes and gene expression counts

source_name: CT26 mouse tumor model

growth_protocol: The adherent colorectal carcinoma cell line CT26 (cat. # CRL-2638, ATCC, Manassas, VA) was expanded and maintained in RPMI-1640 (Roswell Park Memorial Institute medium cat. # SH30021.02 GE Healthcare Life Sciences) supplemented with 10% FBS (cat. # F442-500 Sigma-Aldrich).

extract_protocol:
After treatment, tumors were dissected from the mice. Single cell suspensions were generated using a  tumor  dissociation  kit  (Miltenyi  Biotec,  Bergisch  Gladbach,  Germany)  according  to  the manufacturer’s instructions. CD45+ TILs were enriched from these samples by CD45 positive selection (Stemcell technologies, Vancouver, BC). Cell viability and number were calculated using ViCell Blue and single cell RNA sequencing was performed using Chromium and GEM-RT 3’ V3 chemistry kit according to manufacturer’s instruction (10X Genomics, Pleasanton, CA). Single cell droplets were generated and RT-PCR reactions were performed to barcode the cells and cDNAs. First-strand cDNA were further amplifed and enriched for downstream library prep and sequencing.
According to manufacturer’s instruction (10X Genomics, Pleasanton, CA), full-length cDNA were amplifed from barcoded and reverse transcrited cDNAs. 3'end of cDNA were selected for library generation.  Sequencing  was  performed  on  NextSeq  550  (Illumina,  San  Diego,  CA)  instrument  following  of  manufacturer’s instruction  (10X  Genomics).

treatment_protocol: Samples were treated with vehicle, low dose (10 mg/kg) or high dose (30 mg/kg) PD-1 GITR-L bispecific antibody

value: tumor

value: CD45+ bead enriched TILs


title: day 8 isotype-GITR-L mouse 2 tumor

description: group 3 12 tumor

value: isotype-GITR-L


title: High dose bispecific treated TILs replicate 1

value: high dose (30 mg/kg) PD-1 GITR-L bispecific antibody


title: Low dose bispecific treated TILs replicate 2

value: low dose (30 mg/kg) PD-1 GITR-L bispecific antibody


title: day 8 isotype-GITR-L mouse 1 tumor

description: group 3 11 tumor


title: S4-3

value: Interparietal bone

value: 4 day of ischemic injury in skull


title: CHA732A1

description: Gene expression from islets from 16-week C57BL/KsJ control mice.

value: C57BL/KsJ control

value: Pancreatic islets


title: Gns_1

value: Gns-stimulated patient

value: granulosa cells from pre-ovulatory follicle

value: Yes


title: day 8 anti PD-1 mouse 5 tumor

description: group 2 10 tumor

value: CT26 tumor


title: S4-2


title: Ctrl_2

source_name: pre-ovulatory follicle from natural-cycle patients

value: natural-cycle patient

value: No


title: S4-1


title: day 8 anti PD-1 mouse 3 tumor

description: group 2 8 tumor

value: day 8


title: Ctrl_3


title: Ctrl_1


title: day 8 anti PD-1 mouse 2 tumor

description: group 2 7 tumor


title: 2u_6

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

description: P2 baseline #3

data_processing:
Data Formatting - bcltofastq-2.19.0
Data Cleaning - fastp 0.20.0, --in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j ${SAMPLE}_fastp.json
Genome Alignment - STAR_2.7.0f, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification - subread-1.6.4, featurecounts, -s 0 -t exon -g gene_name
Genome_build: GRCm38.p6 + Gencode-M22 Annotation
Supplementary_files_format_and_content: Raw gene counts

source_name: Heart

extract_protocol:
In preparation for flow cytometry, each heart was minced in 1% Bovine Serum Albumin (BSA, Sigma Alldrich) and 0.1% glucose (Fisher Scientific) in Hank’s Balanced Salt Solution without calcium and magnesium (HBSS, Fisher Scientific). Tissue fragments and solution were collected into a conical tube with 2% fetal bovine serum (Gemini) in PBS. After centrifugation and resuspension into collagenase/dispase solution (Sigma Aldrich), samples were shaken at 37°C for 20 to 30 minutes, with longer time for samples collected at later postnatal stages.  Samples were centrifuged and resuspended in 2% FBS in PBS prior to filtration using a 40 µm filter. Cells were centrifuged and resuspended in 1% BSA/ 0.1% glucose/ HBSS solution for flow cytometry. Endogenous GFP and tdTomato fluorescence were utilized to sort the cells, in which GFP labeled the TCF21-lineage and tdTomato labeled all other cells. BV421 Rat anti-mouse CD140a was used to label the PDGFR-alpha cells (BD Biosciences Part Number BDB562774 at a 1/100 dilution). Dapi (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) at 1:10,000 was used to label live/dead cells (Fisher). Cells were sorted using an 18-color BD fluorescence activated cell sorting (FACS) Aria II (BD biosciences).
Total RNA was isolated using TRIzol Reagent (Thermo Fisher, Carlsbad, CA) per manufacturer’s recommendations. RNA concentration was determined with the NanoDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). 1ng of total RNA was pre-amplified with the SMARTer Ultra Low Input kit v4 (Clontech, Mountain View, CA) per manufacturer’s recommendations. The quantity and quality of the subsequent cDNA was determined using the Qubit Fluourometer (Life Technnologies, Carlsbad, CA) and the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). 150pg of cDNA was used to generate Illumina compatible sequencing libraries with the NexteraXT library preparation kit (Illumina, San Diego, CA) per manufacturer’s protocols. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the NextSeq550 DNA sequencer (Illumina, San Diego, CA). Single end reads of 75nt were generated for each sample.

treatment_protocol: Tcf21-MerCreMer; Rosa-mTmG mice were injected with Tamoxifen to label cardiac fibroblasts at P1, and given apical resection surgery or sham surgery at P2 or P10.  GFP labeled cardiac fibroblasts were isolated for RNA-sequencing at baseline (no injury or sham) at P2 or P10 or 3 days following sham/resection surgery at P2 or P10.

value: Tcf21-lineage cardiac fibroblasts

value: baseline (no treatment)


title: S2-2

value: BALB/c

value: 2 day of ischemic injury in skull


title: S2-3


title: Gns_2


title: day 8 anti PD-1 mouse 1 tumor

description: group 2 6 tumor


title: Vehicle treated TILs replicate 1

value: tumor

value: CD45+ bead enriched TILs

value: vehicle


title: 2u_4

description: P2 baseline #1


title: prp4k3-small RNA seq_R1-repeat3

city: College Station

first: Lin

last: WANG

state: Texas

address: 2123 Norman Borlaug Center Rm112A

institute: Texas A&M University

data_processing:
RNA  Library selection cDNA
small RNA  Library selection size fractionation
Library source transcriptomic
Genome_build: TAIR_10
Supplementary_files_format_and_content: Sequenced reads were mapped to genome by tophat2 to generate bam files  bam files were sorted by samtools  sorted bam files were count by Htseq-count.  use edgeR to get normalized reads

organism: Arabidopsis thaliana

source_name: three-week-old plant leaves

extract_protocol:
Total RNA was extracted using Trizol reagent from leaves of three week-old plants.RNA-seq library was prepared with TruSeq Stranded Total RNA kit (Illumina) according to the manufacturer’s manual. small RNA-seq libarary was prepared according to D. Sun, Z. Ma, J. Zhu, X. Zhang, in Arabidopsis Protocols. (Springer, 2021), pp. 225-254..
RNA libraries were prepared for sequencing using standard Illumina protocols

value: leaves

tag: developmental stage

value: 3 weeks

value: untreatment


title: prp4k3-small RNA seq_R1-repeat2


title: Low dose bispecific treated TILs replicate 1

value: low dose (30 mg/kg) PD-1 GITR-L bispecific antibody


title: Mnase-Seq rpb1-TPY-AAA,FSP+-KRR+3

description:
rpb1-TPY-AAA,FSP+-KRR+3
MNase resistant fraction
rpb1-TPY-FSP.ext150.bw

data_processing:
Reads were aligned to the yeast genome version SacCer3 using Novocraft novoalign version 3.7.1, with adapter trimming, allowing one random multi-mapping alignment.
Duplicate alignments were randomly sub-sampled to a level of 40% relative to non-duplicate reads using bam_partial_dedup, version 1.7, https://github.com/tjparnell/HCI-Scripts/tree/master/BamFile.
Fragment coverage was generated using bam2wig version 1.52 (https://github.com/tjparnell/biotoolbox) with an extension of 150 bp, skipping chrMito and high-copy number features including telomeric and rDNA loci, depth normalized to Reads Per Million, averaging between replicates, and converting to bigWig format.
Genome_build: SacCer3
Supplementary_files_format_and_content: bigWig files representing the nucleosomal 150 bp fragment coverage, normalized to Reads Per Million, and averaged between replicates.

source_name: Whole yeast cells

extract_protocol:
Glycine (final 0.2 M) was added to quench crosslinking and cells were washed with 1X Tris-buffered saline. Cell walls were removed with 500 U lyticase, 37° 20 minutes, or until >90% of cells were spheroplasted and collected by centrifugation. Cells were lysed in MNase digestion buffer and 10 U MNase, then incubated at 37° for 15 minutes, and the reaction stopped, diluted, and crosslinks reversed by incubating 5 hours at 65°. DNA was precipitated with ethanol, then treated with RNase A, followed by Proteinase K digestion and purification on Qiagen Qiaquick columns.
Sequencing libraries were constructed using NEBNext® Multiplex Oligos (Index Primers Set 1 and Set 2) and NEBNext® ChIP-seq Library Prep Reagent Set for Illumina. Ligated samples were purified by electrophoresis through 1.5% agarose, excising the 270 bp mononocleosome band (150 bp + 120 bp adaptors), purified on a Qiagen gel extraction kit. Samples were then subjected to 50 bp single-end sequencing in an Illumina Hiseq2500 sequencer.

tag: growth

value: Rich medium, 30 C, log phase

tag: genotype

tag: sample


title: prp4k3-small RNA seq_R1-repeat1


title: 2u_5

description: P2 baseline #2

tag: cell type


title: day 8 Isotype control mouse 5 tumor

description: group 1 5 tumor

data_processing: Normalization method NanoStringTM nSolver 4.0 advanced analysis, normalised to standards on NanoStringTM panel per their protocol.

extract_protocol: Total RNA processed from formalin fixed paraffin embedded (FFPE) blocks as per NanoStringTM protocols.

value: Isotype control


title: Mnase-Seq rpb1-FSP+-KRR+3

description:
rpb1-FSP+-KRR+3
MNase resistant fraction
rpb1-FSP.ext150.bw


title: S2-1

value: Interparietal bone


title: day 8 anti PD-1 mouse 4 tumor

description: group 2 9 tumor

value: CT26 tumor


title: day 8 Isotype control mouse 4 tumor

description: group 1 4 tumor


title: day 8 Isotype control mouse 3 tumor

description: group 1 3 tumor


title: Mnase-Seq rpb1-TPY-AAA3

description:
rpb1-TPY-AAA3
MNase resistant fraction
rpb1-TPY.ext150.bw


title: Col-0-small RNA seq_R1-repeat3


title: Col-0-small RNA seq_R1-repeat2


title: 2a_6

description: P2 resection + 3 days  #3

value: apical resection


title: day 8 Isotype control mouse 2 tumor

description: group 1 2 tumor

value: day 8


title: Col-0-small RNA seq_R1-repeat1


title: day 8 Isotype control mouse 1 tumor

description: group 1 1 tumor


title: 2s_3

description: P2 sham + 3 days  #1

value: Tcf21-lineage cardiac fibroblasts

value: sham


title: Mnase-Seq spt6-KK-AA3

description:
spt6-KK-AA3
MNase resistant fraction
spt6-KK.ext150.bw


title: se-2-RNA-seq_R1-repeat3


title: 2s_6

description: P2 sham + 3 days  #3


title: Vehicle treated TILs replicate 2


title: 21

description: P2 resection + 3 days  #1


title: se-2-RNA-seq_R1-repeat2


title: Mnase-Seq WT3

description:
WT3
MNase resistant fraction
WT.ext150.bw


title: day 10 anti PD-1 + muGITR-L bispecific mouse 4 Draining lymph node

description: group 5 49 DLN

source_name: draining lymph node

value: draining lymph nodes

value: anti-PD-1 + muGITR-L bispecific

value: day 10


title: 2a_2

description: P2 resection + 3 days  #2


title: 2s_5

description: P2 sham + 3 days  #2


title: Mnase-Seq spt6-R-H3

description:
spt6-R-H3
MNase resistant fraction
spt6-R.ext150.bw


title: se-2-RNA-seq_R1-repeat1


title: Mnase-Seq spt6-R-H, KK-AA3

description:
spt6-R-H, KK-AA3
MNase resistant fraction
spt6-RKK.ext150.bw

value: spt6-R-H, KK-AA3


title: 10u_5P

description: P10 baseline #3

value: baseline (no treatment)


title: 10u_4P

description: P10 baseline #2


title: day 10 anti PD-1 + muGITR-L bispecific mouse 3 Draining lymph node

description: group 5 48 DLN


title: Mnase-Seq rpb1-TPY-AAA,FSP+-KRR+2

description:
rpb1-TPY-AAA,FSP+-KRR+2
MNase resistant fraction
rpb1-TPY-FSP.ext150.bw


title: prp4k3-RNA-seq_R1-repeat3

value: leaves


title: 10u_3

description: P10 baseline #1


title: day 10 anti PD-1 + muGITR-L bispecific mouse 2 Draining lymph node

description: group 5 47 DLN


title: prp4k3-RNA-seq_R1-repeat2

value: 3 weeks


title: Mnase-Seq rpb1-FSP+-KRR+2

description:
rpb1-FSP+-KRR+2
MNase resistant fraction
rpb1-FSP.ext150.bw


title: prp4k3-RNA-seq_R1-repeat1

value: untreatment


title: Mnase-Seq rpb1-TPY-AAA2

description:
rpb1-TPY-AAA2
MNase resistant fraction
rpb1-TPY.ext150.bw


title: day 10 anti PD-1 + muGITR-L bispecific mouse 5 Draining lymph node

description: group 5 50 DLN


title: 10s_6

description: P10 sham + 3 days  #2


title: Col-0-RNA-seq_R1-repeat3


title: day 10 anti PD-1 + muGITR-L bispecific mouse 1 Draining lymph node

description: group 5 46 DLN


title: Mnase-Seq spt6-R-H, KK-AA2

description:
spt6-R-H, KK-AA2
MNase resistant fraction
spt6-RKK.ext150.bw

value: spt6-R-H, KK-AA2


title: day 10 anti PD-1 + isotype-GITR-L mouse 5 Draining lymph node

description: group 4 45 DLN

value: anti-PD-1 + isotype-GITR-L


title: 10s_3

description: P10 sham + 3 days  #1


title: day 10 anti PD-1 + isotype-GITR-L mouse 3 Draining lymph node

description: group 4 43 DLN


title: Col-0-RNA-seq_R1-repeat2


title: day 10 anti PD-1 + isotype-GITR-L mouse 2 Draining lymph node

description: group 4 42 DLN


title: 10a_5

description: P10 resection + 3 days  #3


title: day 10 anti PD-1 + isotype-GITR-L mouse 4 Draining lymph node

description: group 4 44 DLN


title: Col-0-RNA-seq_R1-repeat1


title: 10a_4

description: P10 resection + 3 days  #2


title: Mnase-Seq spt6-KK-AA2

description:
spt6-KK-AA2
MNase resistant fraction
spt6-KK.ext150.bw

value: Rich medium, 30 C, log phase


title: Mnase-Seq WT2

description:
WT2
MNase resistant fraction
WT.ext150.bw


title: 350Veh

city: New York

first: Miguel

last: Fribourg

address: 1 Gustave Levy Pl

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

description:
126 bp paired-end reads
350Veh

data_processing:
Raw RNaseq fastq reads were trimmed with bbtools and QC assesed with FASTQC
Reads were aligned to mouse genome (mm10) using STAR (v. 2.4.0h)
Gene-assignment and count of RNA reads were performed with HTseq.
Genome_build: mm10
Supplementary_files_format_and_content: The processed file includes the feature counts of each gene, arranged in columns for each of the samples

source_name: Treg_ day 14 post-tx, vehicle treated animal

growth_protocol: RNA from CD4+Foxp3-YFP+ T cells cells were  sorted from the spleen of BALB/c transplant recipients at day 14 post-transplant

extract_protocol:
RNA from the sorted cells was isolated using the RNeasy Plus Micro kit (QIAGEN).
Quality control was performed by bioanalyzer (Agilent), and RNA samples with an RNA integrity number (RIN) > 8 were processed for library preparation using SMARTer Ultra Low Input reagent (Takara) and Nextera XT DNA (Illumina) library preparation kits
Libraries were sequenced with paired-end reads of 126bp on a HiSeq2500 sequencer (Illumina) to reach 50 million read pairs per sample. For each group, IFN or vehicle, and genotype, data are derived from three distinct mice, with separate processing from cell sorting to sequencing.

treatment_protocol: Mice were transplant recipients of BALB/c hearts, and were treated with CTLA-4 Ig and IFNb or vehicle.

value: Spleen

value: Treg (CD4+Foxp3+ cells)

value: Foxp3-YFP C57BL/6 background

value: Vehicle


title: 101

description: P10 resection + 3 days  #1

value: Tcf21-lineage cardiac fibroblasts

value: apical resection


title: Mnase-Seq rpb1-TPY-AAA,FSP+-KRR+1

description:
rpb1-TPY-AAA,FSP+-KRR+1
MNase resistant fraction
rpb1-TPY-FSP.ext150.bw


title: Mnase-Seq spt6-R-H2

description:
spt6-R-H2
MNase resistant fraction
spt6-R.ext150.bw


title: βC1-OX-V17A-2/BSCTV-IR-Bisulfite-seq_rep3

data_processing:
PCR duplicated reads were removed and the unique reads with read counts above 5 were retained for cytosine methylation analysis
Genome_build: TYLCCNV(AJ319675.1);BSCTV(U02311.1)
Supplementary_files_format_and_content: the processed data files contain the unique sequence and their counts

source_name: leaves

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5046), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)94. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).

tag: infection

value: BSCTV


title: day 10 anti PD-1 + isotype-GITR-L mouse 1 Draining lymph node

description: group 4 41 DLN

tag: strain

value: draining lymph nodes


title: 325IFN

description:
126 bp paired-end reads
325IFN

source_name: Treg_ day 14 post-tx, IFNbeta treated animal

tag: treatment

value: Interferon beta


title: day 10 isotype-GITR-L mouse 5 Draining lymph node

description: group 3 40 DLN

tag: tissue

value: isotype-GITR-L

value: day 10


title: 10s_7

description: P10 sham + 3 days  #3

value: sham


title: Mnase-Seq rpb1-FSP+-KRR+1

description:
rpb1-FSP+-KRR+1
MNase resistant fraction
rpb1-FSP.ext150.bw


title: 324IFN

description:
126 bp paired-end reads
324IFN


title: day 10 isotype-GITR-L mouse 4 Draining lymph node

description: group 3 39 DLN

tag: time point


title: Mnase-Seq rpb1-TPY-AAA1

description:
rpb1-TPY-AAA1
MNase resistant fraction
rpb1-TPY.ext150.bw


title: Mnase-Seq spt6-R-H, KK-AA1

description:
spt6-R-H, KK-AA1
MNase resistant fraction
spt6-RKK.ext150.bw

value: spt6-R-H, KK-AA1


title: day 10 isotype-GITR-L mouse 3 Draining lymph node

description: group 3 38 DLN


title: βC1-OX-V17A-2/BSCTV-IR-Bisulfite-seq_rep1

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5044), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)92. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: 323Veh

description:
126 bp paired-end reads
323Veh


title: day 10 isotype-GITR-L mouse 2 Draining lymph node

description: group 3 37 DLN


title: day 10 isotype-GITR-L mouse 1 Draining lymph node

description: group 3 36 DLN


title: βC1-OX-V17A-1/BSCTV-IR-Bisulfite-seq_rep3

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5043), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)91. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: 321Veh

description:
126 bp paired-end reads
321Veh


title: βC1-OX-V17A-1/BSCTV-IR-Bisulfite-seq_rep2

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5042), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)90. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: 318Veh

description:
126 bp paired-end reads
318Veh


title: Mnase-Seq spt6-R-H1

description:
spt6-R-H1
MNase resistant fraction
spt6-R.ext150.bw


title: βC1-OX-2/BSCTV-IR-Bisulfite-seq_rep3

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5040), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)88. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: Mnase-Seq spt6-KK-AA1

description:
spt6-KK-AA1
MNase resistant fraction
spt6-KK.ext150.bw


title: βC1-OX-V17A-1/BSCTV-IR-Bisulfite-seq_rep1

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5041), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)89. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: βC1-OX-2/BSCTV-IR-Bisulfite-seq_rep2

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5039), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)87. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: Mnase-Seq WT1

description:
WT1
MNase resistant fraction
WT.ext150.bw


title: EE03 [miRNA-seq]

city: Granada

first: Francisco

last: Hernandez-Torres

state: Granada

address: Avda. de la Investigación, 11

department: Dept. of Biochemistry, Molecular Biology III and Immunology

institute: Universidad de Granada

data_processing:
For trimming and alignment of raw data, fastq sequences reads were uploaded to the European version of Galaxy platform (Afgan et al. Nucleic Acids Res, 2016). Reads were trimmed with Trim Galore software (Galaxy Version 0.4.3.1) and aligned to the built- in mouse reference genome mm10 with RNA STAR Gapped- read mapper for RNA-seq data (Galaxy Version 2.6.0b-2) (Dobin et al. Bioinformatics, 2013).
Parameters for mRNA alignment : --sjdbOverhang 50 --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.08--alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1
Parameters for microRNA alignment : ---sjdbOverhang 1 --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 10 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 16 --outFilterMatchNminOverLread 0 --alignIntronMax 1 --alignSJDBoverhangMin 1000 --alignEndsType EndToEnd
Reads were assigned to mRNAs and microRNAs by using “featureCounts” function from R package “Rsubread” (Liao et al., 2019) version 1.28.1 and mouse annotation file release M19, GRCm38.p6. Uniquely, mapped reads were used to calculate gene expression.
Genome_build: Galaxy built- in mouse reference genome mm10
Supplementary_files_format_and_content: mRNA_counts.xlsx: Matrix table with raw gene counts for every mRNA by sample.
Supplementary_files_format_and_content: miR_counts.xlsx: Matrix table with raw gene counts for every microRNA by sample.

source_name: Embryonic epicardial cells

growth_protocol: PE samples were obtained by manually dissected proepicardial organs of mouse E9.5 embryos. EE samples were obtained by FACS-sorting epicardial cells from mouse E10.5 embryos. At least 5 embryos were collected on each of biological samples. Three distinct samples were analysed per condition.

extract_protocol:
Total RNA from sample was extracted by using RNAqueousTM-Micro Total RNA Isolation Kit (Ambion, AM1931) following manufacturer’s instructions.
[RNA-seq] 2.5 ng of total RNA were used to amplify the cDNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara). 1 ng of amplified cDNA was used to generate barcoded libraries using the Nextera XT DNA library preparation kit (Illumina). Basically, cDNA is fragmented and adapters are added in a single reaction followed by an amplification and clean up. The size of the libraries was checked using the Agilent 2100 Bioanalyzer High Sensitivity DNA chip and their concentration was determined using the Qubit® fluorometer (ThermoFisher Scientific). Libraries were sequenced on a HiSeq 2500 (Illumina) and processed with RTA v1.18.66.3. FastQ files for each sample were obtained using bcl2fastq v2.20.0.422 software (Illumina).
[miRNA-seq] 500 pg of total RNA were used to generate barcoded miRNA-seq libraries using the Bioo NEXTflex Small RNA (BiooScientific). Briefly, 3´ and 5´ SR adapters were first ligated to the RNA sample. Next, reverse transcription followed by PCR amplification was used to enrich cDNA fragments with adapters at both ends. Adapter-ligated cDNA fragments from different samples were pooled and run in a 6% polyacrylamide gel. The 147 nt band, corresponding to the pooled miRNA libraries, was purified from the gel. Finally, the quantity and quality of the pooled miRNA libraries were determined using the Agilent 2100 Bioanalyzer High Sensitivity DNA chip. Libraries were sequenced on a HiSeq 2500 (Illumina) and processed with RTA v1.18.66.3. FastQ files for each sample were obtained using bcl2fastq v2.20.0.422 software (Illumina).

treatment_protocol: No treatment was applied.

value: FACS-sorted epicardial cells


title: EE02 [miRNA-seq]


title: βC1-OX-V17A-2/BSCTV-IR-Bisulfite-seq_rep2

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5045), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)93. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: day 10 anti PD-1 mouse 3 Draining lymph node

first: Kyle

address: 1500 Seaport Blvd

description: group 2 33 DLN


title: EE01 [miRNA-seq]


title: 322IFN

description:
126 bp paired-end reads
322IFN


title: βC1-OX-2/BSCTV-IR-Bisulfite-seq_rep1

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5038), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)86. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: day 10 anti PD-1 mouse 2 Draining lymph node

description: group 2 32 DLN


title: βC1-OX-1/BSCTV-IR-Bisulfite-seq_rep3

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5037), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)85. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: PE03 [miRNA-seq]

source_name: Proepicardial cells

value: Dissected proepicardial cells


title: day 10 anti PD-1 mouse 1 Draining lymph node

description: group 2 31 DLN


title: day 10 Isotype control mouse 5 Draining lymph node

description: group 1 30 DLN

value: Isotype control


title: PE01 [miRNA-seq]


title: βC1-OX-1/BSCTV-IR-Bisulfite-seq_rep2

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5036), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)84. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: PE02 [miRNA-seq]


title: day 10 Isotype control mouse 4 Draining lymph node

description: group 1 29 DLN


title: Col-0/BSCTV-IR-Bisulfite-seq_rep3

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5034), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)82. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: day 10 anti PD-1 mouse 4 Draining lymph node

description: group 2 34 DLN


title: day 10 Isotype control mouse 2 Draining lymph node

description: group 1 27 DLN


title: Col-0/BSCTV-IR-Bisulfite-seq_rep1

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5032), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)80. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: day 10 anti PD-1 mouse 5 Draining lymph node

description: group 2 35 DLN


title: EE03 [RNA-seq]


title: EE02 [RNA-seq]


title: day 10 Isotype control mouse 3 Draining lymph node

description: group 1 28 DLN


title: Col-0/BSCTV-IR-Bisulfite-seq_rep2

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5033), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)81. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: EE01 [RNA-seq]


title: day 10 Isotype control mouse 1 Draining lymph node

description: group 1 26 DLN

extract_protocol: Total RNA processed from formalin fixed paraffin embedded (FFPE) blocks as per NanoStringTM protocols.


title: PE03 [RNA-seq]


title: 60-24-T2_input

city: East Lansing

first: Dae Kwan

last: Ko

state: MI

address: 612 Wilson Rd.  Plant Biology RM 122

department: Plant Research Laboratories

institute: Michigan State University

data_processing:
RNAseq analysis: RNA-seq libraries were constructed using the Illumina TruSeq Stranded mRNA Library (Illumina, San Diego, CA, USA) and sequenced in single-end mode on the Illumina HiSeq 4000 platform (50-nt) at Research Technology Support Facility Genomics Core at Michigan State University (RTSF-MSU). The quality of raw reads was evaluated using FastQC (version 0.11.5). Reads were cleaned for quality and adapters with Cutadapt (version 1.8.1) using a minimum base quality of 20 retaining reads with a minimum length of 30 nucleotides after trimming. Quality-filtered reads were aligned to the Col-0 reference genome (TAIR10) using Bowtie (version 2.2.4) and TopHat (version 2.0.14) with a 10 bp minimum intron length and 15,000 bp maximum intron length. Fragments per kilobase exon model per million mapped reads (FPKM) were calculated using TAIR10 gene model annotation with Cufflinks (version 1.3.0).
ChIP-seq analysis: The quality of raw ChIP-seq reads was evaluated using FastQC (version 0.11.5). Reads were cleaned for quality and adapters with Cutadapt (version 1.8.1) using a minimum base quality of 20 retaining reads with a minimum length of 30 nucleotides after trimming. Quality-filtered reads were aligned to the Col-0 reference genome (TAIR10) using Bowtie (version 1.1.2) with parameters “-n 2 -m 3 -k 1 --threads 7 --best --chunkmbs 256 -q”. Duplicated reads were removed using Samtools (version 1.8). Peak calling was performed using MACS2 (version 2.1.2) in individual samples with input samples pooled for DMSO-only and Tm treated samples and with a relaxed threshold of P-value (--pvalue=1e-2), as recommended by the IDR pipeline (https://sites.google.com/site/anshulkundaje/projects/idr). Peaks across replicates with an IDR < 0.05 were retained for further analysis.
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text file: for RNA-seq: The normalized read values (FPKM) for gene expression in all samples. Sample name consists of genotype, treatment, time-point and biological replicate with hyphen. 28, bzip28. 60, bzip60.
Supplementary_files_format_and_content: for ChIP-seq, UPR-specific binding peak coordinates, annotated genes and scores

source_name: Whole seedlings

growth_protocol: Surface-sterilized seeds were plated on half-strength Linsmaier Skoog (LS) medium (Caisson Labs, Ontario, Canada) supplemented with 1% sucrose (Sigma-Aldrich, St. Louis, MO, USA), and 1.2% Agar (Acumedia, Lansing, MI, USA). Appropriate antibiotics was also added for screening of transgenic lines. After stratification in the dark at 4 °C for 2 days, plates were transferred to a controlled growth chamber with 80 μmol m−2 s−1 under 16 h light:8 h dark with temperature 22 °C.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed in two biological replicates using the NEBNext Ultra II DNA Library Prep Kit (New England BioLabs, Beverly, MA, USA) according to manufacturer’s protocol.

treatment_protocol: 5-day-old seedlings were transferred to half-strength LS liquid buffer containing either 0.5 g/mL Tm (Sigma-Aldrich, St. Louis, MO, USA) or DMSO alone as mock, and treated for 6 hours. After the incubation, the seedlings were transferred to 100x100 square petri dishes with grid (Fisher Scientific, Hampton, NH, USA) containing half-strength LS medium (Caisson Labs, Ontario, Canada) supplemented with 1% sucrose (Sigma-Aldrich, St. Louis, MO, USA), 1.2% Agar (Acumedia, Lansing, MI, USA).

value: whole seedlings

tag: ecotype background

value: 500 ng/mL Tunicamycin treatment

tag: time (hours)

tag: chip antibody


title: βC1-OX-1/BSCTV-IR-Bisulfite-seq_rep1

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5035), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)83. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: day 8 anti PD-1 + muGITR-L bispecific mouse 5 Draining lymph node

city: Redwood City

last: Halliwill

institute: Abbvie Inc

description: group 5 25 DLN

value: anti-PD-1 + muGITR-L bispecific

value: day 8


title: day 8 anti PD-1 + muGITR-L bispecific mouse 4 Draining lymph node

description: group 5 24 DLN


title: 60-24-T1_input


title: day 8 anti PD-1 + muGITR-L bispecific mouse 2 Draining lymph node

description: group 5 22 DLN


title: control-HT rep3 RNA-seq

city: Lincoln

first: Qi

state: NE

address: 354C Hardin NW

department: Statistics

institute: University of Nebraska Lincoln

description: CNTNAP-58 RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Merge the RNA-seq reads from two lanes to one single fastq file.
RNA-seq reads were processed by RSEM pipeline, which called Bowtie internally allowing at most two mismatches and keeping reads mapped to multiple locations, and the multi-mapping reads were distributed fractionally based on RSEM model.We used mm9 assembly as reference genome and GENCODE M1 (NCBIM37) as the gene model. chrY was removed because our subjects were all female.
genome build: mm9
processed data files format and content: RSEM output at gene-level and at isoform-level in the format of tab-delimited text, including calculated expected count, TPM and FPKM for each sample

molecule: polyA RNA

source_name: control-HT rep3 RNA-seq

extract_protocol:
Mice were sacrificed (2 hours after lights on) and whole brains were extracted and immediately flash frozen in 2-methylbutane and dry ice. Striatum tissue was excised by micropunch (1.53 to -0.95 mm posterior to bregma) and approximately 30 milligrams of tissue was homogenized with glass beads (Sigma) and DNA/RNA were extracted using AllPrep DNA/RNA mini kit (Qiagen).
5hmC-enriched libraries were generated using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina sequencing, according to the manufacturer’s protocol. Briefly, the 5hmC-enriched DNA fragments were purified after the adapter ligation step using AMPure XP beads (Agencourt A63880). Approximately 100 ng of total RNA was used for sequence library construction following instructions of NuGen mRNA sample prep kit (cat# 0348). In brief, total RNA was copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. These cDNA fragments went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. These products were gel purified and enriched with PCR to create the final cDNA libraries.

treatment_protocol: Pregnant dams (carrying WT and Cntnap2 het embryos) were exposed to 7 days of variable stress starting at embryonic day 12.5; Offspring were ear-tagged at (postnatal day) (P) 12 and left undisturbed until weaning day (P18), at which time the mice were group housed with same sex littermates.

tag: cntnap2 genotype

value: Heterozygous

tag: prenatal condition

value: Non-stressed

value: brain

tag: brain region

value: striatum

tag: gender

value: female


title: control-WT rep3 RNA-seq

description: CNTNAP-54 RNA-seq

source_name: control-WT rep3 RNA-seq

value: Wild type


title: PE02 [RNA-seq]

tag: developmental stage


title: PE01 [RNA-seq]


title: 60-24-T2_chip

value: GFP (Millipore, ab290)


title: day 8 anti PD-1 + muGITR-L bispecific mouse 3 Draining lymph node

description: group 5 23 DLN

value: draining lymph nodes


title: day 8 anti PD-1 + muGITR-L bispecific mouse 1 Draining lymph node

description: group 5 21 DLN


title: 60-24-T1_chip


title: 60-24-D2_chip

value: mock treatment


title: 60-24-D2_input


title: day 8 anti PD-1 + isotype-GITR-L mouse 5 Draining lymph node

description: group 4 20 DLN

value: anti-PD-1 + isotype-GITR-L


title: 60-24-D1_input


title: day 8 anti PD-1 + isotype-GITR-L mouse 4 Draining lymph node

description: group 4 19 DLN


title: control-WT rep2 RNA-seq

description: CNTNAP-46 RNA-seq

source_name: control-WT rep2 RNA-seq


title: 60-24-D1_chip


title: control-HT rep2 RNA-seq

description: CNTNAP-52 RNA-seq

source_name: control-HT rep2 RNA-seq


title: day 8 anti PD-1 + isotype-GITR-L mouse 3 Draining lymph node

description: group 4 18 DLN


title: control-WT rep1 RNA-seq

description: CNTNAP-45 RNA-seq

source_name: control-WT rep1 RNA-seq


title: 60-12-T2_input


title: control-HT rep1 RNA-seq

description: CNTNAP-47 RNA-seq

source_name: control-HT rep1 RNA-seq


title: 60-12-T2_chip


title: day 8 anti PD-1 + isotype-GITR-L mouse 1 Draining lymph node

description: group 4 16 DLN


title: stress-WT rep3 RNA-seq

description: CNTNAP-43 RNA-seq

source_name: stress-WT rep3 RNA-seq

value: Stressed


title: day 8 isotype-GITR-L mouse 5 Draining lymph node

description: group 3 15 DLN

value: isotype-GITR-L


title: stress-WT rep2 RNA-seq

description: CNTNAP-41 RNA-seq

source_name: stress-WT rep2 RNA-seq


title: day 8 anti PD-1 + isotype-GITR-L mouse 2 Draining lymph node

description: group 4 17 DLN


title: 60-12-T1_chip


title: 60-12-T1_input


title: day 8 isotype-GITR-L mouse 4 Draining lymph node

description: group 3 14 DLN


title: stress-HT rep3 RNA-seq

description: CNTNAP-42 RNA-seq

source_name: stress-HT rep3 RNA-seq


title: day 8 isotype-GITR-L mouse 3 Draining lymph node

description: group 3 13 DLN


title: stress-HT rep2 RNA-seq

description: CNTNAP-40 RNA-seq

source_name: stress-HT rep2 RNA-seq


title: stress-WT rep1 RNA-seq

description: CNTNAP-39 RNA-seq

source_name: stress-WT rep1 RNA-seq


title: 60-12-D2_chip


title: stress-HT rep1 RNA-seq

description: CNTNAP-38 RNA-seq

source_name: stress-HT rep1 RNA-seq


title: 60-12-D2_input


title: control-HT rep3 5hmC-distribution

description:
processed data file: 5hmc_het_control-wt_control.csv, 5hmc_het_stress-het_control.csv
CNTNAP-58 5hmC-Chipseq

data_processing:
Illumina Casava1.7 software used for basecalling.
5hmC reads were aligned to the mm9 genome assembly by Bowtie 0.12.7 allowing no more than two mixmatches, an only keeping uniquely mapped reads.
R package MOSAiCS was used to call peaks from each sample, adjusting for mappability, GC contents and ambiguity score.
Reshape the peaks as 1kb windows around its summit (found by R package segvis), merge the peaks from all three replicates in the same group, and define one such merged peak as a peak for this group if it overlapped with peaks from at least two subjects in thisgroup
For each comparison of two groups, merge the peaks of the two groups as the candidate regions for DhMR identification. Extend the mapped reads to its average length (estimated by SPP for each sample), and count the number of extended reads from each sample in each such candidate region.
genome build: mm9
processed data files format and content:  comma-delimited text of raw 5hmc read counts in the candidate regions for DhMR analysis for each contrast.

source_name: control-HT rep3 5hmC-Chipseq


title: day 8 isotype-GITR-L mouse 2 Draining lymph node

description: group 3 12 DLN

source_name: draining lymph node


title: 60-12-D1_input


title: day 8 isotype-GITR-L mouse 1 Draining lymph node

description: group 3 11 DLN


title: 60-0-T2_input


title: genomic DNA from RNA039VAT

city: Hong Kong

first: Nana

last: Jin

address: CUHK, Sha tin, NT

country: Hong Kong

institute: CUHK

description: genomic DNA from RNA039VAT

hyb_protocol: Bisulfite conversion of DNA was conducted using the EZ DNA methylation kit (Zymo Research)

scan_protocol: DNA methylation was quantified using the Illumina Infinium MethylationEPIC (EPIC) BeadChip (Illumina, CA) run on an Illumina iScan System (Illumina) using the manufacturer’s standard protocol.

data_processing: First, to reduce bias in probe-binding efficiency due to differences in individual genetic makeup, probes that overlapped with SNPs in the last three bases of the target sequence were removed. Second, the Greedycut algorithm was used for iterative removal of probes that produced unreliable measurements. Third, probes that did not target CpG sites or were located on sex chromosomes were removed. The remaining probes were subjected to background correction using the ENmix method and normalization using the beta-mixture quantile normalization method.

label: Cy5 and Cy3

source_name: genomic DNA from RNA039VAT

label_protocol: Standard Illumina Protocol

extract_protocol: Total DNA samples were prepared using proteinase K digestion and phenol extraction.

value: F

value: VAT

tag: disease

value: NoDM


title: genomic DNA from RNA062VAT

description: genomic DNA from RNA062VAT

source_name: genomic DNA from RNA062VAT


title: 60-12-D1_chip

source_name: Whole seedlings

value: whole seedlings

tag: genotype


title: genomic DNA from RNA037VAT

description: genomic DNA from RNA037VAT

source_name: genomic DNA from RNA037VAT

value: DM


title: genomic DNA from RNA041VAT

description: genomic DNA from RNA041VAT

source_name: genomic DNA from RNA041VAT


title: genomic DNA from RNA035VAT

description: genomic DNA from RNA035VAT

source_name: genomic DNA from RNA035VAT


title: day 8 anti PD-1 mouse 5 Draining lymph node

description: group 2 10 DLN

value: day 8


title: control-WT rep3 5hmC-distribution

description:
processed data file: 5hmc_het_stress-wt_control.csv, 5hmc_wt_stress-wt_control.csv, 5hmc_het_control-wt_control.csv
CNTNAP-54 5hmC-Chipseq

source_name: control-WT rep3 5hmC-Chipseq

value: Non-stressed


title: genomic DNA from RNA014VAT

description: genomic DNA from RNA014VAT

source_name: genomic DNA from RNA014VAT

value: M


title: genomic DNA from RNA022VAT

description: genomic DNA from RNA022VAT

source_name: genomic DNA from RNA022VAT


title: genomic DNA from RNA024VAT

description: genomic DNA from RNA024VAT

source_name: genomic DNA from RNA024VAT


title: control-HT rep2 5hmC-distribution

description:
processed data file: 5hmc_het_control-wt_control.csv, 5hmc_het_stress-het_control.csv
CNTNAP-52 5hmC-Chipseq

source_name: control-HT rep2 5hmC-Chipseq

value: Heterozygous

value: brain

value: striatum


title: day 8 anti PD-1 mouse 4 Draining lymph node

description: group 2 9 DLN


title: genomic DNA from RNA045VAT

description: genomic DNA from RNA045VAT

source_name: genomic DNA from RNA045VAT


title: genomic DNA from RNA031VAT

description: genomic DNA from RNA031VAT

source_name: genomic DNA from RNA031VAT


title: day 8 anti PD-1 mouse 3 Draining lymph node

description: group 2 8 DLN


title: genomic DNA from RNA048VAT

description: genomic DNA from RNA048VAT

source_name: genomic DNA from RNA048VAT


title: 60-0-T1_input

value: 500 ng/mL Tunicamycin treatment


title: day 8 anti PD-1 mouse 2 Draining lymph node

description: group 2 7 DLN

value: draining lymph nodes


title: genomic DNA from RNA054VAT

description: genomic DNA from RNA054VAT

source_name: genomic DNA from RNA054VAT


title: genomic DNA from RNA008VAT

description: genomic DNA from RNA008VAT

source_name: genomic DNA from RNA008VAT


title: genomic DNA from RNA003VAT

description: genomic DNA from RNA003VAT

source_name: genomic DNA from RNA003VAT


title: day 8 anti PD-1 mouse 1 Draining lymph node

description: group 2 6 DLN

source_name: draining lymph node


title: genomic DNA from RNA062SAT

description: genomic DNA from RNA062SAT

source_name: genomic DNA from RNA062SAT

value: SAT


title: control-WT rep1 5hmC-distribution

description:
processed data file: 5hmc_het_stress-wt_control.csv, 5hmc_wt_stress-wt_control.csv, 5hmc_het_control-wt_control.csv
CNTNAP-45 5hmC-Chipseq

source_name: control-WT rep1 5hmC-Chipseq

value: Wild type

value: female


title: genomic DNA from RNA044VAT

description: genomic DNA from RNA044VAT

source_name: genomic DNA from RNA044VAT


title: genomic DNA from RNA042VAT

description: genomic DNA from RNA042VAT

source_name: genomic DNA from RNA042VAT


title: genomic DNA from RNA054SAT

description: genomic DNA from RNA054SAT

source_name: genomic DNA from RNA054SAT


title: 60-0-T1_chip

source_name: Whole seedlings

value: GFP (Millipore, ab290)


title: genomic DNA from RNA011VAT

description: genomic DNA from RNA011VAT

source_name: genomic DNA from RNA011VAT

value: F


title: genomic DNA from RNA047VAT

description: genomic DNA from RNA047VAT

source_name: genomic DNA from RNA047VAT

value: VAT


title: day 8 Isotype control mouse 5 Draining lymph node

description: group 1 5 DLN

value: Isotype control


title: control-HT rep1 5hmC-distribution

description:
processed data file: 5hmc_het_control-wt_control.csv, 5hmc_het_stress-het_control.csv
CNTNAP-47 5hmC-Chipseq

source_name: control-HT rep1 5hmC-Chipseq


title: stress-WT rep3 5hmC-distribution

description:
processed data file: 5hmc_het_stress-wt_stress.csv, 5hmc_wt_stress-wt_control.csv
CNTNAP-43 5hmC-Chipseq

source_name: stress-WT rep3 5hmC-Chipseq

value: Stressed


title: genomic DNA from RNA004VAT

description: genomic DNA from RNA004VAT

source_name: genomic DNA from RNA004VAT

value: NoDM


title: 60-0-D2_chip

value: whole seedlings

value: mock treatment


title: 60-0-D2_input


title: day 8 Isotype control mouse 3 Draining lymph node

description: group 1 3 DLN

value: day 8


title: stress-HT rep3 5hmC-distribution

description:
processed data file: 5hmc_het_stress-wt_control.csv, 5hmc_het_stress-het_control.csv, 5hmc_het_stress-wt_stress.csv
CNTNAP-42 5hmC-Chipseq

source_name: stress-HT rep3 5hmC-Chipseq

value: Heterozygous


title: day 8 Isotype control mouse 4 Draining lymph node

description: group 1 4 DLN


title: 60-0-D1_chip


title: stress-HT rep2 5hmC-distribution

description:
processed data file: 5hmc_het_stress-wt_control.csv, 5hmc_het_stress-het_control.csv, 5hmc_het_stress-wt_stress.csv
CNTNAP-40 5hmC-Chipseq

source_name: stress-HT rep2 5hmC-Chipseq

value: brain


title: 60-0-D1_input


title: stress-WT rep2 5hmC-distribution

description:
processed data file: 5hmc_het_stress-wt_stress.csv, 5hmc_wt_stress-wt_control.csv
CNTNAP-41 5hmC-Chipseq

source_name: stress-WT rep2 5hmC-Chipseq

value: striatum


title: Eml4-Alk Lung

city: Cambridge

first: Sangeeta

middle: N

last: Bhatia

state: MA

address: 77 Massachusetts Avenue

institute: Massachusetts Institute of Technology

description: Model of Eml4-Alk NSCLC; 11-12 wks post tumor induction

data_processing:
Illumina NovaSeq6000 sequencer on an Illumina NovaSeq SP flow cell
Raw gene expression matrices were generated for each sample by the Cell Ranger (v.3.0.2) Pipeline coupled with mouse reference version GRCm38
The output filtered gene expression matrices were analyzed by Python software (v.3.9.0) with the scanpy package (v.1.7.2)
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw counts; 10x-Genomics-formatted hdf5 file.
Supplementary_files_format_and_content: Filtered matrix table with raw counts; 10x-Genomics-formatted hdf5 file.

source_name: Lung

extract_protocol:
Eml4-Alk mice (10–12 weeks post tumor induction) and age-matched C57BL/6 healthy controls (Jackson Labs; 18–22 weeks) were euthanized by isoflurane overdose, and lungs were excised and separated into lobes. For tumor-bearing lungs, tumors were separated from healthy tissue using a dissecting microscope. Tissue was minced, treated with digestion buffer (Hank’s Balanced Salt Solution + 2% heat-inactivated FBS, supplemented with DNase and collagenase), and incubated at 37C for 30 minutes with rotation. Samples were filtered using a 70 μm filter and diluted with RPMI-1640 + 2% heat-inactivated FBS. Cell suspension was centrifuged at 1800 rpm for 5 minutes and the pellet was resuspended in ACK lysis buffer for 2 minutes, followed by quenching with buffer (PBS + 2% heat-inactivated FBS). Cell suspension was centrifuged and supernatant was discarded. CD45 cell depletion and viability enrichment was performed according to manufacturer’s instructions (StemCell Technologies). Single cells were processed using the 10X Genomics Single Cell 3’ platform using the Chromium Single Cell 3’ Library & Gel Bead Kit V2 kit (10X Genomics), per manufacturer’s protocol.
10X Genomics Single Cell 3' platform; Chromium Single Cell 3' Library & Gel Bead Kit V2

value: lung

tag: age

value: 18-22 wks; 11-12 wks post tumor induction

value: Eml4-Alk translocation


title: 60-0-T2_chip

value: 500 ng/mL Tunicamycin treatment


title: genomic DNA from RNA005VAT

description: genomic DNA from RNA005VAT

source_name: genomic DNA from RNA005VAT


title: day 8 Isotype control mouse 2 Draining lymph node

description: group 1 2 DLN

source_name: draining lymph node

value: draining lymph nodes


title: 15_S3

city: Helsinki

first: Iiris

last: Hovatta

address: Haartmaninkatu 3

department: Department of Psychology and Logopedics

country: Finland

institute: University of Helsinki

data_processing:
Each sample was run mixed in all runs and lanes. RNA-sequencing reads for each sample were merged from three  Illumina NextSeq 500 runs totalling 12 lanes. Reads were aligned to mouse and human genomes using STAR aligner, version (Dobin et al. 2013) and annotated to genes using HTSeq (Anders et al. 2015).
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: Tab delimeted text file containing unnormalized (raw) read counts per feature.

source_name: Mouse cortex, no transplantation

growth_protocol: iPSC-astrocyte progenitors: The primary cells were reprogrammed with Cytotune 2.0 iPS Sendai Reprogramming Kit for Oct4, Sox2, Klf4, and c-myc. The emerged colonies were individually subcloned. For differentiation, iPSCs were cultured in feeder-free conditions with Matrigel-coating and Essential 8 culture medium. Astroglial differentiation was carried out as described (Stem Cell Reports. 2017;9:1885-1897) by maintaining neural progenitor spheres in astrocyte differentiation medium in suspension for 6–7 months before dissociation. Transplantation: hiPSC-astrocyte progenitors (100,000 cells/µl in PBS) dissociated from sphere cultures were transplanted into newborn Rag1 knockout mouse (B6.12957-Rag1tm1Mom/J, The Jackson Laboratory) forebrain using the published protocol  (Kim, et al., 2014). Cell transplantation was performed by injecting 300,000 cells into the brain at 5 locations: (0.8, 1.0, -1.5); (-0.8, 1.0, -1.5); (0.8, 2.0, -1.5); (-0.8, 2.0, -1.5); (0.0, -1.0, -1.5). The mice were killed when they were 11 months old and frontal cortex was separated.

extract_protocol:
Total RNA was extracted using Trizol and cleaned using RNeasy Mini Kit. The RNA quality was analyzed on the Agilent 2100 Bioanalyzer™ using an RNA6000 assay.
Sequencing libraries were prepared with Illumina NextSeq and SureSelect Strand Specific RNA Seq kits.

tag: sample number

tag: mouse strand

value: cortex

tag: group status

value: non-transplanted

tag: mouse gender

value: female

tag: sample type

value: Mouse cortex, no transplantation


title: 28-24-T2_input

tag: tissue

tag: treatment


title: 28-24-T1_chip

tag: ecotype background

tag: time (hours)

value: GFP (Millipore, ab290)