title: ser33 rep 2

tag: genotype

tag: biological replicate

value: rep 2

tag: technical replicate

value: tech rep 1


title: TimeSeriesFST_55_vHC_2h

status: Public on Mar 25 2021

type: SRA

city: Zürich

first: Lukas

middle: Matthias

last: von Ziegler

address: Winterthurerstrasse 190

department: D-HESZ

country: Switzerland

institute: ETH Zürich

description: polyA RNA

library_source: transcriptomic

data_processing:
Adaptor trimmed with cutadapt (v 1.15), maximum error rate of 0.05 and a minimum length of 15
Pseudoalignment using kallisto (version 0.44.0) on the GENCODE M17 transcriptome
Aggregation on the protein coding level
Genome_build: GRCm38
Supplementary_files_format_and_content: .h5 files with kallisto output (pseudoaligned read counts). Files are futher zipped

molecule: polyA RNA

organism: Mus musculus

source_name: hippocampus

growth_protocol: Mice are originally all from a C57BL/6J Background. More details about mouselines can be found in the metadata. Age of the mice is between 2 and 3 months

extract_protocol:
Trizol
illumina TrueSeq or Illumina Smartseq2 (see samples)

treatment_protocol: Homecage (no stress, control group) or 6 min 18°C swim stress

tag: condition

value: Swim

tag: timepoint

tag: region

value: vHC

tag: Sex

value: Male

tag: hemisphere

value: both

tag: animalnumber

tag: experiment

value: TimeSeriesFST

tag: block

tag: mousetype

value: WT

tag: mouseline

tag: libraryprotocol

value: illumina TruSeq

tag: sampleprocessing

value: WholeRNA


title: 391 D28 R1

city: Cuernavaca

first: Gamaliel

last: Lopez

state: Morelos

address: Ave. Universidad s/n, Chamilpa

department: Genómica Evolutiva

country: Mexico

institute: Centro de Ciencias Genómicas

description: 391 D28 R1

data_processing:
Raw reads were quality checked and trimmed using fastqc (version 0.11.9) and Trim_Galore (version 0.6.5)
Quality reads were aligned with the Mus musculus from NCBI (assembly GRCm38.p6) as the reference genome, using BWA_MEM (version 0.7.17)
Read counts were obtained using htseq-count (version 0.13.5)
The differential expressed genes were identified considering those with a p-value of <0.01 by DESeq2 (version 3.7)
Genome_build: Mus musculus from NCBI (assembly GRCm38.p6) was used as the reference genome
Supplementary_files_format_and_content: All the raw counts for each gene (and replicates) are in the spreadsheet processed_data.xlsx

source_name: lung

growth_protocol: The genetic material was obtained from BALB/c mouse lungs infected with ~250,000 bacteria per 100 uL of solution, for each of the Beijing strains.

extract_protocol:
RNA was obtained from lungs stored at -80 ° C using the Quick-RNA Miniprep Kit Zymo Research cat. R1054 / R1055 following the manufacturer's instructions.
cDNA_oligo_dT

treatment_protocol: The infected lungs were obtained after euthanasia at days 3, 14 and 28 post-infection for 323 Beijing-Like and at days 3, 14, 28 and 60 post-infection for 391 Beijing-Classic.

tag: strain

value: BALB/c

tag: age

value: six weeks

value: male

tag: infection

value: Classical-Beijing strain 391

tag: time

value: post-infection D28


title: sam1 rep 1, technical rep 2

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

country: USA

institute: Stowers Institute

data_processing:
Samples were sequenced on 3 lanes total of a HiSeq and data was processed with Casava 1.8.2.
Reads were aligned to yeast genome sacCer3 from UCSC with ensembl transcript definition from Ensembl 72 using tophat (2.0.13) with -g 1
Downstream analysis was done in R using edgeR with TMM normalization.
Genome_build: sacCer3
Supplementary_files_format_and_content: tab-delimited text, edger RPKMs

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Cells were grown in YPD medium to an OD600 of 0.7-1.0

extract_protocol:
The RNA was extracted with Rneasy mini kit.
RNA libraries were prepared for sequencing using a Ribo-depletion stranded illumina RNA-seq protocol.

tag: genotype

tag: biological replicate

value: rep 1

tag: technical replicate

value: tech rep 2


title: sam1 rep 1


title: by4741 rep 3

value: rep 3


title: TimeSeriesFST_41_vHC_2h

description: polyA RNA

tag: condition

tag: timepoint

tag: region


title: EHE 1

city: Cleveland

first: Brian

middle: P

last: Rubin

state: OH

address: 9620 Carnegie Ave NE2-215

department: Cancer Biology

institute: Cleveland Clinic

data_processing:
Gapped aligment was performed to the hg38 genome with HISAT2 v2.1.0
Raw counts were created with Featurescounts v1.6.4
FPKM abundance measurements were generated with Cufflinks v2.2.1.3
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: EHE Tumor

extract_protocol:
Tumors from either surgical resection or autopsy were cold preserved at -80˚C till sample processing. Total RNA was isolated with the Qiagen RNAeasy kit.
RNA libraries were prepared for sequencing using the standard DNBSeq protocol (BGI).

tag: tissue

value: Epithelioid hemangioendothelioma (EHE)


title: EHE 5


title: TimeSeriesFST_44_dHC_0min

description: polyA RNA

value: Homecage

value: dHC

tag: Sex

tag: hemisphere

tag: animalnumber

tag: experiment


title: 391 D14 R2

description: 391 D14 R2

value: post-infection D14


title: 391 D60 R1

description: 391 D60 R1

value: post-infection D60


title: ser33 rep 2, technical rep 2

value: rep 2


title: 391 D28 R2

description: 391 D28 R2


title: TimeSeriesFST_40_dHC_3h

description: polyA RNA

value: Swim

value: Male

value: both

value: TimeSeriesFST

tag: block

tag: mousetype

value: WT

tag: mouseline

tag: libraryprotocol


title: EHE 3


title: by4741 rep 2

value: tech rep 1


title: by4741 rep 2, technical rep 2


title: 391 D14 R3

description: 391 D14 R3

tag: strain

value: BALB/c

tag: age

value: six weeks

value: male

tag: infection

value: Classical-Beijing strain 391


title: 391 D3 R2

description: 391 D3 R2

tag: time

value: post-infection D3


title: Kir2.1-Off replicate 2 [p5_kir_2]

first: Congrong

middle: Ron

last: Yu

state: Missouri

institute: Stowers Insitute for Medical Research

description: processed data file: Kir_norm_counts.txt

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18
PEA Data: Raw FASTQ files were concatenated across all flow-cell lanes
Selective alignment was performed w/ Salmon v1.3.0 on each sample FASTQ to mm10 transcriptome (ENSEMBL Release 100) with 'salmon quant --index salmon_index -libType SR --unmatedReads sample.fq --seqBias --gcBias'
Count normalization was performed with the DESeq function using DESeq2 v1.30.0
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited matrix tables with DESeq2 normalized gene counts for every gene and every sample

source_name: Kir2.1-Off_olfactory epithelium

extract_protocol:
Olfactory epithelial tissue was removed directly into Trizol reagent for RNA harvesting.
Kir Data: Illumina mRNA-Seq Sample Prep Kit (Cat#RS-930-1001) was used with 2 ug of total RNA for construction of sequencing libraries.
PEA Data: Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold Set A (Cat#RS-122-2301) and Ribo-Zero Gold Set B (Cat#RS-122-2302) was used with 7.5 ug of total RNA for construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PEA-treated mice were exposed to PEA continuously from P0 until P5

tag: strain background

tag: genotype/variation

value: postnatal day 5

tag: treatment

value: Olfactory Epithelium


title: TimeSeriesFST_39_vHC_3h

description: polyA RNA

tag: condition

tag: timepoint

tag: region

value: vHC

value: illumina TruSeq

tag: sampleprocessing

value: WholeRNA


title: TimeSeriesFST_38_dHC_1h30min

description: polyA RNA

value: dHC

tag: Sex

tag: hemisphere

tag: animalnumber


title: TimeSeriesFST_47_vHC_45min

description: polyA RNA

value: Swim

tag: experiment

tag: block

tag: mousetype


title: Kir2.1-Off replicate 1 [p5_kir_1]

tag: tissue


title: 391 D3 R1

description: 391 D3 R1

tag: strain

tag: age


title: acs2 rep 3, technical rep 2

tag: genotype

tag: biological replicate

value: rep 3

tag: technical replicate

value: tech rep 2


title: TimeSeriesFST_37_vHC_1h30min

description: polyA RNA

value: Male

value: both

value: TimeSeriesFST

tag: mouseline

tag: libraryprotocol


title: Kir2.1 Control replicate 3 [p5_wt_3]

source_name: Kir2.1 Control_olfactory epithelium

tag: strain background

tag: genotype/variation

value: OMP-IRES-tTA het

tag: treatment

value: Control


title: Kir2.1 Control replicate 2 [p5_wt_2]


title: 323 D28 R2

description: 323 D28 R2

value: BALB/c

value: six weeks

tag: Sex

value: male

tag: infection

value: BL strain 323

tag: time

value: post-infection D28


title: acs2 rep 1

value: rep 1

value: tech rep 1


title: by4741 rep 3, technical rep 2


title: Kir2.1 Control replicate 1 [p5_wt_1]

value: postnatal day 5

value: Olfactory Epithelium


title: Kir2.1-Off replicate 3 [p5_kir_3]


title: acs2 rep 1, technical rep 2


title: TimeSeriesFST_35_vHC_3h

description: polyA RNA

tag: condition

value: Swim

tag: timepoint

tag: region

value: vHC

tag: hemisphere

tag: animalnumber

tag: experiment

value: WT

value: illumina TruSeq

tag: sampleprocessing

value: WholeRNA


title: 391 D14 R1

description: 391 D14 R1

tag: strain

tag: age

value: Classical-Beijing strain 391

value: post-infection D14


title: 323 D28 R1

description: 323 D28 R1


title: wt rep 2, technical rep 2

tag: genotype

value: wt

tag: biological replicate

value: rep 2

tag: technical replicate

value: tech rep 2


title: TimeSeriesFST_34_dHC_1h30min

description: polyA RNA

value: dHC

value: Male

value: both

value: TimeSeriesFST

tag: block

tag: mousetype

tag: mouseline

tag: libraryprotocol


title: 323 D14 R2

description: 323 D14 R2

value: BALB/c

value: six weeks

tag: Sex

value: male

tag: infection

value: BL strain 323

tag: time


title: WT_IgG_d14_R1_RNA

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

data_processing:
Basecalling, RTA v1.13
Alignments to mm10 using TopHat v2.12
Annotation, cufflinks v2.2.1, GENCODE v25
Gene quantification with htseq-count v0.6.1p1 using the "intersection-strict" overlapping mode
Genome_build: mm10
Supplementary_files_format_and_content: gene quantification txt file

source_name: LSK

extract_protocol:
RNeasy Plus Mini Kit (Qiagen)
Illumina TruSeq Stranded Total RNA Library Prep Kit

tag: differentiation

value: IgG


title: acs2 rep 3

value: rep 3

value: tech rep 1


title: wt rep 2


title: ML171546 3H Post Dex

city: Parkville

first: Jane

middle: T

last: Seto

state: VIC

address: 50 Flemington Road

country: Australia

institute: Murdoch Children's Research Institute, Royal Children's Hospital

data_processing:
Raw read data was processed using the Illumina BaseSpace RNA Express application (Illumina Inc. 2016)
Sequencing reads were aligned using STAR ultrafast RNA seq aligner in the SAM file format
Reads were counted using HTSeq
genewise count data was analyzed using the R (3.6.0) statistical programming language
Differential expression (DE) was conducted using the voom precision weights approach in the limma (3.40.6) package from the Bioconductor (3.9) project
Genome_build: mm10
Supplementary_files_format_and_content: text

source_name: Skeletal muscle

extract_protocol:
Quadriceps muscles were removed and weighed, flash frozen in liquid nitrogen, and RNA extracted using Trizol reagent. RNA was purified using Qiagen RNA columns and Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols on a Illumina HiSeq 2500

tag: gender

value: KO

tag: treatment

value: Dex

tag: time point

value: 3H Post


title: TimeSeriesFST_36_dHC_3h

description: polyA RNA

tag: condition

value: Swim

tag: timepoint

tag: region

tag: hemisphere

tag: animalnumber

tag: experiment

value: WT

value: illumina TruSeq

tag: sampleprocessing

value: WholeRNA


title: TimeSeriesFST_32_dHC_4h

description: polyA RNA

value: dHC

value: Male

tag: block

tag: mousetype


title: 391 D3 R3

description: 391 D3 R3

tag: strain

tag: age

value: Classical-Beijing strain 391

value: post-infection D3


title: TimeSeriesFST_31_vHC_4h

description: polyA RNA

value: vHC

tag: Sex

value: both

value: TimeSeriesFST

tag: mouseline

tag: libraryprotocol


title: DN2b_6-12-13_RNA

tag: differentiation


title: 323 D28 R3

description: 323 D28 R3

value: BALB/c

value: six weeks

value: male

tag: infection

value: BL strain 323

tag: time

value: post-infection D28


title: 323 D14 R3

description: 323 D14 R3

value: post-infection D14


title: wt rep 1, technical rep 2

tag: genotype

value: wt

tag: biological replicate

value: rep 1

tag: technical replicate

value: tech rep 2


title: WT_IgG_d14_D2_RNA

value: IgG


title: TimeSeriesFST_33_vHC_1h30min

description: polyA RNA

tag: condition

value: Swim

tag: timepoint

tag: region

tag: hemisphere

value: WT

value: illumina TruSeq

value: WholeRNA


title: TimeSeriesFST_29_vHC_45min

description: polyA RNA

value: vHC

value: Male

tag: animalnumber

tag: experiment

tag: block

tag: sampleprocessing


title: WT_IgG_d14_D1_RNA


title: wt rep 1

value: tech rep 1


title: snRNAseq_CTRL_2

data_processing:
Reads were demultiplexed, aligned and quantified with Cell Ranger 4.0.0 (Zheng et al., 2017) using a pre-mRNA transcriptome.
Quality control with scater 1.18.0 and scDblFinder 1.4.0
Normalization with sctransform 0.3.1
SVD and clustering with Seurat 3.2.2
Genome_build: GRCm38
Supplementary_files_format_and_content: snRNAseq.SCE.final.rds.gz contains the final R SingleCellExperiment object (saved as RDS object and gzipped), filtered and containing identities and reduced dimensions.

extract_protocol:
All steps for tissue dissociation were performed on ice. Both hippocampi of the same animal were chopped briefly in 100 μL lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal, 0.2 U/ul recombinant RNase inhibitor in nuclease-free water) and immediately transferred to a dounce homogenizer filled with 1 mL lysis buffer. Tissue was homogenized by 15-20 strokes with each pestle A and pestle B. 2 mL of lysis buffer was added to the dounce homogenizer and the solution was incubated for 5 minutes. The dounce homogenizer was filled with 4 ml wash buffer (1% BSA. 0.2 U/ul recombinant RNase inhibitor in PBS) and homogenate was passed through a 40 µm filter before adding 8 ml wash buffer.  The sample was centrifuged at 500 g for 5 minutes at 4 °C and the pellet was resuspended in 7 mL nuclei suspension buffer (1% BSA, 0.2 U/µl RNaseInhibitor (Superasin) in PBS). Then the sample was centrifuged at 500 g for 5 minutes at 4 °C. The pellet was resuspended in 1 mL nuclei suspension buffer and filtered through a 40 µm, 30 µm and 10 µm filter. Nuclei count was assessed manually by Trypan blue staining and adjusted to a final concentration of 1000 nuclei/µL.
cDNA synthesis and library preparation were conducted following the Chromium Single Cell 3’ Reagent Kit v3 User Guide (CG000183 Rev B, 10X Genomics). 14 PCR cycles were performed for cDNA amplification.
single-nucleus mRNA sequencing

value: Homecage

tag: Sex

value: both

tag: strain

value: 10x single-nucleus mRNAseq


title: 323 D3 R3

description: 323 D3 R3

value: BALB/c

tag: age

value: six weeks

value: male

value: BL strain 323

value: post-infection D3


title: TimeSeriesFST_30_dHC_45min

description: polyA RNA

value: dHC

value: TimeSeriesFST

tag: mousetype

tag: mouseline

tag: libraryprotocol


title: 323 D3 R2

description: 323 D3 R2

tag: infection

tag: time


title: DN2a_6-12-13_RNA

tag: differentiation


title: snRNAseq_CTRL_1

tag: condition


title: DN2a_12-12-12_RNA


title: WT_IgG_d14_R2_RNA

value: IgG


title: 323 D14 R1

description: 323 D14 R1

value: post-infection D14


title: DN2b_12-12-12_RNA


title: snRNAseq_Swim_2

value: Swim

tag: timepoint


title: DN1_6-7-13_RNA


title: smallRNA1_vHC_CTRL

description: short RNA

data_processing:
Reads were trimmed using cutadapt (adapter sequence TGGAATTCTCGGGTGCCAAGG, 0.05 error rate, minimum length of 18)
Reads with the same sequence (including UMI) were then collapsed, and the UMIs trimmed.
Alignment and quantification was performed using Sports 1.0 using the software's full mouse annotation
Genome_build: GRCm38
Supplementary_files_format_and_content: shortRNA_counts.csv contains data for all small RNA counts across samles

growth_protocol: Mice are all from a C57BL/6J Background. Age of the mice is between 2 and 3 months

extract_protocol:
Trizol
Nextflex v3 small RNA

value: CTRL

tag: region

value: Nextflex v3 small RNA


title: smallRNA20_dHC_Swim45min

description: short RNA

value: Male

tag: hemisphere


title: 323 D3 R1

description: 323 D3 R1


title: smallRNA19_vHC_Swim45min

description: short RNA

value: vHC


title: TimeSeriesFST_25_vHC_0min

description: polyA RNA

value: Homecage

tag: animalnumber

value: WT

value: illumina TruSeq

value: WholeRNA


title: CaMKIIa-TRAP_2-2M_19_vHC_0min

description: ribosome bound RNA

value: both

tag: experiment

value: illumina Smartseq2


title: AG3115_LSK_LSK_DNase

library_source: genomic

data_processing:
Basecalling, RTA v1.13
Alignments to GRCh38, BWA v0.7.12
Read processing, Samtools v1.2
Read density, Bedops v2.4.15
Peak calling, Hotspot2 v2.1.1
Genome_build: mm10
Supplementary_files_format_and_content: 5% FDR hotspot peak calls as a .bed file, normalized density bigWig file

molecule: genomic DNA

extract_protocol:
PEG precipitation and size fractionation of DNA
Low-input single-stranded library construction protocol as per PMIDs 23493070 & 26771485
DNase-Seq

value: LSK


title: CaMKIIa-TRAP_2-2M_20_vHC_45min

description: ribosome bound RNA

tag: block


title: TimeSeriesFST_23_vHC_0min

description: polyA RNA

tag: sampleprocessing


title: CaMKIIa-TRAP_2-2M_21_vHC_1h30min

description: ribosome bound RNA

tag: Sex


title: CaMKIIa-TRAP_2-2M_18_vHC_45min

description: ribosome bound RNA


title: TimeSeriesFST_26_dHC_0min

description: polyA RNA


title: DN1_12-5-12_RNA


title: snRNAseq_Swim_1

tag: strain

value: 10x single-nucleus mRNAseq


title: smallRNA18_dHC_CTRL

description: short RNA

value: dHC


title: CaMKIIa-TRAP_2-2M_17_vHC_0min

description: ribosome bound RNA


title: TimeSeriesFST_22_dHC_1h30min

description: polyA RNA

value: TimeSeriesFST


title: AG3099_IgG_LSK_DNase

value: IgG


title: smallRNA16_dHC_Swim45min

description: short RNA


title: smallRNA17_vHC_CTRL

description: short RNA


title: TimeSeriesFST_21_vHC_1h30min

description: polyA RNA


title: TimeSeriesFST_27_vHC_2h

description: polyA RNA


title: BNRIJHsd_Input_Liver

city: Bethesda

first: Kevin

last: Brick

state: MD

address: 5/205 Memorial Drive

department: GBB

institute: NIDDK

description: BNRIJHsd wildtype Input DNA Liver

data_processing:
Basecalls performed using Illumina HCS 1.5.15.1
BIGWIGs:  Reads were aligned to the rn5 reference genome using BWA MEM 0.7.12. a BedGraph was generated from the aligned BAM using genomeCoverageBed (bedtools 2.23.0) and was converted to a BIGWIG using the UCSC bedGraphToBigWig utility (v.190).
PEAKS TABLE:  The pipeline described in Khil et al. Genome Res. 2012 was used to align SSDS reads to the genome (https://github.com/kevbrick/SSDSpipeline.git). Uniquely mapping fragments unambiguously derived from ssDNA (ssDNA type 1) and having both reads with a mapping quality score ≥ 30 were used for identifying hotspot locations (peak calling). NCIS was used to estimate the background fraction for each library. Peak calling was performed using MACS (v.2.1.0.20150420) with the following parameters : --ratio [output from NCIS]  -g mm --bw 1000 --keep-dup all --slocal 5000. (https://github.com/kevbrick/callHotspotsSSDS.git). DSB hotspots within regions previously blacklisted were removed and hotspot strength was calculated as described previously(17).
Genome_build: rn5
Supplementary_files_format_and_content: BIGWIG: Genomic coverage
Supplementary_files_format_and_content: TABLE: SSDS peaks in each strain

organism: Rattus norvegicus

source_name: Liver

extract_protocol:
For DMC1 SSDS, testicular samples were obtained frozen and were directly thawed in 1% paraformaldehyde and gently dissociated. Genomic DNA for whole genome sequencing was extracted from the testicular samples before fixation with the DNeasy Blood and Tissue kit (Qiagen). DMC1 ChIP was performed as described previously (Smagulova et al., 2011; Khil et al., 2012; Brick et al., 2012) with minor modifications.
For H3K4me3 ChIP-Seq, nuclei were isolated from cells using hypotonic lysis. Chromatin was fragmented by sonication. After high speed spin soluble chromatin was removed and used for ChIP.
Sequencing libraries for anti-DMC1 were prepared following the method described in (Khil et al., 2012).  For H3K4me3 ChIP-Seq, libraries were prepared for sequencing using Bio Scientific's NEXTflex ChIP-Seq Kit (protocol version V11.11) without size selection. Amplification of the libraries was done with 20 µL ligation product, 16 ul water, 12 µL NEXTflex ChIP PCR master mix, 2 µL NEXTflex ChIP primer mix and 14-18 cycles of PCR.

tag: tissue

value: Liver

value: BN/RIJHsd

tag: age

value: Adult

tag: genotype

value: wild-type

tag: antibody

tag: sequencing technique

value: DNA-Seq


title: CaMKIIa-TRAP_2-2M_16_vHC_0min

description: ribosome bound RNA

value: vHC

value: Male

tag: mousetype

tag: mouseline

tag: libraryprotocol


title: WKY_Input_Testis

description: WKY wildtype Input DNA Testis

source_name: Testis

value: Testis

value: WKY


title: TimeSeriesFST_28_dHC_2h

description: polyA RNA

tag: condition

value: Swim

tag: timepoint

value: WT

value: illumina TruSeq

value: WholeRNA


title: smallRNA9_vHC_CTRL

description: short RNA

value: CTRL

tag: region

tag: hemisphere

value: both

value: Nextflex v3 small RNA


title: smallRNA8_dHC_CTRL

description: short RNA

value: dHC


title: smallRNA7_vHC_CTRL

description: short RNA


title: BNRIJHsd_Input_Testis

description: BNRIJHsd wildtype Input DNA Testis


title: TimeSeriesFST_20_dHC_3h

description: polyA RNA

tag: animalnumber

tag: experiment

value: TimeSeriesFST


title: TimeSeriesFST_19_vHC_3h

description: polyA RNA

tag: block

tag: sampleprocessing


title: TimeSeriesFST_24_dHC_0min

description: polyA RNA

value: Homecage

tag: Sex


title: WKY_H3K4m3_Testis

description: WKY wildtype H3K4m3 ChIPSeq Testis

tag: tissue

tag: strain

value: Adult

value: Millipore/EMD 07-473

value: ChIP-Seq


title: CaMKIIa-TRAP_2-2M_15_vHC_1h30min

description: ribosome bound RNA

value: vHC

value: illumina Smartseq2


title: BNRIJHsd_H3K4m3_Liver

description: BNRIJHsd wildtype H3K4m3 ChIPSeq Liver

value: Liver

value: BN/RIJHsd

tag: age

tag: genotype

value: wild-type


title: smallRNA6_dHC_Swim45min

description: short RNA

value: Swim

value: Male


title: CaMKIIa-TRAP_2-2M_14_vHC_45min

description: ribosome bound RNA


title: TimeSeriesFST_18_dHC_45min

description: polyA RNA

value: WT

value: illumina TruSeq

value: WholeRNA


title: CaMKIIa-TRAP_2-2M_13_vHC_0min

description: ribosome bound RNA

value: both


title: smallRNA5_vHC_Swim45min

description: short RNA

value: Nextflex v3 small RNA


title: TimeSeriesFST_17_vHC_45min

description: polyA RNA

value: TimeSeriesFST


title: TimeSeriesFST_16_dHC_2h

description: polyA RNA

value: dHC


title: CaMKIIa-TRAP_2-2M_10_vHC_45min

description: ribosome bound RNA


title: TimeSeriesFST_15_vHC_2h

description: polyA RNA


title: CaMKIIa-TRAP_2-2M_12_vHC_1h30min

description: ribosome bound RNA


title: WKY_Input_SSDS_wildtype

description: WKY wildtype Input SSDS

data_processing:
Library strategy: Single Stranded DNA Sequencing (SSDS)
Basecalls performed using Illumina HCS 1.5.15.1
BIGWIGs:  Reads were aligned to the rn5 reference genome using BWA MEM 0.7.12. a BedGraph was generated from the aligned BAM using genomeCoverageBed (bedtools 2.23.0) and was converted to a BIGWIG using the UCSC bedGraphToBigWig utility (v.190).
PEAKS TABLE:  The pipeline described in Khil et al. Genome Res. 2012 was used to align SSDS reads to the genome (https://github.com/kevbrick/SSDSpipeline.git). Uniquely mapping fragments unambiguously derived from ssDNA (ssDNA type 1) and having both reads with a mapping quality score ≥ 30 were used for identifying hotspot locations (peak calling). NCIS was used to estimate the background fraction for each library. Peak calling was performed using MACS (v.2.1.0.20150420) with the following parameters : --ratio [output from NCIS]  -g mm --bw 1000 --keep-dup all --slocal 5000. (https://github.com/kevbrick/callHotspotsSSDS.git). DSB hotspots within regions previously blacklisted were removed and hotspot strength was calculated as described previously(17).
Genome_build: rn5
Supplementary_files_format_and_content: BIGWIG: Genomic coverage
Supplementary_files_format_and_content: TABLE: SSDS peaks in each strain

value: Testis

value: WKY

value: Adult

tag: antibody

tag: sequencing technique

value: Single Stranded DNA Sequencing (SSDS)


title: SHR_Input_SSDS_wildtype

description: SHR wildtype Input SSDS

value: SHR/OlaIpcv


title: CaMKIIa-TRAP_2-2M_9_vHC_45min

description: ribosome bound RNA

value: vHC

tag: mousetype

tag: mouseline

value: illumina Smartseq2


title: smallRNA31_vHC_CTRL

description: short RNA

tag: condition

value: CTRL

tag: libraryprotocol


title: smallRNA14_dHC_CTRL

description: short RNA

tag: timepoint

tag: region


title: smallRNA30_dHC_Swim45min

description: short RNA

value: Swim

tag: hemisphere


title: TimeSeriesFST_13_vHC_4h

description: polyA RNA

value: Male

tag: animalnumber

tag: experiment


title: SHR_DMC1_SSDS_wildtype

description: SHR wildtype DMC1 SSDS

value: wild-type

value: Anti-DMC1 Santa Cruz (C-20, sc 8973)

value: ChIP-Single Stranded DNA Sequencing (SSDS)


title: ML171547 3H Post Dex

tag: gender

value: KO

tag: treatment

value: Dex

tag: time point

value: 3H Post


title: CaMKIIa-TRAP_2-2M_7_vHC_45min

description: ribosome bound RNA

tag: Sex

value: both

tag: block

tag: sampleprocessing


title: TimeSeriesFST_12_dHC_1h30min

description: polyA RNA

value: dHC

value: TimeSeriesFST

value: WT

value: illumina TruSeq

value: WholeRNA


title: SHR_DMC1_SSDS_Prdm9KOHet

description: SHR Prdm9KOHet DMC1 SSDS

tag: tissue

value: Testis

tag: strain

value: SHR/OlaIpcv

tag: age

value: Adult

tag: genotype

tag: antibody


title: smallRNA32_dHC_CTRL

description: short RNA

tag: condition

value: CTRL

tag: mouseline

tag: libraryprotocol

value: Nextflex v3 small RNA


title: TimeSeriesFST_11_vHC_1h30min

description: polyA RNA

value: Swim

tag: timepoint

tag: region

value: vHC

value: Male

tag: hemisphere

tag: mousetype


title: SHR_DMC1_SSDS_Prdm9KO

description: SHR Prdm9KO DMC1 SSDS

value: Anti-DMC1 Santa Cruz (C-20, sc 8973)

tag: sequencing technique

value: ChIP-Single Stranded DNA Sequencing (SSDS)


title: BNRIJHsd_H3K4m3_Testis

description: BNRIJHsd wildtype H3K4m3 ChIPSeq Testis

value: BN/RIJHsd

value: wild-type

value: Millipore/EMD 07-473

value: ChIP-Seq


title: CaMKIIa-TRAP_2-2M_8_vHC_1h30min

description: ribosome bound RNA

value: both

tag: animalnumber

tag: experiment

value: illumina Smartseq2


title: smallRNA28_dHC_Swim45min

description: short RNA

value: dHC

tag: Sex

tag: block


title: CaMKIIa-TRAP_2-2M_6_vHC_0min

description: ribosome bound RNA

value: Homecage

tag: sampleprocessing


title: TimeSeriesFST_9_vHC_3h

description: polyA RNA

value: TimeSeriesFST

value: WT

value: illumina TruSeq

value: WholeRNA


title: TimeSeriesFST_10_dHC_3h

description: polyA RNA

value: Swim


title: CaMKIIa-TRAP_2-2M_4_vHC_1h30min

description: ribosome bound RNA

value: vHC


title: BNRIJHsd_DMC1_SSDS_wildtype

description: BNRIJHsd wildtype DMC1 SSDS

tag: tissue

value: Testis

tag: strain

value: Adult


title: CaMKIIa-TRAP_2-2M_5_vHC_1h30min

description: ribosome bound RNA

value: Male


title: smallRNA27_vHC_Swim45min

description: short RNA

value: Nextflex v3 small RNA


title: CaMKIIa-TRAP_2-2M_3_vHC_45min

description: ribosome bound RNA


title: smallRNA26_dHC_CTRL

description: short RNA

value: CTRL


title: TimeSeriesFST_8_dHC_2h

description: polyA RNA


title: CaMKIIa-TRAP_2-2M_2_vHC_0min

description: ribosome bound RNA


title: CaMKIIa-TRAP_2-2M_11_vHC_0min

description: ribosome bound RNA


title: TimeSeriesFST_7_vHC_2h

description: polyA RNA


title: smallRNA24_dHC_CTRL

description: short RNA


title: CaMKIIa-TRAP_2-2M_1_vHC_1h30min

description: ribosome bound RNA


title: TimeSeriesFST_6_dHC_4h

description: polyA RNA


title: TimeSeriesFST_5_vHC_4h

description: polyA RNA


title: smallRNA22_dHC_Swim45min

description: short RNA


title: smallRNA29_vHC_Swim45min

description: short RNA


title: CAMK2A-TRAP_20_vHC_45min

description: ribosome bound RNA


title: CAMK2A-TRAP_19_vHC_0min

description: ribosome bound RNA


title: TimeSeriesFST_4_dHC_45min

description: polyA RNA


title: smallRNA21_vHC_Swim45min

description: short RNA


title: TimeSeriesFST_3_vHC_45min

description: polyA RNA


title: CAMK2A-TRAP_18_dHC_0min

description: ribosome bound RNA


title: smallRNA23_vHC_CTRL

description: short RNA


title: TimeSeriesFST_2_dHC_0min

description: polyA RNA


title: WKY_DMC1_SSDS_wildtype

description: WKY wildtype DMC1 SSDS

value: WKY

tag: age

tag: genotype

value: wild-type

value: Anti-DMC1 Santa Cruz (C-20, sc 8973)

value: ChIP-Single Stranded DNA Sequencing (SSDS)


title: CAMK2A-TRAP_17_dHC_0min

description: ribosome bound RNA

tag: condition

value: dHC

value: both

value: illumina Smartseq2


title: TimeSeriesFST_14_dHC_4h

description: polyA RNA

value: TimeSeriesFST

value: WT

tag: mouseline


title: smallRNA25_vHC_CTRL

description: short RNA

tag: libraryprotocol


title: CAMK2A-TRAP_16_vHC_45min

description: ribosome bound RNA

tag: timepoint


title: Day2_WT_rep5

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

data_processing:
Trimmomatic version 0.36
HISAT2 (version 2.1.0) mapping
HTSeq (version 0.6.1p1) counts
Genome_build: grcm38
Supplementary_files_format_and_content: counts

source_name: organoid

growth_protocol: Intestinal crypts were isolated from Lgr5-EGFP-IRES-CreERT2 Lgr5-EGFP-IRES-CreERT2.Apcfl/fl or Villin-CreERT2.Apcfl/fl mice. Isolated crypts were resuspended in MatrigelÒ (Corning) and seeded in pre-heated 24-well plates, supplemented with Advanced DMEM/F12 medium containing the following growth factors: mouse EGF 50ng/ml, R-spondin (conditioned medium), Noggin (conditioned medium). For in vitro recombination, 1mM 4OH-Tamoxifen (Sigma) was added to the medium. Recombination of the Apc gene was validated by Droplet Digitalä PCR (Bio-Rad) using EvaGreenâ Supermix (Bio-Rad). Lgr5-EGFP-IRES-CreERT2 organoids, from now on referred to as wild type (WT) organoids, were stably transduced with a red fluorescent mCherry construct (LeGO-C2). The in vitro recombined Lgr5-EGFP-IRES-CreERT2;Apcfl/fl, referred to as Apc-/-, were stably transduced with a green fluorescent Venus construct (LeGO-V2). Conditioned medium (CM) used in these assays was taken from three-day old WT or Apc-/- organoid cultures and freshly supplemented with growth factors R-spondin, Noggin and mEGF.

extract_protocol:
RNA was extracted using the Bioke Nucleospin RNA isolation kit (cat no. 740955).
RNA-seq libraries were prepared using the KAPA RNA HyperPrep with RiboErase (Roche)

value: Intestinal organoid

tag: treatment

tag: background strain

tag: culture day


title: Day4_WTCM_rep3

value: Apc-mutant conditioned medium


title: CAMK2A-TRAP_15_dHC_45min

description: ribosome bound RNA

value: Swim

tag: region

tag: hemisphere

tag: mousetype


title: smallRNA15_vHC_Swim45min

description: short RNA

value: vHC

tag: Sex


title: Day2_APC_rep5

value: Apc mutant


title: Day2_WT_rep4


title: CAMK2A-TRAP_14_dHC_45min

description: ribosome bound RNA

value: Male

tag: animalnumber

tag: experiment

tag: block


title: TimeSeriesFST_1_vHC_0min

description: polyA RNA

value: Homecage

value: illumina TruSeq

tag: sampleprocessing

value: WholeRNA


title: Day2_APC_rep4

tag: tissue


title: smallRNA13_vHC_CTRL

description: short RNA

value: CTRL

value: Nextflex v3 small RNA


title: CAMK2A-TRAP_13_vHC_0min

description: ribosome bound RNA


title: Day4_WTCM_rep1

tag: genotype


title: Day4_WTCM_rep2


title: genomic DNA from Labial salivary gland tissue 130

type: genomic

city: Berkeley

first: Xiaorong

last: Shao

state: CA

address: 431 Stanley Hall

institute: University of California, Berkeley

description: Case

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K/Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using HiScan Reader using standard recommended Illumina scanner setting

data_processing: Minfi

label: Cy5 and Cy3

source_name: Labial salivary gland tissue 130

label_protocol: Standard Illumina Protocol

extract_protocol: Qiagen Allprep DNA/RNA mini kit

tag: gender

value: Female

value: Labial salivary gland tissue

tag: disease status

value: Sjogrens Syndrome


title: genomic DNA from Labial salivary gland tissue 131

description: Non-case

source_name: Labial salivary gland tissue 131

value: symptomatic not Sjogrens


title: genomic DNA from Labial salivary gland tissue 129

description: Case

source_name: Labial salivary gland tissue 129


title: AG3561_LSK_LSK_DNase

tag: differentiation

value: LSK


title: AG3560_IgG_LSK_DNase

value: IgG


title: CAMK2A-TRAP_12_dHC_45min

description: ribosome bound RNA

tag: condition

tag: timepoint

value: dHC

value: both

tag: mouseline

tag: libraryprotocol

value: illumina Smartseq2


title: genomic DNA from Labial salivary gland tissue 127

description: Non-case

source_name: Labial salivary gland tissue 127


title: genomic DNA from Labial salivary gland tissue 128

description: Case

source_name: Labial salivary gland tissue 128


title: CAMK2A-TRAP_10_dHC_45min

description: ribosome bound RNA

value: Swim

tag: region


title: AG3248_LSK_LSK_DNase


title: Day4_APCCM_rep1

value: Intestinal organoid

value: Apc mutant

tag: treatment

value: Apc-mutant conditioned medium

tag: background strain

tag: culture day


title: CAMK2A-TRAP_9_vHC_0min

description: ribosome bound RNA

value: Homecage

value: vHC

tag: Sex

value: Male

tag: hemisphere

tag: animalnumber

tag: mousetype


title: CAMK2A-TRAP_8_dHC_0min

description: ribosome bound RNA

tag: experiment

tag: block

tag: sampleprocessing


title: Day4_APCCM_rep3

tag: tissue

tag: genotype


title: AG3094_DN2b_LSK_DNase

tag: differentiation


title: Day2_WTCM2

value: WT


title: AG3093_DN2a_LSK_DNase


title: Day4_APCCM_rep2


title: CAMK2A-TRAP_7_vHC_0min

description: ribosome bound RNA

tag: condition

tag: timepoint


title: genomic DNA from Labial salivary gland tissue 125

description: Case

source_name: Labial salivary gland tissue 125

tag: gender

value: Female

tag: disease status


title: genomic DNA from Labial salivary gland tissue 124

description: Non-case

source_name: Labial salivary gland tissue 124

value: Labial salivary gland tissue


title: AG3092_DN1_LSK_DNase


title: CAMK2A-TRAP_6_vHC_45min

description: ribosome bound RNA

source_name: hippocampus

tag: region

tag: mouseline

tag: libraryprotocol


title: genomic DNA from Labial salivary gland tissue 126

description: Non-case

source_name: Labial salivary gland tissue 126


title: genomic DNA from Labial salivary gland tissue 121

description: Case

source_name: Labial salivary gland tissue 121

value: Sjogrens Syndrome


title: genomic DNA from Labial salivary gland tissue 122

description: Non-case

source_name: Labial salivary gland tissue 122

value: symptomatic not Sjogrens


title: genomic DNA from Labial salivary gland tissue 123

description: Case

source_name: Labial salivary gland tissue 123


title: AG3091_DN1_LSK_DNase

source_name: LSK


title: Day2_WTCM1

tag: treatment

tag: background strain

tag: culture day


title: genomic DNA from Labial salivary gland tissue 120

description: Case

source_name: Labial salivary gland tissue 120


title: CAMK2A-TRAP_5_dHC_0min

description: ribosome bound RNA

tag: Sex

tag: hemisphere

tag: animalnumber

tag: mousetype


title: CAMK2A-TRAP_4_dHC_0min

description: ribosome bound RNA

tag: experiment

tag: block

tag: sampleprocessing


title: Day2_APCCM3

tag: tissue

tag: genotype


title: Day2_APCCM1


title: Day2_APCCM2


title: Batch II (S2) TCR

city: Amsterdam

first: Pia

last: Kvistborg

state: FOREIGN

address: Plesmanlaan 121

department: Molecular Oncology & Immunology

country: Netherlands

institute: Netherlands Cancer Institute

description:
See 'overall design' for details
library type: TCR

data_processing:
Cell Ranger Software Suite v.3.1.0 with default parameters was used to perform sample de-multiplexing, barcode processing  and  single-cell 5’ unique molecular identifier (UMI) counting
Genome_build: GRCh38
Supplementary_files_format_and_content: Files include filtered feature-barcode matrix files and processed outputs of the 10x VDJ assay.

source_name: Bulk CD8 T cells from COVID-131: TCR, sample 2, batch 2

extract_protocol:
Live bulk CD8 T cells were sorted out and processed according to 10x Genomics Chromium protocol
10x genomics kits were used to produce the Gel Bead-In Emulsions (GEMs) and the resulting sequence libraries (Gene expression library, Feature Barcode library, TCR library) according to manufacturer’s protocol: For batch I, Chromium Next GEM Single Cell 5’ Library and Gel Bead kit v1.1 (10x Genomics, PN-1000167), Chromium Next Gem Single Cell V(D)J Reagent Kit v1.1 (10x Genomic, PN-1000165), Chromium Single Cell 5’ Library Construction Kit (10x Genomics, PN-1000020), Chromium Single Cell 5’ Feature Barcode Library Kit (10x Genomics, PN1000080) and Chromium Next GEM Chip G Single Cell kit (10x Genomics, PN-100127). For batch II, Chromium Next GEM Single Cell 5' Kit v2 (10x Genomics, PN-1000265), Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) (10x Genomic, PN-2000263), Library Construction Kit (10x Genomics, PN-1000190), 5’ Feature Barcode Kit (10x Genomics, PN-1000256) and Chromium Next GEM Chip K Single Cell kit (10x Genomics, PN-1000287). The 3 libraries were combined in relative fractions of 0.785, 0.085 and 0.130 in order to generate sufficient reads per cell for each type of library.

tag: cell type

value: PBMC-derived CD8 T cells

tag: disease state

value: Acute COVID-19


title: Batch II (S2) FB

description:
See 'overall design' for details
library type: feature barcodes

source_name: Bulk CD8 T cells from COVID-131: feature barcodes, sample 2, batch 2


title: CAMK2A-TRAP_3_vHC_45min

description: ribosome bound RNA

tag: condition

tag: timepoint

tag: region


title: RNAseq_circPRE8 HCT116 CRISPRi_sgNORAD-1

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 6000 Harry Hines Blvd., NA6.200A

department: Molecular Biology

institute: UT Southwestern Medical Center

description:
total RNA extracted using Qiagen RNAeasy kit; polyA-selection using oligo-dT beads
circPRE8sgNORAD1

data_processing:
Reads were mapped to the hg38 reference genome using STAR (Dobin et al, Bioinformatics 2013).
Mapped reads were assigned to genes using featureCounts (v1.6.0) without considering the strand.
Differntial expression analysis was performed using EdgeR (v3.24.0).
Genome_build: hg38
Supplementary_files_format_and_content: A table of normalized read counts for mapped genes is provided.

growth_protocol: HCT116 cells were grown in McCoy's 5A media supplemented with 10%FBS and 1X Antibiotic-antimycotic solution.

extract_protocol:
Total RNA was extracted from cell pellets using Qiagen RNAeasy kit with DNAse I on-column digestion according to the manufacturer's instructions.
Libraries were prepared by GENEWIZ (New Jersey) using an Illumina HiSeq 2x150bp platform.

treatment_protocol: N/A.

value: CRISPRi, circPRE8

tag: sgrna received

value: sgNORAD

tag: cell line


title: CAMK2A-TRAP_2_vHC_0min

description: ribosome bound RNA

value: both

tag: mouseline

tag: libraryprotocol

value: illumina Smartseq2


title: RNAseq_circPRE2 HCT116 CRISPRi_sgNORAD-2

description:
total RNA extracted using Qiagen RNAeasy kit; polyA-selection using oligo-dT beads
circPRE2sgNORAD2

value: CRISPRi, circPRE2


title: CAMK2A-TRAP_1_dHC_45min

description: ribosome bound RNA

value: Swim

value: dHC

tag: Sex

tag: hemisphere


title: Batch II (S1) TCR

source_name: Bulk CD8 T cells from COVID-131: TCR, sample 1, batch 2


title: RNAseq_circPRE8 HCT116 CRISPRi_sgNORAD-2

description:
total RNA extracted using Qiagen RNAeasy kit; polyA-selection using oligo-dT beads
circPRE8sgNORAD2


title: RNAseq_circPRE2 HCT116 CRISPRi_sgNORAD-1

description:
total RNA extracted using Qiagen RNAeasy kit; polyA-selection using oligo-dT beads
circPRE2sgNORAD1


title: CMVTRAP_18_vHC_0min_TRAP_PostIP

description: ribosome bound RNA

value: Homecage

tag: animalnumber

value: CMV-TRAP

tag: mousetype

value: CMV-nuTRAP


title: Batch II (S2) GE

description:
See 'overall design' for details
library type: gene expression

source_name: Bulk CD8 T cells from COVID-131: gene expression, sample 2, batch 2


title: genomic DNA from Labial salivary gland tissue 118

description: Non-case

source_name: Labial salivary gland tissue 118

tag: gender

tag: disease status


title: RNAseq_Parental HCT116 CRISPRi_sgNORAD-2

description:
total RNA extracted using Qiagen RNAeasy kit; polyA-selection using oligo-dT beads
HCTCIsgNORAD2

value: CRISPRi, parental


title: genomic DNA from Labial salivary gland tissue 117

description: Non-case

source_name: Labial salivary gland tissue 117

value: Female

tag: tissue


title: CMVTRAP_17_vHC_45min_TRAP_PreIP

description: total RNA

value: vHC

tag: experiment

tag: block

tag: sampleprocessing


title: genomic DNA from Labial salivary gland tissue 111

description: Non-case

source_name: Labial salivary gland tissue 111

value: Labial salivary gland tissue


title: Batch II (S1) FB

source_name: Bulk CD8 T cells from COVID-131: feature barcodes, sample 1, batch 2

tag: cell type

tag: disease state


title: Batch I (S2) TCR

source_name: Bulk CD8 T cells from COVID-087, -096, -117, -143 and -153: TCR, sample 2, batch 1


title: genomic DNA from Labial salivary gland tissue 113

description: Non-case

source_name: Labial salivary gland tissue 113

value: symptomatic not Sjogrens


title: genomic DNA from Labial salivary gland tissue 112

description: Non-case

source_name: Labial salivary gland tissue 112


title: Batch II (S1) GE

source_name: Bulk CD8 T cells from COVID-131: gene expression, sample 1, batch 2

value: PBMC-derived CD8 T cells


title: Batch I (S2) FB

source_name: Bulk CD8 T cells from COVID-087, -096, -117, -143 and -153: feature barcodes, sample 2, batch 1

value: Acute COVID-19


title: CMVTRAP_15_vHC_45min_TRAP_PostIP

description: ribosome bound RNA

source_name: hippocampus

tag: condition

tag: timepoint

tag: region


title: CMVTRAP_16_vHC_0min_TRAP_PreIP

description: total RNA

tag: mouseline


title: genomic DNA from Labial salivary gland tissue 109

description: Non-case

source_name: Labial salivary gland tissue 109


title: genomic DNA from Labial salivary gland tissue 114

description: Case

source_name: Labial salivary gland tissue 114

value: Sjogrens Syndrome


title: Batch I (S2) GE

source_name: Bulk CD8 T cells from COVID-087, -096, -117, -143 and -153: gene expression, sample 2, batch 1


title: CMVTRAP_14_vHC_45min_TRAP_PostIP

description: ribosome bound RNA

tag: libraryprotocol


title: RNAseq_Parental HCT116 CRISPRi_sgNORAD-1

description:
total RNA extracted using Qiagen RNAeasy kit; polyA-selection using oligo-dT beads
HCTCIsgNORAD1

tag: genotype

tag: sgrna received

value: sgNORAD

tag: cell line


title: RNAseq_Parental HCT116 CRISPRi_sgControl-2

description:
total RNA extracted using Qiagen RNAeasy kit; polyA-selection using oligo-dT beads
HCTCIsgNC2

value: sgControl


title: Batch I (S1) TCR

source_name: Bulk CD8 T cells from COVID-087, -096, -117, -143 and -153: TCR, sample 1, batch 1


title: RNAseq_Parental HCT116 CRISPRi_sgControl-1

description:
total RNA extracted using Qiagen RNAeasy kit; polyA-selection using oligo-dT beads
HCTCIsgNC1


title: CMVTRAP_13_vHC_45min_TRAP_PreIP

description: total RNA

tag: Sex

tag: hemisphere

value: both

tag: animalnumber

tag: mousetype

value: illumina Smartseq2


title: genomic DNA from Labial salivary gland tissue 107

description: Case

source_name: Labial salivary gland tissue 107

tag: gender

tag: tissue

tag: disease status


title: genomic DNA from Labial salivary gland tissue 119

description: Case

source_name: Labial salivary gland tissue 119


title: genomic DNA from Labial salivary gland tissue 110

description: Non-case

source_name: Labial salivary gland tissue 110


title: Batch I (S1) FB

source_name: Bulk CD8 T cells from COVID-087, -096, -117, -143 and -153: feature barcodes, sample 1, batch 1

tag: cell type


title: input for SAR-seq in primary neuron

city: Shanghai

first: Wei

last: Wu

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science

country: China

data_processing:
Library strategy: SAR-seq
SAR-seq, END-seq, ChIP-seq, SEAL, and ATAC-seq reads were aligned to the reference genome (hg19 for human i3Neuron and iMuscle, mm10 for mouse pre B cells or rn6 for rat primary neurons) using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1 for END-seq and -n 2 -l 50 -m 1 for the rest. RNA-seq reads were aligned by STAR (v2.7.6a). Functions “view” and “sort” of samtools (v 1.6) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools bamToBed command. Mitochondrial reads were removed in SAR-seq for intensity comparisons.
We used MACS (v1.4.3) to call SAR-seq, XRCC1 ChIP-seq and ATAC-seq peaks. SAR-seq XRCC1, and CTCF ChIP-seq peaks with >10 fold-enrichment over background were kept. Peaks of hisone modification determined by ChIP-seq peaks were called by SICER with default parameters. Peaks within blacklisted regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were filtered. As peaks of ddN S1-END-seq are always clustered, subpeaks were called by the PeakSplitter tool of PeakAnalyzer with parameters -c 15 -v 0.6.
BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig from UCSC pre-compiled utilities for visualization at UCSC genome browser
.
Genome_build: hg19 for human, mm10 for mourse, rn6 for rat.
Supplementary_files_format_and_content: bigwig

source_name: Primary rat cortical neurons at embryonic day 18

growth_protocol: For neuronal differentiation, 20-25 million iPSCs were plated on day 0 onto a 15 cm plate in N2 media composed of knockout DMEM/F12 media (Life Technologies Corporation, Cat. No. 12660012) with N2 supplement (Life Technologies Corporation, Cat. No. 17502048), 1x GlutaMAX (Thermofisher Scientific, Cat. No. 35050061), 1x MEM nonessential amino acids (NEAA) (Thermofisher Scientific, Cat. No. 11140050), 10 µM ROCK inhibitor (Y-27632; Selleckchem, Cat. No. S1049), and 2 µg/mL doxycycline (Clontech, Cat. No. 631311). N2 media was changed once a day for two more days. Day 3 cells were replated onto freshly-prepared poly-L-ornithine- (PLO; 0.1 mg/ml; Sigma, Cat. No. P3655-10MG) coated dishes as follows: Cells were washed with PBS, dissociated with accutase for 10 minutes at 37°C, washed and plated in i3Neuron Culture Media: BrainPhys media (STEMCELL Technologies, Cat. No. 05790) supplemented with 1x B27 Plus Supplement (ThermoFisher Scientific, Cat. No. A3582801), 10 ng/mL BDNF (PeproTech, Cat. No. 450-02), 10 ng/mL NT-3 (PeproTech, Cat. No. 450-03), 1 mg/mL mouse laminin (Sigma, Cat. No. L2020-1MG), and 2 µg/mL doxycycline (Clontech, Cat. No. 631311).For 10 cm plates used in SAR-seq or CHIP-seq, 12-15 million neurons were plated. For 15 cm plates 30-45 million neurons were plated. For ibidi slides used in imaging experiments, 0.2 million neurons per well were plated. Unless otherwise noted, i3Neurons were fed on day 6 during a half media change and harvested on day 7. For i3Neurons cultured beyond 7 days, half media changes were conducted three times per week. In some experiments pre-differentiated i3Neurons were frozen on day 3 in 90% fetal bovine serum (Sigma Aldrich, Cat. No. ES-009-B) and 10% DMSO (Mediatech Inc., Cat. No. 25-950-CQC), and then thawed rapidly at 37°C, followed by removal of FBS/DMSO and plating in i3Neuron Culture Media. We did not detect any differences for experiments where day 3 neurons were thawed or plated immediately following differentiation.

extract_protocol:
Cells were washed with PBS, incubated with accutase for 5-10 mins, collected with a cell scrapper, pelleted at 200 × g for 5 minutes and resuspended in cold 0.1% BSA in PBS. Cold methanol was then added dropwise during slow vortexing to 80% final concentration. Samples were kept on ice for 20 minutes and then stored at -20C until processing.
Copper catalyzes azide-alkyne click chemistry. For biotin labeling via Click-iT reaction, cells were first washed 1x in PBS, permeabilized with 0.2% Triton-X100/PBS for 10 minutes on ice, and then washed 1x in PBS. Then the following were added in order: 3 mM copper sulfate (Sigma), 50 M biotin azide (ThermoFisher, Cat. No. B10184), and 1X Click-iT additive (ThermoFisher, Cat. No. C10424) for 2 hours shaking at room temperature. Cells were then washed one time in PBS and lysed in 50 mM Tris pH 8.0 with 1% SDS and Proteinase K overnight at 37°C. DNA was extracted with UltraPure Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v) (Invitrogen) according to manufacturer’s instructions, followed by 2.5:1 volume ethanol and 1:10 volume sodium acetate precipitation. DNA pellets were resuspended in TE buffer and sheared to 150-200 bp fragments using Covaris S220 sonicator at 10% duty cycle, 175 peak incident power, 200 cycles per burst, for 240 seconds. DNA was again precipitated by 2.5:1 volume ethanol and 1:10 volume sodium acetate and resuspended in TE buffer. Biotin-EdU fragments were pulled down using MyOne Streptavidin C1 Beads (ThermoFisher, Cat. No. 650-01). Before pulldown, 35 L of Dynabeads were washed two times with 1 mL 1X Wash and Binding buffer (1X W&B) (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1 M NaCl, 0.1% Tween20) on a DynaMag-2 magnetic separator (Invitrogen, Cat. No. 12321D) and resuspended in 2X W&B (10 mM Tris-HCl pH8.0, 2 mM EDTA, 2 M NaCl, 0.2% Tween20). Equal volume of Dynabeads in 2X W&B were added to DNA in TE and incubated at 24°C shaking in a ThermoMixer C at 800 rpm for 30 minutes. Dynabeads bound to biotin-EdU fragments were washed three times in 1 mL of 1X W&B, two times in 1 mL EB, and one time in 1mL 1X T4 DNA Ligase Buffer (NEB). Dynabeads were resuspended in 50 L end-repair reaction mix (1X T4 DNA Ligase Buffer, 0.4 mM of dNTPs, 2.7 U of T4 DNA polymerase (NEB), 9 U of T4 Polynucleotide Kinase (NEB), and 1 U of Klenow fragment (NEB)) and incubated at 24°C shaking at 800 rpm for 30 minutes. Dynabeads were washed one time in 1mL 1X W&B, two times in 1mL EB, and one time in 1 mL NEBuffer 2 (NEB) and resuspended in 50 L of A-tailing reaction mix (1X NEB dA-Tailing Buffer and 20 U Klenow fragment exo- (NEB)), followed by incubation at 37°C shaking at 800 rpm for 30 minutes. Dynabeads were then washed again 1x in 1 mL NEBuffer 2 and resuspended in 115 L of ligation reaction mix (1X Quick Ligase Buffer (NEB), 6000 U Quick Ligase (NEB), 5 nM annealed TruSeq truncated adapter) and incubated at 25°C shaking at 600 rpm for 20 minutes. Ligation reaction was stopped by adding 50 mM EDTA, and Dynabeads were washed three times in 1 mL 1X W&B, three times in 1 mL EB, and finally resuspended in 8 L EB + 10 L 2X Kapa HiFI HotStart Ready Mix (Kapa Biosciences). 10 mM primers 5’-CAAGCAGAAGACGGCATACGA- GATXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T-3’ and 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCC CTACACGACGCTCTTCCGATC*T-3’ (* indicates a phosphothiorate bond and a NNNNNN TruSeq index sequence) were added with 37 L PCR reaction mix (20 L 2X Kapa HiFI HotStart Ready Mix, 17 L H2O) for final volume of 60 L. DNA was amplified using PCR program: 98°C, 45 seconds; 15 cycles [98°C, 15 seconds; 63°C, 30 seconds; 72°C, 30 seconds]; 72°C, 5 minutes. PCR products were separated from DynaBeads and cleaned using 1.8X volume AMPure Beads XP. 150-200 bp bands were isolated on 2% agarose gel and purified using QIA-quick Gel Extraction Kit (Qiagen). Prior to sequencing using Illumina NextSeq 550 (75 bp single read), library concentrations were calculated by KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems).    To specifically sequence only EdU-incorporated strands of DNA (Strand-Specific SAR-seq), SAR-seq was followed exactly as above with additional steps prior to PCR amplification. After washing three times in 1 mL 1X W&B and three times in 1 mL EB post-ligation, Dynabeads were washed in 50 L 1X SSC buffer and resuspended in 20 L of 0.15 M NaOH for 10 minutes at room temperature to denature DNA strands. Beads were placed back on the DynaMag-2 magnetic separator and washed one time with 20 L 0.1 M NaOH, one time with 1 mL 1X W&B, two times with 1 mL EB, and resuspended in 8 L EB + 10 L 2X Kapa HiFI HotStart Ready Mix. Primers and PCR reaction mix were added as above.

treatment_protocol: Neurons and iMuscle cells were incubated with 20 M EdU for 18 hours, unless otherwise noted.

value: rat cortical neurons

value: WT

tag: treatment

value: NT

tag: dose

tag: harvested day

value: day7 (post plating)

tag: molecule subtype

value: EdU incorporated DNA


title: Batch I (S1) GE

source_name: Bulk CD8 T cells from COVID-087, -096, -117, -143 and -153: gene expression, sample 1, batch1

tag: disease state


title: CMVTRAP_12_vHC_45min_TRAP_PostIP

description: ribosome bound RNA

data_processing:
Adaptor trimmed with cutadapt (v 1.15), maximum error rate of 0.05 and a minimum length of 15
Pseudoalignment using kallisto (version 0.44.0) on the GENCODE M17 transcriptome
Aggregation on the protein coding level
Genome_build: GRCm38
Supplementary_files_format_and_content: .h5 files with kallisto output (pseudoaligned read counts). Files are futher zipped

tag: condition

value: Swim

tag: timepoint

tag: region

tag: experiment

value: CMV-TRAP

tag: block

value: CMV-nuTRAP

tag: mouseline

tag: libraryprotocol

tag: sampleprocessing


title: CMVTRAP_11_vHC_0min_TRAP_PostIP

description: ribosome bound RNA

value: Homecage

value: vHC

tag: Sex

value: Female

tag: hemisphere

tag: animalnumber

tag: mousetype


title: AG3558_IgG_LSK_DNase

source_name: LSK

tag: differentiation

value: IgG


title: SAR-seq in rat primary neuron

institute: Center for Excellence in Molecular Cell Science

tag: cell type

tag: genotype

tag: treatment

value: Aphidicolin (APH) added two hours after plating

tag: dose

value: 5 uM


title: input for 5hmC SEAL

data_processing:
Library strategy: SEAL
SAR-seq, END-seq, ChIP-seq, SEAL, and ATAC-seq reads were aligned to the reference genome (hg19 for human i3Neuron and iMuscle, mm10 for mouse pre B cells or rn6 for rat primary neurons) using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1 for END-seq and -n 2 -l 50 -m 1 for the rest. RNA-seq reads were aligned by STAR (v2.7.6a). Functions “view” and “sort” of samtools (v 1.6) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools bamToBed command. Mitochondrial reads were removed in SAR-seq for intensity comparisons.
BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig from UCSC pre-compiled utilities for visualization at UCSC genome browser
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: iNeuron

growth_protocol: For neuronal differentiation, 20-25 million iPSCs were plated on day 0 onto a 15 cm plate in N2 media composed of knockout DMEM/F12 media (Life Technologies Corporation, Cat. No. 12660012) with N2 supplement (Life Technologies Corporation, Cat. No. 17502048), 1x GlutaMAX (Thermofisher Scientific, Cat. No. 35050061), 1x MEM nonessential amino acids (NEAA) (Thermofisher Scientific, Cat. No. 11140050), 10 M ROCK inhibitor (Y-27632; Selleckchem, Cat. No. S1049), and 2 g/mL doxycycline (Clontech, Cat. No. 631311). N2 media was changed once a day for two more days. Day 3 cells were replated onto freshly-prepared poly-L-ornithine- (PLO; 0.1 mg/ml; Sigma, Cat. No. P3655-10MG) coated dishes as follows: Cells were washed with PBS, dissociated with accutase for 10 minutes at 37°C, washed and plated in i3Neuron Culture Media: BrainPhys media (STEMCELL Technologies, Cat. No. 05790) supplemented with 1x B27 Plus Supplement (ThermoFisher Scientific, Cat. No. A3582801), 10 ng/mL BDNF (PeproTech, Cat. No. 450-02), 10 ng/mL NT-3 (PeproTech, Cat. No. 450-03), 1 mg/mL mouse laminin (Sigma, Cat. No. L2020-1MG), and 2 g/mL doxycycline (Clontech, Cat. No. 631311).For 10 cm plates used in SAR-seq or CHIP-seq, 12-15 million neurons were plated. For 15 cm plates 30-45 million neurons were plated. For ibidi slides used in imaging experiments, 0.2 million neurons per well were plated. Unless otherwise noted, i3Neurons were fed on day 6 during a half media change and harvested on day 7. For i3Neurons cultured beyond 7 days, half media changes were conducted three times per week. In some experiments pre-differentiated i3Neurons were frozen on day 3 in 90% fetal bovine serum (Sigma Aldrich, Cat. No. ES-009-B) and 10% DMSO (Mediatech Inc., Cat. No. 25-950-CQC), and then thawed rapidly at 37°C, followed by removal of FBS/DMSO and plating in i3Neuron Culture Media. We did not detect any differences for experiments where day 3 neurons were thawed or plated immediately following differentiation.

extract_protocol: 5hmC-Seal was performed as previously described with modifications. Briefly, 80 μg genomic DNA was resuspended in TE buffer and sonicated to 200 bp fragments using a Covaris S220 sonicator. Fragmented DNA was precipitated by ethanol and sodium acetate and resuspended in TE buffer. The selective 5hmC chemical labeling was performed in 100 μl glucosylation buffer (50 mM HEPES buffer pH 8.0, 25 mM MgCl2) containing above fragmented DNA, β-GT (NEB, Cat. No. M0357), UDP-Azide-Glucose (Active Motif, Cat. No. 55020), and incubated at 37°C for 1.5 hr. After the reaction, DNA was cleaned up with QIAquick Nucleotide Removal Kit. The labeled DNA was eluted with ddH2O, after which 1mM DBCO-PEG4-Biotin (Click Chemistry Tools) was added and incubated at 37°C for 2 hours. Then, the biotin-labeled DNA was pulled down by C1 Streptavidin beads (ThermoFisher, Cat. No. 650-01) for 30 minutes at room temperature. The captured DNA fragments were processed for library construction as described in SAR-seq (above).  For 5fC-SEAL, we modified the previously described protocol, which reduces 5fC to 5hmC using NaBH452. We labeled the newly generated 5hmC (derived from 5fC reduction with NaBH4) with an azide-modified glucose as described above for 5hmC-Seal. In brief, 80 μg of fragmented i3Neurons genomic DNA was incubated in 100 μl glucosylation buffer (50 mM HEPES buffer pH 8.0, 25 mM MgCl2) containing unmodified UDP-Glucose (NEB, Cat No. M0357), and β-GT for 1.5 hours at 37°C. The labeled DNA was cleaned up with QIAquick Nucleotide Removal Kit. Then, an equal volume of freshly prepared NaBH4 (Aldrich, Cat. No. 213462) solution was added to the glucose-blocked DNA solution. The reaction mixture was vortexed and incubated in a Thermomixer for 15 minutes at room temperature. The chemical labeling and capture were performed as described above for 5hmC-SEAL.

tag: harvested day

value: neuron differentiated from iPSC


title: CMVTRAP_10_vHC_45min_TRAP_PreIP

description: total RNA

extract_protocol:
Trizol
illumina TrueSeq or Illumina Smartseq2 (see samples)

tag: condition

tag: timepoint

value: both


title: genomic DNA from Labial salivary gland tissue 116

description: Non-case

source_name: Labial salivary gland tissue 116

tag: gender

tag: tissue

value: Labial salivary gland tissue

tag: disease status

value: symptomatic not Sjogrens


title: XRCC1 ChIP-seq in rat primary neuron

data_processing:
SAR-seq, END-seq, ChIP-seq, SEAL, and ATAC-seq reads were aligned to the reference genome (hg19 for human i3Neuron and iMuscle, mm10 for mouse pre B cells or rn6 for rat primary neurons) using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1 for END-seq and -n 2 -l 50 -m 1 for the rest. RNA-seq reads were aligned by STAR (v2.7.6a). Functions “view” and “sort” of samtools (v 1.6) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools bamToBed command. Mitochondrial reads were removed in SAR-seq for intensity comparisons.
We used MACS (v1.4.3) to call SAR-seq, XRCC1 ChIP-seq and ATAC-seq peaks. SAR-seq XRCC1, and CTCF ChIP-seq peaks with >10 fold-enrichment over background were kept. Peaks of hisone modification determined by ChIP-seq peaks were called by SICER with default parameters. Peaks within blacklisted regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were filtered. As peaks of ddN S1-END-seq are always clustered, subpeaks were called by the PeakSplitter tool of PeakAnalyzer with parameters -c 15 -v 0.6.
BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig from UCSC pre-compiled utilities for visualization at UCSC genome browser
Genome_build: hg19 for human, mm10 for mourse, rn6 for rat.
Supplementary_files_format_and_content: bigwig, bed

extract_protocol:
Cells were fixed in 1% formaldehyde. Cells were sonicated, lysates clarified, and protein-DNA complexes immunoprecipitated.
Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads).  libraries were prepared and sequenced following standard Illumina protocols

value: rat cortical neurons

tag: chip antibody

value: 2.6 ug, Novus, Cat. No. NBP1-87154

value: day8 post plating


title: genomic DNA from Labial salivary gland tissue 108

description: Case

source_name: Labial salivary gland tissue 108

value: Sjogrens Syndrome


title: H3K4me1 ChIP-seq in rat primary neuron

value: 5 ug, Abcam #8895


title: genomic DNA from Labial salivary gland tissue 104

description: Non-case

source_name: Labial salivary gland tissue 104


title: 5hmC SEAL-seq rep1


title: AsisI-DOX SAR-seq in preB

description: Cells were arrested in G1 with 3 μM imatinib for 24 hours, followed by addition of 3 μg/mL doxycycline for 24 hours, and then further addition of 1 μM 4OHT for 18 hours to induce AsiSI nuclear localization

source_name: Abelson-transformed pre-B cell

value: Abelson-transformed pre-B cell

value: WT

value: NT

tag: molecule subtype

value: EdU incorporated DNA


title: 5fC SEAL-seq rep2


title: PARGi PAR ChIP-seq in preB wih AsisI induction

value: 3 uM imatinib for 24 hrs for cell arrest; next, 3 ug/mL doxycyline for 24 hours to express AsiSI; next, 1 uM 4OHT for 18 hrs to induce AsiSI nuclear localization; next, 10 uM PARG inhibitor 20 mins prior to harvest

value: 5 ug, Millipore-Sigma MABE1016


title: CMVTRAP_7_vHC_0min_TRAP_PreIP

description: total RNA

source_name: hippocampus

value: Homecage

tag: region

value: vHC

tag: Sex

value: Female

tag: experiment

value: CMV-TRAP

tag: block

value: CMV-nuTRAP

tag: mouseline

tag: libraryprotocol

value: illumina Smartseq2

tag: sampleprocessing


title: 5hmC SEAL-seq rep2

tag: cell type

value: neuron differentiated from iPSC


title: CMVTRAP_8_vHC_0min_TRAP_PreIP

description: total RNA

tag: hemisphere

value: both

tag: animalnumber

tag: mousetype


title: genomic DNA from Labial salivary gland tissue 101

description: Non-case

source_name: Labial salivary gland tissue 101

value: Labial salivary gland tissue

value: symptomatic not Sjogrens


title: CMVTRAP_6_vHC_45min_TRAP_PreIP

description: total RNA

tag: condition

value: Swim

tag: timepoint


title: Day2_WTCM3

source_name: organoid

tag: tissue

value: Intestinal organoid

tag: genotype

tag: treatment

value: Apc-mutant conditioned medium

tag: background strain

tag: culture day


title: genomic DNA from Labial salivary gland tissue 103

description: Case

source_name: Labial salivary gland tissue 103

tag: gender

tag: disease status

value: Sjogrens Syndrome


title: PAR ChIP-seq in preB wih AsisI induction

value: Abelson-transformed pre-B cell

value: 3 uM imatinib for 24 hrs for cell arrest; next, 3 ug/mL doxycyline for 24 hours to express AsiSI; next, 1 uM 4OHT for 18 hrs to induce AsiSI nuclear localization

tag: chip antibody

tag: harvested day


title: CMVTRAP_5_vHC_45min_TRAP_PostIP

description: ribosome bound RNA

tag: region

tag: Sex

tag: experiment

tag: block

tag: mouseline

tag: libraryprotocol


title: PAR ChIP-seq in preB wihout AsisI induction

tag: cell type

value: 3 uM imatinib for 24 hrs for cell arrest

value: 5 ug, Millipore-Sigma MABE1016


title: CAMK2A-TRAP_11_vHC_45min

description: ribosome bound RNA

tag: condition

tag: timepoint

value: vHC

value: Male

tag: hemisphere

tag: animalnumber

tag: mousetype

tag: sampleprocessing


title: CMVTRAP_4_vHC_45min_TRAP_PreIP

description: total RNA

value: Female

value: CMV-TRAP


title: genomic DNA from Labial salivary gland tissue 102

description: Case

source_name: Labial salivary gland tissue 102

tag: gender

tag: tissue


title: NT for MMS SAR-seq in iNeuron rep2

tag: genotype

value: WT

tag: treatment

value: NT

tag: dose

tag: molecule subtype

value: EdU incorporated DNA


title: input for 5fC SEAL-seq

tag: harvested day

value: neuron differentiated from iPSC


title: genomic DNA from Labial salivary gland tissue 105

description: Non-case

source_name: Labial salivary gland tissue 105

value: Labial salivary gland tissue

tag: disease status

value: symptomatic not Sjogrens


title: genomic DNA from Labial salivary gland tissue 106

description: Non-case

source_name: Labial salivary gland tissue 106


title: Skin CD4+ (MD-scATAC_51)

city: Regensburg

first: LIT

last: NGS-Core

address: Franz-Josef-Strauß-Allee 11

department: NGS-Core

country: Germany

institute: Leibniz Institute for Immunotherapy

description:
Mouse_Gnotobiotic_CD4_barcodes.tsv
Mouse_Gnotobiotic_CD4_fragments.tsv.gz
Mouse_Gnotobiotic_CD4_matrix.mtx
Mouse_Gnotobiotic_CD4_peaks.bed
Mouse_Gnotobiotic_CD4_singlecell.csv
Mouse_Gnotobiotic_CD4_Seurat.RDS

data_processing:
Fastq files were processed using Cell Ranger atac version 1.1.0. Read filtering, alignment, peak calling and count matrix generation from fastq files were done per sample using cellranger-atac count with the reference genome assembly mm10 provided by 10xGenomics (refdata-cellranger-atac-mm10-1.1.0).
Subsequently, barcodes with less than 5000 read-pairs (1000 read-pairs for tumor T cells), more than 20% read-pairs with low mapping quality, more than 90% read-pair duplicates, more than 10% read-pairs from mitochondrial DNA or annotation as multiplet were filtered out.
Barcodes and peaks of the CD4+ T cells from normal tissues, tumor tissue and tissues from gnotobiotic mice were each combined into an aggregate matrix using cellranger-atac aggr without library size normalization.
Fragments from barcodes with more than 50,000 fragments passed filters were randomly subsampled to 50,000 fragments.
Fragments were loaded into R (version 3.6.0) using the package Seurat (version 3.1.2). The peak-barcode matrix was binarized and normalized using the TF-IDF transformation. Singular value decomposition and UMAP were applied for dimensionality reduction.
Genome_build: mm10
Supplementary_files_format_and_content: Output from Cell Ranger atac is described at https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac. RDS files contain final processed matrices stored in a Seurat R object. and meta data

source_name: Skin CD4+

growth_protocol: SPF mice were housed under specified pathogen-free conditions at the central animal facility of the university clinics in Regensburg. Germ-free animals were housed under germ-free conditions at the Helmholtz Center for Infection Research in Braunschweig.

extract_protocol:
T cells were isolated and pre-enriched as described in the associated publication. Afterwards, they were stained with live/dead dye and surface antibodies as described. Cells were then sorted on an BDTM FACSAriaTM IIu or FACSAriaTM FUSION cell sorter using 85 µm nozzle size and 4-way-purity sort mode into 1.5 ml tubes filled with FACS buffer. Sample and post-sort quality control were recorded where applicable and are displayed in supplementary figures of the manuscript.
Cells were pelleted by centrifugation. Supernatant was removed and cells were resuspended in 0.04%BSA-PBS buffer. Cells were centrifuged, supernatant was completely removed and chilled nuclei lysis buffer was added. Lysis was performed for 2 minutes at 4°C, followed by addition of 50 µl washing buffer. After centrifugation, supernatant was removed and 45 µl chilled diluted nuclei buffer was added. After centrifugation, supernatant was removed and 7µl chilled diluted nuclei buffer was added. Nuclei were counted (if applicable) and transposition mix was prepared with 5 µl of nuclei suspension based on manufacturer’s protocol. Transposition was performed for one hour at 37°C, followed by supplementation of master mix and beads, loading on 10X Chromium Next GEM Chip H and processing on 10X Chromium Controller. GEM incubation was performed with 12 cycles of PCR. Library was prepared according to protocol with cycle numbers dependent on input nuclei concentration. Libraries were sequenced on an Illumina NextSeqTM 550 with NextSeqTM 500/550 High Output Kit v2.5 (75 cycles).

value: Skin

tag: breeding condition

value: Germ-free breeding

value: CD3+TCRb+CD45+CD8-CD4+ T cells


title: Colon CD4+ (MD-scATAC_49)

source_name: Colon CD4+

value: Colon


title: NT for MMS SAR-seq in iNeuron rep1


title: AsisI+DOX SAR-seq in preB

value: Abelson-transformed pre-B cell

value: DOX

value: 3 ug/mL


title: genomic DNA from Labial salivary gland tissue 96

description: Non-case

source_name: Labial salivary gland tissue 96


title: 5fC SEAL-seq rep1


title: genomic DNA from Labial salivary gland tissue 98

description: Non-case

source_name: Labial salivary gland tissue 98


title: genomic DNA from Labial salivary gland tissue 100

description: Case

source_name: Labial salivary gland tissue 100

value: Sjogrens Syndrome


title: genomic DNA from Labial salivary gland tissue 97

description: Case

source_name: Labial salivary gland tissue 97


title: VAT CD4+ (MD-scATAC_47)

source_name: VAT CD4+

value: VAT


title: CMVTRAP_2_vHC_45min_TRAP_PostIP

description: ribosome bound RNA

value: Swim

tag: region

value: vHC

tag: Sex

value: Female

value: both

tag: experiment

tag: block

value: CMV-nuTRAP

tag: mouseline

tag: libraryprotocol

value: illumina Smartseq2


title: CMVTRAP_1_vHC_0min_TRAP_PreIP

description: total RNA

tag: condition

value: Homecage

tag: timepoint

tag: hemisphere

tag: animalnumber

value: CMV-TRAP

tag: mousetype


title: LeftvsRight_48_dHC_Right_0min

description: polyA RNA

value: dHC

value: Male

value: Right

value: LeftvsRight

value: WT

value: illumina TruSeq

tag: sampleprocessing

value: WholeRNA


title: LeftvsRight_47_vHC_Right_0min

description: polyA RNA


title: Spleen CD25+ (MD-scATAC_46)

source_name: Spleen CD25+

tag: tissue

value: Spleen

value: Germ-free breeding

tag: cell type

value: CD3+TCRb+CD45+CD8-CD4+CD25+ T cells


title: 18hrs SAR-seq in iNeuron rep2

source_name: iNeuron

value: neuron differentiated from iPSC

tag: genotype

tag: treatment

value: NT

tag: dose

tag: harvested day

tag: molecule subtype

value: EdU incorporated DNA


title: MMS SAR-seq in iNeuron rep2

value: 15 min. MMS


title: genomic DNA from Labial salivary gland tissue 115

description: Case

source_name: Labial salivary gland tissue 115

tag: gender

value: Female

value: Labial salivary gland tissue

tag: disease status

value: Sjogrens Syndrome


title: genomic DNA from Labial salivary gland tissue 95

description: Case

source_name: Labial salivary gland tissue 95


title: HER2 tumor CD25+ (MD-scATAC_27)

description:
Mouse_Tumor_CD4_barcodes.tsv
Mouse_Tumor_CD4_fragments.tsv.gz
Mouse_Tumor_CD4_matrix.mtx
Mouse_Tumor_CD4_peaks.bed
Mouse_Tumor_CD4_singlecell.csv
Mouse_Tumor_CD4_Seurat.RDS

source_name: HER2 tumor CD25+

value: HER2 transgenic tumor

tag: breeding condition

value: Specified pathogen free breeding


title: MMS SAR-seq in iNeuron rep1


title: Spleen CD4+ (MD-scATAC_44)

source_name: Spleen CD4+

value: CD3+TCRb+CD45+CD8-CD4+ T cells


title: 8hrs SAR-seq in iNeuron rep1


title: 8hrs SAR-seq in iNeuron rep2


title: LeftvsRight_45_vHC_Left_0min

description: polyA RNA

source_name: hippocampus

value: Homecage

tag: region

value: vHC

tag: Sex

value: Male

value: Left

tag: experiment

value: LeftvsRight

tag: block

tag: mouseline

tag: libraryprotocol


title: genomic DNA from Labial salivary gland tissue 94

description: Non-case

source_name: Labial salivary gland tissue 94

value: symptomatic not Sjogrens


title: genomic DNA from Labial salivary gland tissue 92

description: Non-case

source_name: Labial salivary gland tissue 92


title: LeftvsRight_44_dHC_Right_45min

description: polyA RNA

tag: condition

value: Swim

tag: timepoint

value: dHC

tag: hemisphere

value: Right

tag: animalnumber

tag: mousetype

value: WT

value: illumina TruSeq

tag: sampleprocessing

value: WholeRNA


title: HER2 tumor CD4+ (MD-scATAC_25)

source_name: HER2 tumor CD4+

tag: tissue

tag: cell type


title: Lung CD4+ (MD-scATAC_40)

description:
Mouse_Normal_CD4_barcodes.tsv
Mouse_Normal_CD4_fragments.tsv.gz
Mouse_Normal_CD4_matrix.mtx
Mouse_Normal_CD4_peaks.bed
Mouse_Normal_CD4_singlecell.csv
Mouse_Normal_CD4_Seurat.RDS

source_name: Lung CD4+

value: Lung


title: 4hrs SAR-seq in iNeuron rep2

value: neuron differentiated from iPSC

tag: genotype

tag: treatment

value: NT

tag: dose

tag: harvested day

tag: molecule subtype

value: EdU incorporated DNA


title: LeftvsRight_46_dHC_Left_0min

description: polyA RNA

tag: region

tag: Sex

tag: experiment


title: LeftvsRight_43_vHC_Right_45min

description: polyA RNA

tag: block

tag: mouseline

tag: libraryprotocol


title: 18hrs SAR-seq in iNeuron rep1


title: Skin CD4+ (MD-scATAC_23)

source_name: Skin CD4+

value: Skin

tag: breeding condition

value: Specified pathogen free breeding

value: CD3+TCRb+CD45+CD8-CD4+ T cells


title: HER2 tumor CD4+ (MD-scATAC_24)

value: HER2 transgenic tumor


title: LeftvsRight_42_dHC_Left_45min

description: polyA RNA

tag: condition

tag: timepoint

value: Male

tag: hemisphere

value: Left

tag: animalnumber


title: genomic DNA from Labial salivary gland tissue 91

description: Case

source_name: Labial salivary gland tissue 91

tag: gender

value: Female

tag: tissue

value: Labial salivary gland tissue

tag: disease status

value: Sjogrens Syndrome


title: 4hrs SAR-seq in iNeuron rep1

tag: cell type

tag: genotype

tag: treatment

tag: dose


title: genomic DNA from Labial salivary gland tissue 93

description: Case

source_name: Labial salivary gland tissue 93


title: genomic DNA from Labial salivary gland tissue 99

description: Case

source_name: Labial salivary gland tissue 99


title: genomic DNA from Labial salivary gland tissue 89

description: Non-case

source_name: Labial salivary gland tissue 89

value: symptomatic not Sjogrens


title: LeftvsRight_41_vHC_Left_45min

description: polyA RNA

value: Swim

tag: region

value: vHC

tag: Sex

value: LeftvsRight

tag: mousetype

value: WT

tag: sampleprocessing


title: VAT CD4+ (MD-scATAC_19)

source_name: VAT CD4+

value: VAT


title: Spleen CD25+ (MD-scATAC_21)

source_name: Spleen CD25+

value: Spleen

value: CD3+TCRb+CD45+CD8-CD4+CD25+ T cells


title: genomic DNA from Labial salivary gland tissue 88

description: Non-case

source_name: Labial salivary gland tissue 88


title: genomic DNA from Labial salivary gland tissue 87

description: Case

source_name: Labial salivary gland tissue 87


title: 2hrs SAR-seq in iNeuron rep1

source_name: iNeuron

value: neuron differentiated from iPSC

value: NT

tag: harvested day

tag: molecule subtype

value: EdU incorporated DNA


title: genomic DNA from Labial salivary gland tissue 90

description: Case

source_name: Labial salivary gland tissue 90


title: Skin CD4+ (MD-scATAC_9)

value: Skin

tag: breeding condition

value: Specified pathogen free breeding

value: CD3+TCRb+CD45+CD8-CD4+ T cells


title: 1hr SAR-seq in iNeuron rep2


title: CMVTRAP_9_vHC_0min_TRAP_PostIP

description: ribosome bound RNA

tag: condition

value: Homecage

tag: timepoint

value: Female

value: both

tag: experiment

value: CMV-TRAP

tag: block

value: CMV-nuTRAP

tag: mouseline

tag: libraryprotocol

value: illumina Smartseq2


title: LeftvsRight_39_vHC_Right_45min

description: polyA RNA

value: Swim

value: vHC

value: Male

tag: hemisphere

value: Right

tag: animalnumber

value: LeftvsRight

value: illumina TruSeq

value: WholeRNA


title: Spleen CD25+ (MD-scATAC_8)

tag: tissue

value: Spleen

tag: cell type

value: CD3+TCRb+CD45+CD8-CD4+CD25+ T cells


title: LeftvsRight_38_dHC_Left_45min

description: polyA RNA

tag: region

value: dHC

value: Left

value: WT


title: VAT CD4+ (MD-scATAC_5)

value: VAT

value: Specified pathogen free breeding

value: CD3+TCRb+CD45+CD8-CD4+ T cells


title: SAR-seq in Muscle rep2

source_name: iMuscle

growth_protocol: To generate skeletal muscle myoblasts from human iPSCs, we engineered a doxycycline-inducible vector harboring a MyoD1transcription factor transgene immediately followed by a co-inducible short hairpin RNA targeting Oct4 and selection marker/fluorescent proteincassette (MyoD-O iPSCs), similar to previous methods. We used the PiggyBacTM system to facilitate delivery and genome integration of thetransgene cassette. To increase transposase expression in iPSCs, we subcloned the PiggyBacTM transposase under a long version of the eF1a promoter,and co-transfected this transposase vector with the MyoD1 donor vector into iPSCs using lipofectamine stem (Thermofisher Scientific, Cat. No.STEM00015). Transfection rates were approximately 55% based on fluorescence of a co-expressed reporter gene, and we were able to obtain 100%MyoD1-O iPSCs after puromycin selection of iPSCs harboring stable integration of the transcription factor cassette. To induce myogenic differentiation, MyoD-O iPSCs were dissociated using accutase (37  C for 10 minutes) and resuspended in myogenic induction media (MIM) and plated with 3x106 iPSCs per 10 cm dish. The MyoD-O iPSCs differentiation was modified from a recent report. The MIM contained DMEM/F12 HEPES (Gibco, Cat. No. 11-330-032) supplemented to a final concentration of 1 mM sodium pyruvate, 1x MEM nonessential amino acids (NEAA) (Thermofisher Scientific, Cat. No. 11140050), 0.1 mM 2-mercaptoethanol (Gibco, Cat. No. 21985023), 10   g/mL insulin (Roche , Cat. No. 11376497001), 2   g/mL doxycycline and 10   M RI. After plating the MyoD-O iPSCs in MIM at day 0, fresh media was supplied daily until 80% confluency or more (day 6). Myoblast morphology was observed beginning at day 2 followed by myotube-like morphology at day 5. On day 6, the glycogen synthase kinase 3 (GSK-3) inhibitor, CHIR 99021, was administered for 48 hours to enhance myoblast differentiation and stimulate fusion (3   M, Tocris, Cat. No. 4423) as reported by others. At day 9 post-doxycycline, the differentiating myoblasts were harvested.

value: muscle cell differentiated from iPSC

tag: genotype

tag: treatment

value: NT

tag: dose

value: EdU incorporated DNA


title: 1hr SAR-seq in iNeuron rep1

value: neuron differentiated from iPSC

tag: harvested day


title: SAR-seq in Muscle rep1

tag: molecule subtype


title: LeftvsRight_37_vHC_Left_45min

description: polyA RNA

source_name: hippocampus

value: Swim

value: vHC

tag: Sex

value: Male

tag: mousetype

tag: sampleprocessing


title: LeftvsRight_40_dHC_Right_45min

description: polyA RNA

tag: condition

tag: timepoint

value: Right

tag: experiment

value: LeftvsRight

value: illumina TruSeq


title: genomic DNA from Labial salivary gland tissue 85

description: Non-case

source_name: Labial salivary gland tissue 85

tag: gender

value: Female

value: Labial salivary gland tissue

tag: disease status

value: symptomatic not Sjogrens


title: genomic DNA from Labial salivary gland tissue 86

description: Non-case

source_name: Labial salivary gland tissue 86


title: strandness SAR-seq in iNeuron rep3

value: WT


title: Spleen CD4+ (MD-scATAC_1)

source_name: Spleen CD4+

value: Spleen

tag: breeding condition


title: strandness SAR-seq in iNeuron rep2


title: LeftvsRight_35_vHC_Right_0min

description: polyA RNA

value: Homecage

tag: hemisphere

tag: animalnumber

tag: block

tag: mouseline

tag: libraryprotocol

value: WholeRNA


title: ST142DAF14SolarSHADINGDelayedR3

city: Valdivia

first: Javier

last: Canales

state: Los Ríos

address: Campus Isla Teja s/n

department: Instituto de Bioquimica y Microbiologia

country: Chile

institute: Universidad Austral de Chile

data_processing:
Sequenced reads were pseudo-aligned to the publicly available Brassica napus transcriptome obtained from Ensembl Plants using kallisto (v0.46)
RNA-seq data was normalized using the R package sleuth
Genome_build: AST_PRJEB5043_v1
Supplementary_files_format_and_content: tab-delimited text files include tpm values for each sample

organism: Brassica napus

growth_protocol: A ﬁeld experiment in two sowing dates was carried out at the Austral Farming Exper-imental Station in Valdivia, Chile (39° 47’ S., 73° 14’ W.). In this experiment three sources of variation were evaluated in rapeseed: (i) genotype (two adapted spring rapeseed hy-brids: Lumen and Solar (chosen for having similar phenology and adapted to southern Chile), (ii) sowing date (optimum and late sowing date) and (iii) source-sink (S-Sratio) ra-tios (control without manipulation and a reduced S-Sratio with black nets intercepting 75% of solar radiation from the beginning of flowering [BBCH 61] to 15 days after flowering (DAF)). Treatments were arranged in a split–split-plot design with three replicates, where sowing date was assigned to main plots, the S-Sratio to subplots and genotypes to sub-sub plots [16]. The rapeseed plants were sown at a plant density of 55 plants m-2

extract_protocol:
Total RNA extraction was performed using a method adapted for Brassica seeds (Graeber et al., 2011;doi:10.1105/tpc.111.084103) with 100 mg of each sample and using NucleoSpin® Gel and PCR columns
RNA quality analysis, libraries construction and sequencing were performed by Novogene (Beijing, China) using standard Illumina protocols

tag: days after flowering

tag: genotype

value: Solar

tag: treatment

value: SHADING

tag: sowing date

value: Delayed

tag: replicate


title: Colon CD4+ (MD-scATAC_4)

source_name: Colon CD4+

tag: tissue

value: Colon

value: Specified pathogen free breeding

tag: cell type

value: CD3+TCRb+CD45+CD8-CD4+ T cells


title: ST138DAF14SolarSHADINGDelayedR2


title: strandness SAR-seq in iNeuron rep1

value: neuron differentiated from iPSC

value: NT

tag: dose

tag: harvested day

tag: molecule subtype

value: EdU incorporated DNA


title: CPT sgControl for sgPNKP SAR-seq iNeuron rep2

value: sgControl

value: 2hrs Camptothecin+18 hrs EdU

value: 25 uM (for Camptothecin)


title: genomic DNA from Labial salivary gland tissue 82

description: Case

source_name: Labial salivary gland tissue 82

tag: gender

value: Female

value: Labial salivary gland tissue

tag: disease status

value: Sjogrens Syndrome


title: LeftvsRight_32_dHC_Right_45min

description: polyA RNA

tag: condition

value: Swim

tag: timepoint

tag: region

value: dHC

tag: Sex

value: Male

tag: hemisphere

value: Right

tag: experiment

value: LeftvsRight

tag: mousetype

value: WT

value: illumina TruSeq

tag: sampleprocessing


title: ST118DAF7SolarSHADINGDelayedR3

tag: days after flowering

tag: genotype

value: Solar

tag: treatment

value: SHADING

tag: sowing date

value: Delayed


title: LeftvsRight_33_vHC_Left_0min

description: polyA RNA

value: Homecage

value: vHC

value: Left

tag: animalnumber

tag: block

tag: mouseline

tag: libraryprotocol

value: WholeRNA


title: ST134DAF14SolarSHADINGDelayedR1

tag: replicate


title: CPT sgPNKP SAR-seq iNeuron rep2

tag: cell type

value: neuron differentiated from iPSC

value: sgPNKP

value: 2hrs Camptothecin+18 hrs EdU

tag: dose

value: 25 uM (for Camptothecin)

tag: harvested day

tag: molecule subtype

value: EdU incorporated DNA


title: LeftvsRight_31_vHC_Right_45min

description: polyA RNA

tag: condition

value: Swim

tag: timepoint

tag: region

tag: Sex

value: Male

tag: hemisphere


title: genomic DNA from Labial salivary gland tissue 79

description: Non-case

source_name: Labial salivary gland tissue 79

tag: gender

value: Female

tag: tissue

value: Labial salivary gland tissue

tag: disease status

value: symptomatic not Sjogrens


title: CPT sgPNKP SAR-seq iNeuron rep1

tag: genotype

tag: treatment


title: genomic DNA from Labial salivary gland tissue 81

description: Case

source_name: Labial salivary gland tissue 81

value: Sjogrens Syndrome


title: LeftvsRight_30_dHC_Left_45min

description: polyA RNA

value: dHC

tag: animalnumber

tag: experiment

value: LeftvsRight

tag: block

tag: mousetype

value: WT

tag: mouseline

value: illumina TruSeq

tag: sampleprocessing


title: LeftvsRight_36_dHC_Right_0min

description: polyA RNA

value: Homecage

value: Right

tag: libraryprotocol


title: NT sgPNKP SAR-seq iNeuron rep2

tag: cell type

value: neuron differentiated from iPSC

value: NT

tag: dose

tag: harvested day

tag: molecule subtype


title: genomic DNA from Labial salivary gland tissue 76

description: Case

source_name: Labial salivary gland tissue 76


title: LeftvsRight_29_vHC_Left_45min

description: polyA RNA

tag: condition

tag: timepoint

tag: region

value: vHC

tag: Sex

tag: hemisphere

value: Left

value: WholeRNA


title: ST094DAF14SolarSHADINGOptimalR3

tag: days after flowering

tag: genotype

value: Solar

tag: treatment

value: SHADING

tag: sowing date

value: Optimal

tag: replicate


title: CPT sgControl for sgPNKP SAR-seq iNeuron rep1

value: sgControl

value: 2hrs Camptothecin+18 hrs EdU

value: 25 uM (for Camptothecin)

value: EdU incorporated DNA


title: genomic DNA from Labial salivary gland tissue 78

description: Non-case

source_name: Labial salivary gland tissue 78

tag: gender

value: Female

tag: tissue

value: Labial salivary gland tissue

tag: disease status

value: symptomatic not Sjogrens


title: LeftvsRight_34_dHC_Left_0min

description: polyA RNA

value: Homecage

value: dHC

value: Male

tag: animalnumber

tag: experiment

value: LeftvsRight

tag: block

tag: mousetype

value: WT

tag: mouseline

tag: libraryprotocol

value: illumina TruSeq

tag: sampleprocessing


title: ST114DAF7SolarSHADINGDelayedR2

value: Delayed


title: genomic DNA from Labial salivary gland tissue 84

description: Case

source_name: Labial salivary gland tissue 84

value: Sjogrens Syndrome


title: genomic DNA from Labial salivary gland tissue 75

description: Case

source_name: Labial salivary gland tissue 75


title: genomic DNA from Labial salivary gland tissue 83

description: Non-case

source_name: Labial salivary gland tissue 83


title: ST110DAF7SolarSHADINGDelayedR1

value: Solar

value: SHADING


title: ST090DAF14SolarSHADINGOptimalR2

value: Optimal


title: LeftvsRight_27_vHC_Right_0min

description: polyA RNA

tag: condition

tag: timepoint

tag: region

value: vHC

tag: Sex

value: Right

value: WholeRNA


title: NT for ETO SAR-seq in iNeuron rep2

tag: cell type

value: neuron differentiated from iPSC

tag: genotype

tag: treatment

value: NT

tag: dose

tag: harvested day

tag: molecule subtype

value: EdU incorporated DNA


title: NT for ETO SAR-seq in iNeuron rep1


title: ST086DAF14SolarSHADINGOptimalR1

tag: days after flowering

tag: sowing date

tag: replicate


title: genomic DNA from Labial salivary gland tissue 73

description: Case

source_name: Labial salivary gland tissue 73

tag: gender

value: Female

tag: tissue

value: Labial salivary gland tissue

tag: disease status


title: genomic DNA from Labial salivary gland tissue 72

description: Case

source_name: Labial salivary gland tissue 72


title: genomic DNA from Labial salivary gland tissue 74

description: Case

source_name: Labial salivary gland tissue 74


title: ST070DAF7SolarSHADINGOptimalR3


title: genomic DNA from Labial salivary gland tissue 80

description: Non-case

source_name: Labial salivary gland tissue 80

value: symptomatic not Sjogrens


title: ST066DAF7SolarSHADINGOptimalR2


title: ST062DAF7SolarSHADINGOptimalR1


title: genomic DNA from Labial salivary gland tissue 70

description: Case

source_name: Labial salivary gland tissue 70


title: 2hrs SAR-seq in iNeuron rep2

source_name: iNeuron


title: ETO SAR-seq in iNeuron rep1

value: Etoposide

value: 50 uM


title: LeftvsRight_26_dHC_Left_0min

description: polyA RNA

source_name: hippocampus

value: Homecage

value: dHC

value: Male

tag: hemisphere

value: Left

tag: animalnumber

tag: experiment

value: LeftvsRight

tag: block

tag: mousetype

value: WT

tag: mouseline

tag: libraryprotocol

value: illumina TruSeq

tag: sampleprocessing


title: ETO SAR-seq in iNeuron rep2

tag: cell type

tag: genotype

tag: treatment

tag: dose


title: LeftvsRight_23_vHC_Right_45min

description: polyA RNA

tag: condition

value: Swim

tag: timepoint

tag: region

value: vHC

tag: Sex

value: Right


title: APH sgControl for sgPOLB SAR-seq iNeuron rep2

value: neuron differentiated from iPSC

value: sgControl

value: 24hrs APH +18hrs EdU

value: 50 uM (for APH)

tag: harvested day

tag: molecule subtype


title: genomic DNA from Labial salivary gland tissue 71

description: Case

source_name: Labial salivary gland tissue 71

tag: gender

value: Female

tag: tissue

value: Labial salivary gland tissue

tag: disease status

value: Sjogrens Syndrome


title: SC141DAF14SolarCONTROL DelayedR3

tag: days after flowering

value: Solar

value: CONTROL

tag: sowing date

value: Delayed

tag: replicate


title: genomic DNA from Labial salivary gland tissue 69

description: Case

source_name: Labial salivary gland tissue 69


title: SC137DAF14SolarCONTROL DelayedR2


title: LeftvsRight_28_dHC_Right_0min

description: polyA RNA

value: Homecage

value: dHC

value: Male

tag: hemisphere

tag: animalnumber

tag: experiment

tag: block

tag: mousetype

tag: mouseline

tag: libraryprotocol

tag: sampleprocessing

value: WholeRNA


title: LeftvsRight_24_dHC_Right_45min

description: polyA RNA

tag: condition

value: Swim

tag: timepoint

tag: region

tag: Sex

value: LeftvsRight

value: WT

value: illumina TruSeq


title: LeftvsRight_22_dHC_Left_45min

description: polyA RNA

value: Left


title: APH sgControl for sgPOLB SAR-seq iNeuron rep1

tag: cell type

value: neuron differentiated from iPSC

tag: genotype

value: sgControl

tag: treatment

value: 24hrs APH +18hrs EdU

tag: dose

tag: harvested day

tag: molecule subtype

value: EdU incorporated DNA


title: NT sgControl for sgPOLB and sgPNKP SAR-seq iNeuron rep2

value: NT


title: LeftvsRight_21_vHC_Left_45min

description: polyA RNA

value: vHC

tag: hemisphere

tag: animalnumber


title: SC133DAF14SolarCONTROL DelayedR1

tag: days after flowering

value: Solar

value: CONTROL

tag: sowing date

tag: replicate


title: NT sgControl for sgPOLB and sgPNKP SAR-seq iNeuron rep1


title: genomic DNA from Labial salivary gland tissue 67

description: Non-case

source_name: Labial salivary gland tissue 67

tag: gender

value: Female

tag: tissue

value: Labial salivary gland tissue

tag: disease status

value: symptomatic not Sjogrens


title: LeftvsRight_20_dHC_Right_0min

description: polyA RNA

tag: condition

value: Homecage

tag: timepoint

value: dHC

value: Male

value: Right

tag: experiment

tag: block

tag: mousetype

tag: mouseline

tag: libraryprotocol

tag: sampleprocessing

value: WholeRNA


title: SC117DAF7SolarCONTROL DelayedR3

tag: genotype

tag: treatment

value: Delayed


title: LeftvsRight_25_vHC_Left_0min

description: polyA RNA

tag: region

tag: Sex

tag: hemisphere

value: Left

tag: animalnumber

value: LeftvsRight

value: WT

value: illumina TruSeq


title: SC113DAF7SolarCONTROL DelayedR2

tag: days after flowering

tag: sowing date

tag: replicate


title: LeftvsRight_19_vHC_Right_0min

description: polyA RNA

tag: condition


title: genomic DNA from Labial salivary gland tissue 65

description: Non-case

source_name: Labial salivary gland tissue 65

tag: gender

tag: tissue

tag: disease status


title: APH sgPOLB SAR-seq iNeuron rep2

tag: cell type

value: neuron differentiated from iPSC

value: sgPOLB

value: 24hrs APH +18hrs EdU

tag: dose

value: 50 uM (for APH)

tag: harvested day

tag: molecule subtype

value: EdU incorporated DNA


title: LeftvsRight_17_vHC_Left_0min

description: polyA RNA

tag: timepoint

value: vHC

tag: experiment

tag: block

tag: mousetype

tag: mouseline

tag: libraryprotocol

tag: sampleprocessing


title: genomic DNA from Labial salivary gland tissue 64

description: Case

source_name: Labial salivary gland tissue 64

value: Female

value: Labial salivary gland tissue

value: Sjogrens Syndrome


title: genomic DNA from Labial salivary gland tissue 66

description: Case

source_name: Labial salivary gland tissue 66


title: NT sgPOLB SAR-seq iNeuron rep2

tag: genotype

tag: treatment

value: NT


title: SC093DAF14SolarCONTROL OptimalR3

tag: days after flowering

value: Solar

value: CONTROL

tag: sowing date

value: Optimal

tag: replicate


title: SC089DAF14SolarCONTROL OptimalR2


title: LeftvsRight_16_dHC_Right_0min

description: polyA RNA

tag: condition

value: Homecage

tag: region

value: dHC

tag: Sex

value: Male

tag: hemisphere

value: Right

tag: animalnumber

value: WholeRNA


title: CMVTRAP_3_vHC_0min_TRAP_PostIP

description: ribosome bound RNA

tag: timepoint

value: both

value: CMV-TRAP

value: CMV-nuTRAP

value: illumina Smartseq2


title: LeftvsRight_18_dHC_Left_0min

description: polyA RNA

value: Left

tag: experiment

value: LeftvsRight

value: WT

value: illumina TruSeq


title: NT sgPOLB SAR-seq iNeuron rep1

tag: cell type

value: neuron differentiated from iPSC

value: sgPOLB

value: NT

tag: dose

tag: harvested day

tag: molecule subtype

value: EdU incorporated DNA


title: SC109DAF7SolarCONTROL DelayedR1

value: Solar

value: CONTROL

value: Delayed


title: SC085DAF14SolarCONTROL OptimalR1

value: Optimal


title: LeftvsRight_15_vHC_Right_0min

description: polyA RNA

value: Homecage

value: vHC

value: Male

value: Right

tag: block

tag: mousetype

tag: mouseline

tag: libraryprotocol

tag: sampleprocessing

value: WholeRNA


title: sgControl SAR-seq for sgPOLB in iNeuron rep2

tag: genotype

value: sgControl

tag: treatment


title: NT sgPNKP SAR-seq iNeuron rep1

value: sgPNKP


title: genomic DNA from Labial salivary gland tissue 63

description: Non-case

source_name: Labial salivary gland tissue 63

tag: gender

value: Female

tag: tissue

value: Labial salivary gland tissue

tag: disease status

value: symptomatic not Sjogrens


title: LeftvsRight_14_dHC_Left_0min

description: polyA RNA

tag: condition

tag: region

value: dHC

tag: Sex

tag: hemisphere

value: Left

tag: animalnumber

value: LeftvsRight

value: WT

value: illumina TruSeq


title: APH sgPOLB SAR-seq iNeuron rep1

tag: cell type

value: neuron differentiated from iPSC

value: sgPOLB

value: 24hrs APH +18hrs EdU

tag: dose

value: 50 uM (for APH)

tag: harvested day

value: EdU incorporated DNA


title: sgControl SAR-seq for sgPOLB in iNeuron rep1

value: NT

tag: molecule subtype


title: LeftvsRight_13_vHC_Left_0min

description: polyA RNA

value: Homecage

tag: timepoint

value: vHC

value: Male

tag: experiment

tag: block

tag: mousetype

tag: mouseline

value: WholeRNA


title: genomic DNA from Labial salivary gland tissue 62

description: Case

source_name: Labial salivary gland tissue 62

tag: gender

value: Female

value: Labial salivary gland tissue

value: Sjogrens Syndrome


title: POLB sg2 SAR-seq in iNeuron rep2

tag: genotype

tag: treatment


title: SC065DAF7SolarCONTROL OptimalR2

tag: days after flowering

value: Solar

value: CONTROL

tag: sowing date

value: Optimal

tag: replicate


title: LeftvsRight_12_dHC_Right_45min

description: polyA RNA

tag: condition

value: Swim

tag: region

value: dHC

tag: Sex

tag: hemisphere

value: Right

value: LeftvsRight

value: WT

tag: libraryprotocol

value: illumina TruSeq

tag: sampleprocessing


title: SC069DAF7SolarCONTROL OptimalR3


title: genomic DNA from Labial salivary gland tissue 77

description: Non-case

source_name: Labial salivary gland tissue 77

tag: tissue

tag: disease status

value: symptomatic not Sjogrens


title: LT126DAF14Lumen SHADINGDelayedR2

value: Lumen

value: SHADING

value: Delayed


title: genomic DNA from Labial salivary gland tissue 60

description: Case

source_name: Labial salivary gland tissue 60


title: genomic DNA from Labial salivary gland tissue 61

description: Non-case

source_name: Labial salivary gland tissue 61


title: POLB sg1 SAR-seq in iNeuron rep1

tag: cell type

value: neuron differentiated from iPSC

value: sgPOLB

value: NT

tag: dose

tag: harvested day

tag: molecule subtype

value: EdU incorporated DNA


title: genomic DNA from Labial salivary gland tissue 58

description: Non-case

source_name: Labial salivary gland tissue 58

tag: gender

value: Female

value: Labial salivary gland tissue


title: LeftvsRight_10_dHC_Left_45min

description: polyA RNA

tag: timepoint

value: Male

value: Left

tag: animalnumber

tag: experiment

tag: block

tag: mousetype

tag: mouseline

value: WholeRNA


title: genomic DNA from Labial salivary gland tissue 59

description: Non-case

source_name: Labial salivary gland tissue 59


title: POLB sg2 SAR-seq in iNeuron rep1

tag: genotype

tag: treatment


title: sgControl SAR-seq for sgXRCC1 in iNeuron rep2

value: sgControl