title: sgElavl1 rep2

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Raw reads were trimmed using cutadapt (v1.14) using the following parameters: -O 5 --match-read-wildcards --times 2 -e 0.0 --quality-cutoff 6 -m 18 -b TCGTATGCCGTCTTCTGCTTG ATCTCGTATGCCGTCTTCTGCTTG CGACAGGTTCAGAGTTCTACAGTCCGACGATC GATCGGAAGAGCACACGTCTGAACTCCAGTCAC AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
Trimmed reads were mapped to and filtered of mouse-specific repeat elements (RepBase 18.05) with STAR (2.4.0i) using the following parameters: --alignEndsType  EndToEnd  --genomeDir  repbase  --genomeLoad  NoSharedMemory  --outBAMcompression  10  --outFileNamePrefix  condition1  --outFilterMultimapNmax  10  --outFilterMultimapScoreRange  1  --outFilterScoreMin  10  --outFilterType  BySJout  --outReadsUnmapped  Fastx  --outSAMattrRGline  ID:foo  --outSAMattributes  All  --outSAMmode  Full  --outSAMtype  BAM  Unsorted  --outSAMunmapped  Within  --outStd  Log  --readFilesIn  r1.fastq  r2.fastq  --runMode  alignReads  --runThreadN  8
Reads unmapped to repeat elements were mapped to the mouse genome with STAR using the same parameters as the previous step, using an mm9 index in place of the repeat element index
Subread featureCounts (-a gencode.vM1.annotation.gtf -s 2 -p -o counts.txt RN2c.bam) was used to count features using mouse annotations (Gencode vM1)
Genome_build: mm9
Supplementary_files_format_and_content: counts.txt contains read counts from mm9-mapped BAM files

growth_protocol: RN2c cells were cultured in RPMI supplemented with 10% FBS, at a maximum density of 1 million cells per mL.

extract_protocol:
RNA was coprecipitated with GlycoBlue (ThermoFisher #AM9516) following manufacturers protocol; in brief, 3uL (final concentration 45ug/mL) of GlycoBlue was added to TrizolLS-separated aqueous phase followed by one volume isopropanol and incubated at -20C for 30 min before pelleting RNA by centrifugation. Isolated RNA was treated with DNase I (ThermoFisher #EN0521) which was inactivated by addition of EDTA and incubation at 65C.
PolyA+ RNA libraries were generated using NEBNext PolyA mRNA Magnetic Isolation Module (E7490) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L) and indexed using NEBNext Multiplex Oligos for Illumina (E6440L). 100bp paired-end sequencing was performed on the Illumina HiSeq 1500 with depth of 50 million reads per sample.

treatment_protocol: Cells were transduced with lentiviral-packaged sgRNA targeting Elavl1 and, as control, Ano9. 72 hours following transduction live 7AAD- GFP+ cells were isolated by FACS and RNA was extracted by TrizolLS (ThermoFisher # 10296028) following manufacturers protocol.

tag: cell line

value: murine MLL-AF9/NrasG12D acute myeloid leukemia cell line

tag: genotype/variaton


title: Input_hPGC_wk8_F_r2

status: Public on Jan 18 2023

type: SRA

city: Cambridge

first: Walfred

last: Tang

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

library_source: genomic

data_processing:
Paired-end ChIP-seq reads were quality- and adaptor-trimmed by Trim Galore (v0.4.1) using default parameters.
Trimmed reads were mapped to the human reference genome (UCSC GRCh38/hg38) and 680 drosophila (UCSC dm6) by Bowtie 2 (v2.3.4.1) with options ‘--local -X 2000 --no-mixed --no-discordant’, hence retaining properly paired reads with a maximum fragment length of 2000 bp.
Unmapped reads, non-primary reads, supplementary alignment and QC-failed reads were removed using samtools view with option ‘-F 2828’. Duplicated reads were marked and removed by the MarkDuplicates function in Picard Tools (Broad Institute). Subsequently, fragments mapped to hg38 blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/hg38.blacklist.bed.gz), non-canonical hg38 contigs and mitochondrial DNA (chrM) were removed.
Prior to peak calling, libraries were subsampled using Picard DownSampleSam so that each library contains approximately the same number of paired-end reads.
Peaks were called following the Encode replicated peak calling guidelines (https://www.encodeproject.org/pipelines/ENCPL272XAE/) with modifications to accommodate for paired-end libraries. To obtain high resolution of peaks, narrow peak call was used for all marks. Histone peaks were called using the input reads as background. Peaks were initially called for each biological replicate (downsampled to similar read depth), for the pooled replicates, and for the pooled pseudoreplicates of each biological replicate using MACS2 with a relaxed p-value threshold of 0.05 (options: ‘-g 3e9 --keep-dup all -p 0.05’). Each pseudoreplicate consists of half the reads of each biological replicate, chosen at random without replacement. Narrow peaks from the pooled replicate set were retained if they overlapped peaks from both biological replicates or peaks from both pooled pseudoreplicates. The thresholds of overlap were set at 30% by peak length for histone peaks. This peak calling strategy allows for the retention of marginal peaks in one replicate to be rescued by a strong biological replicate. To obtain a final high confidence peak set, the reproducible peaks were further filtered using the MACS2 q-value (false discovery rate <0.001).
Assembly: hg38
Supplementary files format and content: Reproducible peaks of the two biological replicates in macs2 narrowPeak format

molecule: genomic DNA

organism: Homo sapiens

source_name: Gonad

extract_protocol:
Cells were thawed on ice, incubated with 2 µl of 1 % Triton X-100, 1 % Sodium deoxycholate and digested with Micrococcal Nuclease (MNase) (NEB). MNase activity was blocked by addition of 11 µl 100 mM EDTA and cell lysate was incubated for 1 h in 400 µl of IP buffer at 4 °C followed by 2 h incubation in the presence of 5 µl blocked protein A/G beads (blocking buffer: 100 µg/ml yeast tRNA, 0.1 % BSA in IP buffer). After the removal of the protein A/G beads, the pre-cleared cell lysate was added to the antibody bead complex (antibody was incubated with 5 µl blocked protein A/G beads for 3 h on 4 °C) overnight at 4 °C. Unbound chromatin was removed, and beads were sequentially washed for 4 min for 1.) two times with low salt wash buffer, 2.) two times with high salt buffer, and 3.) two times with LiCl wash buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 250 mM LiCl, 1 % NP-40, 1 % Sodium deoxycholate). To elute the bound DNA, beads were incubated in Proteinase K digestion buffer (20 mM HEPES pH 8.0, 1 mM EDTA, 0.5 % SDS, 1 mg/ml RNase, 0.4 mg/ml Proteinase K) for 15 min at 55 °C and 1 h at 65 °C. The DNA was purified from the eluate through AMPure XP beads following the manufacturer’s instructions and eluted in 20 µl EB buffer (MinElute Reaction Cleanup Kit; Qiagen).
ULI-NChIP-seq libraries were generated by the KAPA Hyper Prep Kit (KAPA Biosystems) according to manufacturer’s protocol. To minimize adaptor dimer formation, the NEBNext Adaptor and NEBNext Index PCR Primers from the NEBNext® Multiplex Oligos for Illumina (Index Primers Set 1) (NEB, E7335S) were used. After library amplification, libraries were purified by AMPure XP beads with double-sided size selection. The libraries were subjected to paired-end sequencing on HiSeq 4000 sequencing system (Illumina)

tag: tissue

value: Gonad

tag: cell type

value: Primordial germ cells

tag: Sex

value: Female

tag: chip antibody


title: sgControl rep2

state: CA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

value: transduced with lentiviral-packaged sgRNA control


title: Blood_dnAML_3_450K

type: genomic

city: Gliwice

first: Agnieszka

last: Cecotka

address: Kozielska, 9/8

department: Department of Data Science and Engineering

country: Poland

institute: Politechnika Śląska

hyb_protocol: standard Illumina protocol

scan_protocol: 750ng DNA at a concentration of at least 20ng/ul was sent to NXT-DX (Ghent, Belgium) and run on the Human Methylation 450K BeadChip array for DNA methylation analysis. Samples were first sent for analysis using the 450K array, but due to discontinuation, some patient samples were repeated on the Infinium Human Methylation EPIC BeadChip array. 500ng DNA at a concentration of at least 20ng/ul was sent to NXT-DX and run on the EPIC array for DNA methylation analysis

data_processing: Filtering and BMIQ normalization with ChAMP

label: Cy3 and Cy5

source_name: Blood, de novo AML

label_protocol: standard Illumina protocol

extract_protocol: DNA was extracted from human bone marrow aspirate samples using the DNeasy® Blood & Tissue kit (Qiagen, Manchester, UK) according to the manufacturer's instructions. DNA quantity was measured by Quant-iT™ PicoGreen™ dsDNA Assay Kits (Thermo Fisher Scientific, Paisley, U.K.) and quality assessed by agarose gel electrophoresis using 1.3% agarose gel.

tag: gender

value: male

tag: age


title: H3K9me3_Soma_wk9_F_r1

description: H3K9me3_Soma_wk9_F_pool_final_q3.narrowPeak

value: Gonadal somatic cells


title: Blood_dnAML_3

value: female


title: H3K9me3_Soma_wk10_M_r2

description: H3K9me3_Soma_wk10_M_pool_final_q3.narrowPeak

value: Male


title: Multiple psychotic episodes, responder, hospital arrival, rep12

city: Santiago de Compostela

first: Roberto Carlos

middle: Agís

last: Balboa

state: Coruña

address: Travesía da Choupana s/n

department: Movement Disorders Group (AC22)

country: Spain

institute: Health Research Institute of Santiago de Compostela (IDIS)

data_processing:
myBrain-Seq v0.1.0 (https://github.com/sing-group/my-brain-seq)
Sequence reads were trimmed for adaptor sequence using myBrain-Seq
Trimmed sequences were aligned to GRCh38 using myBrain-Seq.
Quantification and annotation of the aligned sequences to miRBase v.22 was performed using myBrain-Seq.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include miRNA quantification values for each sample.

extract_protocol:
PAXgene ® Blood microRNA Kit from Qiagen (PreAnalytiX GmbH, Hombrechtikon, Switzerland).
NEBNext Multiplex Small RNA Sample Prep Set for illumina (New England biolabs, Ipswich, MA, USA)

value: Peripheral blood

value: M

tag: disease state

value: MR

tag: alcohol

value: no

tag: tobacco

tag: illegal drugs

value: yes

tag: medication group

value: Antipsychotics

tag: medication subgroup

value: Other antipsychotics


title: Melanoma_softtismet_P08-area3 [P08_Sof-3]

city: Dresden

first: Michael

last: Seifert

address: Fetscherstr. 74

country: Germany

institute: TU Dresden

hyb_protocol: Bisulfite conversion was executed with the Zymo EZ Methylation Kit following purification with Zymo DNA Clean Kit (Zymo Research, Irvine, USA). DNA was finally treated with the Infinium HD FFPE Restore kit before hybridization to the Illumina Infinium MethylationEPIC (850K) beadchip (both Illumina, San Diego, USA).

scan_protocol: The bead chips were scanned by iScan (Illumina, San Diego, USA).

data_processing:
Normalization was done by the R function preprocessFunnorm of the R package minfi utilizing the gender of patients. The CpGs were further filtered to exclude polymorphic and off-target probes based on data from McCartney et al. 2016 (PMID: 27330998). Beta values were computed for each CpG in each sample.
MelanomaMetastases_MatrixProcessed.txt: Beta values
MelanomaMetastases_MatrixSignal.txt: unmethylated and methylated signal intensities

source_name: Melanoma soft tissue metastasis

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from a 2 mm punch biopsy of the selected tumor area of the FFPE sample using the Maxwell16 FFPE Plus LEV DNA purification kit on a Maxwell 16 extractor (Promega, Madison, USA). DNA concentration was determined by a Qubit dsDNA BR Assay Kit (Thermo Scientific, Waltham, USA) and 500 ng DNA was used for further analysis.

tag: tissue type

value: Melanoma soft tissue metastasis


title: Multiple psychotic episodes, responder, hospital discharge, rep12


title: Multiple psychotic episodes, responder, hospital discharge, rep11


title: H3K9me3_Soma_wk10_M_r1


title: Melanoma_softtismet_P08-area2 [P08_Sof-2]


title: Multiple psychotic episodes, responder, hospital arrival, rep11


title: VCR+RCM [m12]

city: Cincinnati

first: Jose

last: Gomez-Arroyo

state: Ohio

address: 3333 Burnet Ave

department: Pulmonary and Critical Care Medicine

institute: University of Cincinnati

data_processing:
Reads were aligned to the GRCm38 mouse genome and quantified using an index transcriptome version of GRCm38 using Kallisto using standard settings
Raw counts were normalized using DESeq2
Differential gene expression between conditions was performed using DEseq2
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include estimated counts and TPM for each Sample

source_name: tumor

extract_protocol:
RNA was harvested using Rneasy kit (Qiagen) using the recommended protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for all samples using Illumina TruSeq Stranded mRNA Prep to generate poly-A enriched, non-stranded RNA libraries, using manufacturers protocol.

value: tumor

tag: tumor cell_line_injected

value: Rd76-9 injected into the flank

tag: genotype

value: WT

tag: strain

tag: treatment

value: Vincristine +  RCM1 nanoparticle-folic acid


title: VCR+RCM [m11]

tag: tissue


title: sgElavl1 rep1

tag: cell line

tag: cell type

value: murine MLL-AF9/NrasG12D acute myeloid leukemia cell line

tag: genotype/variaton

value: transduced with lentiviral-packaged sgRNA targeting Elavl1


title: Blood_dnAML_2_450K

tag: gender

value: male


title: H3K9me3_hPGC_wk9_F_r2

description: H3K9me3_hPGC_wk9_F_pool_final_q3.narrowPeak

value: Gonad

value: Primordial germ cells

tag: Sex

value: Female

tag: chip antibody


title: VCR+RCM [m10]


title: Multiple psychotic episodes, responder, hospital discharge, rep10

value: Peripheral blood

value: M

tag: age

tag: disease state

tag: alcohol


title: Melanoma_softtismet_P08-area1 [P08_Sof-1]


title: H3K9me3_hPGC_wk9_F_r1


title: Melanoma_brainmet_P08 [P08_B]

source_name: Melanoma brain metastasis

value: Melanoma brain metastasis


title: Blood_dnAML_1_450K

value: female


title: Melanoma_livermet_P09 [P09_Liv]

source_name: Melanoma liver metastasis

value: Melanoma liver metastasis


title: Blood_dnAML_1

value: missing


title: Multiple psychotic episodes, responder, hospital arrival, rep10

value: MR

value: no

tag: tobacco

value: yes

tag: illegal drugs

tag: medication group

value: Antipsychotics

value: Other antipsychotics


title: Multiple psychotic episodes, responder, hospital discharge, rep9

value: F

tag: medication subgroup


title: H3K9me3_hPGC_wk10_M_r2

description: H3K9me3_hPGC_wk10_M_pool_final_q3.narrowPeak

value: Male


title: H3K9me3_hPGC_wk10_M_r1


title: RCM [m7]

value: tumor

tag: tumor cell_line_injected

value: Rd76-9 injected into the flank

tag: genotype

value: WT

value: RCM1 nanoparticle-folic acid


title: Melanoma_brainmet_P09 [P09_B]

tag: tissue type


title: Multiple psychotic episodes, responder, hospital arrival, rep9

tag: tissue

value: Peripheral blood


title: H3K4me3_Soma_wk8_M_r2

description: H3K4me3_Soma_wk8_M_pool_final_q3.narrowPeak

value: Gonad

value: Gonadal somatic cells


title: VCR [m6]

tag: strain

tag: treatment

value: Vincristine


title: Multiple psychotic episodes, responder, hospital arrival, rep15

value: M

value: Butyrophenone derivatives


title: Multiple psychotic episodes, responder, hospital discharge, rep8

value: MR

value: Diazepines, oxazepines, thiazepines and oxepines


title: H3K4me3_Soma_wk8_M_r1

tag: cell type


title: RCM [m9]


title: Melanoma_brainmet_P02 [P02_B]

tag: gender

value: male

value: Melanoma brain metastasis


title: VCR [m5]


title: Multiple psychotic episodes, responder, hospital arrival, rep8

tag: Sex

value: no

value: yes

value: Antipsychotics


title: VCR [m4]

value: tumor


title: Multiple psychotic episodes, responder, hospital discharge, rep7

value: F


title: H3K4me3_Soma_wk8_F_r1

description: H3K4me3_Soma_wk8_F_pool_final_q3.narrowPeak

value: Female

tag: chip antibody


title: H3K4me3_hPGC_wk8_M_r2

description: H3K4me3_hPGC_wk8_M_pool_final_q3.narrowPeak

value: Primordial germ cells

value: Male


title: Multiple psychotic episodes, responder, hospital discharge, rep6

value: Peripheral blood

tag: age

value: Benzamides


title: RCM [m8]

value: Rd76-9 injected into the flank

value: WT

value: RCM1 nanoparticle-folic acid


title: H3K4me3_Soma_wk8_F_r2

value: Gonad

value: Gonadal somatic cells


title: Control [m3]

value: Vehicle control (Empty nanoparticle + RCM1 nanoparticle-folic acid)


title: Melanoma_skinmet_P04-area2 [P04_Ski-2]

source_name: Melanoma skin metastasis

value: male

value: Melanoma skin metastasis


title: Control [m2]


title: H3K4me3_hPGC_wk8_M_r1


title: Control [m1]


title: Melanoma_skinmet_P04-area1 [P04_Ski-1]


title: H3K4me3_hPGC_wk8_F_r2

description: H3K4me3_hPGC_wk8_F_pool_final_q3.narrowPeak


title: Multiple psychotic episodes, responder, hospital discharge, rep5

tag: disease state

value: MR

value: no

value: Diazepines, oxazepines, thiazepines and oxepines


title: Melanoma_lymphmet_P02 [P02_Lym]

source_name: Melanoma lymph node metastasis

value: Melanoma lymph node metastasis


title: VisiumSample16SOR

city: Iowa City

first: Yann

last: Vanrobaeys

state: IA

address: 169 Newton Road

department: Neuroscience and Pharmacology

institute: University of Iowa

data_processing:
Raw files were processed with spaceranger-1.3.1.
Outputs for each samples are provided in tar.gz files.
Assembly: mm10

molecule: polyA RNA

source_name: brain

extract_protocol:
Mouse brain section per mouse was cut at 10 µm thickness and mounted onto each Visium slide capture area. After H&E staining, each bright-field image was taken as described in the Spatial Transcriptomics procedure. Tissue permeabilization was performed for 18 minutes, as established in the tissue optimization assay.  The Visium Spatial Gene Expression Slide & Reagent kit (10X Genomics) was used to generate sequencing libraries for Visium samples.
For Visium Spatial Transcriptomic libraries were constructed according to the 10x Visium library construction protocol and sequenced by Illumina NovaSeq6000.

value: brain

tag: condition

value: spatial object recognition training


title: Melanoma_brainmet_P04 [P04_B]

value: Melanoma brain metastasis


title: H3K4me3_hPGC_wk8_F_r1

value: Primordial germ cells

value: Female


title: VisiumSample15HC

value: home cage


title: Melanoma_lymphmet_P06 [P06_Lym]


title: Melanoma_lungmet_P03 [P03_Lun]

source_name: Melanoma lung metastasis

value: female

value: Melanoma lung metastasis


title: Multiple psychotic episodes, responder, hospital arrival, rep5

value: Peripheral blood

value: F

tag: alcohol

tag: tobacco

value: Antipsychotics


title: H3K4me1_Soma_wk8_M_r2

description: H3K4me1_Soma_wk8_M_pool_final_q3.narrowPeak

value: Gonad

value: Gonadal somatic cells

value: Male


title: Melanoma_brainmet_P03 [P03_B]


title: Multiple psychotic episodes, responder, hospital arrival, rep7

value: MR

value: no

tag: illegal drugs

tag: medication group


title: H3K4me1_Soma_wk8_M_r1


title: Multiple psychotic episodes, responder, hospital discharge, rep4

tag: medication subgroup

value: Other antipsychotics


title: Melanoma_brainmet_P06-area2 [P06_B-2]

value: male


title: VisiumSample13HC

value: brain


title: H3K4me1_Soma_wk8_F_r2

description: H3K4me1_Soma_wk8_F_pool_final_q3.narrowPeak


title: Multiple psychotic episodes, responder, hospital arrival, rep4


title: VisiumSample10SOR

value: spatial object recognition training


title: Multiple psychotic episodes, responder, hospital discharge, rep3

value: yes


title: H3K4me1_Soma_wk8_F_r1

value: Female


title: VisiumSample9HC

value: home cage


title: Multiple psychotic episodes, responder, hospital arrival, rep3


title: Melanoma_lymphmet_P17-area1 [P17_Lym-1]

value: Melanoma lymph node metastasis


title: sgControl rep1

tag: cell line

value: murine MLL-AF9/NrasG12D acute myeloid leukemia cell line

tag: genotype/variaton

value: transduced with lentiviral-packaged sgRNA control


title: VisiumSample8HC

tag: tissue


title: Multiple psychotic episodes, responder, hospital discharge, rep2

value: Peripheral blood

value: M


title: Melanoma_brainmet_P17 [P17_B]

tag: tissue type

value: Melanoma brain metastasis


title: Melanoma_lungmet_P18-area2 [P18_Lun-2]

value: Melanoma lung metastasis


title: VisiumSample7HC


title: Multiple psychotic episodes, responder, hospital arrival, rep2

value: Antipsychotics


title: H3K4me1_hPGC_wk8_F_r2

description: H3K4me1_hPGC_wk8_F_pool_final_q3.narrowPeak

value: Gonad

value: Primordial germ cells


title: VisiumSample14SOR


title: Multiple psychotic episodes, responder, hospital discharge, rep1

value: MR

value: Other antipsychotics


title: Melanoma_brainmet_P06-area1 [P06_B-1]

value: male


title: Melanoma_brainmet_P67-area1 [P67_B-1]

value: female


title: H3K4me1_hPGC_wk8_F_r1


title: Melanoma_lymphmet_P17-area2 [P17_Lym-2]


title: Melanoma_lungmet_P18-area1 [P18_Lun-1]


title: Melanoma_brainmet_P18 [P18_B]


title: Multiple psychotic episodes, responder, hospital arrival, rep21

value: yes


title: VisiumSample5HC

value: brain


title: H3K27me3_Soma_wk9_M_r2

description: H3K27me3_Soma_wk9_M_pool_final_q3.narrowPeak

value: Gonadal somatic cells

value: Male

value: H3K27me3(Cell Signaling,9733,8)


title: Multiple psychotic episodes, responder, hospital arrival, rep6

value: Benzamides


title: Melanoma_skinmet_P28 [P28_Ski]

value: Melanoma skin metastasis


title: Multiple psychotic episodes, non-responder, hospital discharge, rep21

value: Peripheral blood

value: M

value: MNR

value: no

value: Diazepines, oxazepines, thiazepines and oxepines


title: VisiumSample4SOR

value: spatial object recognition training


title: VisiumSample3SOR_


title: Melanoma_brainmet_P28 [P28_B]

value: Melanoma brain metastasis


title: H3K27me3_Soma_wk9_M_r1

value: Gonad


title: Multiple psychotic episodes, non-responder, hospital arrival, rep21

value: Antipsychotics


title: H3K27me3_Soma_wk9_F_r2

description: H3K27me3_Soma_wk9_F_pool_final_q3.narrowPeak

value: Female


title: H3K4me1_hPGC_wk8_M_r1

description: H3K4me1_hPGC_wk8_M_pool_final_q3.narrowPeak

value: Primordial germ cells


title: Multiple psychotic episodes, non-responder, hospital discharge, rep20


title: Melanoma_lungmet_P39 [P39_Lun]

value: female

value: Melanoma lung metastasis


title: VisiumSample2SOR

value: brain

value: male


title: H3K27me3_Soma_wk9_F_r1

value: Gonadal somatic cells

value: H3K27me3(Cell Signaling,9733,8)


title: H3K27me3_hPGC_wk9_M_r2

description: H3K27me3_hPGC_wk9_M_pool_final_q3.narrowPeak

value: Male


title: Melanoma_brainmet_P39 [P39_B]


title: Multiple psychotic episodes, non-responder, hospital arrival, rep20

value: Peripheral blood

value: M


title: Melanoma_lymphmet_P42-area2 [P42_Lym-2]

value: Melanoma lymph node metastasis


title: VisiumSample1SOR


title: Multiple psychotic episodes, non-responder, hospital discharge, rep19

value: F

value: MNR

value: no

value: Aliphatic side chain phenothiazines


title: BulkSOR4

extract_protocol:
Dorsal hippocampi were dissected and immediately stored at -80°C in RNAlater solution. For RNA total extraction, hippocampi were homogenized in Qiazol using stainless steel beads. Chloroform was then added, and the homogenate was centrifuged at 12,000 x g at RT for 15 min. Aqueous phase containing RNA was precipitated using ethanol and then cleaned using the RNeasy kit. RNA was eluted in nuclease-free water, treated with DNase at RT for 25 min and precipitated in ethanol, sodium acetate (pH 5.2) and glycogen overnight at -20C. Precipitated RNA samples were centrifuged at top speed at RT for 20 min, washed with 70% ethanol and centrifuged at top speed for 5 min, dried and resuspended in nuclease free water.
For bulk RNA-seq librairies were prepared using Ribo-Zero gold sample preparation kit. Library concentrations were measured using KAPA Illumina Library Quantification Kit. Polled libraries were sequenced on Illumina NovaSeq6000 sequencer with 150-bp Paired-End chemistry.

value: spatial object recognition training


title: H3K27me3_hPGC_wk9_M_r1

value: Gonad


title: Multiple psychotic episodes, non-responder, hospital arrival, rep19

value: Antipsychotics


title: Melanoma_lymphmet_P42-area1 [P42_Lym-1]


title: H3K27me3_hPGC_wk9_F_r2

description: H3K27me3_hPGC_wk9_F_pool_final_q3.narrowPeak

value: Primordial germ cells

value: Female


title: BulkSOR1

value: brain


title: Multiple psychotic episodes, non-responder, hospital arrival, rep18

value: Butyrophenone derivatives


title: H3K27me3_hPGC_wk9_F_r1


title: Melanoma_brainmet_P42 [P42_B]

value: male

value: Melanoma brain metastasis


title: BulkSOR2


title: H3K27me3_hPGC_wk7_M_r2

description: H3K27me3_hPGC_wk7_M_pool_final_q3.narrowPeak

value: Male

value: H3K27me3(Cell Signaling,9733,8)


title: BulkHC4

value: home cage


title: rDM-Ins_RepC

city: Maastricht

first: Christoph

middle: S

last: Börlin

address: Watermolen 28

country: Netherlands

institute: Mosa Meat

data_processing:
Basecalling was performed using Guppy version 5.0.16 in the Super-accurate setting (minimal q-score threshold of 10) with automatic de-multiplexing and barcode removal.
The filtered reads were mapped to the bovine transcriptome (ARS-UCD1.2) using Minimap2 71 with the default settings for Oxford Nanopore reads (-ax map-ont), and then subsequently quantified using Salmon.
The data analysis was performed using DEseq2, with tximport for importing the quantified data from Salmon. Batch correction for the 3 separate batches of mRNA extraction and cDNA making was done using Combat-Seq from the SVA package.
Assembly: ARS-UCD1.2
Supplementary files format and content: .sf = Salmon quantification output
Supplementary files format and content: .csv = Normalized CPM data including batch correction obtained from DEseq2

organism: Bos taurus

source_name: MSC

extract_protocol:
mRNA was extracted using the Dynabeads® mRNA DIRECT™ Micro Kit (ThermoFischer). Subsequently 1ng of mRNA was reversed transcribed into cDNA using the Maxima H Minus Reverse Transcriptase (ThermoFisher) and the primers from the PCR-cDNA Barcoding kit (SQK-PCB109, Oxford Nanopore Technologies).
Library prep including cDNA barcode was performed using the PCR-cDNA Barcoding kit (SQK-PCB109, Oxford Nanopore Technologies)

value: MSC

tag: treatment

value: rDM without insulin

tag: batch


title: rDM-HC-PR_RepC

tag: cell type

value: rDM without hydrocortisone and progesterone


title: Multiple psychotic episodes, non-responder, hospital discharge, rep17

value: Peripheral blood

tag: Sex

value: F

value: MNR

value: no

value: Other antipsychotics


title: BulkHC3


title: rDM-Ros_RepC

value: rDM without rosiglitazone


title: Multiple psychotic episodes, non-responder, hospital arrival, rep17

value: Antipsychotics


title: H3K27me3_hPGC_wk7_M_r1

value: Gonad

value: Primordial germ cells

tag: chip antibody


title: H3K27me3_hPGC_wk7_F_r2

description: H3K27me3_hPGC_wk7_F_pool_final_q3.narrowPeak

value: Female


title: BulkHC2

value: brain

value: male


title: BulkSOR3

value: spatial object recognition training


title: Multiple psychotic episodes, non-responder, hospital arrival, rep16

tag: age

value: yes

value: Diazepines, oxazepines, thiazepines and oxepines


title: rDM_RepC

value: MSC

value: rDM


title: Multiple psychotic episodes, non-responder, hospital arrival, rep15

value: Peripheral blood

value: M

tag: disease state


title: Multiple psychotic episodes, non-responder, hospital discharge, rep18

value: MNR

value: Butyrophenone derivatives


title: rDM-Ros_RepB


title: Multiple psychotic episodes, non-responder, hospital arrival, rep14

value: no


title: BulkHC1

tag: condition

value: home cage


title: H3K27me3_hPGC_wk7_F_r1

value: H3K27me3(Cell Signaling,9733,8)


title: rDM-HC-PR_RepB

value: rDM without hydrocortisone and progesterone


title: H3K27ac_Soma_wk8_M_r2

description: H3K27ac_Soma_wk8_M_pool_final_q3.narrowPeak

value: Gonad

value: Gonadal somatic cells

value: Male


title: H3K27ac_Soma_wk8_F_r2

description: H3K27ac_Soma_wk8_F_pool_final_q3.narrowPeak

value: Female


title: Multiple psychotic episodes, non-responder, hospital arrival, rep11

tag: alcohol

value: Antipsychotics


title: H3K27ac_hPGC_wk8_M_r2

description: H3K27ac_hPGC_wk8_M_pool_final_q3.narrowPeak

value: Primordial germ cells


title: H3K27ac_Soma_wk8_F_r1


title: rDM-HC-PR_RepA


title: H3K27ac_hPGC_wk8_M_r1


title: Multiple psychotic episodes, non-responder, hospital arrival, rep9

tag: tobacco

value: Diazepines, oxazepines, thiazepines and oxepines


title: rDM-Ins_RepA

value: MSC

value: rDM without insulin


title: Multiple psychotic episodes, non-responder, hospital arrival, rep8

value: Peripheral blood

value: yes

tag: illegal drugs


title: FL_nan_h3k27ac_input_rep2

city: New York

first: Kaustav

last: Mukherjee

state: NY

address: 1 Gustave Levy Place

department: Cell, Developmental and Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie 2.1 after trimming 25 nucleotides from the 3' end and in the sensitive-local mode.
Samtools v1.1 was used to convert sam files to sorted bam files
Deeptools v3.5 bamCompare function was used to convert individual bam files from each ChIP experiment to input-normalized bigwig files using the rpkm method
kentUtils v302.1 bigWigMerge was used to merge the input-normalized bigwig files into one bedgraph, sort the bedgraph file, and then convert the bedgraph to an input-normalized bigwig file using bedGraphToBigWig
Homer was used to generate tag directories from bam files of each ChIP-experiment and peaks were called using the region parameter with 125bp window size and maximum peak size of about 250bp. Peaks were filtered based on 4-fold enrichment above input with a q-value threshold of 0.01. Peaks were converted to bed files using the pos2bed.pl Homer script
Assembly: UCSC mouse mm10
Supplementary files format and content: bigwig for ChIP and ATAC, bam for ChIP input, bed for EKLF peaks determined by Homer

source_name: embryonic day E13.5 fetal liver

extract_protocol:
Fetal livers were dissected from E13.5 mouse embryos and mechanically dispersed into single cells by gentle pipetting and straining through a 70µM filter into ice-cold PBS containing 2% FBS. Primary fetal liver cells were crosslinked in 1% formaldehyde and cell pellets were stored at -80ºC. Frozen cells were thawed and resuspended in MNase lysis buffer (0.2% NP-40, 10mM NaCl, 10mM Tris pH 8.0) and kept on ice for 15 mins. Cells were pelleted and resuspended in MNase lysis buffer with 1mM CaCl2, 40 units Micrococcal nuclease (MNase) and incubated at 37ºC for 15 minutes. The MNase reaction was stopped by adding EDTA to a final concentration of 2mM and nuclei were pelleted by centrifugation. The pellet was resuspended in 1X RIPA buffer with 1X Protease Inhibitor Cocktail and sonicated using a cup-horn sonicator (Ultrasonic VC505) at 80 Amplitude for 50 cycles with pulses of 40s on and 50s off. The lysed and fragmented chromatin was cleared by centrifugation and 5%v/v was stored at -80ºC as input. 5-10µg of antibody (depending on the titer) was added to the lysate along with a control IgG (for enrichment estimation) and antibody-lysate mixture was incubated at 4ºC for 16h (overnight). The lysate-antibody mixture was then incubated with Protein-A or Protein-G Dynabeads, depending on the antibody serotype, for 2h at 4ºC. Immunoprecipitated complexes on Dynabeads were then washed three times in 1X RIPA with protease inhibitors, and three times in wash buffer containing 0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris pH 8.0, 500mM NaCl, and protease inhibitors. This was followed by three washes in wash buffer containing 1% NP-40, 1% sodium deoxycholate, 1mM EDTA, 10mM Tris pH 8.0, and 250 mM LiCl. Finally, beads were washed three times in 1X TE buffer containing 10mM Tris pH 8.0 and 1mM EDTA. Elution was performed by adding elution buffer containing 10mM Tris pH 8.0, 1mM EDTA, 200mM NaCl and 1% SDS and incubating at 65ºC in a Thermomixer (Eppendorf Cat# 5382000023) with gentle mixing for 20 mins. Eluate containing ChIP DNA and input chromatin was removed and incubated at 65ºC with gentle mixing overnight for reverse crosslinking. DNA was treated with 0.1µg/µl Proteinase K for 1h at 55ºC followed by purification using Phenol:chloroform extraction and ethanol precipitation. ATAC-Seq was performed exactly as in (Buenrostro et al., 2013; Buenrostro et al., 2015).
ChIP-Seq libraries were made using a Neb Next DNA Ultra II DNA library preparation kit following manufacturer’s instructions. Libraries were quantified using Qubit fluorometer (Invitrogen) and library quality was assessed using a high-sensitivity DNA kit on Agilent Bioanalyzer, followed by Illumina next generation sequencing with single-end 100bp reads

value: embryonic day E13.5 fetal liver

value: Klf1 / Klf1-Nan

value: primary erythroid

tag: genotype

value: Nan/+


title: H3K27ac_hPGC_wk8_F_r2

description: H3K27ac_hPGC_wk8_F_pool_final_q3.narrowPeak


title: rDM_RepA

value: rDM


title: H3K27ac_Soma_wk8_M_r1


title: Multiple psychotic episodes, non-responder, hospital arrival, rep13

value: M

value: MNR

value: no

tag: medication group

tag: medication subgroup


title: H3K27ac_hPGC_wk8_F_r1

value: Gonad


title: FL_wt_h3k27ac_input_rep2

tag: cell line

value: Nan strain WT


title: rDM_RepB


title: Multiple psychotic episodes, non-responder, hospital discharge, rep7

tag: tissue

value: F

value: Antiepileptics

value: Fatty acid derivatives


title: FL_nan_h3k27ac_input_rep1


title: GD_rep3

city: Hefei

first: Xiaolin

last: Wang

address: Huangshan Road

country: China

institute: USTC

description:
Linear_RNAs-new.txt.gz
CircRNA_RNAs-new.txt.gz

data_processing:
The adaptors were trimmed with Cutadapt to obtain clean reads. The data quality was then checked with FastQC and the low-quality (Q value ≤ 20) reads were removed.
Reads were aligned to the human reference genome (hg19) with Bowtie2 (-v 1). For linear RNAs including lncRNAs and mRNAs, the corresponding reads were counted with BEDtools and read per million (RPM) was used to calculate levels for lncRNAs and mRNAs.
For circRNA prediction, find_circ and CIRI2 were applied to identify high-confidence back-spliced junctions (BSJs).
Assembly: hg19
Supplementary files format and content: tab-delimited text files include reads for each Sample

source_name: HeLa cells

extract_protocol:
Total RNA was extracted by TRIzol reagent (Invitrogen, 15596026) according to the manufacturer’s instructions.
Libraries were constructed by the TruSeq Ribo Profile Library Prep Kit (Illumina, RPHMR12126) according to the manufacturer’s instructions.

value: HeLa cells

value: human cervical carcinoma cells

value: WT

value: Glucose deprivation for 6h


title: H2AK119u1_Soma_wk9_M_r1

description: H2AK119u1_Soma_wk9_M_pool_final_q3.narrowPeak

value: Gonadal somatic cells

value: Male

value: H2AK119ub(Cell Signaling,8240,6)


title: rDM-Ins_RepB

value: MSC

value: rDM without insulin


title: GD_rep4


title: H2AK119u1_Soma_wk9_F_r1

description: H2AK119u1_Soma_wk9_F_pool_final_q3.narrowPeak

value: Female


title: rDM-Ros_RepA

value: rDM without rosiglitazone


title: Multiple psychotic episodes, non-responder, hospital arrival, rep12

value: Peripheral blood

value: MNR

value: yes

value: Antipsychotics

value: Diazepines, oxazepines, thiazepines and oxepines


title: Multiple psychotic episodes, non-responder, hospital arrival, rep10

value: M

value: no


title: FL_wt_h3k27ac_input_rep1

value: embryonic day E13.5 fetal liver

value: Klf1 / Klf1-Nan

value: primary erythroid

value: Nan strain WT


title: TG_rep4

value: HeLa cells

value: human cervical carcinoma cells

value: WT

value: 300 nM TG  for 6 h


title: FL_nan_h3k27ac_chip_rep3

value: Nan/+

value: anti-H3K27ac, Abcam


title: Multiple psychotic episodes, non-responder, hospital arrival, rep6

value: Peripheral blood

value: Other antipsychotics


title: TG_rep3


title: FL_nan_h3k27ac_chip_rep2


title: Multiple psychotic episodes, non-responder, hospital discharge, rep5

value: F

value: MNR

value: yes

value: Antiepileptics

value: Benzodiazepine derivatives


title: Ctrl_rep4

value: Mock


title: H2AK119u1_hPGC_wk9_M_r1

description: H2AK119u1_hPGC_wk9_M_pool_final_q3.narrowPeak

value: Gonad

value: Primordial germ cells

value: Male

value: H2AK119ub(Cell Signaling,8240,6)


title: H2AK119u1_hPGC_wk10_M_r2

value: Female


title: Ctrl_rep3

value: HeLa cells

value: human cervical carcinoma cells

value: WT


title: FL_nan_h3k27ac_chip_rep1

value: embryonic day E13.5 fetal liver

value: Klf1 / Klf1-Nan

value: primary erythroid

value: Nan/+

value: anti-H3K27ac, Abcam


title: Multiple psychotic episodes, non-responder, hospital arrival, rep7

description:
MNR007A
MNR007A was discarded from the bioionformatic analysis due to the poor sequencing quality.  For that reason, it is not present in all-counts.txt.

value: Peripheral blood

value: F

value: MNR

value: yes

value: no

value: Fatty acid derivatives


title: Multiple psychotic episodes, non-responder, hospital discharge, rep4

value: Antipsychotics

value: Other antipsychotics


title: Multiple psychotic episodes, non-responder, hospital arrival, rep4


title: ATAC_Soma_wk7_M_r2

data_processing:
Paired-end ATAC-seq reads were quality- and adaptor-trimmed by Trim Galore (v0.4.1) using default parameters.
Trimmed reads were mapped to the human reference genome (UCSC GRCh38/hg38) by Bowtie 2 (v2.3.4.1) with options ‘--local -X 2000 --no-mixed --no-discordant’, hence retaining properly paired reads with a maximum fragment length of 2000 bp.
Unmapped reads, non-primary reads, supplementary alignment and QC-failed reads were removed using samtools view with option ‘-F 2828’. Duplicated reads were marked and removed by the MarkDuplicates function in Picard Tools (Broad Institute). Subsequently, fragments mapped to hg38 blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/hg38.blacklist.bed.gz), non-canonical hg38 contigs and mitochondrial DNA (chrM) were removed. To adjust the read start sites to represent the center of the transposon binding event, all reads aligning to the positive strand were offset by +4 bp, and all reads aligning to the negative strand were offset -5 bp.
Prior to peak calling, paired-end reads with fragment size < 120 bp were extracted using deepTools alignmentSieve. These reads were considered nucleosome-free and were used to determine open chromatin regions. Subsequently, libraries were subsampled using Picard DownSampleSam so that each library contains approximately the same number of paired-end reads.
Peaks were called following the Encode replicated peak calling guidelines (https://www.encodeproject.org/pipelines/ENCPL272XAE/) with modifications to accommodate for paired-end libraries. To obtain high resolution of peaks, narrow peak call was used for all marks. Histone peaks were called using the input reads as background. Peaks were initially called for each biological replicate (downsampled to similar read depth), for the pooled replicates, and for the pooled pseudoreplicates of each biological replicate using MACS2 with a relaxed p-value threshold of 0.05 (options: ‘-g 3e9 --keep-dup all -p 0.05’). Each pseudoreplicate consists of half the reads of each biological replicate, chosen at random without replacement. Narrow peaks from the pooled replicate set were retained if they overlapped peaks from both biological replicates or peaks from both pooled pseudoreplicates. The thresholds of overlap were set at 20% for ATAC peaks. This peak calling strategy allows for the retention of marginal peaks in one replicate to be rescued by a strong biological replicate. To obtain a final high confidence peak set, the reproducible peaks were further filtered using the MACS2 q-value (false discovery rate <0.0001).
Assembly: hg38
Supplementary files format and content: Reproducible peaks of the two biological replicates in macs2 narrowPeak format

extract_protocol:
Cells were sorted directly into Nuclei EZ Storage Buffer (Sigma, NUC-101) and stored at -80 °C. ATAC-seq libraries were prepared following the Omni-ATAC protocol described by Corces et al. (2017). Briefly, cells were washed in cold PBS and resuspended in cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water). Cells were then lysed in 50 μl of RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin. After lysis, 1 ml of RSB containing 0.1% Tween-20 was added. Cell pellet was resuspended in 50 μl of transposition mix (25 μl 2x TD buffer, 2.5 μl TDE1 Tagment DNA Enzyme (Nextera DNA Library Prep Kit, FC-121-1031), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl water) by pipetting up and down six times. The 2X TD buffer was composed of 20 mM Tris-HCl pH 7.6, 10 mM MgCl2, 20% Dimethyl Formamide in water. Transposition reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 1,000 r.p.m. Reactions were cleaned up with MinElute Reaction Cleanup Kit (Qiagen).
Tagmented DNA was amplified using the KAPA HiFi HotStart Real-Time Library Amp Kit (Roche) with modified Nextera dual indexed primers as listed in Table 1. Amplified libraries were purified using Ampure XP beads (Beckman Coulter) with double-sided size selection (1st bead selection: 0.5x; 2nd bead selection: 1.2x) according to manufacturer’s protocol. Quantified and validated libraries (~ 150-1000 bp) were subjected to pair-end sequencing on HiSeq 4000 sequencing system (Illumina).

value: Gonad

value: Gonadal somatic cells

value: Male


title: Multiple psychotic episodes, non-responder, hospital arrival, rep5

value: Antiepileptics

value: Benzodiazepine derivatives


title: FL_wt_h3k27ac_chip_rep3

value: embryonic day E13.5 fetal liver

value: Klf1 / Klf1-Nan

value: Nan strain WT


title: ATAC_Soma_wk7_M_r1


title: FL_wt_h3k27ac_chip_rep1

value: primary erythroid

value: anti-H3K27ac, Abcam


title: FL_nan_cbp_input_rep2

value: Nan/+


title: H2AK119u1_Soma_wk10_F_r2

value: Female

value: H2AK119ub(Cell Signaling,8240,6)


title: Multiple psychotic episodes, non-responder, hospital arrival, rep3

value: Peripheral blood

value: M

value: MNR

value: no

value: yes

value: Diazepines, oxazepines, thiazepines and oxepines


title: Multiple psychotic episodes, non-responder, hospital discharge, rep3

value: Antipsychotics


title: FL_nan_cbp_input_rep1


title: ATAC_hPGC_wk7_M_r2

value: Gonad

value: Primordial germ cells

value: Male


title: Multiple psychotic episodes, non-responder, hospital discharge, rep6

value: Other antipsychotics


title: ATAC_hPGC_wk7_M_r1


title: Multiple psychotic episodes, non-responder, hospital discharge, rep2

value: Butyrophenone derivatives


title: ATAC_hPGC_wk7_F_r2


title: FL_wt_cbp_input_rep2

value: embryonic day E13.5 fetal liver

value: Klf1 / Klf1-Nan

value: primary erythroid

value: Nan strain WT


title: Multiple psychotic episodes, non-responder, hospital arrival, rep2


title: ATAC_hPGC_wk7_F_r1

value: Female


title: FL_wt_cbp_input_rep1


title: H2AK119u1_hPGC_wk9_F_r1

description: H2AK119u1_hPGC_wk9_F_pool_final_q3.narrowPeak

value: H2AK119ub(Cell Signaling,8240,6)


title: FL_wt_h3k27ac_chip_rep2

value: anti-H3K27ac, Abcam


title: Multiple psychotic episodes, non-responder, hospital discharge, rep1

value: Peripheral blood

value: F

value: MNR


title: FL_nan_cbp_chip_rep2

value: Nan/+

value: anti-CBP, CST


title: NQXQ

city: Zhengzhou

first: Zhenqiang

last: Sun

address: No 1, Jianshe Road

institute: The First Affiliated Hospital of Zhengzhou University

description: Tumor and adjacent non-cancerous tissues collected within 29mins after surgery

data_processing:
Illumina Casava1.8 software used for basecalling.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome using Tophat2 package.
The mapped reads of each sample were assembled using StringTie, all transcriptomes were merged to reconstruct a comprehensive transcriptome.
Unmapped reads were still mapped to genome using tophat-fusion. CIRCExplorer2 was used to denovo assemble the mapped reads to circular RNAs at first; Then, back splicing reads were identified in unmapped reads by tophat-fusion and CIRCExplorer2. All samples were generated unique circular RNAs.
Genome_build: Homo_sapiens Ensembl release-87
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Adjacent non-cancerous tissues

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 10 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ Magnetic Gold Kit (Illumina, San Diego, USA).Then the left RNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina, San Diego, USA).

value: Normal, adjacent non-cancerous tissues


title: Control, rep44

source_name: Control

value: M

value: C

value: no


title: FL_nan_cbp_chip_rep3


title: NCDZ

description: Tumor and adjacent non-cancerous tissues collected within 28mins after surgery


title: Multiple psychotic episodes, non-responder, hospital arrival, rep1

value: Antipsychotics

value: Diazepines, oxazepines, thiazepines and oxepines


title: FL_wt_cbp_chip_rep3

value: embryonic day E13.5 fetal liver

value: Klf1 / Klf1-Nan


title: NXCZ

description: Tumor and adjacent non-cancerous tissues collected within 30mins after surgery


title: Control, rep43


title: Control, rep42


title: NZGT

description: Tumor and adjacent non-cancerous tissues collected within 31mins after surgery


title: u2os-HAPSTR2_siNT_3

city: Chicago

first: Marc

last: Mendillo

state: IL

address: 303 E Superior St

institute: Northwestern University

data_processing:
RNA-seq: Sequence quality was assessed with FastQC v0.11.2, Fastq files were trimmed using bbduk from BBTools v35.92 according to Lexogen QuantSeq manufacturer parameters, mapped to hg38 using STAR v2.6.0 and gene annotations from Ensembl 78. HTSeq was used to count uniquely mapped reads.
Assembly: hg38
Supplementary files format and content: htseq counts tables provide normalized count estimates of uniquely mapped RNAseq reads

source_name: cancer cell line

growth_protocol: Cells were grown at 37°C and 5% CO2 according to manufacturer's guidelines

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit using the Qiashredder for homogenization
NEBNext magnetic poly(A) enrichment followed by NEBNext Ultra Directional Library Prep

treatment_protocol: See sample section

value: cancer cell line

value: bone cancer

value: siNT


title: Control, rep41


title: u2os-HAPSTR2_siNT_2


title: NGDX

description: Tumor and adjacent non-cancerous tissues collected within 26mins after surgery


title: FL_wt_cbp_chip_rep1

value: primary erythroid

value: Nan strain WT


title: FL_nan_cbp_chip_rep1


title: Control, rep40

value: Peripheral blood

value: F

value: yes


title: NDX

description: Tumor and adjacent non-cancerous tissues collected within 27mins after surgery


title: TZGT

description: Tumor and adjacent non-cancerous tissues collected within 25mins after surgery

source_name: Colon adenocarcinoma

value: Tumor, colon adenocarcinoma


title: FL_nan_eklf_input_rep2

value: Nan/+


title: u2os-HAPSTR2_siNT_1


title: TXCZ

description: Tumor and adjacent non-cancerous tissues collected within 24mins after surgery


title: Control, rep39


title: Control, rep38


title: u2os-HAPSTR2_siHAPSTR1_3


title: FL_nan_eklf_input_rep1


title: u2os-HAPSTR2_siHAPSTR1_2


title: TCDZ

description: Tumor and adjacent non-cancerous tissues collected within 22mins after surgery


title: FL_wt_eklf_input_rep2


title: VisiumSample6HC

value: brain

value: male

value: home cage


title: Control, rep37

value: C

value: no


title: TQXQ

description: Tumor and adjacent non-cancerous tissues collected within 23mins after surgery


title: FL_wt_cbp_chip_rep2

value: embryonic day E13.5 fetal liver

value: anti-CBP, CST


title: u2os-EV_siNT_3

value: cancer cell line

value: WT


title: TDX

description: Tumor and adjacent non-cancerous tissues collected within 21mins after surgery


title: FL_nan_eklf_chip_rep3

description:
EKLF_nan_norm_rpkm.bw
n_peaks_125_250_sig_fold.bed

value: Klf1 / Klf1-Nan

value: 7B2a anti-eklf


title: FL_wt_eklf_input_rep1

value: primary erythroid

value: Nan strain WT


title: Control, rep35

value: Peripheral blood

value: F


title: u2os-EV_siNT_2

value: bone cancer

value: siNT


title: TGDX

description: Tumor and adjacent non-cancerous tissues collected within 20mins after surgery

value: Tumor, colon adenocarcinoma


title: FL_nan_eklf_chip_rep2

value: Nan/+


title: u2os-EV_siNT_1


title: FL_nan_eklf_chip_rep1


title: Control, rep33


title: u2os-EV_siHAPSTR1_3


title: FL_wt_eklf_chip_rep3

description:
EKLF_wt_norm_rpkm.bw
w_peaks_125_250_sig_fold.bed


title: u2os-EV_siHAPSTR1_2


title: CML-A input

description: eCLIPseq

data_processing:
Sequenced reads were removed of inline barcodes and reformatted to include randomers in read headers with eclipdemux (v0.0.1). Args: --length 10
Reads were then trimmed with cutadapt (1.9.1). Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -g g_adapters.fasta -A A_adapters.fasta -a a_adapters.fasta (fasta sequences generated from parsebarcodes.sh within the eclip 0.1.5+ pipeline)
Reads were then trimmed once more with cutadapt (1.9.1) to remove double-ligation events. Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -A A_adapters.fasta (fasta sequences generated from parsebarcodes.sh within the eclip 0.1.5+ pipeline)
Trimmed reads were then mapped with STAR (2.4.0i) against a mouse-specific repeat element database (RepBase 18.05). Args: --runThreadN 16 \  --genomeDir mouse_repbase \  --readFilesIn path/to/read1 path/to/read2 \  --outFileNamePrefix out_prefix \  --outReadsUnmapped Fastx \  --outSAMtype BAM Unsorted \  --outSAMattributes All \  --outSAMunmapped Within \  --outSAMattrRGline ID:foo \  --outFilterType BySJout \  --outFilterMultimapNmax 30 \  --outFilterMultimapScoreRange 1 \  --outFilterScoreMin 10 \  --alignEndsType EndToEnd
Unmapped reads filtered of repeat elements were then mapped with STAR (2.4.0i) against a mouse genome (mm9). Args: --runThreadN 16 \  --genomeDir genomedir \  --readFilesIn /path/to/read1 /path/to/read2 \  --outFileNamePrefix out_prefix \  --outReadsUnmapped Fastx \  --outSAMtype BAM   Unsorted \  --outSAMattributes All \  --outSAMunmapped Within \  --outSAMattrRGline ID:foo \  --outFilterType BySJout \  --outFilterMultimapNmax 1 \  --outFilterMultimapScoreRange 1 \  --outFilterScoreMin 10 \  --alignEndsType EndToEnd
Aligned reads were sorted with samtools (1.4.1)
Sorted reads were collapsed with barcodecollapsepe.py included in eclip 0.1.5+ pipelines. Args: -o preRmDup.bam -m metrics_file -b rmDup.bam
PCR de-duped reads from each inline barcode were then merged with samtools (1.4.1) merge (merged.bam)
Merged alignments were split to keep just read2 using samtools (1.4.1) view. Args: -h -b -f 128
Read2 BAM files were used to identify peak clusters with Clipper (1.2.2). Args: --species mm9 --bam path/to/input.bam --timeout 3600000 --maxgenes 1000000 --save-pickle --outfile path/to/output.bam
Peak clusters were normalized using read2 BAM files for IP against read2 BAM files for INPUT with peaksnormalize.pl (overlap_peakfi_with_bam_PE.pl), included in eclip 0.1.5+.
Overlapping normalized peak regions were merged with compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat.pl, included within eclip-0.1.5+
Normalized peak files were ranked by entropy score (make_informationcontent_from_peaks.pl included within the merge_peaks pipeline) and used as inputs to IDR (2.0.2) to determine reproducible peaks.
Reproducible peaks were annotated by overlapping peak regions with Gencode vM1 annotations
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include -log10pValues and Log2FoldChange values for each IDR peaks called after cutoff of 3,3 in each parameter

source_name: blast crisis CML bone marrow

growth_protocol: Blast crisis CML model was generated as described in Neering et al., Blood 2007. 20.000 blast crisis CML cells were transplated via tail-vein injection into C57Blk/6 recipient mice. 24 h prior to transplantation, mice were sublethally irradiated (1 x 580 Rad).

extract_protocol:
blast crisis CML cells were freshly harvested, crushed in IMDM + 3% FBS, passed through 40 uM cell strainers followed by red blood cell lysis. Cells were incubated with a cocktail of lineage specific antibodies (CD5, CD11b, CD19, B220, Gr-1 and TER119, Stemcell Technologies) for negative selection of Lin- cells using an EasyStep immunomagnetic column (Stemcell Technologies). 20 million cells were per sample were subsequently washed in PBS and UV-crosslinked at 400mJ/cm2 on ice. Samples were then pelleted, snap-frozen and stored at -80°C.
Pellets were lysed in iCLIP lysis buffer, treated with RNAse I for 5 min at 37°C, followed by immunoprecipitation using 10 μg anti-ELAVL1 mouse monoclonal IgG (ab170193, Abcam) and 125 μL M-280 Sheep-α-Mouse IgG Dynabeads (ThermoFisher #11201D) per sample. After stringent rounds of washing, samples were dephosphorylated (FastAP; ThermoFisher, T4 PNK; NEB), 3’ ligation (on-bead) with a barcoded RNA adapter followed using T4 RNA Ligase (NEB). Samples were again stringently washed, run on standard protein gels and transferred to nitrocellulose membranes. The region spanning 36-115 kDa was then isolated, followed by extraction of RNA from the membranes and reverse transcription (AffinityScript; Agilent). A DNA adapter containing a 5’ random-mer was then ligated (3’), followed by cleanup of the samples and PCR amplification. Libraries were size-selected (175-350 bp) and purified from 3% low melting temperature agarose gels, followed by sequencing on the Illumine HiSeq 2500 platform (paired-end).

tag: antibody manufacturer

tag: antibody catalog #

tag: strain

value: blast crisis CML bone marrow


title: FL_wt_eklf_chip_rep2

tag: cell type


title: CML-B

description: eCLIPseq

value: abcam


title: Control, rep36

tag: Sex

value: C

value: no


title: u2os-HAPSTR2_siHAPSTR1_1

tag: treatment


title: Control, rep30

value: M

tag: age


title: CML-A

description: eCLIPseq


title: FL_wt_eklf_chip_rep1

value: embryonic day E13.5 fetal liver

tag: chip antibody


title: Control, rep29

tag: disease state


title: u2os-EV_siHAPSTR1_1

value: cancer cell line

value: WT


title: h661_siNT_3

value: lung cancer

value: siNT+siNT


title: NoPP-4

city: Columbia

first: Sathesh

middle: K

last: Sivasankaran

state: MO

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

description:
NoPP_barcodes.tsv.gz
NoPP_features.tsv.gz
NoPP_matrix.mtx.gz

library_source: transcriptomic single cell

data_processing:
Read were aligned using CellRanger v4.0.6
Assembly: Genome build Sus Scrofa 11.1 (Annotation build Sus Scrofa 11.1.97)
Supplementary files format and content: Raw count matrix (matrix.mtx), cell barcodes (barcode.tsv), gene feature table (feature.tsv) files in gunzipped format

organism: Sus scrofa

source_name: small intestine

extract_protocol:
Tissues were transported to the lab in Hank’s balanced salt solution (HBSS; Gibco 14175) containing 2 mM ethylenediaminetetraacetic acid (EDTA; Invitrogen AM9261), 2 mM L-glutmaine (Gibco 25030), and 0.5% bovine serum albumin (BSA; Sigma A9418). In the lab, tissues werelongitudinally opened and gently rinsed with phosphate-buffered saline (PBS; (pH 7.2, made in-house) to remove luminal contents. From ileum, tissue was grossly dissected into regions containing or lacking Peyer’s patches. Between 1.5-2grams of tissue were weighed and used for cell isolationfrom each sample. Cells were isolated by incubating tissuesin 30mL mucus dissociation solution (5 mM dithiothretol [DTT; Invitrogen 15508, 2% fetal calf serum [FCS; Gibco 26140-079, heat-inactivated before use] in HBSS) for 20minutes, followed by two incubations in 30mL fresh epithelial removal solutions (5 mM EDTA, 2% FCS in HBSS) for 25 minutes each. Each incubation was carried out in a shaking incubator at 37°C, 200 rpm. From each tube of epithelial removal solution,cells were centrifuged atroom temperature (RT) for 10 minutes, 200 xg and resuspended in 2 mM L-glutamine, 2% FCS in HBSS. Viable cells were enriched via density gradient centrifugation with Percoll (1.088 g/mL) and poured over a 40 micron nylon filter.
Single-cell libraries were prepared with the manufacturer’s protocol for Chromium Single Cell 3’ v3 Chemistry (10X Genomics CG000183). Equal amounts of each samples were sequenced on an Illumina HiSeq 3000 with 2x100 paired-end sequencing.

value: Ileum

tag: tissue dissection

value: Ileum without Peyer's patches

tag: breed

value: Mixed-breed

value: 7.5 weeks

tag: gender

value: Female


title: H3K4me1_hPGC_wk8_M_r2

description: H3K4me1_hPGC_wk8_M_pool_final_q3.narrowPeak

source_name: Gonad

value: Gonad

value: Primordial germ cells

value: Male


title: NoPP-3


title: Control, rep28

value: Peripheral blood

tag: alcohol

tag: tobacco

tag: illegal drugs


title: Th0 ITA 2

city: Sapporo

first: Kuniyuki

last: Aso

address: Kita 14, Nishi 5, Kita-ku

country: Japan

institute: Hokkaido university

data_processing:
The resultant libraries were then quantified and sequenced by Illumina NovaSeq according to the manufacturer’s instructions (Illumina, San Diego, CA, USA) with 150 bp paired-end configuration. The library preparation and sequencing were performed by GENEWIZ.
The raw sequencing reads with low quality, and adapter sequences were removed using Cutadapt v 2.1.
The trimmed reads were mapped to the mm10 (Ensembl 99) and quantified using STAR v 2.7.1a.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: spleen

growth_protocol: Naive CD4+ T cells isolated from C57BL/6J spleen by magnetic cell sorting with the naïve CD4+ T Cell Isolation kit (Miltenyi Biotec). Approximately 0.3 million naive CD4+ T cells were plated into 48-well-plate pre-coated with goat anti-hamster IgG (MP Biomedicals). For Th0 differentiation, cells were stimulated for 2-3 days with anti-CD3 and anti-CD28 antibodies (CD3: 0.25 μg/mL, CD28: 0.5 μg/mL).

extract_protocol:
Total RNA was extracted from T cells in the presence or absecnce ITA 6 mM on day2 using RNeasy Plus Micro Kit (QIAGEN) according to the manufacturer’s instructions.
For RNA-sequencing, total RNA was quantified and qualified by NanoDrop and Qubit RNA Assay (Thermo Fisher Scientific), and by RNA ScreenTape on TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). 500 ng total RNA with RIN 7 or higher was used for poly-A mRNA enrichment (NEBNext Poly(A) mRNA Magnetic Isolation Module) and the following library preparation by NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs), according to the manufacture’s protocol.

treatment_protocol: All cells were cultured in RPMI 1640 medium containing 10% FBS, 0.1% 2-mercaptoethanol, and penicillin-streptomycin at 37°C under 5% CO2. Itaconate (ITA; Sigma-Aldrich) were prepared as 750 mM stock solutions in phosphate buffered saline (PBS) and diluted directly into culture media.

value: spleen

value: T cells

tag: genotype

value: wild type

value: treated with ITA for 2 days


title: Control, rep34

tag: tissue

value: F

value: C

value: no

tag: medication group

tag: medication subgroup


title: Th0 ITA 3


title: h661_siNT_2

value: cancer cell line

tag: cell line

value: lung cancer

value: WT

value: siNT+siNT


title: NoPP-2

value: Ileum

value: Ileum without Peyer's patches

value: Mixed-breed

value: 7.5 weeks


title: Control, rep27

value: M


title: h661_siNT_1

tag: cell type


title: Th0 ITA 1


title: CML-B input

description: eCLIPseq

tag: antibody manufacturer

tag: antibody catalog #

tag: strain

value: blast crisis CML bone marrow


title: Control, rep31

value: Peripheral blood

tag: Sex

tag: age


title: Control, rep26

tag: disease state

value: yes


title: NoPP-1

tag: tissue dissection

tag: breed

value: Female


title: Th0 Ctrl 3

value: spleen

value: T cells

value: wild type

tag: treatment

value: untreated


title: JEJ-4

description:
JEJ_barcodes.tsv.gz
JEJ_features.tsv.gz
JEJ_matrix.mtx.gz

value: Jejunum

value: Jejunum collected ~3 feet distal to pylorus

tag: gender


title: Control, rep25

value: C

tag: alcohol

value: no

tag: tobacco

tag: illegal drugs


title: Control, rep24

tag: tissue

tag: medication group


title: Th0 Ctrl 2

tag: genotype


title: h661_siHAPSTR2_2

value: cancer cell line

tag: cell line

tag: cell type

value: lung cancer

value: WT


title: JEJ-3

value: Mixed-breed

value: 7.5 weeks


title: h661_siHAPSTR2_1


title: Th0 Ctrl 1


title: JEJ-1


title: Control, rep21

value: F

tag: medication subgroup


title: h661_siHAPSTR1_2


title: h661_siHAPSTR1_1


title: JEJ-2


title: Control, rep22

value: Peripheral blood


title: IPP-3

description:
IPP_barcodes.tsv.gz
IPP_features.tsv.gz
IPP_matrix.mtx.gz

value: Ileum

value: Ileum with Peyer's patches


title: IPP-4

value: Female


title: h661_siHAPSTR2_3


title: Control, rep19


title: h661_DKD_2


title: IPP-2


title: m678_neg

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

data_processing:
RNA-seq reads were pseudoaligned with Kallisto using the genome build GRCm38.p6.
RNA-seq gene expression values were computed following DESeq2 analysis pipeline.
scRNA- and snRNA-seq reads were aligned by cellranger using the genome build GRCh38.10/GRCh38.p13.
QC, normalization, clustering and downstream analysis were performed by scater, scran and Seurat packages.
Integration of datasets was performed using Harmony package.
Mapping analysis and gene enrichment analysis were performed using SingleR and fgsea packages respectively.
Assembly: GRCh38.10/GRCh38.p13
Assembly: GRCm38.p5/GRCm38.p6
Supplementary files format and content: RNA-seq: Tab-delimited .txt files include 5 columns: Ensembl transcripts identifier, transcript length, effective transcript length, estimated counts and transcripts per million.
Supplementary files format and content: scRNA- and snRNA-seq: Raw count matrices from Cell Ranger.

extract_protocol:
FAPs were directly sorted into 700 μl RNA lysis buffer, and RNA extraction was performed using RNeasy Plus Micro Kit (74034 QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols.
Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry).

value: total hindlimb muscles

value: muscle fibro-adipogenic progenitors


title: m671_pos


title: m673_pos


title: m673_neg


title: m678_pos


title: h661_DKD_1


title: Control, rep18

value: M


title: h661_siHAPSTR1_3


title: Control, rep23


title: m671_neg


title: Homo sapiens PBL, LPS

city: Minato-ku

first: Kei

last: Sato

state: Tokyo

address: 4-6-1 Shiroganedai

department: Department of Microbiology and Immunology

institute: The Institute of Medical Science, The University of Tokyo

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (10x Genomics).
Assembly: Homo sapiens: GRCh38.p13 (RefSeq accession: GCF_000001405.39); Pan troglodytes: Clint_PTRv2 (RefSeq accession: GCF_002880755.1); Macaca mulatta: Mmul_10 (RefSeq accession: GCF_003339765.1); Rousettus aegyptiacus: mRouAeg1.p (RefSeq accession: GCF_014176215.1)
Supplementary files format and content: HDF5 format including count matrices

source_name: peripheral blood

growth_protocol: One million PBMCs were maintained in 500 μl RPMI 1640 (Sigma-Aldrich, Cat# R8758-500ML).

extract_protocol:
One day post infection, infected/stimulated PBMCs were centrifuged and resuspended with PBS.
Library construction was performed following the manufacter’s instructions (Next GEM Single Cell 3' Reagent Kits v3.1, 10x Genomics). Briefly, PBMCs were washed with PBS, then resuspended in the master mix.  Cells, gel-beads and oils were loaded into the Next GEM chip G to generate GEMs using Chromium controller. Reverse transcription were performed in each GEM and barcoded cDNA were produced. After cDNA amplification, enzymatic fragmentation end repair, A-tailing, adaptor ligation and index PCR were processed. QC for constructed libraries were conducted by Agilent Bioanalyzer.

treatment_protocol: One million PBMCs were infected with HSV-1 or SeV at a multiplicity of infection 0.1. LPS (Sigma-Aldrich, Cat# L5024-10MG) was added at 200 ng/ml final concentration. One day post infection, infected/stimulated PBMCs were used for scRNA-seq.

value: peripheral blood

value: PBMC

value: LPS


title: m665_pos


title: Control, rep16

value: C

value: no


title: DUOD-4

description:
DUOD_barcodes.tsv.gz
DUOD_features.tsv.gz
DUOD_matrix.mtx.gz

value: Duodenum

value: Duodenum collected immediately following pylorus


title: Control, rep20


title: Control, rep17


title: h661_DKD_3

value: cancer cell line

value: lung cancer

value: WT


title: DUOD-3

value: Mixed-breed

value: 7.5 weeks


title: Control, rep15

value: Peripheral blood


title: Homo sapiens PBL, SeV

description: 10x Genomics

value: SeV


title: m665_neg

value: total hindlimb muscles


title: DUOD-2

value: Female


title: Homo sapiens PBL, HSV-1

description: 10x Genomics


title: m632_pos

value: muscle fibro-adipogenic progenitors


title: Control, rep14

value: M


title: m632_neg


title: Homo sapiens PBL, mock

description: 10x Genomics

value: peripheral blood

value: PBMC

value: Mock


title: Control, rep13

value: F

value: C

value: no


title: FAPS30_all_E1

description:
single cell RNA
10x scRNA-Seq

value: all mononucleated cells of the muscle


title: DUOD-1

value: Duodenum

value: Duodenum collected immediately following pylorus


title: Control, rep12


title: hESC_naiveJ_WT_IAA_cloneI

data_processing:
Adaptor sequences were removed by Trim Galore(v0.4.1) using the default parameters
Reads were mapped to the human reference genome (UCSC GRCh38/hg38) using STAR(2.7.1a) (parameters: ‘--outFilterMismatchNoverLmax 0.05 --outFilterMultimapNmax 50 --outMultimapperOrder Random’) guided by the Gencode Human Release 30 comprehensive gene annotation.
Raw read counts per gene were extracted by the featureCounts function of the Subread package(1.6.2) using the default parameters. Normalized read counts and differentially expressed genes were obtained using DEseq2(1.26.0) in R(3.6.2)/Bioconductor(3.10.1).
Assembly: hg38
Supplementary files format and content: Excel table with mRNA expression level [log2(normalised counts +1)]

extract_protocol:
RNA was extracted using the PicoPure RNA Isolation Kit including an on-column DNase 1 digest (Qiagen 79254) following the manufacturer’s instruction.
RNA-seq libraries were generated from 2 to 5 ng of total RNA using SMARTer® Universal Low Input RNA Kit for Sequencing (Takara Bio) according to manufacturer's protocol.

value: Naive hESC

value: Wild-type

value: Male

value: IAA


title: hESC_naiveJ_WT_IAA_cloneA


title: hESC_naiveJ_SETDB1AID_IAA_cloneE

value: SETDB1-AID knock-in


title: wild-type, RNaseI, RNA-seq, Replicate 1

city: Freiburg

first: Rick

last: Gelhausen

state: Baden Württemberg

address: Georges-Köhler-Allee 106

department: Department of Computer Science

institute: Albert-Ludwigs-University Freiburg

description: Total RNA extracted from WT strain biological, DNaseI digested, rRNA depleted, fragmented and subjected to cDNA library preparation

data_processing:
Base calling with Illumina NextSeq RTA v2.4.11
FASTQ conversion with bcl2fastq v2.20.0.422
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) version 2.1 (cutadapt parameters: -q 20 --trim-n -m 10 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) (HRIBO 1.6.0)
Mapping with segemehl 0.3.4 (HRIBO 1.6.0)
rRNA filtering was done using samtools 1.9 (HRIBO 1.6.0)
Coverage files were created using HRIBO 1.6.0
bigwig files were generated with full read coverage and normalized to the size of the minimal sample size among all samples.
Assembly: GCA_000025685.1
Supplementary files format and content: bigwig format files containing normalized read coverage for each sample
Supplementary files format and content: The overview.xlsx file contains ORF predictions, together with expression values for all samples.

organism: Haloferax volcanii

source_name: archaea

growth_protocol: For Ribo-seq sample preparation, H. volcanii cells were grown to exponential phase (OD600nm 0.4). Bacteria were cultivated aerobically at 45°C in rich media (Hv_YPC medium)

extract_protocol:
RNA was extracted from fractions or cell pellets for total RNA using hot phenol-chloroform-isoamyl alcohol (25:24:1, Roth) or hot phenol (Roth), respectively, as described previously (Sharma et al. 2007).
Total RNA was first rRNA-depleted, fragmented then subjected to cDNA library preparation. Size selcted RNA for Riboseq samples were directly subjected to cDNA library preparation. The obtained small RNA samples were first treated with Antarctic Phosphatase and re-phosphorylated with T4 Polynucleotide Kinase (PNK). Then,   oligonucleotide adapters were ligated to the 5' and 3' ends of the RNA samples. First-strand cDNA   synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The   resulting cDNA was amplified with PCR using a high fidelity DNA polymerase.

treatment_protocol: No treatment applied during growth.

value: archaea

tag: strain

value: wild type

value: no treatment

tag: molecule type

value: rRNA-depleted, fragmented total RNA


title: IECs, PTBP1_KO_3

city: URBANA

first: Ullas

middle: Valiya

last: Chembazhi

state: Illinois

address: 600 S Mathews Avenue

department: Biochemistry

institute: UIUC

description:
Cufflink_gene_exp.csv
5 MATS files

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina).
Adaptors were trimmed from the reads using trimmomatic V0.38
Reads were mapped to the genome using STAR_2.6.1d
Differential splicing analysis was performed using rMATs v4.0.2(turbo).  All the RAW data files(WT1/2/3 as controls and PTBP1_KO_1/2/3 as experimental dataset) were processed together using rMATS pipeline, to obtain the alternative splicing events.  The 5 MATS files(unprocessed rMATS outputs) describe these, with each file describing a different alternative splicing type (SE-skipped exon, A5SS-alternate 5'splice site, A3SS-alternative 3'splice site, MXE-mutually exclusive exon and RI-retained intron).
FPKM/TPM values were calculated and compared between sets of samples using Cufflinks package
Genome_build: mm10
Supplementary_files_format_and_content: Cuffdiff and rMATs output

source_name: intestinal epithelial cells

extract_protocol:
Small intestines were harvested and cut into ~5 cm fragments and open longitudinally and washed with ice-cold PBS. After villi were gently scraped off, the fragments were incubated in 2 mM EDTA/PBS with gentle shaking at 4°C for 30 minutes. Intestinal fragments were then washed with cold PBS and vortexed, and the supernatant fractions were collected and filtered through 70 μm pore cell strainers. The filtrate was centrifuged at 200 g for 5 minutes  and the pelleted crypt cells were collected for RNA-Seq analysis.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina).

treatment_protocol: Tamoxifen was administrated by single daily injections for two consecutive days at the dose of 100 mg/kg of body weight. Crypt cells were isolated 20 hours post second tamoxifen injection.

value: Intestine

value: intestinal epithelial cells (IECs)

tag: age

value: 60 days

value: Tamoxifen (100 mg/kg)


title: Control, rep10

data_processing:
myBrain-Seq v0.1.0 (https://github.com/sing-group/my-brain-seq)
Sequence reads were trimmed for adaptor sequence using myBrain-Seq
Trimmed sequences were aligned to GRCh38 using myBrain-Seq.
Quantification and annotation of the aligned sequences to miRBase v.22 was performed using myBrain-Seq.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include miRNA quantification values for each sample.

extract_protocol:
PAXgene ® Blood microRNA Kit from Qiagen (PreAnalytiX GmbH, Hombrechtikon, Switzerland).
NEBNext Multiplex Small RNA Sample Prep Set for illumina (New England biolabs, Ipswich, MA, USA)

value: Peripheral blood

tag: Sex

value: F

tag: disease state

value: C

value: no


title: wild-type, MNase, RNA-seq, Replicate 2

description: Total RNA extracted from WT strain biological replicate 2, DNaseI digested, rRNA depleted, fragmented and subjected to cDNA library preparation


title: wild-type, RNaseI, RIBO-seq, Replicate 1

description: RNA purified from WT ribosome footpints, size selected and subjected to cDNA library preparation

value: ribosome footprint generated by RNase


title: wild-type, MNase, RNA-seq, Replicate 1

description: Total RNA extracted from WT strain biological replicate 1, DNaseI digested, rRNA depleted, fragmented and subjected to cDNA library preparation


title: IECs, PTBP1_KO_1

description:
Cufflink_gene_exp.csv
5 MATS files


title: schulthess_10_GM

description:
single cell RNA
10x scRNA-Seq

value: gluteus minimus muscle

value: all mononucleated cells of the muscle


title: IPP-1

value: Ileum

tag: tissue dissection

value: Ileum with Peyer's patches

tag: breed

value: Mixed-breed

value: 7.5 weeks

value: Female


title: schulthess_10_RF1

description:
single cell RNA
10x scRNA-Seq

value: rectus femoris muscle


title: wild-type, MNase, RIBO-seq, Replicate 1

value: archaea

value: wild type

tag: treatment

value: no treatment

value: ribosome footprint generated by MNase


title: IECs, WT_2

description:
Cufflink_gene_exp.csv
5 MATS files

value: Intestine

value: intestinal epithelial cells (IECs)

value: 60 days

value: Tamoxifen (100 mg/kg)


title: wild-type, MNase, RIBO-seq, Replicate 2


title: Control, rep11

value: Peripheral blood

value: M

value: C

tag: alcohol

value: no


title: GM2

description:
single nuclei RNA
10x snRNA-Seq

value: gluteus minimus muscle

value: all mono- and multinucleated cells of the muscle


title: Control, rep7

tag: tobacco


title: IECs, WT_1

description:
Cufflink_gene_exp.csv
5 MATS files


title: Control, rep6

tag: illegal drugs


title: Brain hippocampal CA1 region HPC0h RIP-seq

city: Guangzhou

first: Astrame

last: Chen

address: Xinzao town, Panyu district

institute: Guangzhou Medical University

data_processing:
raw data were generated after sequencing, image analysis, base calling and quality filtering on Illumina sequencer
Firstly, Q30 was used to perform quality control. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.3).
Then, trimmed reads from all samples were pooled, and piano software was used to predict novel piRNAs. The trimmed reads were aligned to the merged rat piRNA databases (known piRNA from piRNABank plus the newly predicted piRNAs) using Novoalign software (v3.02.12) with at most one mismatch.
The counts of piRNA mapped tags were defined as the raw expression counts of that piRNA, and normalized by TPM method.
Differentially expressed piRNAs were filtered by ttest. PiRNA-binding transposon and targets were predicted by miranda software (v3.3a).
piRNA-targets networks were plotted by cytoscape software (v2.8.0), and the GO and KEGG pathway analysis were performed.
Genome_build: piRNAbank
Supplementary_files_format_and_content: Table with raw counts for every piRNA and every sample in excel format.

organism: Rattus norvegicus

source_name: Brain hippocampal CA1 region

extract_protocol:
total RNA was extracted using Trizol reagent (Invitrogen)
Total RNA of each sample was used to prepare the piRNA sequencing library, which included the following steps:1) 3'-adaptor ligation;2) 5'-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) Size selection of ~150 bp PCR amplicons(corresponding to ~30 nt piRNAs)  The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 50 cycles on Illumina HiSeq sequencer following the manufacturer's instructions.

value: Wistar

tag: tissue

value: Brain hippocampal CA1 region

value: 7-8 weeks-old


title: Control, rep5

tag: medication group


title: Brain hippocampal CA1 region IgG RIP-seq


title: IECs, PTBP1_KO_2

description:
Cufflink_gene_exp.csv
5 MATS files

tag: genotype


title: hESC_naiveJ_SETDB1AID_IAA_cloneB

city: Cambridge

first: Walfred

last: Tang

address: Tennis Court Road

institute: University of Cambridge

tag: cell line

value: Naive hESC

value: SETDB1-AID knock-in

value: Male

value: IAA


title: GM1

description:
single nuclei RNA
10x snRNA-Seq

tag: cell type


title: Control, rep9

city: Santiago de Compostela

first: Roberto Carlos

last: Balboa

address: Travesía da Choupana s/n

institute: Health Research Institute of Santiago de Compostela (IDIS)

tag: medication subgroup


title: Brain hippocampal CA1 region tGCI26h RIP-seq

tag: strain


title: Control, rep4

value: F


title: Control, rep8


title: RF1

description:
single nuclei RNA
10x snRNA-Seq

value: rectus femoris muscle


title: Brain hippocampal CA1 region Sham RIP-seq


title: Treg ITA 1

data_processing:
The resultant libraries were then quantified and sequenced by Illumina NovaSeq according to the manufacturer’s instructions (Illumina, San Diego, CA, USA) with 150 bp paired-end configuration. The library preparation and sequencing were performed by GENEWIZ.
The raw sequencing reads with low quality, and adapter sequences were removed using Cutadapt v 2.1.
The trimmed reads were mapped to the mm10 (Ensembl 99) and quantified using STAR v 2.7.1a.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: processed_data_files_raw_counts.tsv: Matrix table with raw gene counts for every gene and every sample.

source_name: spleen T cells

growth_protocol: Naive CD4+ T cells isolated from C57BL/6J spleen by magnetic cell sorting with the naïve CD4+ T Cell Isolation kit (Miltenyi Biotec). Approximately 0.3 million naive CD4+ T cells were plated into 48-well-plate pre-coated with goat anti-hamster IgG (MP Biomedicals) and stimulated for 2-3 days with anti-CD3 and anti-CD28 antibodies (CD3: 0.25 μg/mL, CD28: 0.5 μg/mL). For each T cell differentiation, subset-specific cytokines and antibodies were further supplemented. For Th17 differentiation, cells were cultured with anti-IL-4 (2 μg/mL), anti-IFNγ (2 μg/mL), IL-6 (30 ng/mL), and TGF-β (0.3 ng/mL). For Treg differentiation, cells were cultured with anti-IL-4 (2 μg/mL), anti- IFNγ (2 μg/mL), IL-2 (20 ng/mL), and TGF-β (1 ng/mL).

extract_protocol:
Total RNA was extracted from Th17- and Treg-polarizing T cells with or without ITA on day2 using RNeasy Plus Micro Kit (QIAGEN) according to the manufacturer’s instructions.
For RNA-sequencing, total RNA was quantified and qualified by NanoDrop and Qubit RNA Assay (Thermo Fisher Scientific), and by RNA ScreenTape on TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). 500 ng total RNA with RIN 7 or higher was used for poly-A mRNA enrichment (NEBNext Poly(A) mRNA Magnetic Isolation Module) and the following library preparation by NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs), according to the manufacturer’s protocol.

value: postnatal week 8

value: wild type

value: Treg cells

value: treated with ITA for 2 days


title: Treg ITA 2


title: CRISPR Myoblast [CRISPR_3]

city: Burjassot

first: Ruben

last: Artero

state: Valencia

address: C/ Doctor Moliner, 50

department: Genetics

institute: Universidad de Valencia

data_processing:
Quality control fastqc and trimgallore
Aligment, STAR (version 2.7.3)
Quantification, RSEM (1.3.2)
Assembly: GRCh38.p13
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Muscle Biopsies

extract_protocol:
For each biological replicate, total RNA from 1 × 10^6 cells was extracted using the miRNeasy mini kit (QIAGEN; Hilden, Germany) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Patient derived inmortalized myoblasts

tag: treatment group

value: CRISPR Myoblast


title: Brain hippocampal CA1 region HPC0h rep3 RNA-seq

tag: age


title: Treg ITA 3


title: Treg Ctrl 3

value: untreated


title: CRISPR Myoblast [CRISPR_2]


title: Treg Ctrl 2


title: Control, rep1

value: Peripheral blood

tag: Sex

value: M

value: C

value: no


title: Control, rep3

tag: disease state

value: yes


title: CRISPR Myoblast [CRISPR_1]


title: Brain hippocampal CA1 region HPC0h rep1 RNA-seq

value: Wistar

value: Brain hippocampal CA1 region

value: 7-8 weeks-old


title: Control, rep2


title: Treg Ctrl 1


title: Brain hippocampal CA1 region HPC0h rep2 RNA-seq


title: RF2

description:
single nuclei RNA
10x snRNA-Seq

value: all mono- and multinucleated cells of the muscle


title: SW620-shTEAD4-B

city: shanghai

first: Zhenyu

last: Huang

address: NO. 1665 kongjiang RD.

institute: Colorectal Cancer Research Center of Shanghai

description: TEAD4 knock down

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg18 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GR38p7
Supplementary_files_format_and_content: RNA-seq shTEAD4 in 116,620.xlsx

source_name: SW620 CELL LINE

growth_protocol: DMEM+10%FBS, 5%CO2

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

treatment_protocol: none treatment

tag: tag

value: TEAD4 Knock down


title: LGMDD2 Myoblast [LGMDD2_3]

value: LGMDD2 Myoblast


title: Brain hippocampal CA1 region tGCI26h rep3 RNA-seq


title: Th17 ITA 3

value: postnatal week 8

value: wild type

value: Th17 cells


title: LGMDD2 Myoblast [LGMDD2_2]

value: Patient derived inmortalized myoblasts


title: SW620-shTEAD4-A

description: TEAD4 knock down


title: Brain hippocampal CA1 region tGCI26h rep2 RNA-seq


title: Th17 ITA 2

value: treated with ITA for 2 days


title: SW620-pLKO

description: control

value: control


title: Th17 ITA 1


title: HCT116_shTEAD4-B

description: TEAD4 knock down

source_name: HCT116 CELL LINE


title: Brain hippocampal CA1 region tGCI26h rep1 RNA-seq


title: LGMDD2 Myoblast [LGMDD2_1]


title: Brain hippocampal CA1 region Sham rep3 RNA-seq


title: Control Myoblast [CNT_3]

value: Unaffected derived inmortalized  myoblasts

value: Control Myoblast


title: HCT116_shTEAD4-A

description: TEAD4 knock down


title: Th17 Ctrl 3

value: untreated


title: Control Myoblast [CNT_2]


title: Th17 Ctrl 2


title: HCT116_pLKO

description: control


title: Control Myoblast [CNT_1]

value: Unaffected derived inmortalized myoblasts


title: Th17 Ctrl 1


title: Virus Detected 284

status: Public on Jan 17 2023

city: Gainesville

first: Cuong

last: Nguyen

state: Florida

address: 2015 SW 16th Ave

institute: University of Florida

description: After the exclusion of samples during quality control, the final case-control data sets comprised 254 patients and 80 control participants. The samples with disclosures in the table are those that have passed QC and population stratification.

hyb_protocol: Genotyping was done using Axiom™ Human Genotyping SARS-CoV-2 Research Array as instructed by the manufacturer (Thermo Scientific).

scan_protocol: The scanning was performed by UF ICBR core using GeneTitan MC Instrument.

data_processing: Axiom Analysis Suite (Thermo Scientific) was used to process the raw data.

source_name: Saliva

label_protocol: Total Genomic DNA were extracted, no label needed

extract_protocol: Clinical specimens of nasopharyngeal swabs were collected in a viral transport medium. DNA was extracted from viral transport medium or directly from tracheal aspirates by Maxwell® RSC Blood DNA Kit per manufacturer's instructions (Promega Corporation). RNase A was added to samples to remove potential viral RNA. Isolated genomic DNA was quantified by NanoDrop™ One/OneC Microvolume UV-Vis Spectrophotometer (Thermo Scientific).

value: virus detected

value: F

tag: race

value: EUR


title: Brain hippocampal CA1 region Sham rep2 RNA-seq

value: Wistar

value: Brain hippocampal CA1 region

value: 7-8 weeks-old


title: Brain hippocampal CA1 region Sham rep1 RNA-seq


title: Virus Detected 281


title: Virus Detected 282

value: M


title: Virus Detected 280

value: AFR


title: Virus Detected 279


title: Virus Detected 278


title: Virus Detected 276


title: Virus Detected 274


title: Virus Detected 275

value: Unknown


title: Virus Detected 272


title: Virus Detected 277


title: Virus Detected 271


title: Virus Detected 270


title: Virus Detected 267


title: Virus Detected 269


title: Virus Detected 268


title: Virus Detected 264


title: Virus Detected 262


title: Virus Detected 263


title: Virus Detected 261


title: Virus Detected 260


title: Virus Detected 283


title: Virus Detected 258


title: Virus Detected 259


title: Virus Detected 255


title: Virus Detected 257


title: Virus Detected 256


title: Virus Detected 253


title: Virus Detected 273


title: Virus Detected 252


title: Virus Detected 254


title: Virus Detected 251


title: Virus Detected 250


title: Virus Detected 247


title: Virus Detected 245


title: Virus Detected 265


title: Virus Detected 246


title: Virus Detected 248


title: Virus Detected 249

value: SAS


title: Virus Detected 244


title: Virus Detected 266


title: Virus Detected 242


title: Virus Detected 243


title: Virus Detected 241


title: Virus Detected 240


title: Virus Detected 239


title: Virus Detected 236


title: Virus Detected 237


title: Virus Detected 234


title: Virus Detected 232


title: Virus Detected 235


title: Virus Detected 229


title: Virus Detected 231


title: Virus Detected 228


title: Virus Detected 227


title: Virus Detected 226


title: Virus Detected 223


title: Virus Detected 222


title: Virus Detected 219


title: Virus Detected 215

value: EAS


title: Virus Detected 220


title: Virus Detected 217


title: Virus Detected 216


title: Virus Detected 218


title: Virus Detected 214


title: IECs, WT_3

description:
Cufflink_gene_exp.csv
5 MATS files

value: Intestine

value: intestinal epithelial cells (IECs)

value: 60 days

tag: treatment

value: Tamoxifen (100 mg/kg)


title: Virus Detected 213


title: Virus Detected 233


title: Virus Detected 209


title: Virus Detected 211


title: Virus Detected 212


title: Virus Detected 230


title: Virus Detected 206


title: Virus Detected 210


title: Virus Detected 207


title: Virus Detected 203


title: Virus Detected 204


title: Virus Detected 224


title: Virus Detected 202


title: Virus Detected 201


title: Virus Detected 238


title: Virus Detected 225


title: Virus Detected 200


title: Virus Detected 221


title: Virus Detected 199


title: Virus Detected 197


title: Virus Detected 208


title: Virus Detected 196


title: Virus Detected 193


title: Virus Detected 195


title: Virus Detected 194


title: Virus Detected 192


title: Virus Detected 198


title: Virus Detected 189


title: Virus Detected 188


title: Virus Detected 186


title: Virus Detected 187


title: Virus Detected 190


title: Virus Detected 183


title: Virus Detected 181


title: Virus Detected 182


title: Virus Detected 205


title: Virus Detected 180


title: Virus Detected 184


title: Virus Detected 179


title: Virus Detected 178


title: Virus Detected 177


title: Virus Detected 176


title: Virus Detected 173


title: Virus Detected 172


title: Virus Detected 174


title: Virus Detected 171


title: Virus Detected 191


title: Virus Detected 169


title: Virus Detected 165

source_name: Trachael Aspirate


title: Virus Detected 167


title: Virus Detected 170


title: Virus Detected 168


title: Virus Detected 166


title: Virus Detected 185


title: Virus Detected 164


title: Virus Detected 162


title: Virus Detected 161


title: Virus Detected 160


title: Virus Detected 163


title: Virus Detected 158


title: Virus Detected 175


title: Virus Detected 149


title: Virus Detected 157


title: Virus Detected 156


title: Virus Detected 153


title: Virus Detected 151


title: Virus Detected 152


title: Virus Detected 148


title: Virus Detected 147


title: Virus Detected 146


title: Virus Detected 145


title: Virus Detected 143


title: Virus Detected 144


title: Virus Detected 142


title: Virus Detected 141


title: Virus Detected 140


title: Virus Detected 139


title: Virus Detected 137


title: Virus Detected 138


title: Virus Detected 159


title: Virus Detected 150


title: Virus Detected 155


title: Virus Detected 154


title: Virus Detected 136


title: Virus Detected 135


title: Virus Detected 133


title: Virus Detected 131


title: Virus Detected 130


title: Virus Detected 132


title: Virus Detected 129


title: Virus Detected 128


title: Virus Detected 124


title: Virus Detected 123


title: Virus Detected 121


title: Virus Detected 127


title: Virus Detected 122


title: Virus Detected 126


title: Virus Detected 120


title: Virus Detected 119


title: Virus Detected 116


title: Virus Detected 118


title: Virus Detected 114


title: Virus Detected 113


title: Virus Detected 112


title: Virus Detected 111


title: Virus Detected 110


title: Virus Detected 134


title: Virus Detected 106


title: Virus Detected 105


title: Virus Detected 107


title: Virus Detected 109


title: Virus Detected 108


title: Virus Detected 104


title: Virus Detected 103


title: Virus Detected 102


title: Virus Detected 101


title: Virus Detected 100


title: Virus Detected 125


title: Virus Detected 97


title: Virus Detected 94

source_name: Tracheal Aspirate


title: Virus Detected 98


title: Virus Detected 93


title: Virus Detected 92


title: Virus Detected 95


title: Virus Detected 117


title: Virus Detected 115


title: Virus Detected 96


title: Virus Detected 89


title: Virus Detected 87


title: Virus Detected 90


title: Virus Detected 91


title: Virus Detected 86


title: Virus Detected 85


title: Virus Detected 84

source_name: Nasal Swab


title: Virus Detected 82


title: Virus Detected 80


title: Virus Detected 74


title: Virus Detected 75


title: Virus Detected 76


title: Virus Detected 81


title: Virus Detected 79


title: Virus Detected 77


title: Virus Detected 73


title: Virus Detected 78


title: Virus Detected 99


title: Virus Detected 71


title: Virus Detected 68


title: Virus Detected 72


title: Virus Detected 67


title: Virus Detected 69


title: Virus Detected 64


title: Virus Detected 65


title: Virus Detected 70


title: Virus Detected 63


title: Virus Detected 61


title: Virus Detected 59


title: Virus Detected 88


title: Virus Detected 58


title: Virus Detected 57


title: Virus Detected 62


title: Virus Detected 56


title: Virus Detected 83


title: Virus Detected 55


title: Virus Detected 51


title: Virus Detected 53


title: Virus Detected 52


title: Virus Detected 45


title: Virus Detected 54


title: Virus Detected 49


title: Virus Detected 50

value: U


title: Virus Detected 47


title: Virus Detected 48


title: Virus Detected 66


title: Virus Detected 44


title: Virus Detected 42


title: Virus Detected 43


title: Virus Detected 41


title: Virus Detected 37


title: Virus Detected 36


title: Virus Detected 38


title: Virus Detected 39


title: Virus Detected 60


title: Virus Detected 34


title: Virus Detected 30


title: Virus Detected 31


title: Virus Detected 32


title: Virus Detected 33


title: Virus Detected 29


title: Virus Detected 46


title: Virus Detected 27


title: Virus Detected 28


title: Virus Detected 24


title: Virus Detected 21


title: Virus Detected 40


title: Virus Detected 23


title: Virus Detected 17


title: Virus Detected 22


title: Virus Detected 19


title: Virus Detected 16


title: Virus Detected 18


title: Virus Detected 14


title: Virus Detected 35


title: Virus Detected 13


title: Virus Detected 15


title: Virus Detected 12


title: Virus Detected 9


title: Virus Detected 8


title: Virus Detected 10


title: Virus Detected 4


title: Virus Detected 7


title: Virus Detected 6


title: Virus Detected 5


title: Virus Detected 3


title: Virus Detected 1


title: Virus Detected 2


title: Healthy Volunteer 89

value: healthy


title: Healthy Volunteer 88


title: Virus Detected 25

value: virus detected


title: Virus Detected 20


title: Healthy Volunteer 86

value: F


title: Virus Detected 26


title: Healthy Volunteer 84

value: EUR


title: Healthy Volunteer 85


title: Healthy Volunteer 81


title: Healthy Volunteer 83


title: Healthy Volunteer 82


title: Healthy Volunteer 80


title: Healthy Volunteer 79


title: Healthy Volunteer 78


title: Healthy Volunteer 77


title: Healthy Volunteer 76


title: Virus Detected 11


title: Healthy Volunteer 75


title: Healthy Volunteer 73


title: Healthy Volunteer 70


title: Healthy Volunteer 72


title: Healthy Volunteer 71


title: Healthy Volunteer 68


title: Healthy Volunteer 69


title: Healthy Volunteer 66


title: Healthy Volunteer 67


title: Healthy Volunteer 74


title: Healthy Volunteer 63


title: Healthy Volunteer 64


title: Healthy Volunteer 62


title: Healthy Volunteer 87


title: Healthy Volunteer 65


title: Healthy Volunteer 59


title: Healthy Volunteer 60


title: Healthy Volunteer 61


title: Healthy Volunteer 56


title: Healthy Volunteer 57


title: Healthy Volunteer 55


title: Healthy Volunteer 54


title: Healthy Volunteer 52


title: Healthy Volunteer 58


title: Healthy Volunteer 51


title: Healthy Volunteer 53


title: Healthy Volunteer 48


title: Healthy Volunteer 46


title: Healthy Volunteer 47


title: Healthy Volunteer 45


title: Healthy Volunteer 49


title: Healthy Volunteer 43


title: Healthy Volunteer 42


title: Healthy Volunteer 40


title: Healthy Volunteer 39


title: Healthy Volunteer 41


title: Healthy Volunteer 35


title: Healthy Volunteer 36


title: Healthy Volunteer 34


title: Healthy Volunteer 32


title: Healthy Volunteer 33


title: Healthy Volunteer 29


title: Healthy Volunteer 30


title: Healthy Volunteer 26


title: Healthy Volunteer 28


title: Healthy Volunteer 25


title: Healthy Volunteer 24


title: Healthy Volunteer 27


title: Healthy Volunteer 23


title: Healthy Volunteer 31


title: Healthy Volunteer 22


title: Healthy Volunteer 50


title: Healthy Volunteer 20


title: Healthy Volunteer 44


title: Healthy Volunteer 21


title: Healthy Volunteer 15


title: Healthy Volunteer 18


title: Healthy Volunteer 16


title: Healthy Volunteer 19


title: Healthy Volunteer 17


title: Healthy Volunteer 38


title: Healthy Volunteer 37


title: Healthy Volunteer 11


title: Healthy Volunteer 14


title: Healthy Volunteer 12


title: Healthy Volunteer 13


title: Healthy Volunteer 10


title: Healthy Volunteer 9


title: Healthy Volunteer 8


title: Healthy Volunteer 7


title: Healthy Volunteer 6


title: Healthy Volunteer 5


title: Healthy Volunteer 1


title: Healthy Volunteer 3


title: Healthy Volunteer 2


title: Healthy Volunteer 4


title: Lung,12,rep1

city: Solna

first: Paulo

last: Czarnewski

address: Tomtebodavägen 23b

country: Sweden

institute: KTH

description: 10X Genomics

data_processing:
Sequenced ST libraries were processed using Space Ranger 1.0.0 Pipeline (10X Genomics).
Reads were aligned to the human reference genome to obtain an expression matrix.
Assembly: GRCh38-3.0.0
Supplementary files format and content: Matrix tables with raw gene counts for every gene and every sample

source_name: Lung

extract_protocol:
One of the two lungs (preferentially the left), from each donor, was snap frozen in cryomatrix and further used for histological analyses. We cut 10-12μm-thick tissue sections with a cryostat (Leica CM3050S or analogue) and collected them onto poly-lysine coated slides (VWR Cat No. 631-0107)
Spatial Gene Expression libraries (n=9) (6-13 pcw) were generated with the Visium Spatial Gene Expression Slide & Reagent kit (PN-1000184; 10X Genomics Inc.), according to manufacturer's protocol

value: Lung

tag: donor


title: Lung,12,rep3

description: 10X Genomics


title: Lung,12,rep2

description: 10X Genomics


title: Lung,8,rep1

description: 10X Genomics


title: Lung,9,rep1

description: 10X Genomics


title: Lung,10,rep4

description: 10X Genomics


title: Lung,10,rep2

description: 10X Genomics


title: Lung,10,rep1

description: 10X Genomics


title: Lung,10,rep3

description: 10X Genomics


title: Lung,11,rep4

description: 10X Genomics


title: Lung,11,rep2

description: 10X Genomics


title: Lung,7,rep8

description: 10X Genomics


title: Lung,11,rep1

description: 10X Genomics


title: Lung,11,rep3

description: 10X Genomics


title: Lung,7,rep6

description: 10X Genomics