title: ZW2PLASMAB109A18

tag: sample subgroup (condition)

value: Healthy volunteer

tag: visit

tag: pregnant

tag: trimester

tag: date of collection

tag: gender

tag: age group

value: Not specified

tag: ethnicity

value: HiSeq


title: sgTIGRE tumor 3

status: Public on Aug 10 2024

type: SRA

city: Toronto

first: Graham

last: MacLeod

state: ON

address: 144 College Street

department: Pharmaceutical Sciences

country: Canada

institute: University of Toronto

description: tumor_rnaseq_counts.txt | wt3

library_source: transcriptomic

data_processing:
FASTQ files were aligned to the mouse genome (GRCm39) using STAR.
Read counts were extracted and normalized using DESeq2.
Assembly: GRCm39 primary assembly
Supplementary files format and content: tab delimited text file containing DESEQ2 normalized RNA-seq counts from STAR alignment.

molecule: total RNA

organism: Mus musculus

source_name: brain tumor

extract_protocol:
RNA was extracted using the Trizol reagent (invitrogen) and cleaned using the Qiagen RNeasy kit.
50 ng per sample was used for library preparation with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina after the total RNA was depleted using NEBNExt rRNA depletion kit

tag: tissue

value: brain tumor

tag: genotype

tag: treatment

value: sgRNA-TIGRE


title: ZW2PLASMAB109A15

city: New York

first: Klaas

middle: E. A.

last: Max

state: NY

address: 1230 York Avenue

department: RNA Molecular Biology

country: USA

institute: Rockefeller University

data_processing:
Sequencing data were processed using an in-house RNA-sequencing data analysis platform (RSDAP), see Brown et al. (2013) Front. Genet. for details.
Read extractions and demultiplexing was done using extraction lenth of 16 – 45 nt, a minimum 3’ overlap of adapter with 0/1 mismatches of 4/5 nt, respectively, removal of low complexity sequences.
For the read mapping and the generation of the read count matrix table, read annotations used profile annoDB_jul2014c, which included reference sequences for human and virus RNAs based on miRBASE 18 with modifications and HG19.
Supplementary_files_format_and_content: Matrixtable_exRNAdata20210810_cluster_miRNA_read_counts.csv

organism: Homo sapiens

source_name: Platelet depleted plasma

extract_protocol:
Low speed centrifugation (2500 g x 15 minutes, room temperature) was performed, then transfer of supernatant, 2nd round of centrifugation (same parameters), then transfer of supernatant. A self-developed method and self-developed solutions were used for nucleic-acid extraction, nucleic-acid partitioning, and column purification (RNA isolation), see Max et al. (2018) PNAS for details. For exRNA carrier subfractionation, selected samples were fractionated by differential ultracentrifugation into 10,000 xg pellet, 100,000 xg pellet and corresponding supernatant fractions: 11 ml of platelet-depleted plasma was centrifuged at 10,000 × g in 12 ml tubes (Sorvall, #03699) for 30 min. The supernatant was transferred by aspiration into a fresh 15 ml tube and mixed by inversion. Two aliquots of 500 µl of this supernatant were transferred into 1.5 ml microcentrifuge tubes for later RNA isolation. The 10,000 × g fragile pellet was suspended in 2.0 ml of phosphate-buffered saline (PBS), transferred into a 2.0 ml microcentrifuge tube, and centrifuged at 10,000 × g in a microcentrifuge for 30 min. The PBS supernatant was removed by aspiration, and the residual ≤10 µl volume pellet was resuspended in 450 µl PBS. The residual 10 ml of 10,000 × g supernatant was transferred into a 12 ml tube (Sorvall, #03699) and centrifuged at 100,000 × g for 90 min. The supernatant was transferred as described above, and two 500 µl aliquots of the 100,000 × g supernatant were transferred into 1.5 ml microcentrifuge tubes. The 100,000 × g pellet was washed with 10 ml PBS and centrifuged again at 100,000 × g for 90 min. The PBS supernatant was carefully removed as described above. The pellet was resuspended in 450 µl PBS. All pellet and supernatant fractions were flash-frozen in liquid nitrogen. Automated RNA isolation was conducted as previously described {Max:2018km} with the following modifications: Samples were organized in batches of 24 samples of 450 µl full plasma or plasma subfractions. Vesicle fractions were adjusted with PBS to 450 µl. Calibrator Set1, composed of ten 21-nt 5’-phosphorylated RNA oligos was added at an absolute amount of 2 attomoles per oligonucleotide along with the denaturant to each sample.
Large cohort sample library preparations used 3’ adapters, and PCR amplification methodologie, however, P12 family and plasma subfraction samples used novel 3’ adapters and PCR primers to accommodate changes in Illumina flow cell design after HiSeq was discontinued. RNA equivalent to an input 225 µl plasma was spiked with calibrator Set2 composed of another ten 21-nt 5’-phosphorylated RNA oligos at an absolute amount of 1 attomol per oligonucleotide and entered the first step of the cDNA library preparation. In sample libraries of plasma subfraction RNA from 225 µl supernatant or 5 ml pellet was used to which 0.2 attomoles per oligonucleotide of calibrator Set2 was added. After the 3’ ligation, up to 24 samples were multiplexed, size-selected by denaturing 15%, ligated to 5’ adapter, reverse-transcribed and PCR-amplified. To enable comparisons with earlier results (28), the PAGE size-selection limits were maintained at 19 to 45 for the large (n = 496) and P12 family cohorts (n = 12 samples). After discovering that miRNAs were noticeably underrepresented in the 10K and 100K pellet fractions, the size range for all plasma subfraction libraries (4 plasma subfractions, n = 17 samples, each) was adjusted to 19 to 24 nt in favor of miRNAs. cDNA libraries were sequenced as single-lane high-output single-read 75-bp HiSeq 2000 (Large cohort, n = 496 samples) or as Nextseq-500 100-bp single-read runs (P12 family, n = 12 samples; 4 Plasma subfractions, n = 17 samples each). Sequencing data were processed using an in-house RNA-sequencing data analysis platform (RSDAP) using extraction lenth of 16 – 45 nt, a minimum 3’ overlap of adapter with 0/1 mismatches of 4/5 nt, respectively, removal of low complexity sequences. For read annotations, profile annoDB_jul2014c was used, which included reference sequences for definitions for human and virus RNA sequences based on miRBASE 18 with modifications. Calibrator sequences (labeled by set) are: >Set1_cali_01_rc TCCACGACGTCTCATGTATTTC, >Set1_cali_04_rc GGGTACCATACCGGTTGTCTTA, >Set1_cali_17_rc TCATGAGTCCGTACCTTGATTG, >Set1_cali_18_rc ATCATTTACGATTCGGAGCTGT, >Set1_cali_20_rc GATAGTTCGGGATCGCTGTAAC, >Set1_cali_24_rc TGCTACTCCGATCTTTAGCCTC, >Set1_cali_25_rc AGGGCCCTTTAGGCACTAATAG, >Set1_cali_27_rc GTAGCTGTCAGTACGTTCGTGC, >Set1_cali_43_rc TCTAGTTGCGTGATGGAGAGAA, >Set1_cali_44_rc AGCCGCATTTCGTAGTGATATT, >Set2_cali_07_rc GTCCCACTCCGTAGATCTGTTC, >Set2_cali_11_rc GATGTAACGAGTTGGAATGCAA, >Set2_cali_12_rc TAGCATATCGAGCCTGAGAACA, >Set2_cali_14_rc CATCGGTCGAACTTATGTGAAA, >Set2_cali_15_rc GAAGCACATTCGCACATCATAT, >Set2_cali_16_rc TCTTAACCCGGACCAGAAACTA, >Set2_cali_26_rc AGGTTCCGGATAAGTAAGAGCC, >Set2_cali_28_rc TAACTCCTTAAGCGAATCTCGC, >Set2_cali_31_rc AAAGTAGCATCCGAAATACGGA, >Set2_cali_35_rc TGATACGGATGTTATACGCAGC

tag: cohort

value: Large cohort

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: shortid

tag: batch

tag: adapter

tag: individual

value: no

value: F

tag: age

tag: race

value: White

value: Latin

tag: sequencing technology


title: ZW2PLASMAB109A17

tag: sample subgroup (condition)

tag: visit

tag: pregnant

tag: trimester

tag: date of collection

tag: gender


title: sgTIGRE tumor 2

description: tumor_rnaseq_counts.txt | wt2

tag: tissue

tag: genotype

tag: treatment


title: ZW2PLASMAB109A14

tag: cohort

tag: anatomical location

tag: rna source

tag: rna isolation kit

value: M

tag: age group

tag: ethnicity


title: ZW2PLASMAB109A16

tag: shortid

tag: batch

tag: adapter

tag: individual

tag: age

tag: race


title: 786-O_TFE3KD_nodox_rep3

city: Boston

first: Dipanjan

last: Chowdhury

state: MA

address: 4 Blackfan Circle

institute: Dana-Farber Cancer Institute

data_processing:
Paired-end RNA-seq reads were aligned to a Bowtie2 indexed human genome (hg38 sourced from UCSC) using STAR with default settings. For better alignment, the first aligned splicing junctions detected by STAR (SJ.out.tab) were used for STAR alignment again with parameters “--sjdbFileChrStartEnd SJ.out.tab --readFilesIn $R1 $R2 --quantMode TranscriptoomeSAM GeneCounts --sjdbGTFfile $GTF_file --outSAMtype BAM Unsorted SortedByCoordinate”. Then the aligned to transcriptome bam files (AlignedtoTranscriptome.out.bam) were used to quantify gene expression levels by rsem-calculate-expression function from RSEM. Tag per million reads (TPM) from gene expression results files (.genes.results) were extracted and assembled for subsequent differential gene expression analysis by DESeq2.
Assembly: hg38
Supplementary files format and content: genes.results.gz

source_name: cell line

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomyicin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Total RNA was isolated using RNeasy Plus Mini Kit (QIAGEN, #74136)
After the QC procedures, mRNA is enriched using oligo(dT) beads. Then, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. After a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: ccRCC cell line (786-O) and tRCC cell line (FU-UR-1) were transduced with lentivirus expressing doxycycline shRNA against wild type TFE3 and ASPSCR1-TFE3 and selected with 500 mg/mL of G418. Subsequently, the cells were treated with doxycycline at a concentration of 1mg/mL for 5 days. s-TFE tRCC cells were transduced with control sgRNA or sgRNA targeting ASPSCR1-TFE3 for 5 days

value: cell line

tag: cell line

tag: cell type

value: Cancer cell

value: Control


title: ZW2PLASMAB109A13

tag: sample subgroup (condition)

value: Healthy volunteer

tag: visit

tag: pregnant

tag: trimester

tag: date of collection

tag: gender

tag: sequencing technology


title: sgTIGRE-tumor 1

description: tumor_rnaseq_counts.txt | wt1

tag: tissue

tag: genotype

tag: treatment


title: ZW2PLASMAB109A12

tag: cohort

tag: anatomical location

tag: rna source

tag: rna isolation kit

tag: shortid

tag: batch

tag: age group

value: Not specified

tag: ethnicity


title: ZW2PLASMAB109A10

tag: adapter

tag: sample subgroup (condition)

tag: individual

tag: visit

tag: age

tag: race

value: HiSeq


title: ZW2PLASMAB109A11

tag: pregnant

tag: trimester

tag: date of collection

tag: gender

tag: sequencing technology


title: 786-O_TFE3KD_nodox_rep2

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: 42670-14d

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Mapping was performed using CellRanger (v 6.0.1) with default parameters on the mouse reference transcriptome refdata-gex-mm10-2020-A complemented with 2 sequences (EGFP and hPDGFB).
Counts matrices were imported into R (v.4.0.3) and subsequently analyzed using the Seurat package (v 4.3.0). The count matrix was filtered to retain (i) cells bearing between 200 and 7,500 genes, (ii) cells bearing with less than 10% of mitochondrial gene counts, (iii) genes detected in at least 5 cells.
Doublet prediction was performed by sample using DoubletFinder (v 2.0.3). PC neighborhood sizes (pK) were set to the maximum mean-variance normalized bimodality coefficient (BCmvn), and the pANN threshold (nExp) was set to 2.5%.
Gene counts were normalized using regularized negative binomial regression for data normalization and variance stabilization, SCTransform (v 0.3.5). The percentage of mitochondrial genes was used to regress out in a second non-regularized linear regression.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Glioblastoma

growth_protocol: Gliobastomas were induced in mice using the RCAS model system at 5-weeks of age. Mice were monitored by MRI over the next 6 weeks until tumors developed that were at least 30 mm3 in volume.

extract_protocol:
Mice were euthanised with pentobarbitol, intercardiacally perfused with cold PBS, and brains were extracted. Tumor and/or treated lesion were disected from brains and minced in cold PBS for 5 minutes. For each sample, gentleMACS Octo Dissasociator tubes were prepared with 4.8 ml 2% FBS in PBS with 100 mg/ml collagenase/disapse (Sigma-Aldrich). Minced tissue samples were added to dissasociator tubes, then incubated for 30 minutes at 37ºC with constant low-speed rotation. Samples were then centrifuged at 300 g for 5 minutes at 4ºC and pellets were resuspended in 5 ml HBSS on ice. Cells were passed through a sterile 100 µm filter, centrigued again at 300 g for 5 minutes at 4ºC, and pellets were resuspended in myelin removal bead mixture (1800 µl FACS buffer with 200 µl myelin removal beads II (Miltenyi Biotec)), and incubated for 15 minutes at 4ºC. 18 mls of FACS buffer were added to each sample, centrigured at 300 g for 5 minutes at 4ºC, resuspended in 1 ml FACS buffer, and filtered through LS columns (Miltenyi Biotec). Samples were incubated with red blood cell lysis buffer for 15 minutes at room temperature, then centrifuged at 300 g for 5 minutes at 4ºC, and resuspended in 100 µm FACS buffer for 10X Chromium workflow.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction.

treatment_protocol: 3 mice were sacraficed at this time point prior to the initiation of treatment. 6 mice were treated daily with 200 mg/kg BLZ945 (Novartis), 3 were sacraficed 7-days post treatment, 3 at 14-days.

tag: strain

value: Glioblastoma

tag: tumor stage

value: Grade IV

tag: time

tag: replicate


title: ZW2PLASMAB109A8

tag: cohort

value: Large cohort

tag: anatomical location

tag: rna source

tag: rna isolation kit

tag: shortid

tag: batch

tag: adapter

tag: sample subgroup (condition)

tag: individual

tag: visit

tag: age group

tag: ethnicity


title: ZW2PLASMAB109A9

value: Entire cardiovascular system

tag: pregnant

tag: trimester

tag: date of collection

tag: gender

tag: age

tag: race

tag: sequencing technology


title: 786-O_TFE3KD_nodox_rep1

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: 42669-14d

description: 10x Genomics

tag: strain

tag: tumor stage

tag: time

tag: replicate


title: ZW2PLASMAB109A6

tag: cohort

tag: anatomical location

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

tag: shortid

tag: batch

tag: adapter

tag: sample subgroup (condition)

tag: individual

tag: visit

tag: age group

tag: ethnicity


title: sTFE_TFE3KD_rep3

tag: tissue

tag: cell line

value: s-TFE

tag: cell type

tag: genotype

value: ASPSCR1-TFE3 knockout

tag: treatment


title: ZW2PLASMAB109A5

tag: cohort

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: pregnant

value: no

tag: trimester

tag: date of collection

tag: gender

value: F

tag: age

tag: race

tag: sequencing technology


title: sTFE_TFE3KD_rep2


title: 786-O_TFE3KD_dox_rep1

value: TFE3 knockdown

value: dox


title: 42668-UT

description: 10x Genomics

tag: strain

tag: tumor stage

tag: time

value: UT

tag: replicate


title: 786-O_TFE3KD_dox_rep2

tag: tissue

value: cell line

value: Cancer cell


title: ZW2PLASMAB109A4

tag: anatomical location

tag: rna source

tag: rna isolation kit

tag: shortid

tag: batch

tag: adapter

tag: sample subgroup (condition)

value: Healthy volunteer

tag: individual

tag: visit

value: M

tag: age group

tag: ethnicity

value: Latin


title: 42358-7d

description: 10x Genomics

tag: genotype

value: Glioblastoma

value: Grade IV


title: ZW2PLASMAB109A3

tag: cohort

value: Large cohort

value: Entire cardiovascular system

tag: pregnant

tag: trimester

tag: date of collection

tag: gender

tag: age

tag: race

value: White

tag: sequencing technology

value: HiSeq


title: 41420-UT

description: 10x Genomics

tag: strain

tag: tissue

tag: tumor stage

tag: time

tag: replicate


title: ZW2PLASMAB109A1

tag: anatomical location

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: shortid

tag: batch

tag: adapter

tag: sample subgroup (condition)

tag: individual

tag: visit


title: ZW2PLASMAB109A2

tag: cohort

tag: pregnant

value: no

tag: trimester

tag: date of collection

tag: gender

value: F

tag: age

tag: age group

value: Not specified

tag: ethnicity


title: sTFE_Ctrl_sgRNA_rep3

tag: tissue

tag: cell line

value: s-TFE

tag: cell type

tag: genotype

value: Control

tag: treatment


title: sTFE_TFE3KD_rep1

value: cell line

value: Cancer cell

value: ASPSCR1-TFE3 knockout


title: 41415-UT

description: 10x Genomics

tag: strain

tag: tumor stage

tag: time

value: UT

tag: replicate


title: sTFE_Ctrl_sgRNA_rep2


title: ZW2PLASMAB109A7

tag: cohort

tag: anatomical location

tag: rna source

tag: rna isolation kit

tag: shortid

tag: batch

tag: adapter

tag: sample subgroup (condition)

value: Pregnant individual

tag: individual

tag: visit

value: yes

tag: race

tag: sequencing technology


title: ZW2PLASMAB108A22

value: Large cohort

tag: pregnant

tag: trimester

tag: date of collection

tag: gender

tag: age

tag: age group

tag: ethnicity

value: Latin


title: ZW2PLASMAB108A21

tag: cohort

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

value: Healthy volunteer


title: sTFE_Ctrl_sgRNA_rep1

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: ZW2PLASMAB108A20

value: total cell-free biofluid RNA

tag: rna isolation kit

tag: shortid

tag: batch

tag: adapter

tag: sample subgroup (condition)

tag: individual

tag: visit

tag: race

value: HiSeq


title: 41405-7d

description: 10x Genomics

tag: strain

value: Glioblastoma

tag: tumor stage

value: Grade IV

tag: time

tag: replicate


title: ZW2PLASMAB108A19

tag: cohort

tag: anatomical location

tag: rna source

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: pregnant

value: no

tag: trimester

tag: date of collection

tag: gender

value: F

tag: age

tag: age group

value: Not specified

tag: ethnicity

tag: sequencing technology


title: 41397-7d

description: 10x Genomics

tag: genotype

tag: tissue


title: 48hr infected 3

city: New Delhi

first: Bhupendra

middle: Kumar

last: Verma

state: Delhi

address: Ansari Nagar

department: Biotechnology

country: India

institute: All India Institute of Medical Sciences

data_processing:
The trimmed reads (trimmed adaptor bases using cutadapt v 4.0) were filtered based on the read length of min-max 15-50nt.
tRNA fragments (tRFs/tiRNAs) were identified and quantified using MINTmap database (https://cm.jefferson.edu/MINTbase/).
DEseq2 R package was used to calculate differentially expressed tRNA fragments.
Supplementary files format and content: Tab-delimited text file includes raw counts of each sample
Supplementary files format and content: Tab-delimited text file includes RPKM values of each sample

growth_protocol: Huh7 cells were maintained in DMEM medium supplemented with 10% FBS and 1% antibiotics (complete media)

extract_protocol:
Total RNA was extracted using miRNA easy kit (Qiagen)
Total RNA was pretreated with tRF/tiRNA pretreatmet kit (rStar) followed by cDNA synthesis, and PCR amplification, fragments were size-selected on 8% TBE-PAGE gel.  RNA sequencing on an Illumina platform generated FASTQ files. Reads were quality controlled, identified, and quantified using MINTmap database, focusing on exclusive tRNA fragments to avoid ambiguity. Reads with <10 read count were discarded and differential expression analysis was performed through DEseq2.

treatment_protocol: DENV infection was given in serum starved DMEM medium till adosrption period of 2hrs. Following adsorption, media was replaced with complete media.

tag: cell line

tag: cell type

value: Hepatoma

tag: treatment

value: DV infection

value: 50 hrs DENV infection


title: 48hr infected 2

tag: time

value: 49 hrs DENV infection


title: ZW2PLASMAB108A18

tag: cohort

tag: rna isolation kit

tag: shortid

tag: batch

tag: adapter

tag: sample subgroup (condition)

tag: individual

tag: visit

tag: race

value: White


title: 41390-14d

description: 10x Genomics

tag: strain

tag: tumor stage

tag: replicate


title: 48hr infected 1

value: 48 hrs DENV infection


title: ZW2PLASMAB108A23

value: Large cohort

tag: anatomical location

tag: rna source

tag: pregnant

tag: trimester

tag: date of collection

tag: gender

value: M

tag: age

tag: age group

tag: ethnicity

value: Latin

tag: sequencing technology


title: NIP_input_repeat1

city: Shanghai

first: Liufan

last: Yin

state: Shanghai

address: No. 2005, Songhu Road

department: School of Life Science

country: China

institute: Fudan University

library_source: genomic

data_processing:
Cleaned single-end reads were mapped to the reference genome by Bowtie with parameter: -m 1. Reads were normalized as reads per kilobase per million mapped reads (RPKM) in windows of 10 bp using the bamCoverage tool in deepTools. bam files were merged to perform analysis. MACS14 was used to call peak (parameter: -p 0.01, --nomodel --shiftsize 75). MAnorm was used to obtained differentially enriched regions as OsINO80 binding sites compared with NIP. (parameter: Fold=1.1, pvalue<=0.05).
Genome_build: MSU7
Supplementary_files_format_and_content: bigwig files were generated using DeepTools with binsize of 10.

molecule: genomic DNA

organism: Oryza sativa

source_name: 14-day-old seedlings grown up under long-day condition (14 h light at 30°C and 10 h dark at 28°C)

growth_protocol: The husked rice seeds were surface-sterilized by treatment with 0.1% HgCl2 for 20 min and washed with sterilized water. After sterilization, seeds were then cultured on half-strength MS medium in artificial growth chambers under LD conditions (14 h 30 °C : 10 h 28°C, light : dark) for 14 days.

extract_protocol:
ChIP was performed as previously described (Johnson et al., 2002).
ChIP-seq libraries were prepared using the method previously described (Barski, Cuddapah et al. 2007).

tag: tissue

value: 14-day-old seedling

tag: genotype

value: NIP

tag: chip antibody


title: NIP_YFP_repeat2

value: anti-GFP (A-11122, Invitrogen)


title: ZW2PLASMAB108A24

tag: cohort

value: Entire cardiovascular system

value: total cell-free biofluid RNA

tag: rna isolation kit

tag: shortid

tag: batch

tag: adapter

tag: sample subgroup (condition)

value: Healthy volunteer

tag: individual

tag: visit

tag: race

value: HiSeq


title: 0hr infected 3

tag: cell line

tag: cell type

tag: treatment

tag: time

value: 0 hr (2hrs post DENV adsorption)


title: KO-M1-3

city: xi'an

first: Yun

last: Song

address: NO.169 changle west road

institute: The fourth military medical university

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
Counts were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: GRCm38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Bone marrow

extract_protocol:
Bone marrow were isolated and cultured, M-CSF 20ng/ml stimulated 7d, IFN-γ 20ng/mL+LPS 100 ng/mL stimulated 24h, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow derived macrophage(BMDM)

tag: strain

tag: age

value: post natal day 56


title: ZW2PLASMAB108A15

tag: anatomical location

tag: rna source

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: pregnant

value: no

tag: trimester

tag: date of collection

tag: gender

value: F

tag: age group

tag: ethnicity

tag: sequencing technology


title: NIP_YFP_repeat1

tag: tissue

tag: genotype

tag: chip antibody


title: 0hr infected 2

tag: cell line

tag: cell type

value: Hepatoma

value: DV infection


title: ZW2PLASMAB108A14

tag: cohort

value: Large cohort

tag: rna isolation kit

tag: shortid

tag: batch

tag: adapter

tag: sample subgroup (condition)

tag: individual

tag: visit

tag: race

value: Not specified


title: KO-M1-2

tag: strain

tag: age


title: 41407-14d

description: 10x Genomics

value: Glioblastoma

tag: tumor stage

value: Grade IV

tag: time

tag: replicate


title: KO-M1-1

tag: genotype


title: 0hr infected 1

tag: cell line

tag: treatment


title: OsINO80_input_repeat

tag: tissue

value: 14-day-old seedling

tag: chip antibody


title: ZW2PLASMAB108A13

tag: cohort

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

tag: rna isolation kit

tag: shortid

tag: pregnant

tag: trimester

tag: date of collection

tag: gender

tag: age group

tag: ethnicity

tag: sequencing technology


title: WT-M1-3

tag: cell type

tag: strain

tag: age

tag: genotype

value: wild type


title: OsINO80_input_repeat1

tag: tissue

tag: chip antibody


title: NIP_input_repeat2

value: NIP


title: ZW2PLASMAB108A17

tag: cohort

tag: anatomical location

value: total cell-free biofluid RNA

tag: batch

tag: adapter

tag: sample subgroup (condition)

value: Healthy volunteer

tag: individual

tag: visit

value: M

tag: race

value: White

value: Latin

value: HiSeq


title: ZW2PLASMAB108A16

tag: rna source

tag: rna isolation kit

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: shortid

tag: pregnant

value: no

tag: trimester

tag: date of collection

tag: gender

tag: age group


title: mock infected 3

tag: cell line

tag: cell type

value: Hepatoma

tag: treatment

value: mock infection

tag: time

value: 24hrs post seeding


title: WT-M1-2

value: Bone marrow derived macrophage(BMDM)

tag: strain

tag: age

value: post natal day 56

tag: genotype


title: ZW2PLASMAB108A11

tag: cohort

value: Large cohort

tag: anatomical location

tag: batch

tag: adapter

tag: sample subgroup (condition)

tag: individual

tag: visit

value: F

tag: ethnicity

tag: sequencing technology


title: mock infected 2


title: WT-M1-1

value: wild type


title: ZW2PLASMAB108A12

value: Entire cardiovascular system

tag: rna source

tag: rna isolation kit

tag: shortid

tag: pregnant

tag: trimester

tag: date of collection

tag: gender

tag: age group

tag: race


title: OsINO80_YFP_repeat2

tag: tissue

value: 14-day-old seedling

tag: genotype

tag: chip antibody

value: anti-GFP (A-11122, Invitrogen)


title: OsINO80_YFP_repeat1


title: mock infected 1

tag: cell line

tag: cell type

tag: treatment

tag: time


title: scRNA PE (Day 5 + RA), Batch_2

city: Roma

first: Alessio

last: Colantoni

state: RM

address: Piazzale Aldo Moro, 5

department: Dipartimento di Biologia e Biotecnologie "Charles Darwin"

country: Italy

institute: "Sapienza" University of Rome

data_processing:
Illumina base call files were converted to FASTQ files using the Cell Ranger v2.0 program.
FASTQ files were then aligned to the hg19 human reference genome using Cell Ranger.
Cell Ranger count function was used to to produce count matrices for all the cell types.
Assembly: hg19
Supplementary files format and content: Files produced by the Cell Ranger software. barcodes.tsv contains barcodes sequences for cell-associated barcodes, features.tsv contains gene IDs, gene names and the feature type. They are, respectively, column and row indices for matrix.mtx.gz, which contains the UMI counts for each feature and each barcode.

source_name: Pharyngeal Endoderm (PE)

growth_protocol: H9 hESCs were routinely propagated feeder-free in mTeSR1 on cell culture plates previously coated with Matrigelfollowing the manufacturer instructions. Undifferentiated hESCs were propagated and passed at least 3 times after thawing and plated for the differentiation when at 80% of confluence. Cells were maintained in culture and expanded at high quality with particular care to avoid any spontaneous differentiation, which would confound downstream differentiation. The day before the induction of the differentiation, hESCs were washed twice in PBS, dissociated with Accutase, plated in mTeSR1 + Rock Inhibitor (Y27632, 5uM) to promote cell survival and incubated for 12 hours at 37 °C, 5% CO2 for 12 hours. The day after, 30% confluent hESCs were induced to differentiate into definitive endoderm, by incubation with Medium A (Gibco cat. n. A30621-01) for 24 hours and with Medium B (Gibco cat. n. 30624-01) for the following 24 hours at 37 °C, 5% CO2. The third day DE was patterned into AFG by the addition of CDM2 medium with A-83-01, 1uM and DM3189, 250nM. The composition of CDM2 basal medium was as follows: 50% IMDM (+GlutaMAX, +HEPES, +Sodium Bicarbonate; Gibco, 31980-097) + 50% F12 (+GlutaMAX; Gibco, 31765-092) + 1 mg/mL polyvinyl alcohol (Sigma, P8136-250G) + 1% v/v concentrated lipids (Gibco, 11905-031) + 450 µM monothioglycerol (Sigma, M6145) + 0.7 µg/mL insulin (Roche, 1376497) + 15 µg/mL transferrin (Roche, 652202) and incubated at 37 °C, 5% CO2. From day four to day 5, Retinoic Acid 200 nM was added at the CDM2 medium with A-83-01, 1 uM and DM3189, 250 nM and medium was changed every 24 hours.

extract_protocol:
Cells were washed twice with CDM2 medium to remove dead cells and detached using Accutase. Cells were collected and counted using Countess® II Automated Cell Counter. 500,000 cells for each condition were collected in a PBS-0.04%BSA buffer and processed according to the 10X Genomics Single Cell Protocols Cell Preparation Guide (available at https://assets.ctfassets.net/an68im79xiti/56DlUZEsVOWc8sSG42KQis/35cbcf6dcd4b0c0196263ee93815b0ae/CG000053_CellPrepGuide_RevC.pdf). For each cell type, 20,000 cells were loaded per lane on the 10x Genomics Chromium platform, with the goal of capturing 10,000 cells.
Cells were processed for cDNA synthesis and library preparation using 10X Genomics Chromium Version 2 chemistry (catalog number 120234) as per the manufacturer’s protocol. cDNA libraries were checked for quality on the Agilent 4200 Tape Station platform and their concentration was quantified by KAPA qPCR.

value: Pharyngeal Endoderm (PE)

value: Day 5 + RA


title: SLGN-CM-3

city: Lyon

first: Xavier

last: Grand

address: 46 allée d'Italie

country: France

institute: INSERM U1052, UCBL1, ENS de Lyon

data_processing:
Raw reads were pre-processed using fastp and then mapped using hisat2 to the human reference genome (GRCh38.99).
Mapped reads were filtered using samtools and the number of reads per gene was counted using HTSeq.
Quality check of raw and pre-processed reads was performed using fastqc and compiled using multiqc.
Assembly: GRCh38.99
Supplementary files format and content: Tab-delimited csv file containing normalized counts for Homo sapiens samples,

source_name: Liver

growth_protocol: Primary human hepatocytes (PHH) were isolated from human donors (n=3) using a 2-step collagenase perfusion.

extract_protocol:
PHH were lysed with TRI reagent, followed by RNA extraction using the Direct-zol RNA Miniprep kit (Zymo Research).
Libraries were prepared from the purified RNA using the TruSeq Stranded mRNA Sample Preparation kit (Illumina).

treatment_protocol: For each condition, PHH were incubated 72 h at 37°C with 5% CO2 in Williams E culture medium with SLGN- or Mock-CM.

value: Liver

value: Hepatocytes

value: SLGN-CM

tag: batch


title: scRNA AFE (Day 5), Batch_2

source_name: Anterior Foregut Endoderm (AFE)

value: Anterior Foregut Endoderm (AFE)

value: Day 5


title: ZW2PLASMAB108A9

tag: cohort

tag: anatomical location

tag: rna source

value: total cell-free biofluid RNA

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: adapter

tag: sample subgroup (condition)

value: Healthy volunteer

tag: individual

tag: visit

value: no

tag: age

value: Not specified

tag: ethnicity

value: Latin

tag: sequencing technology

value: HiSeq


title: truB KO, Rend-Seq

city: New Haven

first: Wendy

last: Gilbert

state: CT

address: 333 Cedar Street, P.O. Box 208024

institute: Yale University

data_processing:
Adapter trimming and size filtering (cutadapt -a CTGTAGGCACCATCAAT --overlap 2 -m 13)
Read mapping (bowtie2 -a -p 2 –very-sensitive)
Keep unique alignments (samtools view -bSq 3)
5’ and 3’ end counting (bedtools genomecov -d [-3|-5] -strand [-|+])
Peak calling
wig file generation
Assembly: NC_000913_3
Supplementary files format and content: wig files containing 5’ and 3’ end counts
Library strategy: Rend-Seq

organism: Escherichia coli

growth_protocol: Overnight cultures were backdiluted into 15 mL of pre-warmed EZ Rich MOPS Complete media and grown shaking at 37C to OD~0.10-0.15

extract_protocol:
Cultures were pelleted by centrifugation in 15 mL flasks. The media was decanted and the pellets were flash-frozent in liquid nitrogen. For RNA extraction, the pellets were vortexed with 200 uL of RNA extraction solution (18 mM EDTA, 0.025% SDS, 1% 2-mercaptoethanol, 95% formamide), then incubated at 95C for 7 minutes. Cell debris was removed by centrifugation and the extracted RNA was purified from the supernatant by ethanol precipitation and RNEasy column cleanup.
RNA was fragmented by first incubating RNA in water at 95℃ for 2 minutes, then adding Fragmentation Buffer to 1X and incubating for 25 s at 95℃, then quenching with Stop Buffer. RNA fragments 15-45 long were size-selected from a 15% TBE-Urea gel. RNA was dephosphorylated with T4 PNK in at 37℃ for 1 h, then inactivated at 75℃ for 10 min. RNA was precipitated in isopropanol. A 3’ adapter was ligated to the fragments T4 RNA ligase 2 (truncated), in a 20-μL reaction containing 25% PEG-8000, 1X T4 RNA ligase buffer, and 100 pmol of adapter. Ligated RNAs were purified by excision from a TBE-Urea gel. Reverse transcriptions were carried out with SuperScript III, and the RT products were purified and prepared for sequencing.

tag: strain

tag: genotype


title: Mock-CM-3

tag: tissue

value: Mock-CM


title: ZW2PLASMAB108A8

value: Large cohort

value: Entire cardiovascular system

tag: rna isolation kit

tag: shortid

tag: pregnant

tag: trimester

tag: date of collection

tag: gender

value: M

tag: age group

tag: race


title: scRNA AFE (Day 3), Batch_2

tag: cell type

tag: time

value: Day 3


title: truD KO, Rend-Seq


title: truA KO, Rend-Seq


title: ZW2PLASMAB108A7

tag: cohort

tag: anatomical location

tag: rna source

tag: batch

tag: adapter

tag: sample subgroup (condition)

tag: individual

tag: visit

value: F


title: scRNA DE (Day 2), Batch_2

source_name: Definitive Endoderm (DE)

value: Definitive Endoderm (DE)

value: Day 2


title: Mock-CM-2

tag: tissue

value: Liver

value: Hepatocytes

tag: treatment


title: rluA KO, Rend-Seq

tag: strain

tag: genotype


title: ZW2PLASMAB108A6

value: total cell-free biofluid RNA

tag: rna isolation kit

tag: shortid

tag: pregnant

tag: trimester

tag: date of collection

tag: gender

tag: age

value: White

tag: ethnicity

tag: sequencing technology


title: rluF KO, Rend-Seq


title: Mock-CM-1

tag: cell type

tag: batch


title: WT Rend-Seq


title: ZW2PLASMAB108A10

tag: cohort

tag: anatomical location

tag: rna source

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: adapter

tag: sample subgroup (condition)

value: Healthy volunteer

tag: individual

tag: age group

tag: race


title: KC-SLGN-3

growth_protocol: Human Kupffer cells (KCs) were isolated from human donors (n=3) with a 2-phase iodixanol gradient, followed by positive selection based on CD163 expression.

extract_protocol:
KCs were lysed with TRI reagent, followed by RNA extraction using the Direct-zol RNA Miniprep kit (Zymo Research).
Libraries were prepared from the purified RNA using the TruSeq Stranded mRNA Sample Preparation kit (Illumina).
RNA-seq was performed on a NovaSeq 6000 as 42-nt paired-end reads.

treatment_protocol: For each condition, KCs were incubated 24 h at 37°C with 5% CO2 in RPMI-1640 medium with SLGN (150 nM) or DMSO.

tag: tissue

value: Kupffer cells

tag: treatment

value: SLGN


title: SLGN-CM-1

value: SLGN-CM


title: SSc6, TLR8L [NEBNEXTINDEX8], bulkRNA-seq

first: David

last: Oliver

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

data_processing:
Sequencing quality was measured with fastp 19. Reads were then mapped reads in genes counted against the human genome (hg38) with STAR aligner and Gencode v21 20, 21. Differential gene (DEGs) expression analysis was performed in R 22 using the edgeR package 23. Genes with low expression levels (< 3 cpm) were filtered from all downstream analyses. The Benjamini–Hochberg false discovery rate procedure was used to calculate the FDR.
Supplementary files format and content: Tab separated file containing counts per gene across all samples

source_name: pDCs

growth_protocol: pDCs cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: 40 ml blood were collected from 4 SSc patients and pDCs were purified from PBMCs. 1-3 x 104 purified pDCs were cultured in 96 U-bottom well with tissue culture medium or TLR8L (200 μg/ml) for 6h. Total RNA was isolated using RNeasy Plus Mini kit. NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (NEB E6420S) were used to prepare Illumina-compatible sequencing libraries. Quality of all RNA were evaluated with BioAnalyser 2100 (Agilent).

treatment_protocol: pDCs was induced by 100 ug/ml TLR8L for 6h

tag: condition

value: Systemic sclerosis (SSc)

tag: cell line

value: pDCs

value: TLR8L at 200ug/ml, 6h


title: ZW2PLASMAB108A4

value: Large cohort

value: Entire cardiovascular system

tag: rna isolation kit

tag: shortid

tag: visit

tag: pregnant

value: no

tag: trimester

tag: date of collection

tag: gender

value: M

tag: age

value: HiSeq


title: ZW2PLASMAB108A5

tag: cohort

tag: anatomical location

tag: rna source

tag: batch

tag: adapter

value: F

value: Not specified

tag: ethnicity

value: Latin

tag: sequencing technology


title: rluD_CMC_3

data_processing:
Adapter trimming and size filtering using bbduk.sh (parameters: ktrim=r k=10 hdist=1 mink=1)
Read mapping using bbmap (slow=t perfectmode=true k=11 ambiguous=all)
Filter to keep only uniquely mapped reads using samtools
5’ end  counting using bedtools (bedtools genomecov -d -5, use -strand parameter to specify stand), then convert the output to wig format.
Assembly: NC_000913_3
Supplementary files format and content: Two WIG files per sample, with 5’ end read counts for the + and – strands respectively
Library strategy: Pseudo-Seq

extract_protocol:
Cultures were pelleted by centrifugation in 15 mL flasks. The media was decanted and the pellets were flash-frozent in liquid nitrogen. For RNA extraction, the pellets were vortexed with 200 uL of RNA extraction solution (18 mM EDTA, 0.025% SDS, 1% 2-mercaptoethanol, 95% formamide), then incubated at 95C for 7 minutes. Cell debris was removed by centrifugation and the extracted RNA was purified from the supernatant by ethanol precipitation and RNEasy column cleanup.
Total RNA was purified using the QIAGEN RNEasy Plus Mini Kit, which depletes RNAs shorter than 200 nt and removes genomic DNA. rRNA was depleted using either RiboZero or MicrobExpress kits. RNA was fragmented by adding RNA fragmentation buffer, incubating at 95℃ for 22 seconds, then quenched with stop solution. (RNA Fragmentation Reagents). CMC treatment was performed by incubating 40 μL RNA in 5 mM EDTA at 80℃ for 3 minutes, then adding 100 μL of 0.5 M CMC (iN-cyclohexyl-N′-β-(4-methylmorpholinium)ethylcarbodiimide p-tosylate) in BEU buffer (7 M urea, 4 mM EDTA, 50mM bicine,  then incubating at 40℃ for 45 minutes, shaking at 1000 rpm. Mock treatment was performed by incubating adding 100 μL BEU without CMC before incubating. RNAs were precipitated in isopropanol and resuspended in 30 μL of pH 10.4 buffer, then incubated at 50℃ for 2 hours to reverse CMC adducts from guanidines and uridines. RNA fragments were precipitated, then run on a 10% TBE-Urea gel, and fragments 100–115 nt long were excised and purified. RNA 3′ ends were dephosphorylated with T4 PolyNucleotide Kinase, at 37℃ for 1 hour. Enzyme was inactivated at 75℃ for 10 minutes. 3′ adapters were ligated onto RNA fragments using T4 RNA ligase 2 truncated (20 μL reaction with ~3 pmols input RNA, 25% PEG, 5uM Linker-1 [5′ App/CTGTAGGCACCATCAAT/3ddC]) for 2.5 hours at 25℃. Ligated RNAs were purified by size selection. Reverse transcription (RT) was carried out with SuperScriptIII: adapter-ligated RNAs were annealed to the RT primer (oCSB76, CAAGCAGAAGACGGCATACGAGATATTGATGGTGCCTACAG) in 11 μL of water with 25 pmol of the RT primer, incubated at 65℃ for 5 minutes. Reverse transcription proceeded at 50℃ for 30 minutes, with (components). NaOH was added to a final concentration of 0.1M, and the mixture was incubated at 95℃ for 20 minutes to hydrolyze template RNA This solution was mixed with 20 μL of 2X RNA loading dye, and loaded onto a 10% TBE-Urea gel, and truncated products, corresponding to insert sizes of 25-75 nt, were excised and purified. An adapter (oCSB77, /5Phos/NNNNNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT/3SpC3/) was ligated to the 3′ ends of cDNAs as follows: cDNA was incubated for 2 minutes at 75℃ with 8pmols of the adapter and 1 μL of DMSO in a reaction volume of 10.8 μL. Then the rest of the ligation components were added (final reaction volume of 23 μL, 0.9 mM ATP, 20% PEG-8000, 1 μL T4 RNA ligase, high concentration), and the reaction proceeded overnight at 25℃. Partway through the incubation, the reactions were supplemented with an additional 0.5 μL of ligase. The reactions were precipitated, and ligated cDNAs were purified by size selection. After PCR amplification, libraries were sequenced on an Illumina NextSeq, generated 75-nt single-end libraries.

tag: strain

tag: genotype


title: PBMC-4L

first: Yiwen

last: Wang

address: 2005, Songhu Road, Yangpu District

description:
Macrophage-derived foam cell.
10x Genomics

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10x Genomics was used to demultiplex cellular barcodes.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell. barcodes.tsv, features.tsv, matrix.mtx files.

molecule: polyA RNA

source_name: PBMC

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA.
RNA libraries were prepared with Chromium Single cell 3' reagent v3 kits according to the manufacturer's protocol.

tag: cell type

value: PBMC

tag: treatment

value: M-CSF differentiated, oxLDL incubation for 72h


title: SSc4, TLR8L [NEBNEXTINDEX6], bulkRNA-seq

tag: condition

tag: cell line


title: rluC_mock_3


title: ZW2PLASMAB108A2

value: total cell-free biofluid RNA

tag: rna isolation kit

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: shortid

tag: sample subgroup (condition)

value: Healthy volunteer

tag: individual

tag: visit

tag: pregnant

tag: trimester

tag: age group

tag: race

value: White


title: SLGN-CM-2

tag: tissue

value: Liver

value: Hepatocytes

value: SLGN-CM

tag: batch


title: rluC_CMC_3

tag: strain


title: ZW2PLASMAB108A3

tag: cohort

value: Large cohort

tag: anatomical location

tag: rna source

tag: adapter

tag: date of collection

tag: gender

tag: age

tag: ethnicity

tag: sequencing technology


title: KC-SLGN-2

tag: cell type

value: Kupffer cells

tag: treatment

value: SLGN


title: ZW2PLASMAB107A24

value: Entire cardiovascular system

tag: rna isolation kit

tag: shortid

tag: sample subgroup (condition)

tag: individual

tag: visit

tag: pregnant

value: no

tag: trimester


title: KC-DMSO-2

tag: tissue

value: DMSO

tag: batch


title: SSc3, TLR8L [NEBNEXTINDEX2], bulkRNA-seq

tag: condition

value: Systemic sclerosis (SSc)

tag: cell line

value: pDCs

value: medium control,6h


title: rluA_CMC_2

tag: strain

tag: genotype


title: rluD_CMC_2


title: KC-SLGN-1


title: ZW2PLASMAB107A21

tag: cohort

tag: anatomical location

tag: rna source

tag: adapter

tag: date of collection

tag: gender

value: F

tag: age

tag: age group

tag: race

tag: ethnicity

value: HiSeq


title: rluC_mock_2


title: SSc2, TLR8L [NEBNEXTINDEX10], bulkRNA-seq

tag: treatment


title: SSc3, Medium [NEBNEXTINDEX1], bulkRNA-seq


title: SSc4 [SI-GA-B8], scRNA-seq

data_processing:
The sequenced data were analyzed in Cellranger to align reads, generate feature-barcode matrices. A merged dataset were obtained and batch corrected using FastMNN17 in a base of Seurat pipeline18 (https://satijalab.org/seurat/articles/get_started.html). Doublets were removed manually by excluding cells with more than two cell type markers. The trimmed dataset are visualized by UMAP plot.
Supplementary files format and content: A gzip compressed, tab separated file containing barcode counts for each gene in each cell (3 columns: feature, cell, counts)

extract_protocol: Frozen PBMCs from 4 healthy and 4 SSc patient donors were sorted to obtain enriched pDCs (CD3-CD14-CD123+BDCA4+) and T/pDC cell depleted PBMCs (CD3-CD123-BDCA4-) fractions, the two fractions were then remerged at 1:2 ratio. Cell viability of all donors are above 85%. 8000 cells from each donor were loaded to 10x single cell microfluidic chip to obtain around 5000 recovery cells. Libraries were constructed by following the instructions of 10x company (Chromium Single Cell 3’ Reagent kits v3). The 8 libraries were quantified by NEBNext Library Quant Kit (E7630S) and equally merged and sequenced by Novaseq.

tag: tissue

value: PBMC

tag: cell type

value: BLOOD


title: ZW2PLASMAB107A20

value: total cell-free biofluid RNA

tag: rna isolation kit

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: shortid

tag: batch

tag: sample subgroup (condition)

value: Healthy volunteer

tag: individual

tag: visit

tag: pregnant

tag: trimester

value: M

value: Asian

tag: sequencing technology


title: rluC_CMC_2

tag: strain

tag: genotype


title: KPC1199 WT，H3K9me3, Cut&Tag, repeat2

first: JIng

last: Xue

address: No.1630 dongfang road, pudong new district, Shanghai

institute: Renji Hospital, School of Medicine,Shanghai Jiaotong University

data_processing:
Sequenced reads were trimmed for adaptor sequence and to discard reads shorter than 50bp, then mapped to mm10 whole genome using Bowtie2 v. 2.4.2
Reads Per Kilobase of exon per Megabase of library size were calculated using homer annotatePeaks.pl
Peaks were called using MACS2 version 2.2.7.1 with the parameters -B  -t  --broad -g mm --broad-cutoff 0.05
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
Briefly, tumor cell were generated and collected .CUT&Tag assay was performed following the manual of hyperactive pG-Tn5/pA-Tn5 transposase for CUT&Tag kit (TD904, Vazyme).
DNA library were prepared according to manufacturer’s instructions of Trueprep index kit v2 (TD202, Vazyme)

tag: cell line

value: pancreatic tumor cell

value: WT


title: KC-DMSO-1

value: Liver

value: Kupffer cells


title: ZW2PLASMAB107A19

tag: cohort

value: Large cohort

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

tag: adapter

value: no

tag: date of collection

tag: gender

tag: age

tag: age group

tag: race


title: SSc4, Medium [NEBNEXTINDEX5], bulkRNA-seq

tag: condition

value: Systemic sclerosis (SSc)

value: pDCs

tag: treatment

value: TLR8L at 200ug/ml, 6h


title: SSc2, Medium [NEBNEXTINDEX9], bulkRNA-seq

value: medium control,6h


title: ZW2PLASMAB107A18

tag: rna isolation kit

tag: shortid

tag: batch

tag: sample subgroup (condition)

tag: individual

tag: visit

tag: pregnant

value: F

value: Not specified

tag: ethnicity

value: Latin

value: HiSeq


title: WT_CMC_1

tag: strain

tag: genotype

value: Wild-type


title: osino80_input_repeat2

data_processing:
Cleaned paired reads were mapped to the reference genome by Bowtie2. Samtools was used to remove reads with low mapping quality (Q< 20) and potential PCR duplicates. Reads were normalized as reads per kilobase per million mapped reads (RPKM) in windows of 10 bp using the bamCoverage tool in deepTools. MACS2 was used to call peak (parameter: -p 0.001, --nomodel. Foldchange>=3). DiffBind2 was performed to obtained H2A.Z differentially enriched regions considersing H3 dymamics (parameter: bFullLibrarySize=TRUE, filter=1, Fold=1.5, pvalue<=0.05).
Genome_build: MSU7
Supplementary_files_format_and_content: bigwig files were generated using DeepTools with binsize of 10.

tag: tissue

value: 14-day-old seedling

value: osino80 RNAi knockdown mutant

tag: chip antibody


title: SSc6, Medium [NEBNEXTINDEX7], bulkRNA-seq

tag: cell line


title: ZW2PLASMAB107A17

tag: cohort

tag: anatomical location

tag: rna source

value: total cell-free biofluid RNA

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: adapter

value: Healthy volunteer

tag: trimester

tag: date of collection

tag: gender

tag: age

tag: age group

value: Mixed

tag: sequencing technology


title: SSc2 [SI-GA-B6], scRNA-seq

tag: condition

value: PBMC

tag: cell type

value: BLOOD


title: osino80_H3_repeat2

value: anti-H3 (ab1791, Abcam)


title: truD_mock_1

tag: strain


title: SSc1 [SI-GA-B5], scRNA-seq

value: Systemic sclerosis (SSc)


title: truD_CMC_1

tag: genotype


title: ZW2PLASMAB107A16

value: Large cohort

value: Entire cardiovascular system

tag: rna isolation kit

tag: shortid

tag: batch

tag: sample subgroup (condition)

tag: individual

tag: visit

tag: pregnant

value: no

value: M

tag: race

tag: ethnicity


title: osino80_H3_repeat1

tag: tissue

tag: chip antibody


title: KC-DMSO-3

value: Liver

value: Kupffer cells

tag: treatment

value: DMSO


title: HD 4 [SI-GA-B4], scRNA-seq

value: healthy control


title: ZW2PLASMAB107A15

tag: cohort

tag: anatomical location

tag: rna source

tag: adapter

tag: trimester

tag: date of collection

tag: gender

tag: age

tag: age group

value: Asian

tag: sequencing technology

value: HiSeq


title: truC_mock_1

tag: strain

tag: genotype


title: HD 3 [SI-GA-B3], scRNA-seq

tag: condition

tag: cell type


title: WT_mock_1

value: Wild-type


title: ZW2PLASMAB107A22

value: total cell-free biofluid RNA

tag: rna isolation kit

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: shortid

tag: batch

tag: sample subgroup (condition)

value: Healthy volunteer

tag: individual

tag: visit

tag: pregnant

value: F

tag: race

tag: ethnicity


title: SSc3 [SI-GA-B7], scRNA-seq

tag: tissue

value: PBMC

value: BLOOD


title: osino80_input_repeat1

value: 14-day-old seedling

value: osino80 RNAi knockdown mutant

tag: chip antibody


title: ZW2PLASMAB107A13

tag: cohort

value: Large cohort

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

tag: adapter

value: no

tag: trimester

tag: date of collection

tag: gender

tag: age

tag: age group

value: Not specified

value: Latin


title: truB_mock_1

tag: strain

tag: genotype


title: truC_CMC_1


title: osino80_H2AZ_repeat1

value: anti-H2AZ (Li, Liu et al. 2018)


title: osino80_H2AZ_repeat2


title: NIP_input_repeat2

value: NIP


title: NIP_input_repeat1


title: HD 1 [SI-GA-B1], scRNA-seq

tag: condition

value: healthy control

tag: cell type


title: ZW2PLASMAB107A11

tag: rna isolation kit

tag: shortid

tag: batch

tag: sample subgroup (condition)

tag: individual

tag: visit

tag: pregnant

tag: race

value: White

tag: sequencing technology

value: HiSeq


title: Caki-1_VHL-KO_3

city: Durham

first: Meng

last: Jiao

address: 905 S. LaSalle Street

institute: Duke University

data_processing:
We processed the RNA-seq data using the TrimGalore toolkit, which employs cutadapt to trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads.
Only reads that were 20nt or longer after trimming were kept for further analysis. Reads were mapped to the GRCh38.p13 of the human genome and transcriptome using the STAR RNAseq alignment tool.
Reads were kept for subsequent analysis if they mapped to a single genomic location using the SAMtools.
Gene counts were compiled using the HTSeq tool. Only genes that had at least 10 reads in any given library were used in subsequent analysis.
Normalization and differential expression were carried out using the DESeq27 Bioconductor package with the R statistical programming environment.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Caki-1 cell line

growth_protocol: Caki-1 human clear cell carcinoma cells (ATCC  HTB-46™) were cultured following handling instruction of ATCC. Cells were subcultured every 2-3 days.

extract_protocol:
Total RNA was extracted using Trizol.
RNA libraries were prepared for sequencing using standard Illumina Novaseq protocols

treatment_protocol: We used the CRISPR/Cas9 system to generate VHL knockout Caki-1 cells. To produce sgRNA-encoding lentivirus vectors, we used HEK293T cells co-transfected with lentiviral constructs encoding the target sgRNAs and second-generation packaging plasmids psPAX2 and pMD2.G. To generate clonal VHL knockout cell lines, we infected Caki-1 cells with sgRNA-encoding CRISPR/Cas9 lentivirus and cultured them in a complete cell growth medium, selected with puromycin (1mg/ml for Caki-1) for 7-10 days. Cells were then collected to test the expression of target genes by immunoblot.

tag: cell line

value: VHL-knockout

tag: treatment

value: Lenti-CRISPR infection_sgRNA-VHL


title: HD 2 [SI-GA-B2], scRNA-seq

tag: tissue


title: ZW2PLASMAB107A14

tag: cohort

tag: anatomical location

tag: rna source

value: total cell-free biofluid RNA

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: adapter

value: Pregnant individual

value: yes

tag: trimester

tag: date of collection

tag: gender

value: F

tag: age

tag: age group

tag: ethnicity


title: truA_mock_1

tag: strain

tag: genotype


title: Caki-1_VHL-KO_2


title: ZW2PLASMAB107A12

value: Large cohort

tag: rna isolation kit

tag: shortid

tag: batch

tag: sample subgroup (condition)

value: Healthy volunteer

tag: individual

tag: visit

tag: pregnant

tag: race


title: NIP_H3_repeat2

tag: tissue

value: 14-day-old seedling

tag: chip antibody

value: anti-H3 (ab1791, Abcam)


title: ZW2PLASMAB107A10

tag: cohort

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

tag: adapter

value: no

tag: trimester

tag: date of collection

value: Not specified

value: Latin

tag: sequencing technology


title: Caki-1_VHL-KO_1

tag: cell line

tag: genotype

tag: treatment


title: NIP_H3_repeat1

value: NIP


title: ZW2PLASMAB107A9

tag: rna isolation kit

tag: shortid

tag: batch

tag: sample subgroup (condition)

tag: gender

value: M

tag: age

tag: age group

tag: ethnicity

value: HiSeq


title: truA_CMC_1

tag: strain


title: ZW2PLASMAB107A8

tag: cohort

tag: anatomical location

tag: rna source

tag: individual

tag: visit

tag: pregnant

tag: race


title: truB_CMC_1

tag: genotype


title: rsuA_CMC_1


title: Caki-1_VC_2

tag: cell line

value: WT

tag: treatment

value: Lenti-CRISPR infection_vector_only


title: NIP_H2AZ_repeat2

tag: tissue

tag: chip antibody

value: anti-H2AZ (Li, Liu et al. 2018)


title: rsuA_mock_1


title: Caki-1_VC_1


title: Caki-1_VC_3


title: ZW2PLASMAB107A7

value: total cell-free biofluid RNA

tag: rna isolation kit

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: shortid

tag: batch

tag: adapter

tag: sample subgroup (condition)

tag: trimester

tag: date of collection

tag: gender

tag: sequencing technology


title: rluF_mock_1

tag: strain


title: ZW2PLASMAB107A5

tag: cohort

tag: anatomical location

tag: rna source

tag: individual

tag: visit

tag: pregnant

value: F

tag: age

tag: age group

value: White

tag: ethnicity


title: Untreated_2

type: other

scan_protocol: Image pre-processing, puncta detection, transcript decoding and quality score assignment was perofrmed via on-board analysis software Xenium Analyzer.

data_processing:
Xenium analyzer performed read quantification and generated cell by gene count matrix.
matrix.mtx.gz: Gene-barcode matrix in Market Exchange Format (MEX). Columns correspond to individual cells(barcodes), while rows correspond to genes.
features.tsv.gz: Gene feature info
barcodes.tsv.gz: Barcode sequences that correspond to column indices in matrix.mtx.
transcript.csv.gz: Transcript quality and localization info
cells.csv.gz: Cell summary and transcript count info for each identified cell
gene_panel.json.gz: JSON file

molecule: other

extract_protocol: Mice were euthanised with pentobarbitol, intercardiacally perfused with cold PBS and PLP, and brains were extracted. Brains were embedded in OCT and cryosectioned onto Xenium slides. Slides were processed and labelled with the 10X Mouse Brain gene probe panel plus a 100-plex add on gene panel following the 10X Xenium workflow. Single-cell gene expression was measured for each slide on the Xenium Analyzer.

treatment_protocol: 3 mice were sacraficed at this time point prior to the initiation of treatment. 10 mice were treated daily with 200 mg/kg BLZ945 (Novartis), 3 were sacraficed 7-days post treatment, 4 at 28-days and 3 after rebound.

tag: genotype

tag: grade

value: Grade IV

tag: time point

value: UT

tag: replicate


title: ZW2PLASMAB107A6

data_processing:
Sequencing data were processed using an in-house RNA-sequencing data analysis platform (RSDAP), see Brown et al. (2013) Front. Genet. for details.
Read extractions and demultiplexing was done using extraction lenth of 16 – 45 nt, a minimum 3’ overlap of adapter with 0/1 mismatches of 4/5 nt, respectively, removal of low complexity sequences.
For the read mapping and the generation of the read count matrix table, read annotations used profile annoDB_jul2014c, which included reference sequences for human and virus RNAs based on miRBASE 18 with modifications and HG19.
Supplementary_files_format_and_content: Matrixtable_exRNAdata20210810_cluster_miRNA_read_counts.csv

extract_protocol:
Low speed centrifugation (2500 g x 15 minutes, room temperature) was performed, then transfer of supernatant, 2nd round of centrifugation (same parameters), then transfer of supernatant. A self-developed method and self-developed solutions were used for nucleic-acid extraction, nucleic-acid partitioning, and column purification (RNA isolation), see Max et al. (2018) PNAS for details. For exRNA carrier subfractionation, selected samples were fractionated by differential ultracentrifugation into 10,000 xg pellet, 100,000 xg pellet and corresponding supernatant fractions: 11 ml of platelet-depleted plasma was centrifuged at 10,000 × g in 12 ml tubes (Sorvall, #03699) for 30 min. The supernatant was transferred by aspiration into a fresh 15 ml tube and mixed by inversion. Two aliquots of 500 µl of this supernatant were transferred into 1.5 ml microcentrifuge tubes for later RNA isolation. The 10,000 × g fragile pellet was suspended in 2.0 ml of phosphate-buffered saline (PBS), transferred into a 2.0 ml microcentrifuge tube, and centrifuged at 10,000 × g in a microcentrifuge for 30 min. The PBS supernatant was removed by aspiration, and the residual ≤10 µl volume pellet was resuspended in 450 µl PBS. The residual 10 ml of 10,000 × g supernatant was transferred into a 12 ml tube (Sorvall, #03699) and centrifuged at 100,000 × g for 90 min. The supernatant was transferred as described above, and two 500 µl aliquots of the 100,000 × g supernatant were transferred into 1.5 ml microcentrifuge tubes. The 100,000 × g pellet was washed with 10 ml PBS and centrifuged again at 100,000 × g for 90 min. The PBS supernatant was carefully removed as described above. The pellet was resuspended in 450 µl PBS. All pellet and supernatant fractions were flash-frozen in liquid nitrogen. Automated RNA isolation was conducted as previously described {Max:2018km} with the following modifications: Samples were organized in batches of 24 samples of 450 µl full plasma or plasma subfractions. Vesicle fractions were adjusted with PBS to 450 µl. Calibrator Set1, composed of ten 21-nt 5’-phosphorylated RNA oligos was added at an absolute amount of 2 attomoles per oligonucleotide along with the denaturant to each sample.
Large cohort sample library preparations used 3’ adapters, and PCR amplification methodologie, however, P12 family and plasma subfraction samples used novel 3’ adapters and PCR primers to accommodate changes in Illumina flow cell design after HiSeq was discontinued. RNA equivalent to an input 225 µl plasma was spiked with calibrator Set2 composed of another ten 21-nt 5’-phosphorylated RNA oligos at an absolute amount of 1 attomol per oligonucleotide and entered the first step of the cDNA library preparation. In sample libraries of plasma subfraction RNA from 225 µl supernatant or 5 ml pellet was used to which 0.2 attomoles per oligonucleotide of calibrator Set2 was added. After the 3’ ligation, up to 24 samples were multiplexed, size-selected by denaturing 15%, ligated to 5’ adapter, reverse-transcribed and PCR-amplified. To enable comparisons with earlier results (28), the PAGE size-selection limits were maintained at 19 to 45 for the large (n = 496) and P12 family cohorts (n = 12 samples). After discovering that miRNAs were noticeably underrepresented in the 10K and 100K pellet fractions, the size range for all plasma subfraction libraries (4 plasma subfractions, n = 17 samples, each) was adjusted to 19 to 24 nt in favor of miRNAs. cDNA libraries were sequenced as single-lane high-output single-read 75-bp HiSeq 2000 (Large cohort, n = 496 samples) or as Nextseq-500 100-bp single-read runs (P12 family, n = 12 samples; 4 Plasma subfractions, n = 17 samples each). Sequencing data were processed using an in-house RNA-sequencing data analysis platform (RSDAP) using extraction lenth of 16 – 45 nt, a minimum 3’ overlap of adapter with 0/1 mismatches of 4/5 nt, respectively, removal of low complexity sequences. For read annotations, profile annoDB_jul2014c was used, which included reference sequences for definitions for human and virus RNA sequences based on miRBASE 18 with modifications. Calibrator sequences (labeled by set) are: >Set1_cali_01_rc TCCACGACGTCTCATGTATTTC, >Set1_cali_04_rc GGGTACCATACCGGTTGTCTTA, >Set1_cali_17_rc TCATGAGTCCGTACCTTGATTG, >Set1_cali_18_rc ATCATTTACGATTCGGAGCTGT, >Set1_cali_20_rc GATAGTTCGGGATCGCTGTAAC, >Set1_cali_24_rc TGCTACTCCGATCTTTAGCCTC, >Set1_cali_25_rc AGGGCCCTTTAGGCACTAATAG, >Set1_cali_27_rc GTAGCTGTCAGTACGTTCGTGC, >Set1_cali_43_rc TCTAGTTGCGTGATGGAGAGAA, >Set1_cali_44_rc AGCCGCATTTCGTAGTGATATT, >Set2_cali_07_rc GTCCCACTCCGTAGATCTGTTC, >Set2_cali_11_rc GATGTAACGAGTTGGAATGCAA, >Set2_cali_12_rc TAGCATATCGAGCCTGAGAACA, >Set2_cali_14_rc CATCGGTCGAACTTATGTGAAA, >Set2_cali_15_rc GAAGCACATTCGCACATCATAT, >Set2_cali_16_rc TCTTAACCCGGACCAGAAACTA, >Set2_cali_26_rc AGGTTCCGGATAAGTAAGAGCC, >Set2_cali_28_rc TAACTCCTTAAGCGAATCTCGC, >Set2_cali_31_rc AAAGTAGCATCCGAAATACGGA, >Set2_cali_35_rc TGATACGGATGTTATACGCAGC

value: Large cohort

tag: rna isolation kit

tag: shortid

tag: batch

tag: adapter

tag: sample subgroup (condition)

value: Healthy volunteer

tag: trimester

tag: date of collection

tag: race


title: Untreated_3

tag: strain


title: rluE_mock_1


title: Untreated_1


title: rluE_CMC_1


title: K450LM2-1

city: Beijing

first: Zhihua

last: Liu

address: No.17, Panjiayuannanli, Chaoyang District

department: Cancer Institute & Hospital

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
Raw reads quality report was generated using FastQC.
The adapter sequences were remove from the 3’ end of reads with software Trimmomatic(v0.36). Then the filtered reads were mapped to the human (Homo sapiens) genome (version hg19) and transcriptome (gencode v19) using the software STAR (v2.5.1b).
Gene abundance estimation was conducted with the software RSEM (v1.2.29).
The library normlized factor and CPM values were calculated with R package edgeR (v3.8.5). Genes with CPM value greater than 1 in at least two samples were considered to further analysis.
R package edgeR (v3.8.5) was used to compare expression levels between sample pairs. Fold change > 2 and FDR < 0.05 as thresholds to define DEGs.
Genome_build: hg19

source_name: esophagus

growth_protocol: K30LM3 cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) (HyClone, South Logan, UT, USA), penicillin (100 U/ml), and  streptomycin (100 U/ml) at 37℃ in a humidified 5% CO2 incubator.

extract_protocol:
When cells grew to approximately 80% confluence, they were washed twice with pre-chilled PBS, and then total RNAs were harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: esophagus

tag: cell line

tag: cell type

value: Highly metastatic cells derived from K450


title: Rebound_2

value: REB


title: NIP_H2AZ_repeat1

value: 14-day-old seedling

value: NIP

tag: chip antibody


title: K450LM2-3


title: ZW2PLASMAB107A4

tag: cohort

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

tag: individual

tag: visit

tag: pregnant

value: no

tag: gender

tag: age

tag: age group

tag: ethnicity

tag: sequencing technology

value: HiSeq


title: ZW2PLASMAB107A3

tag: rna isolation kit

tag: shortid

tag: batch

tag: adapter

tag: sample subgroup (condition)

tag: trimester

tag: date of collection

tag: race

value: Mixed


title: rluC_mock_1

tag: strain

tag: genotype


title: ZW2PLASMAB107A2

tag: cohort

tag: anatomical location

tag: rna source

value: total cell-free biofluid RNA

tag: individual

tag: visit

value: M


title: rluD_CMC_1


title: Rebound_3

tag: grade

tag: time point

tag: replicate


title: rluC_CMC_1


title: K450-1

tag: tissue

tag: cell line

tag: cell type

value: Parental cells


title: SIRPa KO3

city: Los Angeles

first: Yoshihiro

last: Sakano

state: CA

address: 1450 Biggy street

department: Molecular Microbiology & Immunology

institute: Unversity of Southern California

data_processing:
Partek Flow, version 10.0
Sequence reads were trimmed by quality score (min Phred score 20 from both end, and trimmed reads shorter than 25bp were discarded).
Trimmed reads were mapped to mm10 with GENECODE M25 annotation as a guidance by STAR 2.7.8.
Aligned reads were further quantified to GENCODE M25 with Partek E/M algorithm.
Genes with less than 10 counts in all samples were removed from the analysis. The remaining genes were subjected to differential expression analysis by DESeq2 with median ratio normalization
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw read counts per gene per sample

source_name: lung

extract_protocol:
Cultured ILC2s were recovered, lysed in RLT buffer (Qiagen) and RNA was extracted using the MicroRNeasy kit (Qiagen)
For each sample, a total of 10pg of RNA was used to generate cDNA (SMARTer Ultra Low Input RNA v3 kit, Clontech) for library preparation

value: lung

value: sorted ILC2s


title: rluB_mock_1


title: Rebound_1

value: Grade IV


title: rluB_CMC_1


title: SIRPa KO1


title: rluF_CMC_1


title: 7day_1


title: K450-2


title: K450LM2-2


title: 7day_3


title: rluA_mock_1


title: 7day_2


title: SIRPa KO2


title: ZW2PLASMAB107A1

value: Large cohort

tag: rna isolation kit

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: shortid

tag: batch

tag: adapter

tag: sample subgroup (condition)

tag: pregnant

tag: gender

value: F

tag: age

tag: age group

value: Not specified

tag: ethnicity

value: Latin

tag: sequencing technology


title: K30LM3-2

value: esophagus

value: Highly metastatic cells derived from K30


title: K450-3


title: K30LM3-3


title: K30LM3-1


title: rluA_CMC_1

tag: strain

tag: genotype


title: 28day_3

tag: grade

tag: time point

tag: replicate


title: K30-2

tag: tissue

tag: cell line

tag: cell type


title: WT3


title: K30-3


title: 28day_4


title: 28day_2


title: HEK293_Input

status: Public on Aug 09 2024

city: Austin

first: Svetlana

last: Panina

state: TX

address: 101 East 21st St.

department: Molecular Biosciences

institute: The University of Texas at Austin

data_processing:
After initial assessment of read quality, pThr4_Untreated ChIP-Seq data was mapped onto human reference genome, hg38, with Bowtie2 v. 2.5.0 aligner for paired-end reads using default parameters.
Coverage tracks in .bigwig format were generated from filtered .bam files (mapq > 20) using log2-normalization over Input.
TSS/TES profiling was done using plotProfile on matrices generated with 50-bp bins using the computeMatrix function from the deeptools v.2.2.3
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Briefly, for HA-tagged RPRD1B, HEK293 cells were double crosslinked with 2mM DSG for 15 min followed by secondary fixation with 1% formaldehyde for 10 min at room temperature. Single crosslinking was used for RPB1 ChIP using 1% formaldehyde for 10 min. Crosslinking was quenched with 0.125 M glycine for 5 min. Cells were successively lysed in lysis buffer LB1 (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1× PI), LB2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1× PI) and LB3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1× PI). Chromatin was sonicated to an average size of ~200–500 bp using UCD-200 Biorupter (30s on and 30 s off for 30 min). A total of 5 μg of HA antibody (cat: C29F4), pThr4 antibody (Active Motif, cat: 61361), or pSer2 antibody (Sigma, SKU: MABE953) was pre-mixed in a 50μl volume of Dynabeads protein A or protein G (Invitrogen) and was added to each sonicated chromatin sample and incubated overnight at 4°C. The chromatin-bound beads were washed two times with low salt buffer (0.1% Na Deoxycholate, 1% Triton X-100, 1mM EDTA, 50mM HEPES pH 7.5, 150mM NaCl), once with high salt wash buffer (0.1% Na Deoxycholate, 1% Triton X-100, 1mM EDTA, 50mM HEPES pH 7.5, 500mM NaCl), once with LiCl wash buffer (250mM LiCl, 0.5% NP-40, 0.5% Na-Deoxycholate, 1mM EDTA, 10mM Tris-Cl pH 8.0) and twice in TE buffer. The chromatin was reverse crosslinked overnight at 65°C with shaking at 750rpm. After DNA extraction using phenol-chloroform, the DNA was resuspended in 10mM Tris-HCl pH 8.0.
The extracted DNA was used to construct the ChIP-seq library using the NEBNext Ultra II DNA Library Prep Kit followed by sequencing with an Illumina HiSeq 3000 or NovaSeq X Plus system.

treatment_protocol: To prepare samples for pThr4 ChIP, we treated HEK293 cell lysate with Ssu72/symplekin complex at 4°C for 30 minutes before binding to the 6D7 antibody. To generate T4A and T4WT CTD samples for pSer2 immunoprecipitation, transient transfection of 12 μg of either plasmid was performed using PEI. Following transfection, 2.5 μg of alpha amanitin was added to cells for 48 hours. Finally, to prepare HA-RPRD1B samples, HEK293 were transfected with HA-RPRD1B using PEI (1:7 plasmid to reagent ratio) to overexpress the protein of interest.

value: Human embryonic kidney

tag: chip antibody


title: WT_CMC_deep

value: Wild-type


title: WT2


title: WT_mock_deep


title: K30-1


title: WT1


title: 28day_1


title: Bone injury replicate 2

city: Clayton

first: Mikaël

last: Martino

state: Victoria

address: 15 Innovation Walk

department: Australian Regenerative Medicine Institute

country: Australia

institute: Monash University

description: Processed_Endo_injured_BMS_and_healthy_Spleen_data.csv

data_processing:
Raw fastq files were analysed using the RNAsik pipeline (Tsyganov, K., et al., 2018, Journal of Open Source Software) using STAR aligner (Dobin, A., et al., 2013, Bioinformatics) with Mus musculus GRCm38.
Reads were quantified using featureCounts (Liao, Y., et al., 2014, Bioinformatics) producing the raw genes count matrix and various quality control metrics.
Raw counts (forward stranded reads) were then analysed with Degust web tool (Powell, D.R., et al., 2019, Zenodo) which performs normalisation using trimmed mean of M values (TMM) (Robinson, M.D. and Oshlack, A., 2010, Genome Biol) and differential gene expression analysis using limma/voom (Law, C.W., et al., 2014, Genome Biol)
Samples were batched corrected to account for variation between two different sequencing facilities across replicates. This was done within Degust by adding a covariate to the linear model for each sequencing batch which reduced the noise and improved the power of the test.
Assembly: GRCm38
Supplementary files format and content: csv, gene counts, rows represent genes and each column represents different information, starting from the chromosome, gene name, biotype, followed by read counts corresponding to the individual samples.

source_name: bone

extract_protocol:
RNA was extracted using the RNeasy Plus Micro Kit (Qiagen, #74034) according to the manufacturer’s instructions
Libraries were prepared with the Tecan/Nugen Ovation Solo Library prep kit, starting with 1 ng of input total RNA

value: bone

value: Regulatory T cells

tag: Sex

value: male

value: 10 weeks

tag: treatment

value: calvarial bone defect

tag: time

value: day 7 post-injury


title: HEK293_pThr4_Untreated_rep2

value: pThr4 (ActiveMotif, #61361)


title: 2-cell embryo - Dam-LMNB1 - CBABL6xCAST hybrid - Cbx7-Lap2b & Lap2b injected

city: Utrecht

first: Jop

last: Kind

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Libraries are demultiplexed based on the sample-specific and readout-specific barcode present in R1, using custom pipelines (available at: https://github.com/KindLab/scDamAndTools).
DamID alignment: DamID reads are aligned using bowtie2 (v. 2.3.3.1) with the following parameters: “--seed 42 --very-sensitive -N 1”.
DamID filtering: Alignments with a MAPQ < 10 are removed.
DamID procesing: Using our own custom pipeline (see KindLab GitHub), aligned reads are matched to known GATC positions in the genome to get the number of observations per (strand-specific) GATC position.
DamID processing: GATC-position counts are deduplicated using UMI information to allow a maximum of 4 unique UMIs per GATC position.
DamID processing: Unique GATC counts are summarized in genomic intervals at the desired resolution.
DamID separating allelic data: For samples derived from hybrid mouse crosses, the DamID reads are aligned in paired-end mode to two reference genomes that have the maternal and paternal SNPs incorporated, respectively. Alignments for each read are then compared and reads are assigned to the parent for which the aligned showed the lowest edit distance and highest alignment score. In case of ties, reads were considered to be ambiguous. During read processing, UMIs are flattened across alleles. In other words, if the same UMI is found at the same GATC position between maternal, paternal and ambiguous alleles, only one count is maintained at the parental allele (in case of finding the UMI at for one parent and ambiguous) or the ambiguous allele (in case of finding the UMI at both parental alleles).
CELseq alignment: CELseq R2 reads are aligned using GRCm38 (v. 89) transcript models and hisat2 (v. 2.1.0) with the following paramters: : “--mp 2,0 --sp 4,0”.
CELseq filtering: Alignments with a MAPQ < 10 are removed.
CELseq processing: Using our own custom pipeline (see KindLab GitHub), we assign alignments to genes using a method similar to htseq-count with mode "intersection_strict".
CELseq processing: Transcript counts are deduplicated using UMI information, allowing an unlimited number of UMI-unique counts per gene.
CELseq separating allelic data: For samples derived from hybrid mouse crosses, the CELseq R2 reads are aligned to two reference genomes that have the maternal and paternal SNPs incorporated, respectively. Alignments for each read are then compared and reads are assigned to the parent for which the aligned showed the lowest edit distance and highest alignment score. In case of ties, reads were considered to be ambiguous. During read processing, UMIs are flattened across alleles. In other words, if the same UMI is found for the same gene between maternal, paternal and ambiguous alleles, only one count is maintained at the parental allele (in case of finding the UMI at for one parent and ambiguous) or the ambiguous allele (in case of finding the UMI at both parental alleles).
Assembly: mm10
Supplementary files format and content: CELseq count table: count table containing UMI-unique transcript counts per gene for all single-cell samples
Supplementary files format and content: DamID binary contact table: binary table indicating for each sample which of the 100-kb bins had signal above a threshold to indicate that it was in contact with the Dam-fusion protein
Supplementary files format and content: DamID count table: count table containing UMI-unique GATC counts per 10-kb/100-kb interval for all single-cell samples
Supplementary files format and content: DamID Contact Frequency track: The frequency of single-cell contacts for a paticular bin over all cells of that condition
Supplementary files format and content: DamID combined single-cell track: The combined data of all single cells of that condition, normalized for depth and control (includes both scDamID and scDam&T-seq samples passing DamID thresholds)
Supplementary files format and content: sample annotations: table containing detailed sample information for all single-cell samples
Supplementary files format and content: sample barcodes: sample-specific and readout-specific barcodes that can be used to demultiplex the raw data. CELseq barcodes follow a 3-NNNNNNNN or 3-NNNN-3-NNNN format, where "N" positions indicate the barcode-specific sequence,  the "3" indicates positions of a 3nt UMI sequence. DamID barcodes follow a 3-NNNN-3-NNNNGA or 3-NNNNNNGA format. All DamID barcodes end in "GA", complementing the genomic TC of the cleaved GATC motifs.
Library strategy: scDam&T-seq

source_name: 2-cell embryo

growth_protocol: For the preimplantation embryos: WT mouse embryos were obtained from either B6CBAF1/JxB6CBAF1/J non-hybrid crosses or hybrid crosses between B6CBAF1/J females and CAST/EiJ males. For Eed maternal KO experiments embryos were obtained by mating Eedfl/fl C57BL/6J (control) with PWK/PhJ males or Eedfl/fl;Gdf9-Cre C57BL/6J (maternal KO) females with JF1/MsJ males. Mouse embryos were obtained from super-ovulated females by administering females with mare serum gonadotropin (PMSG) and human chorionic gonadotropin (HCG) via intraperitoneal injections. HCG was injected 2 days after PMSG and that same day females were mated with a male. The next day zygotes were collected, injected with the relevant Dam construct and cultured ex-vivo in M16 (Sigma, MR-016-D) or KSOM medium (Sigma, MR-106-D) until reaching the stage of collection. Ex-vivo culturing was carried out in an incubator at 37C with 5% CO2. For the mESC: F1 hybrid 129/Sv:Cast/Eij mouse embryonic stem cells (mESCs) were cultured on irradiated primary mouse embryonic fibroblasts (MEFs), in ES cell culture media CM+/+; G-MEM (Gibco) supplemented with 10% FBS (Hyclone, Sigma lot no), 1% Pen/Strep, 1x GlutaMAX (Gibco), 1x non-essential amino acids (Gibco), 1x sodium pyruvate (Gibco), 0.1mM β-mercaptoethanol (Sigma) and 10^3U/ml ESGROmLIF (EMD Millipore ESG1107). Cells were split every 3 days and medium was changed every other day.

extract_protocol:
For the preimplantation embryos: At the time of collection, the zona pellucida was remove using Tyrode's acid (Sigma, T1788-100ML), embryos were washed in M2 medium (Sigma, MR-015-D) and dissociated into single cells by incubating in TryplE (Thermo Fisher, 12605010) for approximately 5 minutes and pipetting up an down with a mouth pipet. Embryos were dissociated one by one and the resulting single cells were placed in M2 medium. They were then transferred to a 384-well plate (one single cell per well) containing 5uL of mineral oil and 100nL of CELseq primer (scDam&T) or 100nL of DamID buffer (0.15% NP40 and 2mM dNTPs) using a mouth pipet. For the mESC: Cells were trypsinized and harvested in medium with 20 μg/mL Hoechst 34580 (Sigma 63493) per 1x10^6 cells for 45 minutes at 37°C. The cells were stained for live/dead gating with 1ug/ml propidium iodide and singlets were index sorted based on their Hoechst profile. One cell per well was sorted into 384-well plates (Biorad, HSP3801) using the BD FACS Jazz cell sorter. Wells contained 5 μL filtered mineral oil (Sigma) and 50nL of 0.5uM unique CELseq primer.
The scDam&T protocol and library preparation was performed as previously described in detail (PMID: 32350457).

treatment_protocol: For the mESC: Expression of the Dam-LMNB1 construct was suppressed by addition of 0.5mM indole-3-acetic acid (IAA; Sigma, I5148) during standard culturing. When plated for experiments the cells were passaged 2 times in feeder free conditions on plates coated with 0.1% gelatin in 60% BRL conditioned medium (40% CM+/+ medium and 60% of CM+/+ medium conditioned on Buffalo Rat Liver cells) at 1mM IAA for the final 24 hours before harvesting of the cells. For timed induction of the constructs the IAA is washed out at 6 hourse before harvesting single cells for sorting.

value: 2-cell embryo

value: CBABL6F1 x CAST/EiJ

value: Cbx7-Lap2b or Lap2b mRNA injection

tag: dam-fusion protein


title: 2-cell embryo - Dam-LMNB1 - CBABL6F1 homozygous - WT & Cbx7-Lap2b & Lap2b injected (KIN9024_index13)

value: untreated, Cbx7-Lap2b or Lap2b mRNA injection


title: HEK293_pThr4_Untreated_rep1


title: EpiLC, primed pluripotency, QKO, rep2

city: San Francisco

first: Harold

last: Marin

address: 555 Mission Bay Boulevard South

department: Smith Cardiovascular Institute

institute: University of California San Francisco

description:
QKO_epi_2
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt

data_processing:
Raw sequencing reads were trimmed of the first T overhang using cutadapt (version 2.5) as suggested by Illumina.
Trimmed reads were mapped to the GENCODE primary assembly M30 release of the mouse genome (GRCm39) using STAR (version 2.7.10a): --runMode alignReads --readFilesCommand zcat --clip3pAdapterSeq CTGTCTCTTATA CTGTCTCTTATA --clip3pAdapterMMp 0.1 0.1 --outFilterMultimapNmax 1 --outSAMtype BAM SortedByCoordinate --twopassMode Basic. Bam files were indexed with SAMtools (version 1.10).
The subread featureCounts package (version 1.6.4) and GENCODE M30 primary annotation file was used to generate a read counts table for all conditions.
The subread featureCounts package was used for obtaining read counts on uniquely mapped transposable elements using a custom annotation file made by the Hammell lab.
For multimapping of RNA-seq reads, as recommended by the TEtranscripts authors, STAR parameters were changed from –outFilterMultimapNmax 1 to the following: –outFilterMultimapNmax 100 --winAnchorMultimapNmax 100. A read counts table was generated using the TEcount command from the TEtranscripts package (version 2.2.3) with the following parameters: --sortByPos --format BAM --mode multi. The GENCODE M30 primary annotation file was used for gene annotations and a custom annotation file from the Hammell lab for transposable elements were used to generate a read counts table.
Assembly: mm39
Supplementary files format and content: Tab-delimited text file includes raw counts from uniquely-mapped reads in genes for each sample.
Supplementary files format and content: Tab-delimited text file includes raw counts from uniquely-mapped reads in transposable elements for each sample.
Supplementary files format and content: Tab-delimited text file includes raw counts from multi-mapped reads in genes and transposable elements for each sample.

source_name: EpiLC

growth_protocol: Cells were cultured at 5% CO2 and 37°C. mESCs were grown in serum- and feeder-free 2i + LIF medium: N2B27 basal medium supplemented with the following compounds at a final concentration of 3 μM CHIR-99021 (Selleckchem S1263), 1 μM PD0325901 (Selleckchem S1036), 103 U/mL LIF (MilliporeSigma™ ESG1107), 55 μM β-mercaptoethanol (Gibco™ 21985023), and 1X PenStrep (GenClone 25-512). N2B27 medium was made by mixing equal parts of DMEM:F12 (GenClone 25-503) and Neurobasal medium (Gibco™ 21103049) then adding 1X N-2 (Gibco™ 17502001), 1X B-27 (Gibco™ 17504001) and 2 mM Glutamax (Gibco™ 35050061). mESCs were seeded at 2.11 x 104 cells/cm2 on dishes pre-coated with either Geltrex (Gibco™ A1413202) or Cultrex (Bio-Techne 3445-005-01). mESCs were replenished with fresh 2i + LIF medium after 24 hours then collected at 48 hours for RNAseq. EpiLCs were differentiated by seeding 2.11 x 104 cells/cm2 mESCs into either Geltrex or Cultrex coated dishes containing N2B27 media supplemented with 20 ng/mL FGF (Peprotech 100-18B) and 12 ng/mL Activin A (Peprotech 120-14E). EpiLCs were replenished with fresh differentiation medium after 24 hours then collected at 48 hours for RNAseq.

extract_protocol:
Total RNA was isolated from cells using the RNeasy Plus Mini Kit (QIAGEN 74136). RNA was treated with DNAse using the TURBO DNA-free kit (Invitrogen™ AM1907) prior to prepping libraries. RNA quality was assessed by electrophoresis on a 1% agarose gel and detecting 28S and 18S rRNA bands with ethidium bromide staining (0.6µg/mL).
Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit (Illumina 20040525) was used following the manufacturer’s protocol to prep libraries with a starting RNA input of 500ng. Libraries were amplified using 11 cycles on the thermocycler. Each library was uniquely indexed with IDT for Illumina–DNA/RNA UD Indexes (Illumina 20026121), then pooled together in equimolar amounts. Library concentration was measured using the Qubit dsDNA HS assay kit (Invitrogen Q32851) and Qubit 4 fluorometer. Library size was assayed using the Agilent Bioanalyzer 2100 with the High sensitivity DNA kit.

value: EpiLC


title: mESC, naive pluripotency, QKO, rep4

description:
QKO_naive_4
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt

source_name: mESC

value: mESC


title: EpiLC, primed pluripotency, QKO, rep4

description:
QKO_epi_4
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: 2-cell embryo - Dam-H3K9me3(CBX1) - C57BL6xJF1 hybrid - WT & EEDmKO (KIN8790_index02)

value: C57BL/6J x JF1/Ms:WT & EED mKO

value: CBX1 protein domain (3x)


title: Bone injury replicate 3

tag: age


title: EpiLC, primed pluripotency, QKO, rep1

description:
QKO_epi_1
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: 2-cell embryo - Dam-LMNB1 - CBABL6F1 homozygous - Cbx7-Lap2b injected (KIN8928_index10)

value: Cbx7-Lap2b mRNA injection


title: 2-cell embryo - Dam-only & Dam-LMNB1 - CBABL6F1 homozygous - Cbx7-Lap2b & Lap2b injected (KIN9199)

value: LMNB1; untethered Dam


title: 2-cell embryo - Dam-LMNB1 - CBABL6F1 homozygous - Cbx7-Lap2b & Cbx7-Emd & Cbx7-Lbr injected (KIN8928_index27)

value: Cbx7-Lap2b, Cbx7-Emd, or Cbx7-Lbr mRNA injection


title: Viability experiment - CBX7-Lap2b vs Lap2b - homozygous embryos

data_processing:
Libraries are demultiplexed based on the sample-specific and readout-specific barcode present in R1, using custom pipelines (available at: https://github.com/KindLab/scDamAndTools).
CELseq alignment: CELseq R2 reads are aligned using GRCm38 (v. 89) transcript models and hisat2 (v. 2.1.0) with the following paramters: : “--mp 2,0 --sp 4,0”.
CELseq filtering: Alignments with a MAPQ < 10 are removed.
CELseq processing: Using our own custom pipeline (see KindLab GitHub), we assign alignments to genes using a method similar to htseq-count with mode "intersection_strict".
CELseq processing: Transcript counts are deduplicated using UMI information, allowing an unlimited number of UMI-unique counts per gene.
Assembly: mm10
Supplementary files format and content: CELseq count table: count table containing UMI-unique transcript counts per gene for all single-cell samples
Library strategy: CELseq

source_name: blastocyst

growth_protocol: WT mouse embryos were obtained from B6CBAF1/JxB6CBAF1/J non-hybrid crosses. Mouse embryos were obtained from super-ovulated females by administering females with mare serum gonadotropin (PMSG) and human chorionic gonadotropin (HCG) via intraperitoneal injections. HCG was injected 2 days after PMSG and that same day females were mated with a male. The next day zygotes were collected, injected with the relevant construct and cultured ex-vivo in M16 (Sigma, MR-016-D) or KSOM medium (Sigma, MR-106-D) until reaching the stage of collection. Ex-vivo culturing was carried out in an incubator at 37C with 5% CO2.

extract_protocol:
Embryos were collected nd transferred to a 384-well plate (one embryo per well) containing 5uL of mineral oil and 100nL of CELseq primer (scDam&T) using a mouth pipet.
The CELseq part of the scDam&T protocol and library preparation was performed as previously described in detail (PMID: 32350457).

value: blastocyst

value: Cbx7(CD)-Lap2b or Lap2b mRNA injection


title: EpiLC, primed pluripotency, TKO, rep4

description:
TKO_epi_4
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: EpiLC, primed pluripotency, QKO, rep3

description:
QKO_epi_3
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: 2-cell embryo - Dam-H3K9me3(CBX1) - C57BL6xJF1 hybrid - WT & EEDmKO (KIN8790_index03)


title: EpiLC, primed pluripotency, TKO, rep2

description:
TKO_epi_2
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: EpiLC, primed pluripotency, TKO, rep1

description:
TKO_epi_1
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: mESC, naive pluripotency, TKO, rep4

description:
TKO_naive_4
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: mESC, naive pluripotency, TKO, rep1

description:
TKO_naive_1
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: mESC, naive pluripotency, TKO, rep3

description:
TKO_naive_3
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: mESC, naive pluripotency, QKO, rep3

description:
QKO_naive_3
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: mESC, naive pluripotency, QKO, rep2

description:
QKO_naive_2
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: mESC, naive pluripotency, TKO, rep2

description:
TKO_naive_2
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: mESC, naive pluripotency, LBRKO, rep2

description:
LBRKO_naive_2
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: mESC, naive pluripotency, LBRKO, rep1

description:
LBRKO_naive_1
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: EpiLC, primed pluripotency, LBRKO, rep2

description:
LBRKO_epi_2
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: mESC, naive pluripotency, LBRKO, rep4

description:
LBRKO_naive_4
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: EpiLC, primed pluripotency, LBRKO, rep1

description:
LBRKO_epi_1
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: mESC, naive pluripotency, LBRKO, rep3

description:
LBRKO_naive_3
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: mESC, naive pluripotency, QKO, rep1

description:
QKO_naive_1
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: EpiLC, primed pluripotency, LBRKO, rep4

description:
LBRKO_epi_4
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: EpiLC, primed pluripotency, WT, rep7

description:
WT_epi_7
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt

value: wildtype


title: EpiLC, primed pluripotency, LBRKO, rep3

description:
LBRKO_epi_3
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: EpiLC, primed pluripotency, WT, rep8

description:
WT_epi_8
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: EpiLC, primed pluripotency, WT, rep6

description:
WT_epi_6
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: EpiLC, primed pluripotency, WT, rep4

description:
WT_epi_4
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: EpiLC, primed pluripotency, WT, rep5

description:
WT_epi_5
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: mESC, naive pluripotency, WT, rep7

description:
WT_naive_7
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: mESC, naive pluripotency, WT, rep8

description:
WT_naive_8
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: mESC, naive pluripotency, WT, rep6

description:
WT_naive_6
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: EpiLC, primed pluripotency, TKO, rep3

description:
TKO_epi_3
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: mESC, naive pluripotency, WT, rep4

description:
WT_naive_4
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: EpiLC, primed pluripotency, WT, rep1

description:
WT_epi_1
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: EpiLC, primed pluripotency, WT, rep2

description:
WT_epi_2
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: mESC, naive pluripotency, WT, rep5

description:
WT_naive_5
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: mESC, naive pluripotency, WT, rep2

description:
WT_naive_2
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt