title: hibHSC49

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i701_i507

data_processing:
Raw reads were aligned to the Mus musculus genome build (mm10) using GSNAP with parameters -B 5 -t 24 -n 1 -Q -N 1 (version 2015-09-29 for batch1 and batch2; version 2018-03-25 for batch3 and batch4).
Read counts were computed using HTSeq with parameter -s no (version 0.6.0  for batch1 and batch2; version 0.9.1 for batch3 and batch4).
Cells from which low-quality libraries with insufficient sequencing depths were generated were excluded by setting the threshold of number of mapped reads to >2*105, with mapped reads comprising nuclear genes, mitochondrial genes and ERCCs. A minimum threshold of 20% for reads mapping to known genes was set, in order to exclude empty wells and dead cells. In addition, the threshold for reads mapping to mitochondrial genes was >0.2, to ensure a minimum of 20% of reads to map to non-mitochondrial genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files containing raw counts for each sample (HT-Seq counts)

extract_protocol:
Haematopoietic Stem Cells (HSCs) were extracted from primary mouse bone marrow, derived from C57BL/6 mice(12-16 weks). For this purpose, lineage depleted bone marrow cells were FACS sorted. HSCs were defined as EPCR-high, CD45+, Sca-1-high, CD48-low/neg, CD150+ (ESLAM). HSCs cultured in hibernated conditions (hibHSCs), hibHSCs stimulted with SCF in culture (hibHSC_SCF), freshly isoalted HSCs (fresh_HSC) and fresh_HSCs stimulated with SCF (fresh_HSC_SCF) were sequenced. Cultured HSCs were FACS sorted to be deposited in 96 well plates (one cell per well), containing lysis buffer and subsequently processed using the previously described Smart-Seq2 protocol (Picelli et al., 2014).
Smart-Seq2 protocol performed as previously described (Picelli et al., 2014). Libraries were prepared using Illumina Nextera libraries, single end reads and 50bp read lengths. The pooled libraries were sequenced on an Illumina HiSeq 4000.

value: wild type


title: P18_5F

status: Public on Apr 06 2021

type: SRA

city: Los Angeles

first: Colette

middle: L

last: Picard

state: California

address: 610 Charles E Young Dr East, Room 4045

department: Molecular, Cell and Developmental Biology

country: USA

institute: University of California - Los Angeles

library_source: transcriptomic

data_processing:
Reads were trimmed and quality-filtered using Trim Galore v.0.4.1 and aligned using STAR v.2.7.1a. Reads from Col- Cvi crosses were mapped to a Col-Cvi 'metagenome' (TAIR10 sequence appended to a Cvi 'pseudogenome' generated by substituting the Cvi allele at 576,697 Col-Cvi SNPs). Reads from Col-Ler crosses were mapped to a Col-Ler 'metagenome'. Sequences from ThermoFisher ERCC RNA spike-ins were also appended to the metagenome. Reads that mapped uniquely to the ERCC sequences were extracted and omitted from the rest of the analysis. Procedures and scripts for mapping with the metagenome are available in Picard and Gehring (Methods Mol Biol 2020). Reads overlapping a SNP were identified  using a custom script (Picard and Gehring, 2020) and assigned to parent- of-origin. PCR duplicates were removed using MarkDuplicates from the Picard Toolkit (Broad Institute). Total and allele-specific counts over genes were then obtained using htseq-count v.0.9.1 and the Araport11 gene annotations (excluding new Araport11 annotations antisense to existing TAIR10 genes). Single-nuclei samples with a total of at least 1,500 genes detected (≥ 1 overlapping read) and 1,000 genes well-detected (≥ 5 overlapping reads) prior to removing PCR duplicates were considered high quality and kept for subsequent analyses. Raw total expression counts were normalized to CPM (counts per million) while allelic count data for Col,Cvi reciprocal crosses at 4 DAP were normalized using the same procedure used in DESingle (Miao et al. 2018, Bioinformatics).
Genome_build: Araport 11 (excluding new Araport11 annotations antisense to existing TAIR10 genes)
Supplementary_files_format_and_content: Processed files for each library are tab-delimited with four fields: locus_name, all_counts, [parent1]_counts, [parent2]_counts, corresponding to raw counts of total reads, parent1-derived reads, and parent2-derived reads respectively. Additionally, three matrices are provided: CPM_total_expression.txt contains CPM-normalized total expression data for all 1,437 libraries that passed QC checks (and were not controls). norm_maternal_counts.txt and norm_paternal_counts.txt contain maternal and paternal counts for the 4 DAP Col, Cvi dataset (excluding libraries with few allelic counts; N=748 total), respectively; this subset of the data was used for imprinting analyses. Maternal and paternal counts were normalized according to the procedure used in DESingle (Miao et al. 2018, Bioinformatics), separately for the Col x Cvi and the Cvi x Col dataset.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: seed nuclei

growth_protocol: All parent plants were grown in a growth chamber under 16h light at 50% relative humidity (16h at 22°C and 120μm light, 8h at 20°C and 0μm light).

extract_protocol:
Seeds were manually removed from siliques (~ 2 siliques per sample) into 50 uL Partec nuclei extraction buffer (Partec CyStain UV Precise P system), ground to release nuclei, DAPI stained by adding 400 uL Partec staining buffer, and filtered through a 30 um mesh. For the last four batches, nuclei were then washed 2x in 1:8 Partec extraction buffer:Partec staining buffer. Other batches did not include this was step. Single nuclei from the 3C or 6C peaks were sorted into a 96 well plate using fluorescence-activated nuclei sorting (FANS); each plate also included at least one negative control (no nucleus sorted into the well).
Libraries were prepared according the Smart-seq v2 protocol with a few minor variations and carried out at reduced volume. Nuclei were sorted into 1 μL lysis buffer (0.19% vol/vol Triton-X 100, 2U SUPERase RNase inhibitor, ERCC RNA spike-ins (ThermoFisher). 1 μL poly-A hybridization mix (final conc. 2.5mM/ea. dNTPs + 2.5 μM oligo-dT primer) was added to each well and the plate was incubated at 72°C 3 min before putting back on ice. 2.85 μL RT reaction mix (final concentration 1μM TSO, 1x Maxima RT buffer (Life Technologies), 1M betaine, 5 mM DTT, 6 mM MgCl2, 0.5 U SUPERase RNase-inhibitor, 2 U Maxima RT) was added and RT reaction was performed either in thermocycler with program 42°C 90', 10 x [50°C 2', 42°C 2'], 70°C 15' or in thermomixer. 7.5 μL pre-amp PCR mix (final conc. 1x KAPA HiFi HotStart Readymix (Kapa Biosystems), 0.1 μM IS PCR primer) was added and plate was incubated in thermocycler: 3' 98°C, [cycle #] x [98°C 20'', 67°C 15'', 72°C 6'], 72°C 5'. Number of pre- amplification cycles used varied between 18-21. cDNA was cleaned up using a 0.8x Ampure XP protocol (Beckman Coulter). Final libraries were built from successful cDNA preps using the Nextera XT kit (Illumina) with reduced volume (1/4 or 1/5 standard volumes). Up to 384 libraries were multiplexed together and sequenced on an Illumina HiSeq 2000 using a 40bp single-end protocol, or on an Illumina NextSeq using a 40x40bp paired-end protocol.

treatment_protocol: Plants were emasculated in the afternoon or evening, and pollinated in the morning two days later. Seeds were harvested either 2, 3, 4 or 5 days after pollination, at approximately the same time in the morning.

tag: female parent

value: Cvi

tag: male parent

value: Col

tag: days after pollination

tag: number of nuclei

tag: fans peak

tag: plate/batch

tag: extra wash steps?

value: no

tag: control?


title: hibHSC45

city: Cambridge

first: Daniel

last: Bode

email: db704@cam.ac.uk, 1danielbode@gmail.com

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus

department: Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i711_i506

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow

growth_protocol: For hibernation cultures, Haematopoietic Stem Cells (HSCs), isolated from primary mouse bone marrow, were cultured in the presence of 20 ng/mL IL-11 but absence of Stem Cell Factor (SCF) and (TPO) to retain retain HSCs.

treatment_protocol: Samples including SCF labels were stimulated with Stem Cell Factor (SCF).

tag: strain

tag: tissue

value: Bone marrow

tag: age

value: 12-16 weeks

tag: genotype

tag: batch


title: P18_5D


title: hibHSC52

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i704_i507


title: P18_5C


title: hibHSC51

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i703_i507


title: P18_5B


title: IM9, shBLRF2 sh4, replicate 1

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
RNA-Seq data analyzing was done with rsem (ver. 1.2.3) and hg19 genome with Ensemble transcriptome information
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene

organism: Homo sapiens

source_name: Multiple myeloma IM9 cell line

extract_protocol:
Total RNA was isolated from 1.5 x 106 cells using the Direct-zol microprep kit following the manufacturer’s protocol (Zymo Research)
Sequencing library preparation was then completed using QuantSeq library preparation kit

tag: cell line

tag: blrf2 condition

tag: replicate


title: IM9, shBLRF2 sh3, replicate 2


title: hibHSC53

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i705_i507


title: IM9, shBLRF2 sh3, replicate 1


title: P18_5A


title: P18_4G


title: hibHSC54

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i706_i507


title: P18_4F


title: P18_4E


title: hibHSC55

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i707_i507


title: P18_5H


title: IM9, control condition, replicate 1

value: control


title: IM9, control condition, replicate 2


title: P18_4D


title: P18_4C


title: ARH77, shBLRF2 sh4, replicate 2

source_name: Multiple myeloma ARH77 cell line


title: P18_4A

value: yes - only water used for Nextera library prep


title: hibHSC56

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i710_i507


title: hibHSC57

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i711_i507


title: P18_4B


title: hibHSC58

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i712_i507


title: P18_3E


title: P18_3G


title: hibHSC59

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i714_i507


title: P18_4H


title: ARH77, shBLRF2 sh4, replicate 1


title: P18_3F


title: P18_3C


title: ARH77, shBLRF2 sh3, replicate 1


title: P18_3B


title: hibHSC60

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i715_i507


title: ARH77, control condition, replicate 2


title: hibHSC61

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i701_i508


title: P18_3A


title: P18_2H


title: P18_3D


title: ARH77, control condition, replicate 1


title: hibHSC62

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i702_i508


title: P18_2G


title: EBV negative 8226 cell line

description: EBV negative 8226 cell line

data_processing:
RNA-Seq data analyzing was done with rsem (ver. 1.2.3) and hg19 genome with UCSC transcriptome information
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene

source_name: Multiple myeloma 8226 cell line

extract_protocol:
Total RNA was isolated from 1.5 x 106 cells using the Direct-zol microprep kit following the manufacturer’s protocol (Zymo Research)
Sequencing library preparation was then completed using ScriptSeqRNA library preparation kit

tag: ebv status

value: negative


title: P18_2E

tag: female parent


title: P18_2F

tag: male parent


title: hibHSC63

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i703_i508


title: P18_3H

tag: days after pollination


title: hibHSC64

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i704_i508


title: P18_2D

tag: number of nuclei


title: ARH77, shBLRF2 sh3, replicate 2


title: P18_2C

tag: fans peak


title: EBV positive ARH77 cell line

description: EBV positive ARH77 cell line

value: positive


title: P18_2A

tag: plate/batch


title: P18_2B

tag: extra wash steps?


title: P18_1H

tag: control?

value: yes - two nuclei sorted in same well


title: hibHSC65

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i705_i508

tag: strain


title: UTUC02_T_miRNA

city: Kaohsiung

first: Hsiang

middle: Ying

last: Lee

address: Jhonghua 3rd Rd

country: Taiwan

institute: Kaohsiung Municipal Ta-Tung Hospital

description:
Sample 8
UTUC_miRNA.xlsx

data_processing:
For RNA sequencing:
The sequence was directly determined using sequencing-by-synthesis technology via the TruSeq SBS Kit.
Raw sequences were obtained from the Illumina Pipeline software bcl2fastq v2.0
Trimmomatics was implemented to trim or remove the reads according to the quality score
Qualified reads were analyzed using TopHat/Cufflinks for gene expression estimation.
The gene expression level was calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
CummeRbund was employed to perform statistical analyses of gene expression profiles.
For small RNA sequencing:
Sequencing data was processed with the Illumina software
Initially, the sequences generated went through a filtering process to obtain qualified reads. Trimmomatic was implemented to trim or remove the reads according to the quality score.
Qualified reads were analyzed using miRDeep2 to clip the 3' adapter sequence and discarding reads shorter than 17 nucleotides
Only reads that mapped perfectly to the human genome five or less times were used for miRNA detection
Genome_build: Human genome from Genome Reference Consortium Human GRCh38.p10
Supplementary_files_format_and_content: excel files include gene ID, gene type, gene name, EntrezGene ID, locus and FPKM values for samples 1 to 4; miRNA, raw read counts and normalized values for samples 5 to 8.

source_name: upper tract urothelium

extract_protocol:
After performing radical surgery, specimens were collected within 30 minutes and immediately preserved in a −195.79ºC liquid nitrogen container. Total RNAs of UTUC tumor part and non-tumor part tissues were extracted using Trizol® Reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: upper tract urothelium tumor part

tag: tumor grading

value: high

tag: tumor stage


title: hibHSC67

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i707_i508

tag: age

tag: genotype

tag: batch


title: hibHSC66

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i706_i508


title: P18_1E


title: P18_1C


title: P18_1B


title: UTUC01_N_miRNA

description:
Sample 5
UTUC_miRNA.xlsx

value: upper tract urothelium non-tumor part


title: EBV positive IM9 cell line

description: EBV positive IM9 cell line

tag: cell line


title: hibHSC5

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i705_i502


title: P18_1A

value: yes - no nucleus sorted


title: hibHSC6

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i706_i502


title: P17_12H


title: P18_1D


title: hibHSC4

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i704_i502


title: UTUC02_T_mRNA

description:
Sample 4
UTUC_mRNA.xlsx


title: P17_12G


title: UTUC02_N_mRNA

description:
Sample 3
UTUC_mRNA.xlsx


title: P17_12F


title: UTUC01_T_mRNA

description:
Sample 2
UTUC_mRNA.xlsx


title: P18_1F


title: P17_12E


title: hibHSC3

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i703_i502


title: UTUC02_N_miRNA

description:
Sample 7
UTUC_miRNA.xlsx


title: P18_1G


title: hibHSC2

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i702_i502


title: P17_12B


title: UTUC01_N_mRNA

description:
Sample 1
UTUC_mRNA.xlsx


title: P17_12A


title: UTUC01_T_miRNA

description:
Sample 6
UTUC_miRNA.xlsx


title: P17_12C


title: hibHSC9

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i711_i502


title: hibHSC8

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i710_i502


title: Tau aggregate associated RNA Rep2

city: Boulder

first: Evan

last: Lester

state: CO

address: JSC Biotech bldg

department: Biochemistry

institute: University of Colorado

description: Random hexamer primed RNA

data_processing:
Timmomatic 0.36 to trim Illumina TruSeq3 adapters and low quality reads (options: 2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
Ribosomal reads were filtered out by mapping to a ribosome reference genome (UCSC hg38 humRibosomal.fa) and keeping the unmapped reads.
Reads were then mapped to GRCh38 using STAR v2.6.0c in two pass alignment mode with --outFilterMultimapNmax 20)
FPKM was calculated using the longest transcript lengths taken from from ensembl biomart GRCh38.p13
Genome_build: Genome Reference Consortium Human Build 38

source_name: HEK293 cells expressing P301S-tau RD -YFP and P301S-tau RD-CFP

growth_protocol: HEK293 biosensor cells were grown to 70-80% confluency in 245 mm square tissue culture treated dishes (Corning 07-200-599) in 50mL of DMEM (one plate per biologic replicate).

extract_protocol:
large tau aggregates were enriched for by differential centrifugation and then further purified using fluroescence automated particle sorting. Tau aggregates were denatured and RNA was isolated from all samples using proteinase K, Guanadinium HCL, and Trizol LS reagent.
KAPA RNA HyperPrep Kit with RiboErase

treatment_protocol: 200 ug of WT or P301S tau clarified mouse brain homogenate was transfected per dish using lipofectamine 2000 and incubated at 37C for 24 hours. Tau aggregation was monitored using the Evos M500 Imaging System with a GFP filter. Cells were harvested by scraping, centrifuged at 1500g, snap frozen in liquid nitrogen, and stored at -80C.

value: Transfected with clarified brain homogenate from P301S mice

value: HEK293 Tau-RD-P301S-CFP/YFP

tag: sample

value: Tau aggregates


title: P17_11G

tag: female parent

value: Cvi


title: P17_11F

value: Col

tag: male parent


title: P17_11E

tag: days after pollination

value: no


title: P17_11H

tag: number of nuclei


title: Tau aggregate associated RNA Rep1

description: Random hexamer primed RNA


title: Total RNA Rep2

description: Random hexamer primed RNA

value: total RNA


title: P17_11C

tag: fans peak


title: P17_12D

tag: plate/batch


title: P17_11B

tag: extra wash steps?


title: hibHSC14

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i702_i503

value: Bone marrow

value: 12-16 weeks

value: wild type


title: hibHSC7

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i707_i502


title: P17_11D

tag: control?


title: Total RNA Rep1

description: Random hexamer primed RNA


title: P17_11A


title: P17_10H


title: P17_10F


title: PTB_patient_5

city: Seoul

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequences using Cutadapt v1.2.1, and then aligned to the human reference genome (GRCh38) using TopHat v2.1.1 with parameters -r 100 --library-type fr-firststrand --mate-std-dev 100 -p 24 --bowtie-n.
After the alignment, the number of reads mapped to gene features were counted using HTSeq v0.6.1.
The number of reads counted by HTSeq were normalized using the TMM normalization method provided in the edgeR package. The normalized counts were converted to log2-read-counts after adding one to the normalized counts. The log2-read-counts for the samples were then normalized using the quantile normalization method (MATLAB R2019a).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files including normalized read counts for each sample

source_name: Whole blood

extract_protocol:
Total RNA was isolated from the indicated whole blood samples using TRIzol® RNA Isolation Reagents (Life technologies, Carlsbad, CA), and purification was performed according to the manufacturer’s instructions.
cDNA libraries were generated using TruSeq stranded total RNA sample preparation kit (illumina, San Diego, CA) according to the manufacturer’s protocol.

tag: condition

value: Preterm birth

value: Whole blood


title: PTB_patient_4

tag: tissue


title: P17_10D


title: P17_10G


title: P17_10E


title: hibHSC12

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i715_i502

tag: strain


title: hibHSC11

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i714_i502


title: P17_10C


title: P17_10B


title: PTB_patient_2


title: P17_10A

value: yes - only water used for Nextera library prep


title: hibHSC10

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i712_i502


title: PTB_patient_3


title: hibHSC18

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i706_i503


title: PTB_patient_1


title: P17_9H


title: P17_9F


title: hibHSC17

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i705_i503


title: FTB_control_5

value: Full-term birth


title: P17_9G


title: hibHSC13

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i701_i503


title: hibHSC16

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i704_i503


title: P17_9E


title: FTB_control_4


title: P17_9C


title: hibHSC15

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i703_i503


title: P17_9B


title: P17_9A


title: P17_8G


title: FTB_control_3


title: hibHSC21

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i711_i503


title: FTB_control_2


title: P17_8H


title: P17_8D


title: hibHSC22

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i712_i503


title: P17_8B


title: FTB_control_1


title: P17_8E


title: hibHSC20

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i710_i503


title: P17_8C


title: P17_9D


title: hibHSC19

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i707_i503


title: P17_7H


title: hibHSC23

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i714_i503


title: P17_7E


title: P17_7F


title: hibHSC24

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i715_i503


title: hibHSC26

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i702_i505


title: P17_7C


title: P17_7D


title: P17_7A


title: P17_8F


title: hibHSC29

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i705_i505


title: hibHSC30

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i706_i505


title: P17_6G


title: P17_6E


title: P17_6H


title: P17_8A


title: P17_6F


title: P17_6D


title: P17_7G


title: hibHSC25

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i701_i505


title: P17_6A


title: hibHSC27

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i703_i505


title: hibHSC28

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i704_i505


title: hibHSC33

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i711_i505


title: P17_5H


title: P17_6B


title: P17_5F


title: P17_7B


title: P17_5E


title: hibHSC34

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i712_i505


title: hibHSC31

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i707_i505


title: P17_5D


title: P17_5G


title: P17_5B


title: hibHSC32

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i710_i505


title: P17_4H


title: fresh_HSC190

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i729_i522


title: P17_4G


title: P17_5A


title: fresh_HSC189

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i728_i522


title: P17_4F


title: P17_4D


title: P17_6C


title: P17_4E


title: fresh_HSC188

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i727_i522


title: P17_4C


title: P17_4B


title: P17_4A


title: TEX cells_WY332

city: Ann Arbor

first: Tomasz

last: Cierpicki

state: MI

address: 1150 W Medical Center Dr

department: Pathology

institute: University Of Michigan

library_source: genomic

data_processing:
Peaks were called using either the MACSa or SICERb algorithms. MACS default cutoff is pvalue 1e-7 for narrow peaks and 1e-1 for broad peaks, and SICER default cutoff is FDR 1e-10 with gap parameter of 600 bp. Peak filtering was performed by removing false ChIP-Seq peaks as defined within the ENCODE blacklist.
Spike-in protocols and normalization were used. For comparative analysis, the number of test tags are adjusted by a factor that would result in the same number of usable spike-in Drosophila tags for each sample within a normalization group. The normalization is implemented through random deletion of test sample tags (down-sampling). The normalization factor shows the adjustment relative to standard normalized tag numbers (where the usable tags for each sample within a normalization group would be adjusted to the same number).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

source_name: TEX cells treated with WY332

growth_protocol: 3x10E6 TEX cells were plated in 75mm culture flask

extract_protocol: 25-30x10E6 TEX cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Cells were centrifuged, washed and pellets were stored in -80 till their processing at Active Motif facility, CA.

treatment_protocol: TEX cells were treated with 0.25% DMSO or 25uM WY332 with 0.25% DMSO for 6 days

value: TEX leukemia cells

tag: agent

tag: dose

tag: time

value: 6 days

tag: chip antibody

value: anti-H2Aub (K119) (Cell Signaling Technology #8240, lot number 6)


title: fresh_HSC185

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i723_i522

tag: age

tag: genotype

tag: batch


title: P17_5C

tag: female parent

tag: male parent


title: P17_3H

tag: days after pollination

tag: number of nuclei


title: fresh_HSC186

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i724_i522


title: P17_3F

tag: fans peak

tag: plate/batch


title: P17_3G

tag: extra wash steps?

tag: control?


title: fresh_HSC184

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i722_i522

tag: tissue


title: P17_3D


title: TEX cells_DMSO

source_name: TEX cells treated with DMSO

tag: cell line

value: DMSO


title: P17_3E


title: P17_3B


title: P17_3C


title: fresh_HSC183

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i721_i522

tag: strain


title: P17_3A


title: P17_2E


title: fresh_HSC182

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i720_i522


title: P17_2H


title: P17_2G


title: fresh_HSC180

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i718_i522


title: fresh_HSC181

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i719_i522


title: P17_2F


title: fresh_HSC187

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i726_i522


title: P17_2D


title: P17_2C


title: fresh_HSC179

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i716_i522


title: P17_2B


title: fresh_HSC178

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i729_i521


title: P17_2A


title: P17_1H

value: yes - two nuclei sorted in same well


title: P17_1G


title: P17_1F


title: P17_1C


title: P17_1D


title: P17_1E


title: fresh_HSC175

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i726_i521


title: fresh_HSC174

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i724_i521


title: P17_1B


title: P17_1A

value: yes - no nucleus sorted


title: fresh_HSC176

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i727_i521


title: P16_12H

value: Cvi


title: P16_12G

value: Col


title: fresh_HSC173

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i723_i521


title: P16_12F

value: no


title: fresh_HSC172

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i722_i521


title: P16_12E


title: P16_12D


title: P16_12B


title: P16_11G


title: P16_11H


title: P16_11F


title: fresh_HSC168

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i718_i521


title: P16_11E


title: fresh_HSC170

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i720_i521


title: fresh_HSC177

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i728_i521


title: P16_11D


title: P16_11B


title: P16_11C


title: P16_11A


title: fresh_HSC167

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i716_i521


title: fresh_HSC166

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i729_i520


title: fresh_HSC165

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i728_i520


title: P16_10H


title: fresh_HSC164

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i727_i520


title: P16_10E


title: fresh_HSC171

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i721_i521


title: P16_10D


title: P16_12C


title: fresh_HSC163

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i726_i520


title: P16_10G


title: P16_10B


title: P16_12A


title: P16_10A


title: P16_9H


title: fresh_HSC169

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i719_i521


title: P16_9G


title: fresh_HSC162

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i724_i520


title: fresh_HSC161

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i723_i520


title: P16_9F


title: P16_9D


title: fresh_HSC160

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i722_i520


title: P16_9C


title: fresh_HSC159

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i721_i520


title: P16_9B


title: P16_10F


title: P16_9A


title: P16_8H


title: P16_10C


title: fresh_HSC157

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i719_i520


title: P16_8G


title: P16_8E


title: P16_8F


title: P16_8D


title: P16_8B


title: fresh_HSC155

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i716_i520


title: fresh_HSC154

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i729_i518


title: P16_7H


title: P16_7E


title: P16_7D


title: P16_7C


title: fresh_HSC151

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i726_i518


title: fresh_HSC152

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i727_i518


title: P16_7B


title: fresh_HSC150

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i724_i518


title: P16_7A


title: fresh_HSC158

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i720_i520


title: P16_6H


title: fresh_HSC149

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i723_i518


title: P16_6G


title: P16_6F


title: fresh_HSC148

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i722_i518


title: P16_6E


title: P16_9E


title: fresh_HSC156

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i718_i520


title: P16_8C


title: P16_6D


title: P16_6B


title: fresh_HSC153

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i728_i518


title: P16_6C


title: fresh_HSC147

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i721_i518


title: P16_8A


title: P16_6A


title: P16_7G


title: fresh_HSC146

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i720_i518


title: P16_5G


title: fresh_HSC145

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i719_i518


title: P16_5E


title: fresh_HSC144

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i718_i518


title: P16_5C


title: P16_5H


title: P16_5D


title: P16_5F


title: fresh_HSC143

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i716_i518


title: P16_4G


title: P16_4H


title: P16_5A


title: P16_4E


title: fresh_HSC140

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i727_i517


title: P16_4D


title: P16_4A


title: fresh_HSC139

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i726_i517


title: P16_3H


title: P16_4C


title: P16_4B


title: P16_3G


title: P16_7F


title: fresh_HSC137

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i723_i517


title: P16_3F


title: fresh_HSC138

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i724_i517


title: fresh_HSC136

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i722_i517


title: P16_3E


title: P16_3D


title: P16_3C


title: fresh_HSC135

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i721_i517


title: P16_3B


title: fresh_HSC134

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i720_i517


title: P16_3A


title: P16_4F


title: fresh_HSC141

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i728_i517


title: fresh_HSC133

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i719_i517


title: P16_2H


title: P16_2E


title: P16_2G


title: P16_2D


title: P16_2B


title: P16_2C


title: P16_2A


title: fresh_HSC131

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i716_i517


title: fresh_HSC129

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i728_i516


title: P16_1H


title: fresh_HSC132

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i718_i517


title: P16_1F


title: fresh_HSC130

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i729_i516


title: P16_1E


title: P16_1G


title: P16_1C


title: P16_1D


title: fresh_HSC128

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i727_i516


title: P16_5B


title: P16_1A


title: fresh_HSC126

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i724_i516


title: fresh_HSC127

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i726_i516


title: fresh_HSC125

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i723_i516


title: P15_12H


title: P15_12F


title: P16_2F


title: fresh_HSC124

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i722_i516


title: P15_12C


title: P15_12D


title: fresh_HSC123

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i721_i516


title: P15_12A


title: fresh_HSC122

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i720_i516


title: P15_11H


title: P15_12E


title: P15_11D


title: fresh_HSC120

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i718_i516


title: P15_11F


title: fresh_HSC121

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i719_i516


title: fresh_HSC142

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i729_i517


title: P15_11C


title: P16_1B


title: fresh_HSC119

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i716_i516


title: fresh_HSC118

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i729_i515


title: P15_11B


title: P15_11G


title: P15_11A


title: P15_10H


title: P15_10F


title: P15_10G


title: fresh_HSC117

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i728_i515


title: P15_10E


title: P15_10D


title: fresh_HSC115

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i726_i515


title: fresh_HSC116

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i727_i515


title: P15_10C


title: P15_10B


title: P15_12G


title: P15_12B


title: P15_11E


title: fresh_HSC114

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i724_i515


title: P15_9H


title: fresh_HSC113

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i723_i515


title: P15_9G


title: fresh_HSC112

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i722_i515


title: P15_9D


title: P15_9E


title: P15_9F


title: P15_9C


title: P15_9B


title: P15_9A


title: fresh_HSC110

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i720_i515


title: fresh_HSC111

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i721_i515


title: P15_8H


title: fresh_HSC109

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i719_i515


title: P15_8G


title: P15_8F


title: fresh_HSC108

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i718_i515


title: P15_8D


title: fresh_HSC107

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i716_i515


title: P15_10A


title: P15_8A


title: P15_7H


title: P15_8B


title: P15_8C


title: fresh_HSC106

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i729_i513


title: P15_7F


title: P15_7E


title: fresh_HSC105

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i728_i513


title: P15_7G


title: fresh_HSC104

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i727_i513


title: P15_7D


title: P15_7A


title: P15_7C


title: fresh_HSC102

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i724_i513


title: P15_7B


title: P15_6H


title: fresh_HSC103

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i726_i513


title: P15_8E


title: P15_6F


title: fresh_HSC100

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i722_i513


title: fresh_HSC101

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i723_i513


title: P15_6E


title: P15_6C


title: P15_6A


title: fresh_HSC99

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i721_i513


title: fresh_HSC98

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i720_i513


title: P15_6G


title: P15_5H


title: P15_5G


title: fresh_HSC97

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i719_i513


title: P15_5D


title: P15_5C


title: P15_5B


title: fresh_HSC95

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i729_i522


title: fresh_HSC94

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i728_i522


title: P15_4H


title: P15_4G


title: P15_4F


title: fresh_HSC93

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i727_i522


title: P15_6D


title: P15_4D


title: P15_4E


title: P15_4C


title: P15_4A


title: fresh_HSC90

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i723_i522


title: fresh_HSC91

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i724_i522


title: fresh_HSC92

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i726_i522


title: P15_4B


title: P15_6B


title: fresh_HSC89

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i722_i522


title: P15_3F


title: P15_3E


title: P15_3G


title: fresh_HSC96

description:
HTSeq_counts_SLX12566_batch2.txt.gz
SLX.12566.i718_i513


title: P15_5F


title: fresh_HSC88

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i721_i522


title: P15_3D


title: P15_5E


title: P15_5A


title: P15_3C


title: fresh_HSC87

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i720_i522


title: P15_2H


title: P15_2G


title: P15_3A


title: fresh_HSC86

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i719_i522


title: P15_2F


title: P15_3B


title: fresh_HSC85

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i718_i522


title: P15_2E


title: P15_3H


title: P15_2C


title: fresh_HSC83

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i729_i521


title: P15_2D


title: fresh_HSC82

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i728_i521


title: P15_2A


title: fresh_HSC84

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i716_i522


title: P15_2B


title: fresh_HSC81

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i727_i521


title: P15_1F


title: P15_1D


title: P15_1H


title: P15_1G


title: P15_1C


title: P15_1E


title: P15_1B


title: fresh_HSC79

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i724_i521


title: P15_1A


title: fresh_HSC78

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i723_i521


title: P14_12H


title: P14_12G


title: fresh_HSC77

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i722_i521


title: P14_12E


title: P14_12D


title: P14_12C


title: fresh_HSC76

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i721_i521


title: P14_12F


title: fresh_HSC75

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i720_i521


title: P14_12B


title: P14_12A


title: fresh_HSC73

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i718_i521


title: P14_11G


title: fresh_HSC80

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i726_i521


title: P14_11E


title: fresh_HSC74

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i719_i521


title: P14_11F


title: fresh_HSC72

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i716_i521


title: P14_11C


title: P14_11H


title: P14_11A


title: P14_10H


title: fresh_HSC70

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i728_i520


title: P14_10F


title: P14_10G


title: fresh_HSC71

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i729_i520


title: P14_10E


title: P14_11B


title: fresh_HSC69

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i727_i520


title: fresh_HSC67

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i724_i520


title: fresh_HSC68

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i726_i520


title: P14_10C


title: P14_10B


title: P14_10A


title: P14_9H


title: P14_10D


title: fresh_HSC65

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i722_i520


title: fresh_HSC66

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i723_i520


title: P14_9E


title: P14_9F


title: fresh_HSC64

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i721_i520


title: P14_9C


title: P14_9D


title: fresh_HSC63

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i720_i520


title: P14_11D


title: P14_9A


title: P14_8H


title: fresh_HSC62

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i719_i520


title: fresh_HSC61

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i718_i520


title: P14_8F


title: P14_8G


title: P14_8E


title: fresh_HSC60

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i716_i520


title: P14_8C


title: P14_8D


title: P14_8A


title: fresh_HSC58

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i728_i518


title: P14_7G


title: fresh_HSC57

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i727_i518


title: P14_7H


title: P14_7F


title: P14_9G


title: P14_8B


title: P14_7E


title: P14_7B


title: fresh_HSC55

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i724_i518


title: fresh_HSC56

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i726_i518


title: fresh_HSC54

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i723_i518


title: P14_9B


title: P14_7A


title: P14_6G


title: fresh_HSC53

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i722_i518


title: P14_6E


title: fresh_HSC52

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i721_i518


title: P14_6D


title: fresh_HSC51

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i720_i518


title: P14_6F


title: P14_6C


title: fresh_HSC59

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i729_i518


title: P14_6A


title: fresh_HSC50

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i719_i518


title: P14_5G


title: P14_5H


title: P14_5F


title: P14_5D


title: P14_7C


title: P14_7D


title: P14_5C


title: P14_6H


title: P14_5B


title: fresh_HSC46

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i728_i517


title: P14_5A


title: P14_4G


title: P14_4H


title: fresh_HSC45

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i727_i517


title: P14_4F


title: fresh_HSC44

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i726_i517


title: P14_6B


title: P14_4C


title: P14_4D


title: fresh_HSC43

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i724_i517


title: P14_4A


title: fresh_HSC42

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i723_i517


title: P14_5E


title: P14_3H


title: fresh_HSC48

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i716_i518


title: P14_3G


title: fresh_HSC49

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i718_i518


title: fresh_HSC41

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i722_i517


title: P14_3F


title: fresh_HSC47

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i729_i517


title: P14_3E


title: fresh_HSC40

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i721_i517


title: P14_3D


title: fresh_HSC39

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i720_i517


title: P14_3C


title: P14_3B


title: P14_3A


title: fresh_HSC38

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i719_i517


title: P14_2H


title: P14_2G


title: fresh_HSC37

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i718_i517


title: P14_4E


title: P14_2E


title: P14_4B


title: P14_2F


title: fresh_HSC36

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i716_i517


title: P14_2D


title: fresh_HSC35

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i729_i516


title: fresh_HSC34

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i728_i516


title: P14_2A


title: P14_2B


title: P14_2C


title: fresh_HSC33

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i727_i516


title: P14_1G


title: P14_1H


title: P14_1E


title: P14_1F


title: P14_1D


title: P14_1C


title: P14_1B


title: fresh_HSC32

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i726_i516


title: fresh_HSC31

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i724_i516


title: P14_1A


title: P13_12H


title: P13_12E


title: fresh_HSC28

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i721_i516


title: P13_12F


title: P13_12G


title: fresh_HSC29

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i722_i516


title: P13_12C


title: P13_12D


title: fresh_HSC27

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i720_i516


title: P13_12A


title: fresh_HSC26

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i719_i516


title: P13_11H


title: P13_12B


title: P13_11G


title: fresh_HSC25

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i718_i516


title: P13_11F


title: P13_11E


title: fresh_HSC24

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i716_i516


title: P13_11D


title: P13_11C


title: fresh_HSC23

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i729_i515


title: fresh_HSC30

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i723_i516


title: P13_11B


title: fresh_HSC22

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i728_i515


title: P13_10H


title: P13_10G


title: P13_11A


title: fresh_HSC21

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i727_i515


title: P13_10F


title: P13_10E


title: fresh_HSC20

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i726_i515


title: P13_10C


title: fresh_HSC19

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i724_i515


title: P13_10D


title: P13_10B


title: fresh_HSC18

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i723_i515


title: P13_9H


title: fresh_HSC17

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i722_i515


title: P13_9E


title: P13_9D


title: fresh_HSC16

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i721_i515


title: fresh_HSC15

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i720_i515


title: P13_9C


title: P13_9B


title: P13_9A


title: P13_8H


title: fresh_HSC14

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i719_i515


title: P13_8G


title: fresh_HSC13

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i718_i515


title: P13_8F


title: P13_8D


title: P13_8C


title: fresh_HSC12

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i716_i515


title: P13_8A


title: P13_10A


title: fresh_HSC10

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i728_i513


title: P13_7H


title: P13_9G


title: P13_7E


title: fresh_HSC9

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i727_i513


title: P13_7D


title: P13_7F


title: P13_7C


title: P13_7G


title: fresh_HSC6

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i723_i513


title: P13_6G


title: P13_7B


title: P13_9F


title: fresh_HSC8

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i726_i513


title: fresh_HSC5

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i722_i513


title: P13_6F


title: fresh_HSC11

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i729_i513


title: P13_8E


title: P13_6H


title: fresh_HSC4

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i721_i513


title: P13_6E


title: P13_6D


title: P13_6C


title: fresh_HSC3

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i720_i513


title: P13_6B


title: P13_7A


title: P13_6A


title: fresh_HSC2

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i719_i513


title: P13_5H


title: P13_8B


title: P13_5G


title: P13_5F


title: P13_5E


title: fresh_HSC7

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i724_i513


title: fresh_HSC1

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i718_i513


title: P13_5C


title: P13_5D


title: P13_5A


title: fresh_HSC_SCF95

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i714_i511


title: fresh_HSC_SCF94

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i712_i511


title: P13_5B


title: P13_4G


title: P13_4H


title: P13_4C


title: P13_4E


title: P13_4F


title: P13_4B


title: P13_4D


title: fresh_HSC_SCF93

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i711_i511


title: P13_4A


title: fresh_HSC_SCF92

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i710_i511


title: P13_3G


title: P13_3F


title: fresh_HSC_SCF90

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i706_i511


title: P13_3E


title: fresh_HSC_SCF89

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i705_i511


title: fresh_HSC_SCF88

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i704_i511


title: fresh_HSC_SCF91

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i707_i511


title: P13_3H


title: P13_3D


title: P13_3C


title: fresh_HSC_SCF96

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i715_i511


title: P13_3B


title: P13_3A


title: fresh_HSC_SCF87

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i703_i511


title: fresh_HSC_SCF86

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i702_i511


title: P13_2H


title: P13_2F


title: P13_2E


title: fresh_HSC_SCF84

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i715_i510


title: P13_2B


title: P13_2C


title: P13_2D


title: fresh_HSC_SCF83

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i714_i510


title: P13_2A


title: fresh_HSC_SCF81

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i711_i510


title: P13_1E


title: P13_1G


title: P13_1D


title: fresh_HSC_SCF79

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i707_i510


title: P13_1C


title: P13_1A


title: P12_12H


title: fresh_HSC_SCF77

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i705_i510


title: P12_12F


title: fresh_HSC_SCF78

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i706_i510


title: P13_1B


title: P12_12G


title: fresh_HSC_SCF76

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i704_i510


title: P12_12D


title: fresh_HSC_SCF85

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i701_i511


title: P13_2G


title: fresh_HSC_SCF75

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i703_i510


title: P12_12C


title: P12_12B


title: P12_12A


title: fresh_HSC_SCF82

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i712_i510


title: P13_1H


title: P12_11G


title: fresh_HSC_SCF74

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i702_i510


title: fresh_HSC_SCF80

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i710_i510


title: P12_11F


title: P13_1F


title: P12_11H


title: fresh_HSC_SCF73

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i701_i510


title: P12_11E


title: fresh_HSC_SCF72

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i715_i508


title: fresh_HSC_SCF71

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i714_i508


title: P12_11D


title: P12_11B


title: P12_12E


title: P12_11C


title: fresh_HSC_SCF70

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i712_i508


title: P12_11A


title: P12_10H


title: P12_10G


title: fresh_HSC_SCF69

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i711_i508


title: P12_10F


title: P12_10E


title: fresh_HSC_SCF68

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i710_i508


title: P12_10D


title: P12_10C


title: P12_10B


title: fresh_HSC_SCF67

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i707_i508


title: P12_9H


title: P12_9G


title: fresh_HSC_SCF66

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i706_i508


title: P12_9E


title: fresh_HSC_SCF65

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i705_i508


title: P12_9D


title: P12_9C


title: fresh_HSC_SCF63

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i703_i508


title: P12_9F


title: fresh_HSC_SCF64

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i704_i508


title: fresh_HSC_SCF62

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i702_i508


title: P12_9B


title: P12_8G


title: P12_8H


title: P12_8E


title: fresh_HSC_SCF61

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i701_i508


title: fresh_HSC_SCF60

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i715_i507


title: P12_8C


title: P12_9A


title: P12_8F


title: fresh_HSC_SCF58

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i712_i507


title: P12_8B


title: P12_7H


title: P12_8A


title: fresh_HSC_SCF59

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i714_i507


title: P12_7G


title: P12_10A


title: P12_8D


title: fresh_HSC_SCF57

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i711_i507


title: P12_7F


title: P12_7E


title: fresh_HSC_SCF56

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i710_i507


title: P12_7D


title: fresh_HSC_SCF55

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i707_i507


title: P12_7C


title: fresh_HSC_SCF54

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i706_i507


title: P12_7A


title: P12_7B


title: P12_6H


title: fresh_HSC_SCF53

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i705_i507


title: P12_6G


title: fresh_HSC_SCF52

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i704_i507


title: P12_6C


title: P12_6F


title: P12_6D


title: P12_6E


title: P12_5G


title: fresh_HSC_SCF51

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i703_i507


title: fresh_HSC_SCF49

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i701_i507


title: P12_5H


title: fresh_HSC_SCF50

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i702_i507


title: fresh_HSC_SCF48

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i715_i506


title: P12_5F


title: P12_5D


title: P12_5C


title: P12_5E


title: fresh_HSC_SCF47

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i714_i506


title: P12_4G


title: fresh_HSC_SCF46

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i712_i506


title: P12_4H


title: fresh_HSC_SCF44

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i710_i506


title: P12_4F


title: P12_5A


title: P12_4E


title: fresh_HSC_SCF45

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i711_i506


title: fresh_HSC_SCF43

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i707_i506


title: P12_6B


title: fresh_HSC_SCF42

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i706_i506


title: P12_4A


title: P12_4D


title: P12_6A


title: P12_3G


title: P12_3E


title: P12_3F


title: P12_5B


title: P12_3D


title: fresh_HSC_SCF41

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i705_i506


title: P12_3A


title: fresh_HSC_SCF38

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i702_i506


title: P12_3H


title: P12_3C


title: P12_3B


title: P12_1H


title: fresh_HSC_SCF37

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i701_i506


title: P12_4C


title: P12_1G


title: P12_1E


title: P12_1C


title: P12_4B


title: fresh_HSC_SCF35

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i714_i505


title: P12_1B


title: P12_1D


title: P12_1A


title: fresh_HSC_SCF40

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i704_i506


title: P11_12G


title: fresh_HSC_SCF34

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i712_i505


title: fresh_HSC_SCF33

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i711_i505


title: P11_12H


title: fresh_HSC_SCF39

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i703_i506


title: P11_12B


title: P11_12D


title: P11_12C


title: fresh_HSC_SCF31

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i707_i505


title: fresh_HSC_SCF30

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i706_i505


title: P11_12E


title: P11_11H


title: P11_11G


title: fresh_HSC_SCF36

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i715_i505


title: fresh_HSC_SCF28

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i704_i505


title: P11_11E


title: P12_1F


title: P11_11D


title: P11_11F


title: P11_11C


title: P11_11B


title: fresh_HSC_SCF27

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i703_i505


title: P11_10H


title: fresh_HSC_SCF26

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i702_i505


title: P11_11A


title: P11_12F


title: P11_10G


title: P11_10F


title: P11_10D


title: fresh_HSC_SCF25

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i701_i505


title: P11_12A


title: fresh_HSC_SCF24

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i715_i503


title: fresh_HSC_SCF32

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i710_i505


title: P11_10E


title: fresh_HSC_SCF29

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i705_i505


title: fresh_HSC_SCF21

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i711_i503


title: P11_10A


title: P11_9H


title: P11_10B


title: P11_9G


title: P11_10C


title: fresh_HSC_SCF23

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i714_i503


title: P11_9F


title: fresh_HSC_SCF22

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i712_i503


title: P11_9D


title: fresh_HSC_SCF19

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i707_i503


title: fresh_HSC_SCF20

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i710_i503


title: P11_9C


title: P11_9A


title: P11_9B


title: fresh_HSC_SCF18

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i706_i503


title: P11_8H


title: P11_8G


title: P11_8E


title: P11_8F


title: fresh_HSC_SCF17

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i705_i503


title: fresh_HSC_SCF16

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i704_i503


title: P11_9E


title: P11_8C


title: fresh_HSC_SCF15

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i703_i503


title: nasal swab, healthy donor 1, scRNA-seq

city: Daejeon

first: JUNGMO

last: KIM

state: -- None selected --

address: 291 Daehak-ro, Yuseong-gu

department: Center for Vascular Research

institute: Institute for Basic Science

data_processing:
STAR(v2.7.3a) was used to process single cell 3' RNA-seq outputs. And UMI-tools(v1.1.1) extract UMI from fastq files.
Then, using featureCount(Subread v2.0.1), reads were aligned to human reference genome plus SARS-CoV2 reference genome
Aligned reads were then read by Seurat (v3.2.3) and cell-gene raw expression matrices were made. Then, low quality cells (expressing less than 200 genes and more than 4000 genes)  were removed. Also, genes that are only expressed in less than 3 cells were discarded.
After quality control, expression matrices were log normalized and scaled with Seurat to produce processed data files.
Identification of differentially expressed genes and dimensionality reductions were performed by Seurat.
Genome_build: a customized reference genome in which the SARS-CoV-2 genome (NC_045512.2) was added as an additional chromosome to the human reference genome GRCh38.p13 (GCA_000001405.28).
Supplementary_files_format_and_content: Cell-gene expression matrix of UMI counts for human nasal swab single cell data from healthy donors

source_name: nasal swab

extract_protocol:
After tissue preparation and cell digestion, single-cell suspensions were processed on the BD Rhapsody system following the manufacturer's protocols.
sv

value: nasal swab

tag: disease state

value: COVID-19 negative

tag: gender

value: male


title: P11_8B


title: P11_8A


title: fresh_HSC_SCF14

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i702_i503

value: Bone marrow

value: 12-16 weeks

value: wild type


title: RNAseq ZCCHC4 KO embryos

city: Mexico City

first: David

last: Valle-Garcia

address: Av. Insurgentes Sur 3877, La Fama, Tlalpan

country: Mexico

institute: National Institute of Neurology and Neurosurgery

data_processing:
Reads were aligned with hisat2 (v2.0.4, parameters: --no-unal --rna-strandness R) using the gtf annotation WBcel235 downloaded from Ensembl genes v96 as reference.
Sam files were converted to bam files using samtools (v 1.9, parameters: -bSq 10).
Bigwig files were generated using the bamCoverage program from the deepTools package (v3.3.0, parameters: -bs 20 --normalizeUsing BPM --skipNAs  --ignoreDuplicates).
Gene counts for the Input files (RNAseq experiments) were obtained with the featureCounts program fron the Rsubread package (v 1.34.1, parameters minMQS=10, allowMultiOverlap=F,  largestOverlap=T, strandSpecific=2) using the WBcel235 annotation from Ensembl genes v96.
Normalization and dispersion factors for RNAseq analysis were calculated using the functions calcNormFactors() and estimateDisp() from the edgeR package (v 3.26.1). DEG were calculated using the glmFit() and glmLRT() functions from edgeR. Genes with a |logFC| > 1 and FDR < 1e-5 were considered differentially expressed.
m6A peaks were calculated with the R package exomePeaks (v 2.17) using a FDR cutoff of 1e-10 and a fold enrichment of 10. Only consistent peaks (identified in all replicates) were included. Peaks within genes with low expression level (cpm < 1) were ignored.
Genome_build: WBcel235
Supplementary_files_format_and_content: Log-fold change m6A/Input bigwig files were generated using bamCoverage from the deepTools package (v3.3.0, parameters: -bs 20 --normalizeUsing BPM --skipNAs  --ignoreDuplicates)
Supplementary_files_format_and_content: log2 TPM for RNAseq is generated from normalized counts estimated by edgeR with the rpkm() function
Supplementary_files_format_and_content: BED file containing the estimated m6A peaks for N2 embryos is generated from the output of exomePeaks, aplying the cut-offs values as described

organism: Caenorhabditis elegans

source_name: C elegans embryos

extract_protocol:
mRNA was obtained from total RNA (100 ug) by purifying twice with a rRNA depletion kit (RiboMinus Eukaryote Kit v2) following manufacturer’s instructions.   m6A RIP-seq experiments were performed as previously described (Sendinc, David-Valle et.al, Molecular Cell, 2019). Briefly: 5 g of mRNA are fragmented at 98ºC for 3 min in 200 ul of fragmenting buffer (10 mM Tris pH 7.4, 10 mM ZnCl2) and quenched with 70mM EDTA. 50 L of Protein G Dynabeads (Invitrogen) are incubated with 250 ug of rabbit monoclonal anti-m6A (Cell Signaling Technologies, Cat #56593S) at 4ºC for 30 mins. The beads/antibody slurry is added to the fragmented mRNA and incubated in rotation for 1 h at 4ºC. Beads were washed twice with 200 L of reaction buffer (150 mM NaCl, 10 mM Tris-HCl, 0.1% Triton X-100, pH 7.5), twice with 200 L of low salt buffer (50 mM NaCl, 10 mM Tris-HCl, 0.1% Triton X-100, pH 7.5) and twice with 200 L of high salt buffer (500 mM NaCl, 10 mM Tris-HCl, 0.1% Triton X-100, pH 7.5). Immunoprecipitated RNA was eluted in TRIzol and purified with the RNA clean and concentrator Kit -5 (Zymo, Cat #R1013).
Illumina sequencing libraries are prepared with the NEBNext Ultra II Directional Library Prep Kit for Illumina from NEB (#E7760), following manufacturer's instructions. RNA-Seq libraries are generated from three biological replicates for Input (RNA-Seq) and m6A-immunoprecipitated mRNA. Libraries are sequenced in a NextSeq 550 with an average coverage of 30 million reads per sample.

tag: type

value: Input


title: RNAseq METTL5/ZCCHC4 dKO embryos


title: P11_7H


title: P11_7G


title: fresh_HSC_SCF13

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i701_i503

tag: age


title: P11_7E


title: P11_7C


title: fresh_HSC_SCF12

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i715_i502

tag: genotype


title: P11_7D


title: RNAseq METTL5 KO embryos


title: RNAseq N2 embryos


title: P11_7F


title: m6A-RIP-Seq METTL5/ZCCHC4 dKO embryos

description:
ce11-m6A-METTL5_ZCCHC4_dKO-A-lfc.bw
ce11-m6A-METTL5_ZCCHC4_dKO-B-lfc.bw
ce11-m6A-METTL5_ZCCHC4_dKO-C-lfc.bw

tag: rip antibody

value: 250 ug of a-m6A (Cell Signaling Technologies, Cat #56593S)

value: RIP


title: fresh_HSC_SCF10

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i712_i502

tag: batch


title: P11_7A

tag: female parent

tag: male parent


title: P11_7B

tag: days after pollination

tag: number of nuclei


title: nasal swab, healthy donor 2, scRNA-seq


title: fresh_HSC_SCF9

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i711_i502


title: P11_6F

tag: fans peak

tag: plate/batch


title: fresh_HSC_SCF11

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i714_i502


title: P11_6G

tag: extra wash steps?

tag: control?


title: P11_8D


title: m6A-RIP-Seq METTL5 KO embryos

description:
ce11-m6A-METTL5_KO-A-lfc.bw
ce11-m6A-METTL5_KO-B-lfc.bw


title: P11_6E


title: fresh_HSC_SCF8

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i710_i502

tag: tissue


title: P11_6D


title: P11_6B


title: fresh_HSC_SCF7

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i707_i502

tag: strain


title: m6A-RIP-Seq N2 embryos

description:
m6A-N2-peaks.bed
ce11-m6A-N2-A-lfc.bw
ce11-m6A-N2-B-lfc.bw
ce11-m6A-N2-C-lfc.bw


title: Mutz_MN1_p2

first: Kathrin

last: Bernt

address: 3501 Civic Center Boulevard,

institute: Children's Hospital of philadelphia

data_processing:
Library strategy: 4C
4C pipeline
peakC
Genome_build: GRCh38
Supplementary_files_format_and_content: bw

source_name: Mutz-3 cell line

growth_protocol: UCSD-AML1 were grown in RPMI 1640 medium supplemented with 10% heat inactivated FBS, 1% Penicillin/Streptomycin, and human GM-CSF (10ng/mL). Molm14 and Monomac6 were grown in RPMI 1640 medium supplemented with 10% heat inactivated FBS, and 1% Penicillin/Streptomycin. Mutz-3 cells were grown in 60% α-MEM medium, 20% heat inactivated FBS,  20% HTB-9 supernatant, and supplemented with 1% Penicillin/Streptomycin and 1% L-Glutamine.

extract_protocol:
Briefly, samples were crosslinked, lysed, and sequentially digested with DpnII and Csp6I. Purified DNA was subjected to two rounds of PCR and resulting DNA was sequenced on an Illumina instrument.
Library prep is included in second round of PCR, Illumina NextSeq, 1x75bp single-end reads, multiplexed

tag: cell line

tag: cell type

value: AML

tag: translocation


title: P11_6A


title: P11_6C


title: P11_5G


title: Mutz_MN1_p1


title: P11_5F


title: P11_5H


title: P11_5E


title: MonoMac_MN1_p2

source_name: Monomac6 cell line

value: CTRL


title: fresh_HSC_SCF5

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i705_i502

tag: age


title: fresh_HSC_SCF4

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i704_i502

tag: genotype


title: P11_5D


title: MonoMac_MN1_p1


title: fresh_HSC_SCF3

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i703_i502


title: P11_6H


title: P11_4H


title: P11_5A


title: P11_4G


title: Molm_MN1_p1

source_name: Molm14 cell line


title: fresh_HSC_SCF6

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i706_i502


title: P11_4F


title: P11_5B


title: UCSD_MN1_p1

source_name: UCSD-AML1 cell line


title: H6658, FTO knockdown, IP

city: BeiJing

first: Xueying

last: Yang

address: No. 17, Nanli, Panjiayuan, Chaoyang District, Beijing

country: China

institute: Cancer Hospital, Chinese Academy of Medical Sciences

data_processing:
Basecalls performed using CASAVA version 1.8
circRNA-seq reads were mapped to human genome by BWA-MEM software by default parameters except -T = 19
circRNAs were detected and annotated with CIRI software
Genome_build: hg19
Supplementary_files_format_and_content: methylated_sites.mRNA

source_name: H322 Cell

extract_protocol:
Total RNA was extracted by Trizol reagent
RNA immunoprecipitation was performed with the m6A antibody (Synaptic Syestems,202003).Both the input sample without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra™ RNA Library Prep Kit . Library sequencing was performed on an illumina NovaSeq 6000 instrument with 150bp paired-end reads

value: FTO knockdown

tag: rip antibody

value: m6A antibody (Synaptic Syestems,202003)


title: P11_4D

source_name: seed nuclei


title: fresh_HSC_SCF1

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i701_i502

source_name: Bone marrow

tag: batch


title: P11_4C

tag: female parent


title: UCSD_MN1_p2


title: H6658, FTO knockdown, Input


title: m6A-RIP-Seq ZCCHC4 KO  embryos

description:
ce11-m6A-ZCCHC4_KO-A-lfc.bw
ce11-m6A-ZCCHC4_KO-B-lfc.bw
ce11-m6A-ZCCHC4_KO-C-lfc.bw

tag: type


title: P11_3H

tag: male parent

tag: days after pollination


title: Bulk_Arcuate organoid cells_100d_Maj-2_rep3

first: Hongjun

last: Song

address: 415 Curie Boulevard

institute: University of Pennsylvania

data_processing:
ARCO raw bulk sequencing data were demultiplexed with bcl2fastq2 v2.17.1.14 (Illumina) with adapter trimming using Trimmomatic v0.32 software (Bolger et al., 2014). Alignment was performed using STAR v2.5.2a (Dobin et al., 2013). GENCODE human genome release 28 (GRCh38.p12) was used for alignment. Single cell raw sequencing data was demultiplexed with bcl2fastq2 (Illumina) with adaptor trimming turned off. Additional processing was performed using drop-seq tools v.2.1.0 (Saunders et al., 2018) with GRCh38 as the reference genome, and GENCODE v.28 GTF as the annotation file.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts, each file is a raw counts table for cells obtained from one Dropseq run (single-cell) or one sample (bulk).

source_name: Organoid cells

growth_protocol: Organoids were cultured using modified versions of protocols as previously described (Qian et al., 2019).

extract_protocol:
ARCOs were dissociated using a papain-based neural tissue dissociation kit (Miltenyi Biotech). Frozen hypothalamus pieces were dissociated using Nuclei EZ lysis buffer (Sigma) as previously described (Habib et al., 2017).
Single-cell libraries were constructed as per the Dropseq protocol (Macosko et al., 2015). Bulk RNAseq libraries were constructed using a modified version of the SMARTseq protocol as previously described (Weng et al., 2017).
Single-cell and Bulk RNASeq libraries

treatment_protocol: Organoids were not treated with specific reagents prior to experiments.

value: Organoid


title: H007F, Control, IP

value: control


title: P11_4B

value: Cvi

value: Col

tag: number of nuclei

tag: fans peak


title: P11_3G

tag: plate/batch

tag: extra wash steps?

value: no


title: P11_5C

tag: control?


title: H007F, Control, Input


title: Bulk_Arcuate organoid cells_100d_Maj-2_rep2

tag: tissue


title: fresh_HSC_SCF2

description:
HTSeq_counts_SLX12565_batch1.txt.gz
SLX.12565.i702_i502

tag: strain


title: P11_3F


title: P11_3E


title: Bulk_Arcuate organoid cells_100d_Maj-2_rep1


title: P11_3C


title: P11_4E


title: P11_3D


title: scRNA-seq of IL1b+ TGFb2 treated HUVEC at day7

city: Edinburgh

first: Julie

last: Rodor

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

institute: UNIVERSITY OF EDINBURGH

data_processing:
fastq files obtained from Edinburgh Genomics
Read mapping and generation of the expression matrix was done using CellRanger version 2.1.0 using GRCh38 transcriptome annotation
Genome_build: GRCh38
Supplementary_files_format_and_content: h5 file from CellRanger output

source_name: HUVEC

growth_protocol: Primary endothelial cells (pooled donors HUVEC #C2519A) were purchased from Lonza (Basel, Switzerland) and maintained in endothelial cell growth medium (EGM-2 BulletKit™) (Lonza, Basel, Switzerland) supplemented with foetal bovine serum (FBS) (10%, Life Technologies, Paisley, UK) and Penicillin-Streptomycin (P/S) (100U/ml) (Gibco, Paisley, UK). HUVEC were used between P3 and P8, and kept at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
single cell suspension
Single cell RNA-sequencing libraries were prepared using the Single Cell 3′ Reagent Kit User Guide v2 (10x Genomics)
scRNA-seq - 10X Genomics

treatment_protocol: Endothelial cells were plated at a density of 7 x 104 cells/well in collagen coated 6-well culture plates and were treated with TGF-β2 (10ng/ml, PeproTech NJ, USA) and IL-1β (1ng/ml, PeproTech NJ, USA) for 3 or 7 consecutive day in EGM-2 BulletKit™ supplemented with 10% FBS and refreshed every 24 hours.

tag: treatment

tag: time point (day)


title: scRNA-seq of untreated HUVEC at day7

value: Untreated


title: Bulk_Arcuate organoid cells_100d_Maj-1_rep2


title: Bulk_Arcuate organoid cells_100d_Maj-1_rep3


title: Molm_MN1_p2

tag: cell line

tag: cell type

tag: translocation


title: scRNA-seq of IL1b+ TGFb2 treated HUVEC at day3


title: Bulk_Arcuate organoid cells_100d_Maj-1_rep1


title: P11_1H


title: scRNA-seq of untreated HUVEC at day3


title: P11_4A

value: yes - only water used for Nextera library prep


title: P11_3B


title: P11_1F


title: P11_1E


title: P11_3A


title: scRNA-seq of HUVEC at day0


title: P11_1B


title: Bulk_Arcuate organoid cells_100d_Min-2_rep2


title: GapCTR_Proliferation_3

data_processing:
Fastq files obtained from GENEWIZ
Gene quantification (normalised expression value as FPKM) was obtained using RSEM (options: -bowtie2 -forward-prob 0 -paired-end), based on GENCODE annotation version 26 (primary assembly).
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file with FPKM

source_name: GapmeR control in proliferation HCASMC

growth_protocol: Primary human coronary arterial smooth muscle cells (HCASMC) were maintained in Smooth Muscle Cell Growth Medium 2 (PromoCell) with supplements at 37°C in a humidified atmosphere containing 5% CO2. All cells were used between passages 3-5.

extract_protocol:
miRNeasy mini kit (Qiagen) with on-column DNAse digestion
polyA enriched stranded libraries were prepared and sequenced on Illumina HiSeq by GENEWIZ, Inc.

treatment_protocol:
[Gapmer treatment]  HCASMCs were transfected with Gap143HG or GapCTR (40nM) 24h after plating (plating of 2X10^5 cells for MBCD experiments, of 1.8X10^5 for migration and 1X10^5 for proliferation) using Lipofectamine RNAimax reagent for 5 hours. Additional treatments were performed 24h after transfection.
[MBCD treatment]  HCASMCs were treated with methyl--cyclodextrin (MBCD) loading 10µg/mL in 0.2% Bovine Serum Albumin (BSA) medium for 72 hours or in 0.2% BSA medium for the untreated cells.
[migration treatment]  HCASMCs were starved in 0.2% Foetal Bovine Serum (FBS) medium for 48 hours then scratched with a sterile pipet (~500μm-wide wounds) and replaced with fresh medium for 10 hours.
[proliferation treatment]  HCASMCs were starved in 0.2% Foetal Bovine Serum (FBS) medium for 48 hours. Cells were then treated with Platelet Derived Growth Factor (PDGF)-BB (R&D System) 20ng/mL, or untreated with 0.2% FBS fresh medium for 48 hours.

tag: gapmer

value: GapCTR

tag: condition

value: Proliferation treatment

value: Human Coronary Arterial Smooth Muscle Cells (HCASMCs)

tag: replicate


title: P11_1C

tag: female parent

tag: male parent


title: Bulk_Arcuate organoid cells_100d_Min-2_rep3


title: P11_1D

tag: days after pollination

tag: number of nuclei


title: P11_1A

tag: fans peak

tag: plate/batch

value: yes - no nucleus sorted


title: Bulk_Arcuate organoid cells_100d_Min-2_rep1


title: GapCTR_Proliferation_1


title: GapCTR_Basal-P_3

source_name: GapmeR control in basal-P HCASMC

value: Control Proliferation


title: Bulk_Arcuate organoid cells_100d_Min-1_rep3


title: GapCTR_Proliferation_2


title: Bulk_Arcuate organoid cells_100d_Min-1_rep2


title: P11_1G

tag: extra wash steps?

tag: control?


title: Tex14 heterogyous deeply sequenced

city: San Francisco, CA

first: Rebecca

middle: Garrett

last: Jaszczak

address: 35 Medical Center Way, Room 913D

institute: UCSF

description: Tex14 heterogyous deeply sequenced

data_processing:
cellranger v2.1.0 was run using all default parameters with prebuild mm10 reference genome available from 10X-Genomics
Shallowly sequenced libraries: Seurat v3.1.X was used to select high quality cells and remove cell doublets using the following parameters: genes expressed in at least 3 cells, fewer than 25,000 unique fragments (to exclude cell doublets), greater than 200 genes expressed (to exclude GEMS with no cells), and cells with 7.0% or less mitochondrial gene expression, and cells with less than 0.5% hemogloblin gene expression, to exclude blood cells.
Deeply sequenced libraries: Seurat v3.1.X was used to select high quality cells and remove cell doublets using the following parameters: fewer than 30,000 unique fragments (to exclude cell doublets), greater than 1000 genes expressed (to exclude GEMS with no cells), and cells with 5.0% or less mitochondrial gene expression, cells with less than 0.25% hemoglobin gene expression (to exclude blood cells).
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited text file containing a cell by gene raw count expression table

source_name: Embryonic Ovary

extract_protocol:
Tex14+/- and Tex14-/- ovaries were dissociated and the cells submitted for FACS to concentrate Oct4-GFP+ ovary germ cells. Samples were reecombined with Oct4-GFP- somatic cells. These cell populations were used to create two 10X Chromium Single Cell 3' (v2 Chemistry) single cell RNA sequencing libraries (Cat No: PN-120237, PN-1000009, PN-120262).
10X Chromium Single Cell 3' (v2 Chemistry) single cell RNA sequencing libraries (Cat No: PN-120237, PN-1000009, PN-120262) were created following published protocols available at https://support.10xgenomics.com/single-cell-gene-expression/library-prep/doc/user-guide-chromium-single-cell-3-reagent-kits-user-guide-v2-chemistry.

tag: strain

value: mixed

tag: tissue

value: ovary

tag: age

value: embryonic day 13.5

tag: genotype


title: Bulk_Arcuate organoid cells_100d_Min-1_rep1


title: Tau aggregates 1

description:
Sample 4
MAJIQ_delta_psi.tsv
iREADs_analysis.csv

data_processing:
Timmomatic 0.36 to trim Illumina TruSeq3 adapters and low quality reads (options: 2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
Ribosomal reads were filtered out by mapping to a ribosome reference genome (UCSC hg38 humRibosomal.fa) and keeping the unmapped reads.
Reads were then mapped to GRCh38 using STAR v2.6.0c in two pass alignment mode with --outFilterMultimapNmax 20)
MAJIQ v2.1 and iRead v0.8.5 were used to examine splicing changes in cells with and without tau aggregates
Genome_build: Genome Reference Consortium Human Build 38
Supplementary_files_format_and_content: MAJIQ_delta_psi.tsv (.tsv showingMAJIQ splicing analysis output)
iREADs_analysis.csv (.csv file showing intron retetion analysis using iREADS)

source_name: HEK293 cells expressing P301S-tau RD -YFP and P301S-tau RD-CFP

extract_protocol:
RNA was extracted from cells using Trizol LS reagent
NovoGene Random Hexamer Primed RNA library

treatment_protocol: 200 ug of WT or P301S tau clarified mouse brain homogenate was transfected per dish using lipofectamine 2000 and incubated at 37C for 96 hours. Tau aggregation was monitored using the Evos M500 Imaging System with a GFP filter

tag: cell line

value: Transfected with clarified brain homogenate from P301S mice

value: HEK293 Tau-RD-P301S-CFP/YFP

tag: sample type

value: with tau aggregates


title: No tau aggregates 3

description:
Sample 3
MAJIQ_delta_psi.tsv
iREADs_analysis.csv

value: Mock transfected

value: without tau aggregates


title: No tau aggregates 2

description:
Sample 2
MAJIQ_delta_psi.tsv
iREADs_analysis.csv


title: Tex14 homozygous mutant deeply sequenced


title: GapCTR_Basal-P_2

tag: gapmer

tag: cell type


title: Tau aggregates 2

description:
Sample 5
MAJIQ_delta_psi.tsv
iREADs_analysis.csv


title: Tau aggregates 3

description:
Sample 6
MAJIQ_delta_psi.tsv
iREADs_analysis.csv


title: GapCTR_Basal-P_1

tag: condition

tag: replicate


title: Children Respiratory syncytial virus Pool [RSV-2019-BS]

city: Kansas City

first: Boryana

last: Koseva

state: MO

address: 2420 Pershing Road

department: CMRI

institute: Children's Mercy Hospital

data_processing:
Sequenced reads were processed through the dragen methylation pipeline, duplicates were removed with MarkDuplicates in Picard tools, methylation ratios were determined at each CpG site using Bismark, and CpG sites were filtered to remove sites that: 1) have coverage of less than 10 reads, 2) overlap encode blacklisted regions, and 3) overlap a SNP in dbSNP
Genome_build: WGBS: GRCh37
Supplementary_files_format_and_content: the CpG profile across the genome for each sample in tab deliimited format [chr, start, end, fw_meth_reads, fw_total_reads, fw_meth_frac, rev_meth_reads, rev_total_reads, rev_meth_frac]

extract_protocol:
Nasal specimens were stored at -80⁰C and were brought to room temperature before pooling by age. DNA was isolated with a Qiagen DNeasy Blood and Tissue Kit. 100ng of DNA from each sample was sheared mechanically using a Covaris LE220-plus system to a length of 350 bp. Once the input DNA was at the proper fragment size, the samples were concentrated with a SpeedVac to a volume of 20µL. The samples then underwent bisulfite conversion with an EZ DNA Methylation- Gold kit
Library was prepared according to the standard protocols of the ACCEL-NGS Methyl-Seq Library kit

tag: virus type

value: Respiratory

value: Nasal Mucosa

tag: collection method

value: Copan mid turbinate flocked swabs


title: GapCTR_Migration_3

source_name: GapmeR control in migration HCASMC

value: Migration:scratch assay


title: GapCTR_Migration_2

value: GapCTR


title: Bulk_Arcuate organoid cells_100d_C6-5_rep2

value: Organoid


title: Children Rhinovirus Pool Rep1 [REV-Pool-DNA]

source_name: Children Rhinovirus Pool

value: Rhinovirus


title: E13.5 Tex14 KO2

city: San Francisco

first: Bikem

last: Soygur

address: 35 Medical Center Way, Parnassus, RMB, PodB, 913D

department: Obstetrics, Gynecology & Reproductive Sciences

data_processing:
Aligned with Bismark version 0.14.3 and --non_directional parameter
Genome_build: mm10
Supplementary_files_format_and_content: Read coverage (one bigWig file per sample)
Supplementary_files_format_and_content: CpG methylation percentage (one bigWig file per sample)

source_name: female germ cells

extract_protocol:
E13.0 and E13.5 ovaries were digested in 0.25% Trypsin-EDTA. Germ cells were sorted based on GFP expression (OCT4-GFP+). Cells were lysed using EZ DNA Methylation-DirectTM Kit (Zymo; D5020).
Bisulfite conversion and library preparation was carried out with the Pico Methyl-Seq Library prep kit (Zymo D5455).
Libraries were sequenced on NextSeq 500 High Output and NovaSeq 6000 S1 flow cells 484 yielding to 75-bp, and 50-bp paired-end reads, respectively for whole-genome bisulfite sequencing by post-bisulfite adapter tagging.

value: Mixed genetic background

value: POU5f1-{delta}PE-GFP; Tex14-/-

value: Embryonic day 13.5

value: Germ cell


title: E13.5 Tex14 HET1

value: POU5f1-{delta}PE-GFP; Tex14+/-


title: No tau aggregates 1

description:
Sample 1
MAJIQ_delta_psi.tsv
iREADs_analysis.csv


title: Bulk_Arcuate organoid cells_100d_C3_rep3


title: Bulk_Arcuate organoid cells_100d_C3_rep2


title: Children Human Parainfluenza Virus Type 3 Pool [PIV-3-Pool-DNA]

value: Parainfluenza Type 3


title: GapCTR_Basal-M_3

source_name: GapmeR control in basal-M HCASMC

value: Control Migration

value: Human Coronary Arterial Smooth Muscle Cells (HCASMCs)


title: Children Negative Pool Rep1a [Negative-Pool-DNA]

source_name: Children Negative Pool

value: Control


title: E13.5 Tex14 KO1


title: Bulk_Arcuate organoid cells_100d_C3_rep1


title: E13.0 Tex14 KO

value: Embryonic day 13.0


title: Bulk_Arcuate organoid cells_20d_Maj-2_rep3


title: GapCTR_Basal-M_2


title: E13.0 Tex14 WT

value: POU5f1-{delta}PE-GFP; Tex14+/+


title: GapCTR_Basal-M_1


title: Children Negative Pool Rep1 [Negative-2018-BS]

value: Nasal Mucosa


title: E13.0 Tex14 HET


title: E13.5 Tex14 HET2


title: GapCTR_MBCD_3

source_name: GapmeR control in MBCD HCASMC

value: MBCD treatment


title: Bulk_Arcuate organoid cells_100d_C6-5_rep1


title: Children Rhinovirus Pool Rep2 [Rhino-2019-BS]

value: Copan mid turbinate flocked swabs


title: Children Human metapneumovirus Pool Rep2 [hMPV-2019-BS]

source_name: Children Human metapneumovirus Pool

value: hMPV


title: Bulk_Arcuate organoid cells_20d_Maj-2_rep1

value: Organoid


title: GapCTR_MBCD_2

value: GapCTR


title: P301S Tau-12 IP RNA Rep 2

description:
This dataset is the RNA that is associated with sarkosyl (1%) insoluble tau from the brains of mice expressiong P301L tau (tau aggregates)
Mouse_brain_tau_S12

data_processing:
Timmomatic 0.36 to trim Illumina TruSeq3 adapters and low quality reads (options: 2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
Ribosomal reads were filtered out by mapping to a ribosome reference genome (Ensembl GRCm38 musRibosomal.fa) and keeping the unmapped reads.
Reads were then mapped to GRCm38.p6 using STAR 2.6.0c in two pass alignment mode with --outFilterMultimapNmax 20)
FPKM was calculated using the longest transcript lengths taken from from ensembl biomart GRCm38.p6
Genome_build: Genome Reference Consortium Mouse Build 38 p6
Supplementary_files_format_and_content: csv file containing gene names and FPKM

source_name: Tau-IP IP RNA from P301L mouse (Tg4510)

growth_protocol: Animals were maintained in a facility accredited by the Association for Assessment and Accreditation of Laboratory Animal Care in accord with the Guide for the Care and Use of Laboratory Animals. All procedures were approved by the University of California, San Francisco, Institutional Animal Care and Use Committee. Animals were maintained under standard environmental conditions, with a cycle of 12 hours light and 12 hours dark and free access to food and water.

extract_protocol:
Briefly, tau aggregates were isolated by 1% sarkosyl extraction (to enrich for insoluble proteins) followed by immunoprecipitation of tau using the tau-12 antibody (see Methods section of associated paper for further details).
NuGen Ovation SoLo RNA-seq
Random hexamer primed RNA seq. Ribodepletion following amplification

treatment_protocol: no treatment

value: FvBB6F1-Tg(Camk2a-tTA)1Mmay, (tet)-tdTomato-Syp/EGFP)1.1Luo/J,(tetO-MAPT*P301L)4510 (referred to as rTg4510 or P301L mice)

value: brain

tag: molecule type

value: Random hexamer primed RNA


title: Children Human metapneumovirus Pool Rep1 [HMP-Pool-DNA]


title: Bulk_Arcuate organoid cells_100d_C6-5_rep3


title: GapCTR_Migration_1

value: Migration:scratch assay


title: GapCTR_MBCD_1


title: Children FluB Pool Rep1 [FluB-Pool-DNA]

source_name: Children FluB Pool

value: Influenza Type B


title: P301S Tau-12 IP RNA Rep 1

description:
This dataset is the RNA that is associated with sarkosyl (1%) insoluble tau from the brains of mice expressiong P301L tau (tau aggregates)
Mouse_brain_tau_S11


title: Bulk_Arcuate organoid cells_20d_Maj-1_rep3


title: Bulk_Arcuate organoid cells_20d_Maj-1_rep2


title: WT Tau-12 IP RNA Rep 1

description:
This dataset is the RNA that is associated with sarkosyl (1%) insoluble tau from the brains of mice expressiong WT tau
Mouse_brain_tau_S9

source_name: Tau-12 IP RNA from WT mouse (Tg21221)

value: FvBB6F1-Tg(Camk2a-tTa),(tetO-MAPT*wt)21221 (referred to as rTg21221 or WT tau mice)


title: Bulk_Arcuate organoid cells_20d_Maj-2_rep2


title: Children Negative Pool Rep2 [Negative-2019-BS]


title: Children FluB Pool Rep2 [FluB-2019-BS]


title: WT Tau-12 IP RNA Rep 2

description:
This dataset is the RNA that is associated with sarkosyl (1%) insoluble tau from the brains of mice expressiong WT tau
Mouse_brain_tau_S10


title: Bulk_Arcuate organoid cells_20d_Maj-1_rep1


title: GapCTR_Basal-C_2

source_name: GapmeR control in basal-C HCASMC

value: Control MBCD


title: GapCTR_Basal-C_3

value: Human Coronary Arterial Smooth Muscle Cells (HCASMCs)


title: Bulk_Arcuate organoid cells_20d_Min-2_rep3

source_name: Organoid cells


title: P301L Sarkosyl insoluble RNA Rep2

description:
This dataset is the RNA that is enriched in the sarkosyl (1%) insoluble fraction from the brains of mice expressiong P301L tau
Mouse_brain_tau_S8

source_name: P301L mouse (Tg4510)


title: Bulk_Arcuate organoid cells_20d_Min-2_rep2


title: Children FluA Pool Rep2 [FluA-2019-BS]

source_name: Children FluA Pool

value: Influenza Type A


title: Children FluA Pool Rep1 [FluA-Pool-DNA]


title: Children FluB 2-5y Pool [FB_2-5y_Pool_WGBS]

source_name: Children FluB 2-5y Pool


title: Bulk_Arcuate organoid cells_20d_Min-2_rep1


title: Bulk_Arcuate organoid cells_20d_Min-1_rep2


title: GapCARMN_Proliferation_2

source_name: CARMN depletion in proliferation HCASMC

value: GapCARMN

value: Proliferation treatment


title: GapCARMN_Proliferation_1


title: Bulk_Arcuate organoid cells_20d_Min-1_rep3


title: Children FluB 12-24mo Pool [FB_12-24mo_Pool_WGBS]

source_name: Children FluB 12-24mo Pool

value: Nasal Mucosa


title: Children FluB 6-12mo Pool [FB_6-12mo_Pool_WGBS]

source_name: Children FluB 6-12mo Pool


title: WT Sarkosyl insoluble RNA Rep1

description:
This dataset is the RNA that is enriched in the sarkosyl (1%) insoluble fraction from the brains of mice expressiong WT tau
Mouse_brain_tau_S5

source_name: WT mouse (Tg21221)


title: GapCARMN_Basal-P_3

source_name: CARMN depletion in basal-P HCASMC

value: Control Proliferation


title: GapCARMN_Proliferation_3


title: WT Sarkosyl insoluble RNA Rep2

description:
This dataset is the RNA that is enriched in the sarkosyl (1%) insoluble fraction from the brains of mice expressiong WT tau
Mouse_brain_tau_S6


title: P301L Total RNA Rep1

description:
This dataset is the total, unfractionated RNA from the brains of mice expressiong P301L tau
Mouse_brain_tau_S3

value: total, unfractionated RNA


title: Children FluB 0-6mo Pool [FB_0-6mo_Pool_WGBS]

source_name: Children FluB 0-6mo Pool

value: Copan mid turbinate flocked swabs


title: P301L Total RNA Rep2

description:
This dataset is the total, unfractionated RNA from the brains of mice expressiong P301L tau
Mouse_brain_tau_S4


title: P301L Sarkosyl insoluble RNA Rep1

description:
This dataset is the RNA that is enriched in the sarkosyl (1%) insoluble fraction from the brains of mice expressiong P301L tau
Mouse_brain_tau_S7


title: Children Enterovirus D68 Pool  [EVD68-Pool-DNA]

source_name: Children Enterovirus D68 Pool

value: Enterovirus


title: Bulk_Arcuate organoid cells_20d_C6-5_rep3

value: Organoid


title: GapCARMN_Basal-P_2


title: Children Adenovirus Pool [Adeno-Pool-DNA]

source_name: Children Adenovirus Pool

value: Adenovirus


title: Bulk_Arcuate organoid cells_20d_Min-1_rep1


title: GapCARMN_Basal-P_1


title: GapCTR_Basal-C_1

value: GapCTR


title: Bulk_Arcuate organoid cells_20d_C6-5_rep2


title: Children Coronavirus OC43 Pool Rep1 [Corona-Pool-DNA]

source_name: Children Coronavirus OC43 Pool

value: Coronavirus


title: Bulk_Arcuate organoid cells_20d_C6-5_rep1


title: WT Total RNA Rep1

description:
This dataset is the total, unfractionated RNA from the brains of mice expressiong WT tau
Mouse_brain_tau_S1

value: brain

value: Random hexamer primed RNA


title: GapCARMN_Migration_3

source_name: CARMN depletion in migration HCASMC

value: Migration:scratch assay


title: Bulk_Arcuate organoid cells_20d_C3_rep3


title: WT Total RNA Rep2

description:
This dataset is the total, unfractionated RNA from the brains of mice expressiong WT tau
Mouse_brain_tau_S2

value: FvBB6F1-Tg(Camk2a-tTa),(tetO-MAPT*wt)21221 (referred to as rTg21221 or WT tau mice)


title: Bulk_Arcuate organoid cells_20d_C3_rep1


title: GapCARMN_Basal-M_3

source_name: CARMN depletion in basal-M HCASMC

value: Control Migration

value: Human Coronary Arterial Smooth Muscle Cells (HCASMCs)


title: GapCARMN_Migration_1

value: GapCARMN


title: Bulk_Arcuate organoid cells_20d_C3_rep2


title: GapCARMN_Basal-M_2


title: Single-cell_Arcuate organoid cells_40d_Maj-1


title: Control2_TCR

city: Boston

first: Brian

last: Kalish

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Boston Children's Hospital

data_processing:
Library strategy: TCR-seq
Sequencing data were aligned to the genome and processed using the 10X Genomics Cell Ranger software, version 4.0.0. All cells were combined into a single dataset. Doublets were removed using Scrublet version 0.2.1, and the remaining cells were re-clustered. Mitochondrial genes were filtered from the dataset. Cells with fewer than 250 or more than 2500 unique genes were excluded. Cells were then clustered using the Seurat R package (Version 3.2.3). Specifically, the SCT functionality of Seurat was used to identify cell types that did not depend upon unique aspects of individual samples. Clustering resolution was set to 0.8, and the first 15 principal components were used. The data were log normalized and scaled to 10,000 transcripts per cell. The expression of known marker genes was used to assign each cluster to one of the main cell types. The Seurat FindMarkers function was used to identify genetic markers of cellular subtypes.
Genome_build: hg38
Supplementary_files_format_and_content: counts, filtered_contig_annotations

source_name: Umbilical cord mononuclear cells

extract_protocol:
CBMC aliquots were thawed in a 37˚C water bath and resuspended in RPMI-1640 with 10% FBS (Thermo Fisher). Samples were centrifuged at 350 x g for 7 minutes at 4˚C. Cells were resuspended in 100 microliters of 1X PBS with 2.5% FBS and 2 mM EDTA. Dead cells and red blood cells were depleted using the EasySep Dead Cell Depletion Kit and EasySep RBC Depletion Reagent (Stem Cell), according to manufacturer instructions. Cells were resuspended in RPMI/10% FBS and counted. Cells were loaded on to the 10X Chromium controller at a targeted recovery density of 10,000 cells per sample.
Samples were processed and sequencing libraries were created using the 10X the Chromium Next GEM single-cell V(D)J Reagent Kit v1.1 with human TCR V(D)J Enrichment following manufacturer instructions.
scRNA-seq

value: Umbilical cord mononuclear cells

value: control

tag: developmental stage

value: Term pregnancy


title: Case2_TCR

value: case


title: Control1_TCR


title: Case3_TCR


title: Control3_TCR


title: GapCARMN_Basal-M_1


title: Single-cell_Arcuate organoid cells_40d_Maj-2


title: GapCARMN_MBCD_3

source_name: CARMN depletion in MBCD HCASMC

value: MBCD treatment


title: Single-cell_Arcuate organoid cells_40d_Min-2

source_name: Organoid cells


title: Case1_TCR


title: Control3_RNA

description:
Control_3
MasterNormalizedCountsTable_COVID_010821.tsv

data_processing:
Sequencing data were aligned to the genome and processed using the 10X Genomics Cell Ranger software, version 4.0.0. All cells were combined into a single dataset. Doublets were removed using Scrublet version 0.2.1, and the remaining cells were re-clustered. Mitochondrial genes were filtered from the dataset. Cells with fewer than 250 or more than 2500 unique genes were excluded. Cells were then clustered using the Seurat R package (Version 3.2.3). Specifically, the SCT functionality of Seurat was used to identify cell types that did not depend upon unique aspects of individual samples. Clustering resolution was set to 0.8, and the first 15 principal components were used. The data were log normalized and scaled to 10,000 transcripts per cell. The expression of known marker genes was used to assign each cluster to one of the main cell types. The Seurat FindMarkers function was used to identify genetic markers of cellular subtypes.
Genome_build: hg38
Supplementary_files_format_and_content: counts, filtered_contig_annotations


title: GapCARMN_MBCD_2


title: Single-cell_Arcuate organoid cells_40d_Min-1


title: GapCARMN_Migration_2


title: GapCARMN_MBCD_1


title: sh_LINC00525_2

type: RNA

city: Nanjing

first: Rong

last: Yin

address: Baiziting 42

department: Thoracic Surgery

institute: Nanjing Medical University Affiliated Jiangsu Cancer Hospital

hyb_protocol: Following fragmentation, 10 mg of cRNA were hybridized for 16 hr at 45°C on GeneChip® PrimeView™ Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip® Scanner 3000.

data_processing: Normalized probeset data were generated with Robust Multi-array Averaging (RMA) method.

label: biotin

label_protocol: Biotin-labeled cRNA were prepared using MessageAmp™ Premier RNA Amplification Kit (Ambion) and the protocol of the kit manufacturer from 100 ng total RNA.

growth_protocol: A549 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) (Sigma, USA) supplemented with 10% FBS and 5% CO2 at 37°C.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: we downregulated the expression of LINC00525 utilizing small interference RNA (siRNA) and used scrumble as negative control.

value: non-small cell lungs carcinoma cell line

tag: genotype/variation

value: LINC00526 downregulated


title: Control2_RNA

description:
Control_2
MasterNormalizedCountsTable_COVID_010821.tsv


title: sh_ctrl_2

value: negative control


title: sh_LINC00525_1

value: LINC00525 downregulated