title: ChIP_WT_for_g_del_CTCF_rep2

value: CTCF


title: ChIP_g_del_Rad21_rep2

status: Public on Oct 31 2023

type: SRA

city: Shanghai

first: Xiao

last: Ge

address: No. 800 Dongchuan Road

country: China

institute: Shanghai JiaoTong University

library_source: genomic

data_processing:
Paired-end reads were aligned to the human genome(GRCh37/hg19) using Bowtie (version 1.2.3).
Sam files were then converted into Bam files and indexed. BedGraph files were generated using bigWigToBedGraph software with Bam file as input. Peaks were called using macs14
Assembly: Mus Musculus UCSC mm9
Supplementary files format and content: bigwig and bedGraph files suitable for viewing on UCSC

molecule: genomic DNA

organism: Mus musculus

source_name: cortex

extract_protocol:
2 × 10^6 of cortex neurons or cultured cell were used for one experiment. Neuron cells were first dissected and digested using 0.00625% collagenase.
The neuron suspension or cultured cell were cross-linked using 1% formaldehyde in 10% FBS/PBS for 10 min at room temperature followed by washing twice with PBS solution containing proteinase inhibitors (Roche). Cells were then resuspended and lysed twice with 1ml prechilled lysis buffer containing proteinase inhibitors (Roche) for 10 min with slow rotations. For neuron sample, additional SDS was then added to the lysis solution to adjust final SDS concentration to 0.4% to help sonication. Cells were then sonicated to break DNA fragments to about 100-10000 bp using the Bioruptor system (25% energy, with working time 15s and resting time of 45s, 20cycles). After sonication, lysis buffer not containing SDS was added to adjust final SDS concentration to 0.1% to allow binding of antibodies to proteins while cultured cell move directly to the antibody binding step. After removing the insoluble debris by centrifuging at 14000g for 10 min, the lysate was precleaned with protein-A agarose beads (16-157; Millipore) for 1hr with slow rotation to remove non-specificity binding and incubated with specific antibodies overnight with slow rotation at 4°C. The next day the antibody-protein-DNA complex was purified by adding protein A-agarose beads and incubate for 4hr with slow rotation, followed by washing with low salt buffer, high salt buffer, no salt buffer, LiCl buffer and TE buffer and finally eluted into elution buffer (0.1M NaHCO3, 1% SDS). Reverse cross-link and DNA purification was performed and the sample were prepared into libraries using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme) following the manufacturer’s instruction. The ChIP-seq libraries were sequenced using an Illumina Novaseq6000 platform.

tag: tissue

value: cortex

tag: cell line

tag: cell type

value: cortex neuron

tag: genotype

value: G del


title: ChIP_g_del_CTCF_rep1


title: ChIP_FG_both_DEL_Rad21_rep2

value: FG del


title: ChIP_FG_both_DEL_Rad21_rep1


title: ChIP_CBSF_del_Rad21_rep2

value: F del


title: ChIP_CBSF_del_Rad21_rep1


title: ChIP_WT_H3K9me2_rep3

data_processing:
Paired-end reads were aligned to the mouse genome (M. musculus, UCSC mm9) or human genome(GRCh37/hg19) using Bowtie (version 1.2.3).
Sam files were then converted into Bam files and indexed. BedGraph files were generated using bigWigToBedGraph software with Bam file as input.
Assembly: M. musculus, UCSC mm9 or H.Sapiens UCSC hg19
Supplementary files format and content: bigwig and bedGraph files suitable for viewing on UCSC

extract_protocol:
2 × 106 of cortex neurons or cultured cell were used for one experiment. Neuron cells were first dissected and digested using 0.00625% collagenase.
The neuron suspension or cultured cell were cross-linked using 1% formaldehyde in 10% FBS/PBS for 10 min at room temperature followed by washing twice with PBS solution containing proteinase inhibitors (Roche). Cells were then resuspended and lysed twice with 1ml prechilled lysis buffer containing proteinase inhibitors (Roche) for 10 min with slow rotations. For neuron sample, additional SDS was then added to the lysis solution to adjust final SDS concentration to 0.4% to help sonication. Cells were then sonicated to break DNA fragments to about 100-10000 bp using the Bioruptor system (25% energy, with working time 15s and resting time of 45s, 20cycles). After sonication, lysis buffer not containing SDS was added to adjust final SDS concentration to 0.1% to allow binding of antibodies to proteins while cultured cell move directly to the antibody binding step. After removing the insoluble debris by centrifuging at 14000g for 10 min, the lysate was precleaned with protein-A agarose beads (16-157; Millipore) for 1hr with slow rotation to remove non-specificity binding and incubated with specific antibodies overnight with slow rotation at 4°C. The next day the antibody-protein-DNA complex was purified by adding protein A-agarose beads and incubate for 4hr with slow rotation, followed by washing with low salt buffer, high salt buffer, no salt buffer, LiCl buffer and TE buffer and finally eluted into elution buffer (0.1M NaHCO3, 1% SDS). Reverse cross-link and DNA purification was performed and the sample were prepared into libraries using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme) following the manufacturer’s instruction. The ChIP-seq libraries were sequenced using an Illumina Novaseq6000 platform.

value: cortex-neuron

value: neuron

value: wildtype

tag: antibody

value: Abcam ab1220


title: ChIP_WT_H3K4me3_rep3

value: Millipore 17-614


title: ChIP_WT_H3K9ac_rep3

value: Millipore 06-942


title: ChIP_WT_H3K9me3_rep3

value: Millipore 07-442


title: ChIP_FG_DEL_H3K9me3_rep2

value: CBSfg del -/-


title: ChIP_FG_DEL_H3K4me1_rep2

value: Abcam ab8895


title: ChIP_F_DEL_H3K9me3_rep2

value: CBSf del -/-


title: ChIP_FG_DEL_H3K9ac_rep2


title: ChIP_WT_H3K36me3_rep2

value: Abcam ab9050


title: ChIP_WT_Rad21_rep2

value: Abcam ab992


title: ChIP_FG_DEL_H3K9me2_rep2

value: cortex


title: ChIP_WT_for_g_del_CTCF_rep1

value: CTCF

value: cortex neuron


title: ChIP_F_DEL_H3K4me3_rep2


title: ChIP_F_DEL_H3K4me1_rep2


title: ChIP_g_del_CTCF_rep2

value: G del


title: ChIP_WT_K27ac_rep3

value: Abcam ab4729


title: ChIP_WT_K27ac_rep4

value: cortex-neuron


title: ChIP_WT_K27ac_rep5

value: neuron


title: ChIP_WT_K27ac_rep6

value: wildtype


title: ChIP_WT_CTCF_rep9

value: Millipore 07-729


title: ChIP_WT_K27ac_rep7


title: ChIP_HS7L_del_K27ac_rep2

value: HS7L_del -/-


title: ChIP_HS51bL_to_HS20_del_K27ac_rep2

value: HS51bL_to_HS20_del -/-


title: ChIP_HS7L_del_K27ac_rep1


title: ChIP_HS51bL_to_HS20_del_K27ac_rep1


title: ChIP_HS51bL_to_HS18_del_K27ac_rep2

value: HS51bL_to_HS18_del -/-


title: ChIP_F_DEL_H3K9me2_rep2

value: Abcam ab1220


title: ChIP_HS51bL_to_HS18_del_K27ac_rep1


title: ChIP_HS51bL_del_K27ac_rep1

value: HS51bL_del -/-


title: ChIP_HS18_to_HS20_del_K27ac_rep1


title: ChIP_F_DEL_H3K36me3_rep2

value: CBSf del -/-


title: ChIP_HS19_to_HS20_del_K27ac_rep1


title: ChIP_HS18_to_HS20_del_K27ac_rep2


title: ChIP_HS19_to_HS20_del_K27ac_rep2


title: ChIP_HS51bL_del_K27ac_rep2


title: ChIP_WT_K27ac_rep8


title: ChIP_HS18_del_K27ac_rep2

value: HS18 del -/-


title: ChIP_FG_del_CTCF_rep2

value: CBSfg del -/-


title: ChIP_HS18_del_K27ac_rep1

value: cortex


title: ChIP_FG_del_CTCF_rep1


title: ChIP_F_del_CTCF_rep2


title: ChIP_F_del_CTCF_rep1


title: ChIP_CBSa_K27ac_rep2

value: CBSa mut -/-


title: ChIP_WT_CTCF_rep11


title: ChIP_WT_CTCF_rep10


title: ChIP_CBSa_CTCF_rep2


title: ChIP_CBSa_K27ac_rep1


title: ChIP_FG_CTCF_rep2

data_processing:
For ChIP-seq and ATAC-seq data, paired-end reads were aligned to the mouse genome (M. musculus, UCSC mm9) using Bowtie (version 1.2.3).
Sam files were then converted into Bam files and indexed. BedGraph files were generated using bigWigToBedGraph software with Bam file as input.
Assembly: M. musculus, UCSC mm9
Supplementary files format and content: bigwig and bedGraph files suitable for viewing on UCSC

value: FG del -/-


title: ChIP_F_CTCF_rep1

value: F del -/-


title: ChIP_FG_CTCF_rep1


title: ChIP_A_CTCF_rep2

value: A mut -/-


title: ChIP_A_CTCF_rep1


title: ChIP_WT_CTCF_rep7


title: ChIP_WT_CTCF_rep8


title: ChIP_WT_CTCF_rep6


title: ChIP_WT_CTCF_rep5


title: ChIP_WT_CTCF_rep4


title: ChIP_WT_CTCF_rep2


title: ChIP_WT_CTCF_rep3


title: ChIP_WT_K27ac_rep1

value: Abcam ab4729


title: ChIP_DE_K27ac_rep1

value: neuron

value: D-E del -/-


title: ChIP_HS7L_K27ac_rep1

value: HS7L del -/-


title: ChIP_DE_K27ac_rep2


title: ChIP_BCD_K27ac_rep2

value: BCD del -/-


title: ChIP_BE_K27ac_rep2

value: B-E del -/-


title: ChIP_BE_K27ac_rep1


title: ChIP_E_K27ac_rep1

value: E del -/-


title: ChIP_D_K27ac_rep2

value: D del -/-


title: ChIP_CBSa_CTCF_rep1

value: cortex-neuron

value: Millipore 07-729


title: ChIP_F_CTCF_rep2


title: ChIP_E_K27ac_rep2


title: ChIP_D_K27ac_rep1


title: ChIP_BC_K27ac_rep2

value: BC del -/-


title: ChIP_A_K27ac_rep2


title: ChIP_A_K27ac_rep1


title: ChIP_BC_K27ac_rep1


title: ChIP_WT_for_f_and_fg_del_K27ac_rep2

value: wildtype


title: ChIP_FG_del_K27ac_rep1

value: cortex


title: ChIP_HS7L_K27ac_rep2


title: ChIP_WT_for_f_and_fg_del_K27ac_rep1


title: ChIP_WT_K27ac_rep2


title: ChIP_WT_CTCF_rep1


title: ChIP_f_del_K27ac_rep2


title: ChIP_f_del_K27ac_rep1


title: ChIP_WT_Rad21_rep1

value: Abcam ab992


title: ChIP_BCD_K27ac_rep1


title: ChIP_WT_H3K9me3_rep2

value: Millipore 07-442


title: ChIP_WT_H3K9me2_rep2

value: Abcam ab1220


title: ChIP_WT_H3K9ac_rep2

value: Millipore 06-942


title: ChIP_WT_H3K9ac_rep1


title: ChIP_WT_H3K4me3_rep2

value: Millipore 17-614


title: ChIP_FG_DEL_H3K4me3_rep2

value: neuron

value: FG del -/-


title: ChIP_FG_del_K27ac_rep2

value: Abcam ab4729


title: ChIP_FG_DEL_H3K4me3_rep1


title: ChIP_FG_DEL_H3K9me3_rep1


title: ChIP_FG_DEL_H3K9me2_rep1


title: ChIP_WT_H3K9me2_rep1


title: ChIP_WT_H3K4me1_rep1

value: Abcam ab8895


title: ChIP_FG_DEL_H3K9ac_rep1


title: ChIP_WT_H3K36me3_rep1

value: Abcam ab9050


title: ChIP_WT_H3K4me3_rep1


title: ChIP_FG_DEL_H3K4me1_rep1


title: ChIP_FG_DEL_H3K36me3_rep1


title: ChIP_F_DEL_H3K9me3_rep1

value: F del -/-


title: ChIP_F_DEL_H3K4me3_rep1


title: ChIP_F_DEL_H3K9ac_rep2


title: ChIP_FG_DEL_H3K36me3_rep2


title: ChIP_F_DEL_H3K4me1_rep1


title: ChIP_F_DEL_H3K9me2_rep1


title: ChIP_WT_H3K9me3_rep1


title: ChIP_F_DEL_H3K36me3_rep1


title: H3K27ac_double_KO_del_sample3_rep2

data_processing:
Paired-end reads were aligned to the human genome(GRCh37/hg19) using Bowtie (version 1.2.3).
Sam files were then converted into Bam files and indexed. BedGraph files were generated using bigWigToBedGraph software with Bam file as input. Peaks were called using macs14
Assembly: H.Sapiens UCSC hg19
Supplementary files format and content: bigwig and bedGraph files suitable for viewing on UCSC

organism: Homo sapiens

source_name: cultured cell

extract_protocol:
2 × 106 of cultured cell were used for one experiment. Cells were resuspended in 10 ml 10% FBS/PBS (v/v)
Cultured cell were cross-linked using 1% formaldehyde in 10% FBS/PBS for 10 min at room temperature followed by washing twice with PBS solution containing proteinase inhibitors (Roche). Cells were then resuspended and lysed twice with 1ml prechilled lysis buffer containing proteinase inhibitors (Roche) for 10 min with slow rotations. Cells were then sonicated to break DNA fragments to about 100-10000 bp using the Bioruptor system (25% energy, with working time 15s and resting time of 45s, 20cycles). After sonication, cultured cell move directly to the antibody binding step. After removing the insoluble debris by centrifuging at 14000g for 10 min, the lysate was precleaned with protein-A agarose beads (16-157; Millipore) for 1hr with slow rotation to remove non-specificity binding and incubated with specific antibodies overnight with slow rotation at 4°C. The next day the antibody-protein-DNA complex was purified by adding protein A-agarose beads and incubate for 4hr with slow rotation, followed by washing with low salt buffer, high salt buffer, no salt buffer, LiCl buffer and TE buffer and finally eluted into elution buffer (0.1M NaHCO3, 1% SDS). Reverse cross-link and DNA purification was performed and the sample were prepared into libraries using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme) following the manufacturer’s instruction. The ChIP-seq libraries were sequenced using an Illumina Novaseq6000 platform.

value: cultured cell

value: Human embryonic kidney 293T

value: CBS3 and CBS5 del -/-


title: H3K27ac_double_KO_del_sample2_rep1


title: H3K27ac_double_KO_del_sample1_rep2


title: H3K27ac_double_KO_del_sample2_rep2


title: ChIP_F_DEL_H3K9ac_rep1


title: H3K27ac_double_KO_del_sample1_rep1


title: H3K27ac_CBS5_KO_alone

value: CBS5 del -/-


title: H3K27ac_CBS3_KO_alone

value: CBS3 del -/-


title: H3K27ac_293T_WT_for_double_CBS_KO_rep1

value: wildtype


title: CTCF_del_sample3_rep2


title: CTCF_del_sample1_rep2


title: H3K27ac_293T_WT_for_double_CBS_KO_rep2


title: CTCF_del_sample1_rep1


title: CTCF_del_sample2_rep2


title: CTCF_del_sample2_rep1


title: CTCF_CBS5_del_rep2


title: CTCF_del_sample3_rep1


title: H3K27ac_double_KO_del_sample3_rep1


title: 293T_WT_H3K27ac_rep1


title: CTCF_CBS3_del_rep1


title: 293T_WT_CTCF_rep1


title: mouse olfactory bulb, 50 μm-spot, rep3 [MOB-50-3]

status: Public on Oct 24 2023

city: shanghai

first: di

last: sun

address: pujian road 160

department: institute of molecular medicine

institute: Renji Hospital, School of Medicine, Shanghai Jiao Tong University

description: barcode.txt

library_source: transcriptomic

data_processing:
library strategy: Spatial transcriptomic sequencing
The H&E image was used to accurately distinguish between tissues and backgrounds, with spots outside the tissue being removed. Spots with fewer than 50 observed genes (UMI > 2) were filtered out. And genes with counts in less than 10 spatial spots were discarded. Mitochondrial and ribosomal genes were also removed.
Giotto suite was used to perform spatial gene expression normalization, plotting, dimensionality reduction, spatial domains detection, and differential gene expression analysis. To incorporate spatial information into clustering, we utilized a hidden Markov random field (HMRF) model integrated with Giotto and allocated each cell to one of k spatial domains based on the accepted beta parameter. Furthermore, Giotto's findScanMarkers function was employed to annotate each spatial domain using identified markers.
Assembly: mm10, hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: total RNA

source_name: mouse olfactory bulb

extract_protocol:
Spatial transcriptomic sequencing by Decoder-seq, details in Methods "Dendrimeric DNA coordinate barcoding arrays capture spatial mRNAs of tissues with high efficiency"
Spatial transcriptomic sequencing by Decoder-seq, details in Methods "Amplification, library construction, and sequencing"

value: mouse olfactory bulb


title: mouse olfactory bulb, 15 μm-spot, rep3 [MOB-15-3]

description: barcode.txt


title: Plasma-Stroke-Day 30-Discovery [SH-016-V3-P1]

status: Public on Oct 04 2023

type: RNA

city: Washington

first: Matthew

last: Edwardson

state: DC

address: 4000 Reservoir Rd NW, Building D, Room 207

department: Neurology

country: USA

institute: Georgetown University

description: Stroke

data_processing:
Matrix non-normalized raw Ct values were generated by the Thermo Fisher Connect platform.  Matrix normalized values were generated by delta Ct method using mean miR-16-5p Ct after averaging across all 16 subarrays for each sample
Matrix normalized sheet contains normalized delta Ct values, fold-change sheet contains mean delta Ct stroke vs. mean delta Ct control

label: FAM

source_name: Plasma

label_protocol: Complementary DNA (cDNA) libraries were created using the TaqMan Advanced miRNA cDNA Synthesis Kit (Applied Biosystems, Foster City, CA) using 2 uL of RNA at 5 ng/uL according to the manufacturer's instructions

growth_protocol: Fasting blood samples were collected in the morning by venipuncture using EDTA tubes (Cardinal Health, OH, USA).  Samples were placed on ice, delivered to the biorepository, and centrifuged at 2600 RPM for 10 min at 20○ C.  Platelet-poor plasma was carefully removed with a pipette without disturbing the buffy coat and frozen at -80○ C.  All sample processing was performed within approximately 4 hrs from sample collection.

extract_protocol: The aqueous phase containing total RNA fraction was processed further using the Qiagen miRNeasy Serum/Plasma Kit (QIAGEN, Valencia, CA) to isolate total RNA enriched in miRNA

treatment_protocol: Total RNA was isolated from plasma by first homogenizing plasma samples by adding 1000µL of Qiazol reagent (QIAGEN, Valencia, CA) to 200 µL of plasma and vortexing.  The lysate was further mixed with 200µL of chloroform, vortexed and centrifuged at 4?C for 30 minutes.

tag: disease state

value: Stroke

value: Plasma

tag: study

value: MORSE

tag: cohort

value: Discovery

tag: time point

value: Day 30


title: Plasma-Stroke-Day 30-Discovery [SH009-V3-P1]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [SH-004-V3-P1]

description: Stroke


title: Plasma-Stroke-Day 30- [SH-005-V3-P1]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [SH012-V3-P1]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [SH010-V3-P1]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [SH014-V3-P1]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [SH-015-V3-P1]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [SH-003-V3-P1]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [SH-002-V3-P1]

description: Stroke


title: H3K27ac_293T_WT_for_single_CBS_KO


title: Plasma-Stroke-Day 15-Discovery [SH-016-V2-P1]

description: Stroke

value: Day 15


title: Plasma-Stroke-Day 15-Discovery [SH014-V2-P1]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [SH012-V2-P1]

description: Stroke


title: 293T_WT_CTCF_rep2


title: Plasma-Stroke-Day 15-Discovery [SH-004-V2-P1]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [SH010-V2-P1]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [SH-003-V2-P1]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [SH-002-V2-P1]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [SH-016-V1-P1]

description: Stroke

value: Day 05


title: Plasma-Stroke-Day 15-Discovery [SH-009-V2-P1]

description: Stroke


title: Plasma-Stroke-Day 05- [SH013-V1-P1]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [SH012-V1-P1]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [SH015-V1-P1]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [SH014-V1-P1]

description: Stroke


title: Plasma-Stroke-Day 05- [SH-005-V1-P1]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [SH-004-V1-P1]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [SH-009-V1-P1]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [SH010-V1-P1]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [SH-003-V1-P1]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [142424]

description: Stroke

value: CPASS

value: Validation


title: Plasma-Stroke-Day 05-Discovery [SH-002-V1p1]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [WHC018-0]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [138057]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [WHC007-0]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [SH-015-V2-P1]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [126050]

description: Stroke


title: Plasma-Stroke-- [131223]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [142545]

description: Stroke


title: Plasma-Stroke-- [130390]

description: Stroke


title: Plasma-Stroke-- [138292]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [140421]

description: Stroke


title: Plasma-Stroke-- [134871]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [140630]

description: Stroke


title: Plasma-Stroke-- [WHC20-0]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [128004]

description: Stroke


title: Plasma-Stroke-- [135259]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [132112]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [142342]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [141119]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [133471]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [131449]

description: Stroke


title: Plasma-Stroke-- [128456]

description: Stroke


title: Plasma-Stroke-- [WHC-11-0]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [143950]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [139004]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [128292]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [WHC14-0]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [128667]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [WHC005-0.A5]

description: Stroke


title: Plasma-Stroke-- [133200]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [WHC013-0]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [127564]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [126485]

description: Stroke


title: Plasma-Stroke-- [126264]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [127527]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [WHC006-0]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [142483]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [133835]

description: Stroke


title: Plasma-Stroke-- [132403]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [127809]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [133867]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [126936]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [126979]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [136035]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [WHC004-0]

description: Stroke


title: Plasma-Stroke-- [WHC009-0]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [132751]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [130869]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [128768]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [134924]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [133273]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [135027]

description: Stroke


title: Plasma-Stroke-- [CPASSCEA_019]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [WHC012-0]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [129041]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [WHC005-0.A1]

description: Stroke


title: Plasma-Stroke-- [142429]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [134378]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [127929]

description: Stroke


title: Plasma-Stroke-- [125851]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [126253]

description: Stroke


title: Plasma-Stroke-Day 15-Validation [134587]

description: Stroke


title: Plasma-Control-T1-Discovery/Validation [146081]

description: Control

value: Control

value: BIOREC

value: Discovery/Validation


title: Plasma-Stroke-- [126135]

description: Stroke


title: Plasma-Control-T1-Discovery/Validation [147029]

description: Control


title: Plasma-Control-T1-Discovery/Validation [148378]

description: Control


title: Plasma-Control-T1-Discovery [147496]

description: Control


title: Plasma-Control-T1-Discovery [142409]

description: Control


title: Plasma-Control-T1-Discovery [139774]

description: Control


title: Plasma-Control-T1-Discovery/Validation [141569]

description: Control


title: Plasma-Control-T1-Discovery [144564]

description: Control


title: Plasma-Control-T1-Validation [146619]

description: Control


title: Plasma-Control-T1-Discovery/Validation [146173]

description: Control


title: Plasma-Control-T1-Discovery/Validation [151114]

description: Control


title: Plasma-Control-T1-Discovery/Validation [144533]

description: Control


title: Plasma-Control-T1-Discovery [145678]

description: Control


title: Plasma-Stroke-Day 15-Validation [127805]

description: Stroke


title: Plasma-Control-T1-Discovery [146209]

description: Control


title: Plasma-Stroke-Day 15-Validation [134228]

description: Stroke


title: Plasma-Control-T1-Validation [151668]

description: Control


title: Plasma-Control-T1-Discovery [147591]

description: Control


title: Plasma-Control-T1-Discovery/Validation [147834]

description: Control


title: Plasma-Control-T1-Discovery/Validation [142455]

description: Control


title: Plasma-Control-T1-Discovery/Validation [151532]

description: Control


title: Plasma-Control-T1-Discovery [147492]

description: Control


title: Plasma-Control-T1-Discovery/Validation [151524]

description: Control


title: Plasma-Control-T1-Validation [151649]

description: Control


title: Plasma-Control-T1-Validation [151100]

description: Control


title: Plasma-Control-T1-Validation [151688]

description: Control


title: Plasma-Control-T1-Discovery [144547]

description: Control


title: Plasma-Control-T1-Validation [147141]

description: Control


title: Plasma-Control-T1-Validation [146655]

description: Control


title: Plasma-Control-T1-Discovery [143098]

description: Control


title: Plasma-Control-T1-Discovery [142248]

description: Control


title: Plasma-Control-T1-Validation [151722]

description: Control


title: Plasma-Control-T1-Discovery [148050]

description: Control


title: Plasma-Control-T1-Validation [151528]

description: Control


title: Plasma-Control-T1-Discovery [143242]

description: Control


title: Plasma-Control-T1-Discovery [151823]

description: Control


title: Plasma-Control-T1- [151755]

description: Control


title: Plasma-Control-T1-Validation [146545]

description: Control


title: Plasma-Control-T1-Validation [151548]

description: Control


title: Plasma-Control-T1-Validation [145115]

description: Control


title: Plasma-Control-T1-Discovery/Validation [146615]

description: Control


title: Plasma-Control-T1-Discovery/Validation [147258]

description: Control


title: Plasma-Control-T1-Discovery [146088]

description: Control


title: Plasma-Control-T1-Discovery/Validation [147357]

description: Control


title: Plasma-Control-T1-Discovery [140717]

description: Control


title: Plasma-Control-T1-Validation [147511]

description: Control


title: Plasma-Control-T1-Validation [151683]

description: Control


title: Plasma-Control-T1-Discovery/Validation [151051]

description: Control


title: Plasma-Control-T1-Discovery/Validation [151076]

description: Control


title: Plasma-Control-T1-Validation [145621]

description: Control


title: Plasma-Control-T1-Validation [143206]

description: Control


title: Plasma-Control-T1-Discovery/Validation [144449]

description: Control


title: Plasma-Control-T1-Discovery/Validation [147480]

description: Control


title: Plasma-Control-T1-Validation [151713]

description: Control


title: Plasma-Control-T1-Validation [151658]

description: Control


title: Plasma-Control-T1-Discovery [144481]

description: Control


title: Plasma-Control-T1-Discovery/Validation [142976]

description: Control


title: Plasma-Control-T1-Discovery/Validation [143994]

description: Control


title: Plasma-Control-T1-Discovery/Validation [146683]

description: Control


title: Plasma-Control-T1-Discovery/Validation [144445]

description: Control


title: Plasma-Control-T1-Discovery/Validation [144523]

description: Control


title: Plasma-Control-T1- [151717]

description: Control


title: Plasma-Control-T1-Validation [151127]

description: Control


title: Plasma-Control-T1- [147446]

description: Control


title: Plasma-Control-T1-Validation [146231]

description: Control


title: Plasma-Control-T1-Discovery/Validation [145674]

description: Control


title: Plasma-Control-T1-Discovery/Validation [147019]

description: Control


title: Plasma-Control-T1-Discovery/Validation [147927]

description: Control


title: Plasma-Control-T1- [151932]

description: Control


title: Plasma-Control-T1-Discovery/Validation [148069]

description: Control


title: Plasma-Stroke-Day 30-Discovery [147011]

description: Stroke


title: Plasma-Control-T1-Validation [151759]

description: Control


title: Plasma-Control-T1-Validation [151837]

description: Control


title: Plasma-Stroke-Day 30-Discovery [133656]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [132762]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [144690]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [134776]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [140618]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [143866]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [134970]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [144010]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [130237]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [143614]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [131605]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [131710]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [139852]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [128793]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [138595]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [132001]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [143542]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [145081]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [132477]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [136143]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [140401]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [139906]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [127842]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [129822]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [141999]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [131453]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [132016]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [145746]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [135036]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [140364]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [131457]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [140704]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [131234]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [132032]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [143645]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [138785]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [142537]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [138894]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [139211]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [137671]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [130722]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [140536]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [129858]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [139720]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [133352]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [146679]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [132643]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [134491]

description: Stroke


title: Plasma-Stroke-Day 30-Discovery [134806]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [144513]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [145442]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [143712]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [139668]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [134689]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [143808]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [131486]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [143426]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [138465]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [131576]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [128580]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [143317]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [131841]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [132005]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [137531]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [139929]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [135712]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [144664]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [129418]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [131310]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [140425]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [130028]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [139705]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [141589]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [134851]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [127628]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [129558]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [140489]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [139981]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [131314]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [CPASSCR_054]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [139544]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [131601]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [131940]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [134515]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [140001]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [139072]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [142391]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [138696]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [130302]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [146541]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [134382]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [133245]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [134487]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [142586]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [140261]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [139531]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [131391]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [143376]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [143691]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [131482]

description: Stroke


title: Plasma-Stroke-Day 15-Discovery [138817]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [145140]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [132487]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [143601]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [144397]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [129793]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [138377]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [128504]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [131147]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [131647]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [139814]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [129202]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [143251]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [144560]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [137174]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [127568]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [139673]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [135177]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [131785]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [141529]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [129400]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [134572]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [131511]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [139892]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [139459]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [131195]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [130754]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [138581]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [139888]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [131703]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [142445]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [142268]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [134402]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [138994]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [138789]

description: Stroke


title: Plasma-Stroke-Day 05-Discovery [130157]

description: Stroke


title: WT long read

status: Public on Sep 30 2023

city: WUHAN

first: heng

middle: zhi

last: du

address: 1095 Jiefang Dadao, Wuhan City, Hubei Province, China

institute: Wuhan Tongji Hospital

data_processing:
PacBio SMRTlink generated raw subreads were converted into HiFi circular consensus sequences (CCS)
PacBio IsoSeq v3 pipeline was used to demultiplex the barcodes and remove primers. Additional refine steps included trimming polyA tails and removing concatemers to generate Full Length Non-Concatemer (FLNC) reads.
Hierarchical clustering, iterative clustering and merging steps were performed to obtain consensus isoforms and the full-length (FL) consensus sequences
The high-quality FL transcripts were mapped to the reference genome by using the minimap2
Supplementary files format and content: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: heart

growth_protocol: AC16 cells (ScienCell research laboratories, Carlsbad, CA) were from a single fetal donor, not pooled, and were maintained in medium (ScienCell research laboratories, Cat. #6201), according to the instruction manual.   medium consists of basal medium, foetal bovine serum (FBS),  AC16 cells growth supplement, and penicillin/streptomycin solution.

extract_protocol:
RNA was harvested using Trizol reagent following the instructions.
All of our RNA-seq projects used strand specific kits to construct the libraries.By using next-generation sequencing (NGS) technology, paired-end (PE) sequencing of these libraries was performed based on Illumina HiSeq sequencing platform

value: heart

value: AC16 cells

value: cardiomyocytes

value: WT


title: tRFs/tiRNAs NG3

status: Public on Aug 01 2023

city: Guangzhou

first: Shineng

last: Zhang

state: Guangdong

address: No.107 Yanjiang West Road

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

data_processing:
Total RNA from each sample was quantified using a NanoDrop ND-1000 instrument. Total RNA samples were first pretreated as following to remove some RNA modifications that interfere with small RNA-seq library construction: 3’-aminoacyl (charged) deacylation to 3’-OH for 3’-adaptor ligation, 3’-cP (2’,3’-cyclic phosphate) removal to 3’-OH for 3’ -adaptor ligation, 5’-OH (hydroxyl group) phosphorylation to 5’-P for 5’-adaptor ligation, m1A and m3C demethylation for efficient reverse transcription. Then pretreated total RNA was used to prepare the sequencing library in the following steps: 1) 3’-adapter ligation; 2) 5’-adapter ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of 134∼160bp PCR amplified fragments (corresponding to 14∼40nt small RNA size range). The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as sequencing clusters and sequenced for 50 cycles on Illumina NextSeq 500 system per the manufacturer’s instructions.
Image analysis and base calling are performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8). Sequencing quality are examined by FastQC and trimmed reads (pass Illumina quality filter, trimmed 5’,3’-adaptor bases by cutadapt) are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software. The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2. The abundance of tRF & tiRNA and miRNA are evaluated using their sequencing counts and is normalized as counts per million of total aligned reads (CPM). The tRFs & tiRNAs and miRNAs differentially expressed are screened based on the count value with R package edgeR. Principal Component Analysis (PCA), Correlation Analysis, Pie plots, Venn plots, Hierarchical clustering, Scatter plots and Volcano plots are performed in R or perl environment for statistical computing and graphics of the expressed tRF & tiRNA.
Assembly: H19
Supplementary files format and content: tab-delimited text files include CPM values for each sample

source_name: pancreatic ductal adenocarcinoma

extract_protocol:
The total RNA were extracted with Trizol reagent (Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: pancreatic ductal adenocarcinoma

value: HPAF-II

tag: treatment

value: none glucose


title: tRFs/tiRNAs HG3

value: high glucose


title: DCRT-KO long read

value: DCRT-KO


title: tRFs/tiRNAs NG2


title: tRFs/tiRNAs HG2


title: tRFs/tiRNAs NG1


title: CD34M_GM

city: Los Angeles

first: Quen

last: Cheng

address: 10833 LeConte Ave

institute: UCLA

library_source: genomic single cell

data_processing:
Reads were trimmed, filtered, and aligned to mm10 genome, and peaks were called for each library using the cellranger-atac pipeline (10X Genomics) with default settngs
Assembly: mm10
Supplementary files format and content: 10X Genomics fragments.tsv file, where each line represents a unique ATAC-seq fragment captured by the assay

source_name: hematopoietic stem cell progenitors

growth_protocol: Bone marrow was isolated from C57Bl/6 mice.  HSPC populations were defined using lineage markers cocktail of biotinylated antibodies against CD5, CD11b, CD45R (B220), Gr- 1, 7-4, and Ter-119 and anti-biotin from Miltenyi Biotec; anti-c-Kit (CD117; clone 2B8), and anti-CD34 (clone RAM34) from BD Biosciences; anti-Sca-1 (clone D7), and anti-CD16/32 (clone 93) from BioLegend.

extract_protocol:
Nuclei were isolated using manufacturer’s recommendations (10X Chromium Single Cell ATAC)
Libraries were prepared using manufacturer’s recommenda ons (10X Chromium Single Cell ATAC). Four libraries (two cell types, two treatment condi ons) were sequenced on a Next-seq 500/550 High Output Kit v2.5 (150 cycles).

treatment_protocol: Cells were treated with murine GM-CSF (50 ng/mL) and/or M-CSF (50 ng/mL)

value: hematopoietic stem cell progenitors

value: GM-CSF + M-CSF


title: LKSM

value: LKS

value: M-CSF


title: LKSM_GM


title: CD34M


title: V19 cells, WT, 96h 2i treatment, biol rep 2

status: Public on Jul 18 2023

city: San Antonio

first: Alexey

middle: A

last: Soshnev

state: TX

address: 1 UTSA Cir

department: Neuroscience, Developmental, and Regenerative Biology

institute: University of Texas at San Antonio

data_processing:
Quality assessment of the bulk-RNA-seq data was performed using Multiqc v1.14.
Samples were aligned to the GRCm39 genome using STAR (v. 2.7.10b).
We used featureCounts (v. 2.0.3) to generate a raw counts matrix.
We then created a transformed counts matrix using DESeq2’s (v. 1.40.1) variance-stabilizing-transformation to be used for exploratory analyses of the data such as principal component analysis and clustering. Samples were filtered to only keep gene rows with at least five total counts or higher.
Assembly: mm39
Supplementary files format and content: comma separated file includes raw counts for each sample
Supplementary files format and content: comma separated file includes variance stabilized counts for each sample
Supplementary files format and content: comma separated file is a count matrix that controls for unwanted variation due to batch effects. To do this, we performed RUVg (estimating factors of unwanted variation using control genes) using the RUVseq implementation in DESeq2.

growth_protocol: Cells were grown in vacuum-plasma treated plastic flasks and dishes (Falcon) preincubated with 0.1% gelatin (Embryomax Millipore, ES-006-B), in mES cell media containing Knock-Out DMEM (Gibco 10829018) supplemented with 15% FBS (Gemini 100-525), 2 mM L-Glutamine (Gibco 25030081), 100 U/ml Pennicillin/Streptomycin (Gibco 15140122), 0.1 mM β-mercaptoethanol (Fisher O3446I-100) and 1:1000 LIF (Gemini 400-495). Cells were routinely seeded at 200,000 per 5 ml in T25 with media exchange every 24 hours, and passaged every 48 hours.

extract_protocol:
At specified time points of the time course experiment, media was aspirated from the wells of 12-well plates, followed by a gentle rinse with warm PBS (Corning 21-040-CV) immediate lysis in 1 ml or TRIzol reagent (Thermo 15596026) added directly into the well. Following chloroform addition, the aqueous phase was separated using 5Prime PhaseLock Heavy tubes (QuantaBio 2302830), precipitated with isopropanol, and washed twice with 75% ethanol. Air-dried RNA was resuspended in RNase-free water (Corning 46-000-CM), and 5 μg total RNA per sample were treated with DNAseI using Qiagen RNeasy on-column treatment and cleanup protocol (Qiagen 79254 and Qiagen 74104).
1 μg of DNaseI-treated total RNA was subjected to polyA enrichment using magnetic isolation (NEB E7490), and the mRNA-enriched fraction was converted to barcoded library using NEBNext Ultra II kit (NEB E7770) according to manufacturer’s instructions, using Ampure XP SPRI beads (Beckman Coulter A63881) for size selection, and 96 index primers for barcoding (NEB E6609). Molarity of each library was estimated from electrophoresis profile (Agilent Tapestation) and equimolar amounts were combined in one pool. Sample was sequenced in two Illumina NextSeq 500 High Output 75 SR flowcells, demultiplexed, and merged to combine two runs into single .fastq files

treatment_protocol: For 2i treatment, CHIR99021 and PD0325901 (both from Stemgent) were added at at 3 μM and 1 μM, respectively, and exchanged daily.

value: mouse embryonic stem cells

value: 2i - 96 hours

tag: time


title: V19 cells, WT, 96h 2i treatment, biol rep 3


title: V19 cells, WT, 96h 2i treatment, biol rep 1


title: 1A cells, EED KO, 96h 2i treatment, biol rep 2

value: EED knockout


title: 1A cells, EED KO, 96h 2i treatment, biol rep 1


title: Plasma-Stroke-Day 05-Discovery [140181]

description: Stroke

value: Stroke

value: Plasma

value: BIOREC

value: Discovery

value: Day 05


title: 1A cells, WT, 96h 2i treatment, biol rep 3

value: WT


title: 1A cells, WT, 96h 2i treatment, biol rep 2


title: 1A cells, WT, 96h 2i treatment, biol rep 1


title: 1A cells, EZH2 KO, 96h 2i treatment, biol rep 2

value: EZH2 knockout


title: 1A cells, EZH2 KO, 96h 2i treatment, biol rep 3


title: V19 cells, WT, 48h 2i treatment, biol rep 3

value: 2i - 48 hours


title: V19 cells, WT, 48h 2i treatment, biol rep 2


title: 1A cells, EZH2 KO, 96h 2i treatment, biol rep 1


title: tRFs/tiRNAs HG1

value: pancreatic ductal adenocarcinoma

value: HPAF-II

value: high glucose


title: V19 cells, WT, 48h 2i treatment, biol rep 1


title: 1A cells, EED KO, 48h 2i treatment, biol rep 3


title: 1A cells, EED KO, 48h 2i treatment, biol rep 2


title: 1A cells, WT, 48h 2i treatment, biol rep 1


title: 1A cells, EED KO, 48h 2i treatment, biol rep 1


title: 1A cells, WT, 48h 2i treatment, biol rep 3


title: 1A cells, EED KO, 96h 2i treatment, biol rep 3


title: 1A cells, EZH2 KO, 48h 2i treatment, biol rep 1


title: V19 cells, WT, 24h 2i treatment, biol rep 2

value: 2i - 24 hours


title: 1A cells, EZH2 KO, 48h 2i treatment, biol rep 3


title: V19 cells, WT, 24h 2i treatment, biol rep 3


title: 1A cells, EED KO, 24h 2i treatment, biol rep 3


title: 1A cells, EZH2 KO, 48h 2i treatment, biol rep 2


title: 1A cells, WT, 24h 2i treatment, biol rep 2


title: 1A cells, EED KO, 24h 2i treatment, biol rep 2


title: 1A cells, EZH2 KO, 24h 2i treatment, biol rep 2


title: 1A cells, WT, 24h 2i treatment, biol rep 1


title: 1A cells, EZH2 KO, 24h 2i treatment, biol rep 1


title: V19 cells, WT, 12h 2i treatment, biol rep 3

value: 2i - 12 hours


title: 1A cells, WT, 24h 2i treatment, biol rep 3


title: V19 cells, WT, 12h 2i treatment, biol rep 2


title: V19 cells, WT, 24h 2i treatment, biol rep 1


title: 1A cells, EZH2 KO, 24h 2i treatment, biol rep 3


title: V19 cells, WT, 12h 2i treatment, biol rep 1


title: 1A cells, EED KO, 12h 2i treatment, biol rep 3


title: 1A cells, EED KO, 12h 2i treatment, biol rep 2


title: 1A cells, EED KO, 12h 2i treatment, biol rep 1


title: 1A cells, WT, 12h 2i treatment, biol rep 2


title: 1A cells, WT, 48h 2i treatment, biol rep 2


title: 1A cells, WT, 12h 2i treatment, biol rep 3


title: 1A cells, WT, 12h 2i treatment, biol rep 1


title: 1A cells, EZH2 KO, 12h 2i treatment, biol rep 3


title: 1A cells, EZH2 KO, 12h 2i treatment, biol rep 2


title: 1A cells, EZH2 KO, 12h 2i treatment, biol rep 1


title: V19 cells, WT, 0h 2i treatment, biol rep 3


title: V19 cells, WT, 0h 2i treatment, biol rep 2


title: 1A cells, 1A cells, EED KO, 24h 2i treatment, biol rep 1


title: V19 cells, WT, 0h 2i treatment, biol rep 1


title: 1A cells, EED KO, 0h 2i treatment, bio rep 3


title: 1A cells, WT, 0h 2i treatment, biol rep 2


title: 1A cells, WT, 0h 2i treatment, bio rep 3


title: 1A cells, EED KO, 0h 2i treatment, biol rep 1


title: 1A cells, WT, 0h 2i treatment, biol rep 1


title: 1A cells, EZH2 KO, 0h 2i treatment, biol rep 2


title: 1A cells, EZH2 KO, 0h 2i treatment, biol rep 1


title: 1A cells, EZH2 KO, 0h 2i treatment, biol rep 3


title: mouse olfactory bulb, 50 μm-spot, rep2 [MOB-50-2]

status: Public on Jul 11 2023

description: barcode.txt

data_processing:
*library strategy: Spatial transcriptomic sequencing
The H&E image was used to accurately distinguish between tissues and backgrounds, with spots outside the tissue being removed. Spots with fewer than 50 observed genes (UMI > 2) were filtered out. And genes with counts in less than 10 spatial spots were discarded. Mitochondrial and ribosomal genes were also removed.
Giotto suite was used to perform spatial gene expression normalization, plotting, dimensionality reduction, spatial domains detection, and differential gene expression analysis. To incorporate spatial information into clustering, we utilized a hidden Markov random field (HMRF) model integrated with Giotto and allocated each cell to one of k spatial domains based on the accepted beta parameter. Furthermore, Giotto's findScanMarkers function was employed to annotate each spatial domain using identified markers.
Assembly: mm10, hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

value: mouse olfactory bulb


title: mouse hemibrain, 50 μm-spot [BRAIN-50-1]

description: barcode.txt

source_name: mouse hemibrain

value: mouse hemibrain


title: mouse olfactory bulb, 15 μm-spot, rep1 [MOB-15-1]

description: barcode.txt


title: mouse hippocampus, 15 μm-spot [HM-15-1]

description: barcode.txt

source_name: mouse hippocampus

value: mouse hippocampus


title: mouse olfactory bulb, 50 μm-spot, rep1 [MOB-50-1]

description: barcode.txt


title: mouse olfactory bulb, 15 μm-spot, rep2 [MOB-15-2]

description: barcode.txt


title: clear cell RCC, patient 2, tumor core [ccRCC-2-T]

description: barcode.txt

source_name: renal cancers

value: renal cancers

tag: tissue type

value: clear cell RCC

tag: subject id

value: patient 2


title: chromophobe RCC, patient 2, leading-edge [chRCC-2-L]

description: barcode.txt

value: chromophobe RCC


title: chromophobe RCC, patient 1, tumor core [chRCC-1-T]

description: barcode.txt

value: patient 1


title: clear cell RCC, patient 2, leading-edge [ccRCC-2-L]

description: barcode.txt


title: chromophobe RCC, patient 1, leading-edge [chRCC-1-L]

description: barcode.txt


title: clear cell RCC, patient 3, leading-edge [ccRCC-3-L]

description: barcode.txt

value: patient 3


title: clear cell RCC, patient 1, tumor core [ccRCC-1-T]

description: barcode.txt


title: Day6_Heps_S4_Pf+ [L3Pf8_S12]

status: Public on Jun 01 2023

city: Seattle

first: Research

middle: Scientific

last: Computing

state: WASHINGTON

address: 818 Stewart Street

department: Research Scientific Computing

institute: Seattle Children's Research Institute

description: Smart-seq2 coupled with NEXTERA XT

data_processing:
Plasmodium falciparum sequencing reads mapped to the genome ensemble containing H. sapiens (GRCh38.v106), M. musculus (GRCm39.v106) P. falciparum genome (PlasmoDB-58_Pfalciparum3D7) with STAR 2.7.9.
The alignment was completed with defaul parameters with addition of "--twopassMode Basic" for high quality splice juncion quantification.
The gene count matrix was produced with "--quantMode GeneCounts".
Gene level counts were normalized to transcripts per million (TPM).
Assembly: mm39
Supplementary files format and content: csv files with raw counts matrix for plasmodium faciparum and plasmodium vivax.

organism: Plasmodium falciparum

source_name: FRGN huHep mouse

growth_protocol: FRGN huHep mice were intravenously infected with 3 million PfCsPGFP spz/mouse.

extract_protocol:
Plasmodium falciparum RNA, from sorted infected primary human hepatocytes, was extracted using the miRNeasy Micro Kit (QIAGEN) according to the manufacturer’s instructions, including on-column DNase digestion.
Plasmodium vivax RNA was extracted using TRIzol (Thermo Fisher) and purified using RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions.
RNA libraries for plasmodium falciparum RNA-seq were prepared using SMART-seq v4 Ultra Low Input (Clontech).
RNA libraries for plasmodium vivax RNA-seq were prepared according to the SureSelect XT RNA Target Enrichment for Illumina Multiplexed Sequencing protocol from Agilent.

treatment_protocol:
Harvested hepatocytes on day2, 4,5 or 6 were digested with perfusion buffer I (0.5 mM EGTA in 1x DPBS without Ca2+ and Mg2+) and II (50 ug/ml liberase TL with 800 uM CaCl2 in 1x DPBS), respectively.
The hepatocytes were dispersed in 1x DMEM complete medium and centrifuged twice at low speed (50 rpm) for 2 min at 10oC.
The cell pellet was resuspended in the complete medium and used for FACS sorting.

value: FRGN huHep mouse

value: Plasmodium falciparum NF54

value: hepatocytes

tag: rna label

value: Infected

tag: sample id cat

tag: to concatenate

value: No


title: Day6_Heps_S2_Pf+ [L2Pf6_S6]

description: Smart-seq2 coupled with NEXTERA XT

value: Yes


title: 1A cells, EED KO, 0h 2i treatment, biol rep 2

value: mouse embryonic stem cells

value: EED knockout


title: Day6_Heps_TR2_Pf+ [L2Pf6_S11_TR2]

description: Smart-seq2 coupled with NEXTERA XT


title: Day6_Heps_TR1_Pf+ [L1Pf6_S5_TR2]

description: Smart-seq2 coupled with NEXTERA XT


title: Day6_Heps_S1_Pf+ [L1Pf6_Day6.GFP]

description: Smart-seq2 coupled with NEXTERA XT


title: clear cell RCC, patient 1, leading-edge [ccRCC-1-L]

description: barcode.txt


title: Day6_Heps_TR2_Pf- [L2Pf5_S10_TR2]

description: Smart-seq2 coupled with NEXTERA XT

value: Uninfected


title: Day6_Heps_TR1_Pf- [L1Pf5_S4_TR2]

description: Smart-seq2 coupled with NEXTERA XT


title: Day6_Heps_S1_Pf- [L1Pf5_Day6.NoGFP]

description: Smart-seq2 coupled with NEXTERA XT


title: Day5_Heps_S1_Pf- [L2Pf5_S7]

description: Smart-seq2 coupled with NEXTERA XT


title: Day5_Heps_S3_Pf+ [L3Pf6_S10]

description: Smart-seq2 coupled with NEXTERA XT


title: sporozoite_S1 [SPZ_L1Pf8]

description: Smart-seq2 coupled with NEXTERA XT

source_name: sporozorite

value: sporozoite

value: SPZ


title: Day5_Heps_S1_Pf+ [L1Pf9_S13]

description: Smart-seq2 coupled with NEXTERA XT


title: Day5_Heps_S2_Pf+ [L2Pf6_S8]

description: Smart-seq2 coupled with NEXTERA XT


title: Day5_Heps_S2_Pf- [L3Pf5_S9]

description: Smart-seq2 coupled with NEXTERA XT


title: Day4_Heps_TR2_Pf- [L2Pf3_S8_TR2]

description: Smart-seq2 coupled with NEXTERA XT


title: Day4_Heps_TR1_Pf+ [L1Pf4_S3_TR2]

description: Smart-seq2 coupled with NEXTERA XT


title: Day4_Heps_S3_Pf- [L3Pf3_S4]

description: Smart-seq2 coupled with NEXTERA XT


title: Day4_Heps_MS1_Pf+ [L3Pf4Mix_S6]

description: Smart-seq2 coupled with NEXTERA XT


title: Day2_Heps_MS1_Pf+ [L3Pf2Mix_S3]

description: Smart-seq2 coupled with NEXTERA XT


title: Day4_Heps_S1_Pf+ [L1Pf4_Day4.GFP]

description: Smart-seq2 coupled with NEXTERA XT


title: Day4_Heps_S2_Pf- [L2Pf3_S3]

description: Smart-seq2 coupled with NEXTERA XT


title: Day4_Heps_TR2_Pf+ [L2Pf4_S9_TR2]

description: Smart-seq2 coupled with NEXTERA XT


title: Day4_Heps_TR1_Pf- [L1Pf3_S2_TR2]

description: Smart-seq2 coupled with NEXTERA XT


title: Day4_Heps_S1_Pf- [L1Pf3_Day4.NoGFP]

description: Smart-seq2 coupled with NEXTERA XT


title: Day4_Heps_S4_Pf+ [L3Pf4_S5]

description: Smart-seq2 coupled with NEXTERA XT


title: Day6_Heps_S4_Pf- [L3Pf7_S11]

description: Smart-seq2 coupled with NEXTERA XT


title: Day2_Heps_S2_Pf+ [L2Pf2_S2]

description: Smart-seq2 coupled with NEXTERA XT


title: Day2_Heps_TR2_Pf+ [L2Pf2_S7_TR2]

description: Smart-seq2 coupled with NEXTERA XT


title: Day2_Heps_S3_Pf+ [L3Pf2_S2]

description: Smart-seq2 coupled with NEXTERA XT


title: Day6_Heps_S2_Pf- [L2Pf5_S5]

description: Smart-seq2 coupled with NEXTERA XT


title: Day2_Heps_S3_Pf- [L3Pf1_S1]

description: Smart-seq2 coupled with NEXTERA XT


title: Day2_Heps_S1_Pf+ [L1Pf2_Day2.GFP]

description: Smart-seq2 coupled with NEXTERA XT


title: Day2_Heps_S1_Pf- [L1Pf1_Day2.NoGFP]

description: Smart-seq2 coupled with NEXTERA XT


title: Day2_Heps_TR1_Pf- [L2Pf1_S6_TR2]

description: Smart-seq2 coupled with NEXTERA XT


title: Day2_Heps_S2_Pf- [L2Pf1_S1]

description: Smart-seq2 coupled with NEXTERA XT


title: control_S3 [L1PfM2_S14]

description: Smart-seq2 coupled with NEXTERA XT

value: control


title: Day4_Heps_S2_Pf+ [L2Pf4_S4]

description: Smart-seq2 coupled with NEXTERA XT


title: control_S1 [L1Pf7_Day0.Naive]

description: Smart-seq2 coupled with NEXTERA XT


title: control_S2 [L1PfM1_S13]

description: Smart-seq2 coupled with NEXTERA XT


title: p_viv_PI4K-182

description: Pvivax mRNA enriched using probes; unknown library prep

organism: Plasmodium vivax

value: treated with PI4K inhibitors


title: p_viv_PI4K-181


title: p_viv_Cont177


title: p_viv_PI4K-183


title: p_viv_Cont179


title: Day2_Heps_TR1_Pf+ [L1Pf2_S1_TR2]

description: Smart-seq2 coupled with NEXTERA XT


title: 77 – AD3

status: Public on May 24 2023

city: Vienna

first: Natalia

last: Alkon

address: Währinger Gürtel 18-20

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were demultiplexed, aligned to a reference genome (GrCh38) and counted using Cell Ranger (version 6.1.2; 10x Genomics).
Assembly: GRCh38
Supplementary files format and content: mtx (count matrix in sparse matrix format), barcodes.tsv (barcode ids),  features.tsv: (gene ids)

source_name: Skin Biopsy

extract_protocol:
Single cell suspensions from full thickness skin punch biopsies were generated using the Skin Dissociation Kit by Miltenyi Biotech (Bergisch Gladbach, Germany).
These cells were immediately processed for scRNA-seq by using the Chromium Single Cell Controller and Single Cell 5’ Library & Gel Bead Kit v1.1 (10X Genomics, Pleasanton, CA), following the manufacturer’s suggestions. T-cell receptor (TCR) sequences were enriched from cDNA using the respective reagents, and according to the instructions of the VDJ Kit workflow by 10X Genomics. Sequencing was performed using the Illumina NovaSeq platform and the 150bp paired-end configuration.

value: Skin Biopsy

tag: serum ige (kiu/l)

tag: diagnosis

value: Atopic Dermatitis


title: 81 – AD4

tag: tissue


title: 96 – AD5


title: 74 – AD1


title: p_viv_Cont176

tag: cell line

tag: cell type


title: 75 – AD2


title: LU_m113

status: Public on May 23 2023

city: University Park

first: Elizabeth

last: Jolley

state: PA

address: 239 Chemistry Bldg, Pennsylvania State University

institute: Pennsylvania State University

data_processing:
Cutadapt (1.16)
Bowtie (2.3.4.1)
StructureFold2 modules
Assembly: custom build as described in citation
Supplementary files format and content: processed data files are provided as rtsc files containing reverse transcription stop count on each nucleotide
Library strategy: Structure-seq2

organism: Bacillus subtilis

growth_protocol: Bacillus subtilis PLBS338 cells were grown to mid-exponential phase in a shaking water bath at one of four temperatures, 23C, 30C, 37C, or 42C. Growth was stopped by using frozen slurry killing buffer (containing 10 mM Tris-HCl, 5 mM MgCl2, 25 mM NaN3, 1.5 mM chloramphenicol, and 12.5% ethanol)

extract_protocol:
Cells were pelleted and frozen, and RNA was extracted using RNeasy Mini Kit, then ribosomal RNA was depleted with Ribo-Zero rRNA Removal Kit
Structure-seq2 libraries were prepared using reverse transcription with a random hexamer, ligation of a hairpin adapter, and then amplification incorporating Illumina-specific primers.

treatment_protocol: Samples treated with DMS had a final concentration of 50 mM DMS added to the growth media for 5 min, then reaction was quenched with DTT. Control samples had an equivalent amount of DTT added.

value: Lung

tag: genotype

value: Wild type

tag: growth media

value: LB


title: LU_m122


title: LU_m112


title: LU_m117


title: LU_m116


title: LU_m118


title: LU_m111


title: LU_m121


title: LU_m123


title: LU_m109


title: LU_m106


title: LU_m119


title: LU_m110


title: LU_m107


title: LU_m102


title: LU_m104


title: LU_m100


title: LU_m105


title: LU_m103


title: LU_m99


title: LU_m101


title: LU_m120


title: LU_m97


title: AvrRpm1, 24h, RNA

status: Public on Apr 24 2023

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
10x Genomics Multiome
AvrRpm1_24h_peak.rds

data_processing:
Sequence data were processed to obtain single cell feature counts by running cellranger (v6.0.1) and cellranger-arc (v2.0.0) for snRNA-seq and snATAC-seq, respectively. For snRNA-seq, the –include-introns option was used to align reads to the A. thaliana nuclear transcriptome built with the TAIR10 genome and Araport 11 transcriptome. Count data were analyzed with the R packages Seurat v4 (Hao et al. 2021) and Signac (Stuart et al. 2021).
QC matrices for snATAC-seq were generated by a modified version of loadBEDandGenomeData function in the R package Socrates. ACRs were identified with MACS2 (Zhang et al. 2008) with the following parameters: -g (genomesize)=0.8e8, shift=-50, extsize=100, and --qvalue=0.05, --nomodel, --keep-dup all. Fraction of reads mapping to within 2kb upstrem or 1kb downstream TSS was calculated. Nuclei were filtered with the following criteria: 200 < RNA UMI count < 7000, RNA gene count > 180, 200 < ATAC UMI count <20000, fraction of RNA reads mapped to mitochondrial genome < 5%. Seurat objects of individual samples were merged with the Merge_Seurat_List function of the scCustomize package.
Supplementary files format and content: combined_filtered.rds contains snRNA-seq and snATAC-seq data from all samples after cell filtering
Supplementary files format and content: Processed files except for combined_filtered.rds contains snRNA-seq and snATAC-seq data of each sample before cell filtering

organism: Arabidopsis thaliana

source_name: Leaf

extract_protocol:
Fresh Nuclei purification buffer (NPB; 15mM Tris pH 7.5, 2mM EDTA, 80mM KCl, 20mM NaCl, 0.5mM spermidine, 0.2mM spermine, 1:100 BSA, and 1:100 protease inhibitor cocktail) was prepared before the experiment and chilled on ice. All the following procedures were performed on ice or at 4ºC. Twenty leaves were chopped in 500-1,000 µL of cold NPB with 1:500 Protector RNase IN with a razor blade on ice for 5 min to release nuclei and incubated in 20 mL of NPB. The crude nuclei extract was sequentially filtered through 70 µm and 30 µm cell strainers. Triton-X and NP40 were added to the extract at the final concentration of 0.1% each, and the extract was incubated at 4ºC for 5 min with rotation. The nuclei suspension was centrifuged at 50 x g for 3 min in a swing-rotor centrifuge to pellet non-nuclei debris, and the supernatant was taken. Nuclei were pelleted by centrifugation at 500 x g for 5 min with a swing-rotor centrifuge. When the pellet was green, the pellet was resuspended in 20 mL of NPBd (NPB, 0.1% Triton-X, and 0.1% NP40) with 1:1000 Protector RNase IN by pipetting, followed by centrifugation at 700 x g for 5 min. When the pellet was translucent, this step was skipped. The pellet was then washed by resuspending it in 20 mL of NPB with 1:1000 Protector RNase IN and centrifuging at 500 x g for 5 min with a swing-rotor centrifuge. The pellet was resuspended in 950 µL of 1X Nuclei Buffer (10X Genomics; PN-2000207) with 1:20 Protector RNase IN and 1mM DTT. The nuclei suspension was centrifuged at 50 x g for 3 min in a swing-rotor centrifuge to pellet non-nuclei debris, and the supernatant was taken. This step was repeated one more time. Then, nuclei were counted manually with a hemocytometer. Nuclei were pelleted by centrifugation at 500 x g for 5 min with a swing-rotor centrifuge and removed supernatant leaving approximately 10 µL of buffer. Nuclei were counted again, and up to 16k nuclei were used for the following steps. Single-cell RNA-seq and ATAC-seq libraries were constructed according to the manufacturer’s instruction (10X Genomics, catalog: CG000338). Single-nucleus RNA-seq libraries were sequenced with Illumina NovaSeq 6000 in dual-indexmode with 10 cycles for i7 and i5 index. Single-nucleus ATAC-seq libraries were also sequenced with Illumina NovaSeq 6000 in dual-indexmode with eight and 24 cycles for i7 and i5 index, respectively.
We followed the 10X genomics multiome assay protocols

value: Leaf

tag: cultivar

value: AvrRpm1 24h


title: AvrRpm1, 9h, ATAC

description:
10x Genomics Multiome
AvrRpm1_9h_peak.rds

value: AvrRpm1 9h


title: CNA 10xmultiome 1 RNA (MO C1)

status: Public on May 22 2023

city: Leuven

first: Stein

last: Aerts

state: Vlaams-Brabant

address: O&N4 Herestraat 49 PO Box 602

country: Belgium

institute: KU Leuven

data_processing:
Raw sequencing reads were processed to aligned reads and count matrices using cellranger-arc with standard 10x GRCh38 index. Unfiltered count matrices were converted to h5ad format using scanpy.
library strategy: 10x Multiome
Assembly: GRCh38
Supplementary files format and content: "FULL" fragments.tsv.gz: tab-delimited bed-like fragments file with 5 fields: chromosome, start position, end position, cell barcode and count. Derived from the full sequencing data.
Supplementary files format and content: "FULL" fragments.tsv.gz.tbi: tabix index supplementary to full fragments.tsv.gz files.
Supplementary files format and content: "FIXEDCELLS" fragments.tsv.gz: tab-delimited bed-like fragments file with 5 fields: chromosome, start position, end position, cell barcode and count. Derived from the sequencing data downsampled to the fixed number of cells found in the full sequencing data.
Supplementary files format and content: "FIXEDCELLS" fragments.tsv.gz.tbi: tabix index supplementary to fixedcells fragments.tsv.gz files.
Supplementary files format and content:
h5ad files: scanpy-generated hdf5 formated raw count matrices
barcodes.tsv.gz files: cell barcodes output by CellRanger
features.tsv.gz: feature names (genes) output by CellRanger
matrix.mtx.gz: gene count matrix output by CellRanger

molecule: polyA RNA

source_name: Mixture of PBMC from 2 donors

extract_protocol:
Cryopreserved human PBMCs from a male and female donor were purchased from AllCells and (AllCells, Lot #3030456 and 3030663). Cryopreserved PBMC were thawed according to the 10x Genomics demonstrated protocol CG00039 ("Fresh Frozen Human Peripheral Blood Mononuclear Cells for Single Cell RNA Sequencing"). Briefly, 1 mL of frozen cells was rapidly thawed in a 37 °C water bath and transferred to a 50 mL tube using a 1000 µL wide bore tip. Next, 1 mL of 37 °C pre-warmed medium supplemented with 10% FBS (Thermo Fisher Scientific) was added drop-wise while gently swirling the sample. After 1 minute of incubation at room temperature, 2, 4, 8 and 16 mL of medium with 10% FBS were added drop-wise with 1 minute of incubation at room-temperature inbetween. The cell suspension was then centrifuged at 300 g for 5 min. at room temperature. The pellet was resuspended in 10 mL of medium with 10% FBS, and cells were counted. Unless specified otherwise in technology-specific methods sections, nuclei isolation was performed according to the 10x Genomics demonstrated protocol “Nuclei Isolation for Single Cell ATAC Sequencing”. Briefly, 1 million cells from the cell mix were transferred to a 1.5 mL microcentrifuge tube and centrifuged at 500 rcf for 5 min at 4 °C. The supernatant was removed without disrupting the cell pellet and 100 µL of chilled Lysis Buffer (10 mM Tris-HCl (pH 7.4); 10 mM NaCl; 3 MgCl2; 0.1% Tween-20; 0.1% Nonidet P40 Substitute; 0.01% Digitonin and 1% BSA) were added and pipette mixed 10 times. Samples were then incubated on ice for 3 min. Following lysis, 1 mL of chilled Wash Buffer (10 mM Tris-HCl (pH 7.4); 10 mM NaCl; 3 MgCl2; 0.1% Tween-20 and 1% BSA) was added and pipette mixed. Nuclei were centrifuged at 500 rcf for 5 min at 4 °C and the supernatant removed without disrupting the nuclei pellet. Based on the starting number of cells and assuming a 50% loss during the procedure, nuclei were resuspended into the appropriate volume of chilled Diluted Nuclei Buffer (10x Genomics) in order to achieve a nuclei concentration of 925-2300 nuclei/µL, suitable for a Target Nuclei Recovery of 3000.
PBMC were thawed as described above. Nuclei isolation was slightly different, including RNAse inhibitors to ensure RNA quality. Briefly, two pools of cells (technical replicates) were generated from these two donors by mixing 500,000 cells per donor, in total 1 million cells per pool. Cells were pelleted for 5 mins at 300 rcf at 4oC and washed twice in 1mL wash buffer (10 mM Tris-HCl (pH7.4), 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween-20, 1 mM DTT, 1U/µL RNase inhibitor). After the second wash and final centrifugation, cells were resuspended 0.1 mL chilled Lysis buffer (10 mM Tris, HCL (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40, 0.01% Digitonin, 1% BSA, 1 mM DTT, and incubated for 3 minutes on ice. Nuclei were washed 3 times in 1 mL wash buffer (10 mM Tris-HCl (pH7.4), 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween-20, 1 mM DTT, 1U/µL RNase inhibitor) by spinning down at 500 g for 5 min.  After the last centrifugation cells were resuspended in chilled Nuclei buffer (Nuclei Buffer 1X, 1 mM DTT, 1U/µL RNAse inhibitor) calculated and loaded according to the Chromium Next GEM single cell multiome ATAC + GEX user guide (protocol CG000338 Rev A). For loading onto 10x chips we aimed for a recovery of 3000 nuclei. Following nuclei isolation and transposition, GEMs were generated using GEM Chip J. Post GEM clean-up and pre-amplification PCR were carried out as per user guide. For the ATACseq library 8 cycles of PCR were run, whilst 7 cycles of PCR were performed for cDNA amplification. Of the amplified cDNA 25 % of the material was used for gene expression library construction with 15 cycles of PCR for both technical replicates.

value: Mixture of PBMC from 2 donors

value: PBMC


title: CNA 10xscRNA 3

data_processing:
Raw sequencing reads were processed to aligned reads and count matrices using cellranger-arc with standard 10x GRCh38 index. Unfiltered count matrices were converted to h5ad format using scanpy.
Raw sequencing data was aligned to GRCh38 using cellranger and the raw count matrix was converted to hdf5 format using scanpy.
Assembly: GRCh38
Supplementary files format and content:
h5ad files: scanpy-generated hdf5 formated raw count matrices
barcodes.tsv.gz files: cell barcodes output by CellRanger
features.tsv.gz: feature names (genes) output by CellRanger
matrix.mtx.gz: gene count matrix output by CellRanger

extract_protocol:
Cryopreserved human PBMCs from a male and female donor were purchased from AllCells and (AllCells, Lot #3030456 and 3030663). Cryopreserved PBMC were thawed according to the 10x Genomics demonstrated protocol CG00039 ("Fresh Frozen Human Peripheral Blood Mononuclear Cells for Single Cell RNA Sequencing"). Briefly, 1 mL of frozen cells was rapidly thawed in a 37 °C water bath and transferred to a 50 mL tube using a 1000 µL wide bore tip. Next, 1 mL of 37 °C pre-warmed medium supplemented with 10% FBS (Thermo Fisher Scientific) was added drop-wise while gently swirling the sample. After 1 minute of incubation at room temperature, 2, 4, 8 and 16 mL of medium with 10% FBS were added drop-wise with 1 minute of incubation at room-temperature inbetween. The cell suspension was then centrifuged at 300 g for 5 min. at room temperature. The pellet was resuspended in 10 mL of medium with 10% FBS, and cells were counted.
The cell mix was partitioned into Gel Bead-In-Emulsions by using the Chromium Controller system (10x Genomics), with a target recovery of 5000 total cells. We generated three technical replicates by loading 3 channels of the chip G with the same cell mix. cDNA sequencing libraries were prepared using the Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics, PN-1000268), following manufacturer's instructions. Briefly, after GEM-RT clean up, cDNA was amplified during 12 cycles and cDNA QC and quantification were performed on an Agilent Bioanalyzer High Sensitivity chip (Agilent Technologies). cDNA libraries were indexed by PCR using the PN-220103 Chromium i7 Sample Index Plate. Size distribution and concentration of 3' cDNA libraries were verified on an Agilent Bioanalyzer High Sensitivity chip (Agilent Technologies).


title: CNA 10xscRNA 2


title: AvrRpm1, 24h, ATAC


title: VIB 10xmultiome 1 RNA (MO V1)


title: VIB 10xmultiome 2 RNA (MO V2)


title: CNA 10xmultiome 2 RNA (MO C2)


title: CNA 10xscRNA 1


title: Mock, RNA

description:
10x Genomics Multiome
mock_peak.rds

value: Mock


title: SAN 10xmultiome 1 RNA (MO Sa1)


title: AvrRpm1, 4h, ATAC

description:
10x Genomics Multiome
AvrRpm1_4h_peak.rds

value: AvrRpm1 4h


title: AvrRpm1, 6h, RNA

description:
10x Genomics Multiome
AvrRpm1_6h_peak.rds

value: AvrRpm1 6h


title: AvrRpm1, 4h, RNA


title: DC3000, 24h, ATAC

description:
10x Genomics Multiome
DC3000_24h_peak.rds


title: DC3000, 9h, RNA

description:
10x Genomics Multiome
DC3000_9h_peak.rds


title: DC3000, 9h, ATAC


title: DC3000, 6h, RNA

description:
10x Genomics Multiome
DC3000_6h_peak.rds


title: DC3000, 4h, ATAC

description:
10x Genomics Multiome
DC3000_4h_peak.rds


title: SAN 10xmultiome 2 RNA (MO Sa2)


title: DC3000, 24h, RNA


title: DC3000, 6h, ATAC


title: DC3000, 4h, RNA


title: Mock, ATAC

description:
10x Genomics Multiome
mock_peak.rds


title: AvrRpt2, 24h, ATAC

description:
10x Genomics Multiome
AvrRpt2_24h_peak.rds

value: AvrRpt2 24h


title: AvrRpt2, 24h, RNA


title: AvrRpm1, 9h, RNA


title: AvrRpt2, 6h, RNA

description:
10x Genomics Multiome
AvrRpt2_6h_peak.rds

value: AvrRpt2 6h


title: AvrRpt2, 4h, ATAC

description:
10x Genomics Multiome
AvrRpt2_4h_peak.rds

value: AvrRpt2 4h


title: AvrRpt2, 9h, RNA

description:
10x Genomics Multiome
AvrRpt2_9h_peak.rds

value: AvrRpt2 9h


title: AvrRpm1, 6h, ATAC


title: AvrRpt2, 4h, RNA


title: AvrRpt2, 9h, ATAC


title: AvrRpt2, 6h, ATAC


title: H3K14ac_786O_PBRM1KO_ChIPSeq

status: Public on Feb 11 2023

city: Singapore

first: Xiaosai

last: Yao

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Sequencing reads were mapped against human genome reference hg19 using the Burrows-Wheeler Aligner (BWA) (version 0.6.2) 'mem' algorithm. Only reads with mapQ >10 and with duplicate removed by rmdup were used in the subsequent analysis
Significant peaks were called using MACS2 24 (q-value < 0.01).
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq peaks are in bed format, including 5 columns: "chromosome"  "start of region" "end of region" "peak name" "peak enrichment"

source_name: Cancer cell line

growth_protocol: Cells were grown in RPMI-1640 medium (Sigma) supplemented with 10% fetal bovine serum (Gibco). Cells were maintained in a 5% CO2-humidified incubator at 37°C.

extract_protocol:
For each protein of interest, approximately 2x107 cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and stopped by adding glycine to a final concentration of 0.2M. Chromatin was extracted and sonicated to ~500bp (Vibra cell, SONICS). The total volume of immunoprecipitation was 2 ml and the amount of antibody used was 20 µg. The input DNA was precleared with protein G Dynabeads (LifeTechnologies) for 2 hours at 4°C and then incubated with antibodies overnight at 4°C. Protein G beads were added the following day and mixture was nutated for 3 hours at 4°C. The beads were washed 6 times with wash buffer at room temperature.
At least 10 ng of the amplified DNA was used with NEBNext ChIP-Seq library prep reagent set (NEB). Each library was sequenced to an average depth of 30-50 million reads on HiSeq2500 or HiSeq4000.

treatment_protocol: PBRM1 was knocked out using CRISPR-Cas9 mediated gene editing in 786-O, A498 and HK-2. Wildtype PBRM1 was cloned from normal kidney tissue. cDNA was either cloned into pbabe vector or pLenti-GFP.

tag: source

tag: protein

tag: chip antibody


title: Input_A498_ChIPSeq

value: Input

tag: treatment

value: parental


title: Input_PCS400_ChIPSeq

source_name: primary renal proximal tubule epithelial cells


title: Input_HK2_ChIPSeq

source_name: normal kidney epithelial cell line

value: HK2(ATCC CRL-2190)


title: PBRM1_PCS400_ChIPSeq

value: PBRM1(Bethyl, A301-591A, lot3)


title: WT aortic valve

status: Public on Aug 22 2022

city: Seoul

first: Jae-Hoon

last: Choi

address: 222 Wangsimniro, Seongdong Gu

department: Department of Life Science

country: South Korea

institute: Hanyang University

description:
single-cell RNA-seq
AV_S3

data_processing:
Libraries were mapped to the mouse genome (build mm10) using the Cell Ranger toolkit (v3.0.2).
We applied two quality measures on single cells, the Cell Ranger toolkit (v3.0.2): mitochondrial genes (< 10%) and gene count (range from 200 to 5,000) from the R package Seurat v3.1.1.
Genome_build: mm10
Supplementary_files_format_and_content: RDS (R) files representing: UMI counts (Mouse_AV_raw_UMI_matrix.rds)

source_name: aortic valve

growth_protocol: To induce aortic valve lesions of lipid accumulation by hypercholesterolemia, male Ldlr-/- and Apoe-/- mice (sacrificed at 24- to 26-week-old) fed a western diet at 8- to 10-week-old for 16 weeks. For control, male 12-week-old C57BL/6J WT mice fed a chow diet were used.

extract_protocol:
Mice were sacrificed in a CO2 chamber, and aortic valves were collected in Dulbecco's modified Eagle's medium (DMEM). Aortic valves were minced for a minute. Tissues were digested for 30 minutes with 1000 U/mL collagenase II and 90 U/mL DNase I in Ca2+/Mg2+ DPBS at 37 °C. The number of pooled mice in each experimental group was as follows: 30 mice for the C57BL/6J group (male, 12-week-old), 24 mice for the Ldlr-/- group, and 19 mice in the Apoe-/- group. Only live single-cells (PI negative single cells) were sorted using BD FACS Aria III.
The single-cell suspensions were subjected to 3′ single-cell RNA sequencing aiming for target recovery of 5,000 cells (C57BL/6J; Ldlr-/-) and 3,000 cells (Apoe-/-) using Single Cell A Chip Kit, Single Cell 3' Library, and Gel Bead Kit V2, and i7 Multiplex Kit (10x Genomics). Solutions pertaining to 3′ chemistry and v2 of 10x Genomics were used to barcode individual cells. Libraries were sequenced on an Illumina HiSeq2500.

value: aortic valve

tag: strain

value: wild type

tag: Sex

value: male

tag: diet

value: chow


title: RNA-Seq HSB8073 (RT00390N)

status: Public on Aug 25 2022

city: New haven

first: Nenad

last: Sestan

state: CT

address: 333 Cedar street

department: Neuroscience

institute: Yale University

data_processing:
Cellranger-arc 2.0.1 was used to build the reference genome, read alignment, barcode counting and UMI counting. MACS2 was used for peak calling.
Downstream processing were performed by Seurat and Signac.
Assembly: hg38
Supplementary files format and content: tsv: tab-separated file
Supplementary files format and content: mtx: sparse matrix file
Library strategy: Single Cell Multiome

source_name: dorsolateral prefrontal cortex

extract_protocol:
The brain cell nuclei isolation is a comparable modification of our previous protocols (Zhu et al., 2018, PMID: 30545855; Franjic et al. 2022, PMID: 34798047) with yield improvement for limited tissue (adult and prenatal) and additional removal of debris.
Chromium Single Cell Multiome ATAC + Gene Expression (10x Genomics PN 1000283,PN 1000285)

value: dorsolateral prefrontal cortex

value: Control


title: RNA-Seq HSB6154 (RT00385N)


title: RNA-Seq HSB6195 (2RT00374N)


title: ATAC-Seq HSB8073 (RT00390N)


title: RNA-Seq HSB5871 (RT00382N)


title: ATAC-Seq HSB5871 (RT00382N)


title: ATAC-Seq HSB8050 (RT00383N)


title: Apoe knockout aortic valve

description:
single-cell RNA-seq
ApoE-KO_S1

value: Apoe-/-

value: western diet


title: RNA-Seq HSB8050 (RT00383N)


title: 16

status: Public on Jun 02 2022

city: Philadelphia

first: Tamir

last: Diamond

state: No

address: 3401 Civic Center Blvd

institute: Children's Hospital of Philadelphia/University of Pennsylvania

description: mRNA

data_processing:
Raw reads mapped to the Mus musculus reference transcriptome using Kallisto (version 0.46.2).
Transcript-level counts and abundance data were summarized to gene level using the TxImport package (version 1.16.1).
Differentially expressed genes were identified by linear modeling and Bayesian statistics using the Limma package (3.44.3).
Data was normalized using the TMM method in edgeR package (version 3.30.3).
Normalized data was variance stabilized using the VOOM function in Limma.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_abundance.tsv: Tab-delimited text files include abundance measurements.

source_name: Liver

extract_protocol:
RNA was extracted from ~30mg of liver samples using the RNeasy Mini Kit (Qiagen) according to the manufacturer instructions.
RNA libraries were prepared for sequencing using TruSeq mRNA standard library kits using standard Illumina protocols.

tag: strain/background

tag: group

value: BM IFNgR+/+ and host IFNgR+/+

value: Liver


title: ATAC-Seq HSB6154 (RT00385N)


title: 17

description: mRNA


title: 15

description: mRNA


title: 9

description: mRNA

value: BM IFNgR+/+ and host IFNgR -/-


title: 18

description: mRNA


title: 7

description: mRNA


title: 1

description: mRNA


title: female_SCR_LD_rep_2

status: Public on Apr 13 2022

first: Andrei

last: Chernov

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

data_processing:
FASTQ files were filtered to remove low-quality bases, TruSeq dual-index adapter sequences, and unpaired reads using Trimmomatic
Transcript-level quantification was performed using Salmon (Version 1.3.0) in quasi-mapping mode using the Rn7.2 Rat genome. To correct for systematic biases commonly present in RNA-seq data, both -seqBias and -gcBias features were used.
Transcript- to gene-level conversion was done using Tximeta (Version 3.11).
RNA-seq quantification data quality was assessed using MultiQC (Version 1.9).
DEGs were determined in pairs of samples with SNA and the respective sham-operated controls using DESeq2 package. Datasets normalization was conducted using trimmed means of M-values (TMM) included in DESeq2 package. Statistical parameters for each DEG, including absolute expression, fold change (log2FC), p-values (by Wald test), and false discovery rates (FDR) were computed.
Genome_build: GCA_015227675.2 mRatBN7.2
Supplementary_files_format_and_content: Salmon quant.sf format consisting Entrez IDs, Length, EffectiveLength, abundance measurements (TPM) and number of reads mapping to each transcript (NumReads)

organism: Rattus norvegicus

source_name: Lumbar Dorsal Spinal cord

growth_protocol: Sprague-Dawley rats (n = 3/group, 8-10 weeks old) were obtained from Envigo and housed in a temperature-controlled room (∼22 °C), on a 12-h light/dark cycle, and with free access to food and water. All procedures were conducted during the light cycle.

extract_protocol:
Tissues were submerged in 500 µl RNAlater Stabilization Solution to preserve RNA integrity, placed at 4C overnight, then transferred for storage at -20C.
RNA purification. Lumbar dorsal spinal cord tissues were transferred in Trizol solution and disrupted by mechanical homogenization. Total RNAs were purified using RNeasy RNA purification reagents. RNA concentrations and quality were determined using Nanodrop absorbance ratios at 260/280nm and 260/230nm. RNA integrity was determined using Agilent Bioanalyzer Nano RNA chip. 500 ng of total RNA samples (3 replicates/group) with RIN≥7.0 were used for RNA-seq.
RNA-seq. mRNA libraries were generated following TruSeq Stranded mRNA library preparation protocol (Illumina). In brief, the Poly-A enriched mRNAs were purified using poly-T oligo coupled magnetic beads, followed by mRNA fragmentation, first and second strands synthesis, cleaning on AMPure XP beads, and 3’-adenylation. Barcoded libraries were constructed by ligation of TruSeq dual-index adapters. The quality of RNAseq libraries was validated using qPCR. Libraries were sized on Agilent Bioanalyzer DNA high sensitivity chip and normalized. RNA-seq was performed using the paired-end 100 cycle program on the NovaSeq 6000 system
Base calls were recorded and converted to FASTQ files containing sequencing reads and the corresponding quality scores using Illumina software. Sequencing was conducted until we acquired at least 30 million paired-end reads per sample.

treatment_protocol: Under isoflurane anesthesia, the left sciatic nerve was exposed at the mid-thigh level. Sterile PBS was used a vehicle to dissolve and deliver peptides. OC43 and SCR peptides were dissolved in DMSO, when diluted with PBS to a final concentration of DMSO 2%. Aliquots (10 µg of peptide in 5 μl vehicle) were injected into the sciatic nerve of the left rear hind paw of rats. Quantitative nociception assays were performed by an experimenter blinded to the groups at time points from day 1 to day 21. Tissues were collected at day 21 post-injection. All animal procedures were performed in agreement with the Policy on Humane Care and Use of Laboratory Animals and the protocol approved by the Institutional Animal Care and Use Committee at the VA San Diego Healthcare System.

value: female

value: Sprague-Dawley

value: intrasciatic injection

tag: peptide

value: SCR peptide

tag: time point

value: 21 days


title: female_OC43_LD_rep_3

value: OC43 peptide


title: LU_m114

tag: tissue

value: Lung

value: Wild type

value: LB


title: PBRM1_HK2_ChIPSeq

value: HK2 (ATCC CRL-2190)

value: parental

value: PBRM1(Bethyl, A301-591A, lot3)


title: female_OC43_LD_rep_1


title: female_OC43_LD_rep_2


title: ATAC-Seq HSB6195 (2RT00374N)

value: dorsolateral prefrontal cortex

value: Control


title: Ldlr knockout aortic valve

description:
single-cell RNA-seq
LDLR-KO_S2

value: aortic valve

value: Ldlr-/-

value: male

value: western diet


title: Input_CTCF_KO_rep2

status: Public on Mar 29 2022

city: Amsterdam

first: Mikhail

last: Magnitov

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

data_processing:
RNA-seq:   RNA-seq reads were mapped using STAR v2.6.1c with GENCODE v33 gene annotation. Read counts per gene were obtained using the ‘--quantMode’ parameter in STAR. Differentially expression analysis was performed with edgeR v3.30.0. Quasi-likelihood negative binomial generalized log-linear model and t-test relative to a fold change threshold of 1.5 were used to calculate per gene p-values. The obtained p-values were adjusted with Benjamini–Hochberg correction for multiple testing (FDR). FDR threshold of 0.01 was used to define differentially expressed genes.
ChIP-seq:   ChIP-seq reads were mapped using bowtie v2.2.3 with ‘--no-discordant’ and ‘--no-mixed’ options. Uniquely mapped reads with MAPQ>30 were selected using SAMtools v1.5, PCR duplicates were filtered with Picard MarkDuplicates, reads overlapping with the hg19 blacklist regions were discarded. The bigWig files with the ratio of RPKM-normalized ChIP-seq signal to the input in 50 bp bins were generated using deepTools2 with ‘--pseudocount’ set to 0 1 and ‘--smoothLength’ of 3 bins. Peaks were called using MACS2 with broad-cutoff of 0.1 (H3K9me3 and H3K27me3) in broad peak mode, qvalue of 0.05 (H3K27ac and H3K4me3) and p-value of 0.001 (CTCF) in narrow peak mode.
Hi-C:  Hi-C reads were mapped using bowtie v2.2.3 with the ‘--very-sensitive’ mode and the iterative mapping procedure implemented in hiclib package. Non-uniquely mapped reads, reads mapped on the same fragment and possible PCR duplicates were eliminated. Filtered reads pairs were aggregated into into genomic bins of different sizes to obtain Hi-C contact matrices. Contacts matrices were normalized using the ICE balancing implemented in cooler v0.7.9. Chromatin compartments were annotated using PCA implemented in cooltools v0.3.2 call-compartments function for 100 kb resolution contact matrices. TADs were annotated using the Armatus algorithm implemented in lavaburst package for 20 kb resolution contact matrices.
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq: normalized signal tracks in bigWig format; read counts per gene in TXT format. ChIP-seq: normalized signal tracks in bigWig format; peaks in BED format. Hi-C: contact matrices in MCOOL format; compartment eigenvectors in TXT format; TADs in BED format.

source_name: A549 immortalized cell line

growth_protocol: A549 (K‐RAS G12S) cells were obtained from ATCC (ATCC CCL-185). Cells were cultured in Dulbecco’s modified Eagle’s Medium DMEM (Sigma) supplemented with 10% FBS (Gibco), 1% penicillin/streptomycin (Sigma), maintained at 37°C and 5% CO2.

extract_protocol:
RNA-seq: RNA extraction was performed using RNeasy mini-kit (Qiagen) followed by Turbo DNA-free kit (Ambion).  ChIP-seq: Cells were collected with or without formaline fixation. Chromatin was fragmented by MNase digestion (histone ChIP) or sonication (CTCF ChIP), and immunoprecipitated by different antibodies. DNA was purified using MinElute columns from Qiagen.  Hi-C: Cells were fixed with 2% of formaldehyde, chromatin was digested with DpnII, DNA ends were biotinylated and re-ligated in situ. DNA was purified by reverse-crosslinking, followed by phenol/chloroform extraction, ethanol precipitation and additional purification using AMPure XP magnetic beads. DNA was sheared by sonication, ligation junctions were enriched by Biotin pull-down.
RNA-seq: Libraries were constructed using Truseq stranded total RNA kit (Illumina).  ChIP-seq: Libraries were prepared using the MicroPlex V2 library preparation kit (Diagenode).  Hi-C: Libraries were prepared with standard protocol using TruSeq adapters (Illumina).

treatment_protocol: SETDB1 knockout was performed through CRISPR/Cas9-mediated gene disruption. The sgRNA were synthesized (Sigma) as oligonucleotide DNA sequences and cloned into PX458 plasmid (Addgene, Plasmid #48138). Cloning was performed according to a protocol described by Ran et al. (PMID: 24157548).

tag: cell line

value: SETDB1 knockout (KO)

tag: disease

value: lung adenocarcinoma


title: female_SCR_LD_rep_1

value: female

value: Sprague-Dawley

value: intrasciatic injection

value: SCR peptide


title: Input_CTCF_KO_rep1

tag: genotype


title: Input_CTCF_CT_rep2

value: Control (CT)


title: ChIPseq_CTCF_KO_rep1

description:
input: Input_CTCF_KO_rep1
CTCF_KO.bw
CTCF_KO_peaks.bed

tag: antibody

value: CTCF


title: 12

description: mRNA

value: BM IFNgR+/+ and host IFNgR -/-

value: Liver


title: ChIPseq_CTCF_CT_rep2

description:
input: Input_CTCF_CT_rep2
CTCF_CT.bw
CTCF_CT_peaks.bed


title: ChIPseq_CTCF_CT_rep1

description:
input: Input_CTCF_CT_rep1
CTCF_CT.bw
CTCF_CT_peaks.bed


title: Input_CTCF_CT_rep1


title: Input_histone_CT_rep1


title: Input_histone_CT_rep2


title: ChIPseq_CTCF_KO_rep2

description:
input: Input_CTCF_KO_rep2
CTCF_KO.bw
CTCF_KO_peaks.bed


title: Input_histone_KO_rep2


title: Input_histone_CT_rep3


title: ChIPseq_HK4me3_KO_rep2

description:
input: Input_histone_KO_rep2
H3K4me3_KO.bw
H3K4me3_KO_peaks.bed


title: female_SCR_LD_rep_3

value: 21 days


title: ChIPseq_H3K27ac_KO_rep2

description:
input: Input_histone_KO_rep3
H3K27ac_KO.bw
H3K27ac_KO_peaks.bed


title: ChIPseq_HK4me3_KO_rep1

description:
input: Input_histone_KO_rep1
H3K4me3_KO.bw
H3K4me3_KO_peaks.bed


title: ChIPseq_H3K4me3_CT_rep1

description:
input: Input_histone_CT_rep1
H3K4me3_CT.bw
H3K4me3_CT_peaks.bed


title: ChIPseq_H3K4me3_CT_rep2

description:
input: Input_histone_CT_rep2
H3K4me3_CT.bw
H3K4me3_CT_peaks.bed


title: ChIPseq_H3K27ac_CT_rep2

description:
input: Input_histone_CT_rep3
H3K27ac_CT.bw
H3K27ac_CT_peaks.bed


title: ChIPseq_H3K27ac_KO_rep1

description:
input: Input_histone_KO_rep2
H3K27ac_KO.bw
H3K27ac_KO_peaks.bed


title: RNAseq_KO_rep2

description:
gene_counts.txt
RNAseq_KO.bw


title: ChIPseq_H3K27ac_CT_rep1

description:
input: Input_histone_CT_rep2
H3K27ac_CT.bw
H3K27ac_CT_peaks.bed


title: ChIPseq_H3K27me3_KO_rep1

description:
input: Input_histone_KO_rep2
H3K27me3_KO.bw
H3K27me3_KO_peaks.bed


title: RNAseq_KO_rep1

description:
gene_counts.txt
RNAseq_KO.bw


title: ChIPseq_H3K27me3_KO_rep2

description:
input: Input_histone_KO_rep3
H3K27me3_KO.bw
H3K27me3_KO_peaks.bed


title: ChIPseq_H3K27me3_CT_rep2

description:
input: Input_histone_CT_rep3
H3K27me3_CT.bw
H3K27me3_CT_peaks.bed


title: Input_histone_KO_rep3


title: ChIPseq_H3K27me3_CT_rep1

description:
input: Input_histone_CT_rep2
H3K27me3_CT.bw
H3K27me3_CT_peaks.bed


title: ChIPseq_H3K9me3_KO_rep2

description:
input: Input_histone_KO_rep2
H3K9me3_KO.bw
H3K9me3_KO_peaks.bed


title: ChIPseq_H3K9me3_KO_rep1

description:
input: Input_histone_KO_rep1
H3K9me3_KO.bw
H3K9me3_KO_peaks.bed


title: Input_histone_KO_rep1


title: ChIPseq_H3K9me3_CT_rep2

description:
input: Input_histone_CT_rep2
H3K9me3_CT.bw
H3K9me3_CT_peaks.bed


title: HiC_KO_rep2

description:
HiC_KO.mcool
TADs_KO.bed
compartment_signal.bed


title: HiC_CT_rep1

description:
HiC_CT.mcool
TADs_CT.bed
compartment_signal.bed


title: RNAseq_KO_rep3

description:
gene_counts.txt
RNAseq_KO.bw


title: RNAseq_CT_rep2

description:
gene_counts.txt
RNAseq_CT.bw


title: P121 HC

status: Public on Sep 13 2021

first: Katharina

last: Rindler

address: Waehringer Guertel 18-20

department: Dermatology

data_processing:
Raw sequencing data were demultiplexed, aligned to a reference genome (refdata-cellranger-GRCh38-3.0.0)  and counted using Cell Ranger (version 3.0.2; 10x Genomics).
Genome_build: GrCh38
Supplementary_files_format_and_content: mtx (count matrix in sparse matrix format), barcodes.tsv (barcode ids),  features.tsv: (gene ids)

source_name: skin biopsy

extract_protocol:
For each described sample, one single 6mm punch biopsy was taken and processed immediately. Each sample was cut into small pieces and digested in the C Tube (Miltenyi Biotec, Bergisch Gladbach, Germany) using the enzyme mix as provided by the Whole Skin Dissociation Kit for human (Miltenyi Biotec) in a total volume of 0,5ml RPMI medium with enzymatic supplements as described in the manufacturer's instructions. The sample was then incubated for a total of one hour in a water bath at 37°C. The sample was then further dissociated using the gentleMACS Dissociator (Miltenyi Biotec) running the program h_skin_01. After termination of the program steps 10-14 were conducted as detailed in the manufacturer's instructions. Finally, the cell pellet was resuspended in PBS with 0,08% BSA reaching a total volume of not more than 100µl. A cell aliquot was stained with trypan blue and cell numbers and percentages of dead cells were assessed by manual counting. Samples with not more than 30% dead cells were then subjected to scRNA-seq processing as detailed below.
5' gene expression sequencing was performed using the Chromium Controller and Single Cell 5' Library  (10x Genomics) according to the manufacturer's protocol. Sequencing was performed using the Illumina NovaSeq 6000 platform and the 150bp paired-end configuration.

tag: lesion type

value: healthy control

tag: diagnosis

tag: chemistry

value: Single Cell 5' PE