title: GC B cells, day14, KO mouse 2

status: Public on Sep 19 2023

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: spleen

extract_protocol:
Total RNA was extracted using TRIzol reagent.
Each cDNA was generated using a Clontech SMART-Seq HT Kit (Takara Clontech, Mountain View, CA, USA), and each library was prepared using a Nextera XT DNA Library Prep Kit (Illumina, San Diego, USA).

value: 14 days after NP-KLH-Alum immunization


title: GC B cells, day14, KO mouse 3

type: SRA

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: genotype

tag: treatment


title: GC B cells, day14, KO mouse 1


title: GC B cells, day7, KO mouse 2

value: 7 days after NP-KLH-Alum immunization


title: GC B cells, day14, mouse 3


title: GC B cells, day14, mouse 1


title: GC B cells, day14, mouse 2


title: NB-1 clone#17 DOX+ day8 rep1

status: Public on Sep 26 2023

type: RNA

city: Kitaadachi-gun

first: Hisanori

last: Takenobu

state: Saitama

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

institute: Saitama Cancer Center

description: human", "neuroblastoma", "cell line

hyb_protocol: One-color mixes of labelled cRNA pairs were hybridized to 8x60K whole human genome oligonucleotide microarray (Agilent G4851B), at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit.

scan_protocol: Purified labeled total RNA was hybridized to the expression microarray. Hybridization, the scanning of microarrays (SureScan G4900DA Microarray Scanner), and data extraction from scanned images were conducted according to Agilent protocol version 6.9.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Homo sapiens

source_name: NB-1 clone#17 DOX+ day8 rep1

label_protocol: Two hundred nanograms of total RNA was labeled with Cyanine3 using a Low Input Quick-Amp Labeling Kit (one color, Agilent Technologies) according to the manufacturer’s instructions.

growth_protocol: Human NB cell line NGP and NB-1 were cultured in RPMI1640 (Wako) supplemented with 10% heat-inactivated fetal bovine serum (Invitrogen) and 50 μg/ml penicillin/streptomycin (Wako) in an incubator with humidified air at 37 °C with 5% CO2

extract_protocol: Total cellular RNA for preparing RT–PCR templates was extracted using ISOGEN II (Nippon Gene KK). RNA was extracted at 10 days after shEED-expressing lentiviral infection.

treatment_protocol: Regarding L3MBTL2 KO, we used Dharmacon Edit-RTM CRISPR-Cas9 Gene Engineering with Lentiviral Cas9 Nuclease (Dharmacon Edit-RTM) according to the manufacturer’s protocol. In the preparation of the lentivirus, the packaging cell line HEK 293T (4 × 10^6) was plated on a 10-cm dish and co-transfected the next day with 1.5 μg of each of the shRNA plasmids and 2.0 μg of the packaging vectors (Sigma-Aldrich) using the Fugene HD transfection reagent (Promega) according to the manufacturer’s protocol. Medium was changed the next day and cells were cultured for another 24 h. Conditioned medium was collected and cleared of debris by filtering through a filter with 0.45-μm pores.  Thereafter, NGP and NB-1 cells were infected with the Cas9 lentivirus by lentiviral-conditioned media with 4 μg/mL polybrene. Cas9-expressing cells were selected by blasticidin, a single clone was isolated and expanded, and inducible Cas9 clones were prepared by lentiviral L3MBTL2-sgRNA (Dharmacon Edit-RTM, sgL3MBTL2-1:ATGCACCACTCGTTTCACCG, sgL3MBTL2-2:GAGCCTTCCTCCACTCTCAA). Cells were selected by puromycin, and L3MBTL2-KO was induced by the addition of doxycycline.

tag: cell line


title: GC B cells, day7, mouse 3


title: GC B cells, day7, KO mouse 1


title: IL23KOf_colon_epi

status: Public on Sep 08 2023

description: female

source_name: colon

extract_protocol:
Total RNA was extracted from cells with a miRNeasy Micro kit (Qiagen) following the manufacturer’s instruction.
Library preparation was performed using the TruSeq Stranded mRNA sample prep kit (Illumina, San Diego, CA), according to the manufacturer’s instructions.

tag: tissue

value: colon

value: primary

tag: cell type

value: epithelial cell

tag: Sex

value: female


title: NGP clone#1 DOX+ day8 rep1

description: human", "neuroblastoma", "cell line

source_name: NGP clone#1 DOX+ day8 rep1

value: NGP


title: IL23KOm_colon_epi

description: male

value: male


title: NGP clone#1 DOX- day8 rep2

description: human", "neuroblastoma", "cell line

source_name: NGP clone#1 DOX- day8 rep2


title: GC B cells, day7, mouse 1


title: NB-1 clone#17 DOX- day8 rep2

description: human", "neuroblastoma", "cell line

source_name: NB-1 clone#17 DOX- day8 rep2


title: NGP clone#13 DOX+ day8 rep2

description: human", "neuroblastoma", "cell line

source_name: NGP clone#13 DOX+ day8 rep2


title: NGP clone#13 DOX- day8 rep1

description: human", "neuroblastoma", "cell line

source_name: NGP clone#13 DOX- day8 rep1


title: NB-1 clone#17 DOX+ day8 rep2

description: human", "neuroblastoma", "cell line

source_name: NB-1 clone#17 DOX+ day8 rep2


title: GC B cells, day7, KO mouse 3


title: NB-1 clone#3 DOX- day8 rep2

description: human", "neuroblastoma", "cell line

source_name: NB-1 clone#3 DOX- day8 rep2


title: NB-1 clone#3 DOX+ day8 rep2

description: human", "neuroblastoma", "cell line

source_name: NB-1 clone#3 DOX+ day8 rep2


title: NGP clone#1 DOX- day8 rep1

description: human", "neuroblastoma", "cell line

source_name: NGP clone#1 DOX- day8 rep1


title: NGP clone#13 DOX- day8 rep2

description: human", "neuroblastoma", "cell line

source_name: NGP clone#13 DOX- day8 rep2


title: NB-1 clone#3 DOX+ day8 rep1

description: human", "neuroblastoma", "cell line

source_name: NB-1 clone#3 DOX+ day8 rep1


title: NGP clone#1 DOX+ day8 rep2

description: human", "neuroblastoma", "cell line

source_name: NGP clone#1 DOX+ day8 rep2


title: NB-1 clone#3 DOX- day8 rep1

description: human", "neuroblastoma", "cell line

source_name: NB-1 clone#3 DOX- day8 rep1


title: NB-1 clone#17 DOX- day8 rep1

description: human", "neuroblastoma", "cell line

source_name: NB-1 clone#17 DOX- day8 rep1


title: GC B cells, day7, mouse 2

source_name: spleen


title: IL22KOf_colon_epi

description: female


title: IL23KOf_ileum_epi

description: female

source_name: ileum

value: ileum


title: siXBP1_3

status: Public on Sep 06 2023

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101 base single mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were mapped to the chinese hamster reference genome (GCF_003668045.1) using Hisat2 v2.1.0.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: NCBI chinese hamster reference genome (GCF_003668045.1_CriGri-PICR_genomic.fna)
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

organism: Cricetulus griseus

source_name: Ovary

extract_protocol:
Total RNA was extracted from cells with a miRNeasy kit (Qiagen) following the manufacturer’s instruction.
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).

value: Ovary

value: stably expressing Cdh13

value: CHO cells


title: IL22KOf_ileum_epi

description: female


title: IL23KOm_ileum_epi

description: male


title: IL22KOm_colon_epi

description: male

source_name: colon


title: siXBP1_2


title: NGP clone#13 DOX+ day8 rep1

description: human", "neuroblastoma", "cell line

source_name: NGP clone#13 DOX+ day8 rep1


title: IL22KOm_ileum_epi

description: male


title: Ctrl2


title: siXBP1_1


title: PC-3 cells, (Control) shControl, 2 replicate [miRNA-seq]

status: Public on Aug 21 2023

city: Moscow

first: Anton

last: Zhiyanov

address: 20 Myasnitskaya ulitsa

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

data_processing:
The quality of RNA-Seq FASTQ files was assessed with FastQC v0.11.9.
Adapter sequences were removed with the use of cutadapt v2.10: AGATCGGAAGAGCACACGTCT -- miRNA-Seq 3'-adapter.
IsomiR read count matrices were obtained using IsomiRMap with miRBase v22 annotation.
The standard isomiR notation was utilized: A number after the first ``|'' character denotes the shift from the canonical 5'-end in 5'-3' direction (5'-isomiR notation); an additional ``|'' symbol followed by a number denoted 3'-end shifts (3'-isomiR notation); finally, symbols inside ``(.)'' denoted other nucleotides added to the shifted 3'-end.
Assembly: miRBase v22
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: prostate cancer

growth_protocol: The human prostate adenocarcinoma cell lines PC-3 were grown in DMEM medium containing 4.5g/L glucose (PanEco, Russia) supplemented with 4 mM L-Glutamine (PanEco, Russia), 10% fetal bovine serum (Gibco), 1% penicillin and streptomycin (Gibco) and cultured under the standard cell culture conditions (37◦C, saturated humidity, 5% CO2).

extract_protocol:
According to the manufacturer's instructions, the total RNA was isolated from about $1 \times 10^6$ cells using miRNeasy Mini Kit (Qiagen, Germany).
All RNA samples were treated with DNase I during the isolation procedure.
The RNA yield was determined by UV absorbance using a NanoDrop 1000 spectrophotometer (Peqlab, Germany).
The RNA quality was assessed by analyzing the ribosomal RNA integrity number (RIN) on an Agilent 2000 Bioanalyzer using the RNA 6000 Nano kit (Agilent Technologies, USA).
The RIN values of the isolated RNA samples were 9.5 and higher.
Libraries for miRNA sequencing were prepared from total RNA samples using NEBNext Multiplex Small RNA Library Prep Kit (Illumina, USA).

treatment_protocol:
Stable overexpression of hsa-miR-93-5p isoforms was achieved by a shRNA-mediated approach.
In particular, each of the three double-stranded DNA fragments (in length 65 bp, 68 bp, and 67 bp) containing a 23 base hsa-miR-93-5p sequence (5'-CAAAGTGCTGTTCGTGCAGGTAG) was cloned into the BsmBI restriction sites of the LentiGuide-Hygro lentiviral vector (Addgene #139462, UK) without sgRNA scaffold.
The shRNAs coding by these DNA oligomers differed in the loop sequence only (5'-CTCGAG, 5'-TTCAAGAGA, and 5'-TTCTAGAA).
The same vector containing a short sequence of sgRNA (5'-TTCTCTTGCTGAAAGCTCGA) was used to generate a transduced control cell line (``Control'').
Nucleotide compositions of the obtained lentiviral vectors were confirmed by Sanger sequencing.
Lentiviral particles were obtained as cell-free supernatants by transient transfection of HEK-293T and using GenJect-39 transfection reagent (Molecta, Russia).
Briefly, lentiviral vectors based on pLentiGuide-Hygro were packaged using the second-generation packaging plasmid pCMV-dR8.2 dvpr (Addgene #8455, UK) and pCMV-VSV-G (Addgene #8454, UK) expressing the envelope protein of vesicular stomatitis virus.
The supernatant was harvested 24h and 48h after transfection, 0.45 $\mu$m filtered and was immediately used for transduction or stored at -80C
Target PC-3 cells were plated at 8 x 104 cells in 2 mL medium in each well of a 6-well plate 24 hours before transduction.
After viral particles containing supernatant were added to the cells, the medium was replaced in 3 days, cells were seeded into a 25 cm^2 flask, and hygromycin was added at a concentration of 150 $\mu$g/mL.
The hygromycin selection was carried out for at least two weeks.

value: prostate cancer

value: shControl


title: Ctrl3


title: Ctrl1


title: PC-3 cells, (Control) shControl, 3 replicate [miRNA-seq]


title: PC-3 cells, (sh-miR93#3) shRNA with 5'-UUCUAAAA-3' loop, 1 replicate [miRNA-seq]

value: shRNA with 5'-UUCUAAAA-3' loop


title: PC-3 cells, (Control) shControl, 1 replicate [miRNA-seq]


title: PC-3 cells, (sh-miR93#2) shRNA with 5'-UUCAAGAGA-3' loop, 2 replicate [miRNA-seq]

value: shRNA with 5'-UUCAAGAGA-3' loop


title: PC-3 cells, (sh-miR93#1) shRNA with 5'-CUCGAG-3' loop, 3 replicate [miRNA-seq]

value: shRNA with 5'-CUCGAG-3' loop


title: PC-3 cells, (sh-miR93#2) shRNA with 5'-UUCAAGAGA-3' loop, 1 replicate [miRNA-seq]


title: PC-3 cells, (Control) shControl, 2 replicate [mRNA-seq]

data_processing:
The quality of RNA-Seq FASTQ files was assessed with FastQC v0.11.9.
Adapter sequences were removed with the use of cutadapt v2.10: AGTCGGAGGCCAAGCGGTCTTAGGAAGACAA -- miRNA-Seq 3'-adapter.
Adapter-free mRNA-Seq reads were mapped to the reference human genome (GENCODE GRCh38) with STAR v2.7.5b.
Assembly: GENCODE GRCh38, GENCODE genome annotation (release 34)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
According to the manufacturer's instructions, the total RNA was isolated from about $1 \times 10^6$ cells using miRNeasy Mini Kit (Qiagen, Germany).
All RNA samples were treated with DNase I during the isolation procedure.
The RNA yield was determined by UV absorbance using a NanoDrop 1000 spectrophotometer (Peqlab, Germany).
The RNA quality was assessed by analyzing the ribosomal RNA integrity number (RIN) on an Agilent 2000 Bioanalyzer using the RNA 6000 Nano kit (Agilent Technologies, USA).
The RIN values of the isolated RNA samples were 9.5 and higher.
According to the manufacturer’s instructions, libraries for mRNA sequencing were prepared from total RNA samples using the MGIEasy RNA Library Prep Set (MGI, China).


title: PC-3 cells, (Control) shControl, 3 replicate [mRNA-seq]


title: PC-3 cells, (sh-miR93#1) shRNA with 5'-CUCGAG-3' loop, 2 replicate [miRNA-seq]


title: PC-3 cells, (sh-miR93#3) shRNA with 5'-UUCUAAAA-3' loop, 1 replicate [mRNA-seq]


title: PC-3 cells, (sh-miR93#1) shRNA with 5'-CUCGAG-3' loop, 1 replicate [miRNA-seq]


title: PC-3 cells, (sh-miR93#2) shRNA with 5'-UUCAAGAGA-3' loop, 3 replicate [mRNA-seq]


title: PC-3 cells, (sh-miR93#3) shRNA with 5'-UUCUAAAA-3' loop, 3 replicate [mRNA-seq]


title: PC-3 cells, (sh-miR93#1) shRNA with 5'-CUCGAG-3' loop, 2 replicate [mRNA-seq]


title: PC-3 cells, (sh-miR93#2) shRNA with 5'-UUCAAGAGA-3' loop, 1 replicate [mRNA-seq]


title: PC-3 cells, (sh-miR93#1) shRNA with 5'-CUCGAG-3' loop, 3 replicate [mRNA-seq]


title: rG16_RR

status: Public on Aug 14 2023

source_name: basilarcartilage

extract_protocol:
RNA was harvested using QIAzol Lysis Reagent (Qiagen) from Laser Microdissection of frozen section samples.
Each Illumina sequencing library was prepared using SMARTer Stranded Total RNA-seq Kit v2 -Pico Input Mammalian (Takara Bio).

value: basilarcartilage

value: Gli1CreERT2; Tomato flox

value: Tamoxifen injection at P3


title: PC-3 cells, (sh-miR93#3) shRNA with 5'-UUCUAAAA-3' loop, 2 replicate [mRNA-seq]


title: rG14_FP


title: rG16_FP


title: PC-3 cells, (sh-miR93#1) shRNA with 5'-CUCGAG-3' loop, 1 replicate [mRNA-seq]


title: PC-3 cells, (sh-miR93#2) shRNA with 5'-UUCAAGAGA-3' loop, 2 replicate [mRNA-seq]


title: severe stroke, S386 (miRNA)

status: Public on Aug 11 2023

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
On the generated reads, StrandNGS software (Strand Life Science Pvt. Ltd.) was used for adapter trimming (AGATCGGAAGAGCACACGTCT) , mapping, and quantification.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw count values for each sample

source_name: whole blood

extract_protocol:
Total RNA isolation was performed using a PAXgene™ Blood RNA System (BD Bioscience, San Jose, CA). The collection tubes were stored after blood collection until further analysis at -30°C.
RNA libraries were prepared using NEBNext Small RNA Library Prep Kit (New England BioLabs Inc.).

value: whole blood

tag: national institutes of health stroke scale

value: NIHSS ≥ 8

tag: diagnosis

value: severe stroke


title: rG11_FP


title: rG11_RR


title: rG14_RR


title: PC-3 cells, (sh-miR93#3) shRNA with 5'-UUCUAAAA-3' loop, 2 replicate [miRNA-seq]


title: severe stroke, S210 (miRNA)


title: severe stroke, S170 (miRNA)


title: severe stroke, S235 (miRNA)


title: severe stroke, S127 (miRNA)


title: moderate stroke, M358 (miRNA)

value: NIHSS < 8

value: moderate stroke


title: PC-3 cells, (Control) shControl, 1 replicate [mRNA-seq]


title: moderate stroke, M275 (miRNA)


title: moderate stroke, M232 (miRNA)


title: moderate stroke, M120 (miRNA)


title: moderate stroke, M104 (miRNA)


title: moderate stroke, M226 (miRNA)


title: moderate stroke, M275 (mRNA)

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101+101-base paired-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

extract_protocol:
Total RNA isolation was performed using a PAXgene™ Blood RNA System (BD Bioscience, San Jose, CA). The collection tubes were stored after blood collection until further analysis at -30°C.
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).


title: moderate stroke, M232 (mRNA)


title: moderate stroke, M226 (mRNA)


title: moderate stroke, M120 (mRNA)


title: severe stroke, S386 (mRNA)


title: severe stroke, S235 (mRNA)


title: severe stroke, S127 (mRNA)


title: severe stroke, S170 (mRNA)


title: moderate stroke, M104 (mRNA)


title: severe stroke, S107 (miRNA)


title: healthy control, 76m (mRNA)

value: control

value: healthy


title: healthy control, 69f (mRNA)


title: healthy control, 2 (miRNA)


title: severe stroke, S107 (mRNA)


title: KO98 [RNA-seq]

status: Public on Jul 24 2023

data_processing:
Sequencing was performed on HiSeq 3000 platform in a 100-base single-end mode.
Illumina RTA 2.7.7 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 5000000.
Assembly: mm10
Supplementary files format and content: *_FPKM.txt: Tab-delimited text files include FPKM values for each sample.

growth_protocol: ESCs were grown in serum/LIF medium.

extract_protocol:
Total RNA was extracted from WT, KO #98, and Rescue #22 ESCs using an RNA purification kit (NucleoSpin RNA Plus; MACHEREY-NAGEL).
Library preparation was performed using the TruSeq Stranded mRNA sample prep kit (Illumina, San Diego, CA), according to the manufacturer’s instructions.

value: embryonic stem cells

value: Zfp296 KO


title: healthy control, 70m (mRNA)


title: healthy control, 4 (miRNA)


title: ST22 [ATAC-seq]

library_source: genomic

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 151+151-base paired-end mode.
Illumina RTA v3.4.4 software was used for base calling.
ATAC-seq reads were aligned to mm10 genome using Bowtie2 version v2.3.5.1.
Narrow peak coordinate data was generated by MACS2 version 2.2.7.1 software.
Assembly: mm10
Supplementary files format and content: narrow peak coordinate data (output of MACS2).

molecule: genomic DNA

extract_protocol:
Genomic DNA of WT, KO #98, and Rescue #22 ESCs were extracted using the ATAC-Seq Kit (Cat#53150; Active Motif, Carlsbad, CA).
Tagmentase-loaded (Diagenode) was used for tagmentation reaction. PCR amplification of tagmented DNA were performed using the ATAC-Seq Kit (Active Motif).

value: Zfp296 rescue


title: Ty1Ces1 [ChIP-seq]

data_processing:
Sequencing was performed on HiSeq 2500 platform in a 101-base single-end mode.
ChIP-seq reads were aligned to mm10 genome using Bowtie version 1.1.1.
Narrow peak coordinate data were generated by MACS2 version 2.0.10 software.
Assembly: mm10
Supplementary files format and content: narrow peak coordinate data (output of MACS2).

extract_protocol:
DNA samples for ChIP-seq were prepared from Ty1-ZFP296-producing Zfp296-KO #98 ESCs using the SimpleChIP Enzymatic Chromatin IP Kit (Cat#9003; Cell Signaling).
Libraries were prepared using the TruSeq ChIP Sample Prep Kit (Illumina, San Diego, CA).

value: Ty1-tagged ZFP296 expression in Zfp296 KO

tag: chip antibody

value: Ty1-tag (Diagenode; MAb-054-050)


title: EB3 [RNA-seq]

value: wild-type


title: EB3 [ATAC-seq]


title: KO98 [ATAC-seq]

value: Zfp296 knockout


title: ST10 [RNA-seq]

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10
Supplementary files format and content: *_FPKM.txt: Tab-delimited text files include FPKM values for each sample.

extract_protocol:
Total RNA was extracted from WT, KO #156, and Rescue #10 ESCs using an RNA purification kit (NucleoSpin RNA Plus; MACHEREY-NAGEL).
Library preparation was performed using the TruSeq Stranded mRNA sample prep kit (Illumina, San Diego, CA), according to the manufacturer’s instructions.


title: KO156 [RNA-seq]


title: moderate stroke, M358 (mRNA)


title: severe stroke, S210 (mRNA)


title: si5a_8_2

status: Public on Jul 17 2023

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 101-base single-end mode.
Illumina RTA 1.18.64 software was used for base calling.
Sequenced reads were mapped to the rat reference genome sequences (rn6) using TopHat v2.1.1 in combination with Bowtie2.
The number of fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

organism: Rattus norvegicus

source_name: cardiomyocyte

extract_protocol:
Total RNA was extracted using an miRNeasy Mini Kit (Qiagen).
Library preparation was performed using a TruSeq Stranded mRNA sample preparation kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

value: cardiomyocyte

value: Wistar

value: Wnt5a siRNA with cell strech


title: si5a_8_3


title: si5a_8_1


title: siCont_8_3

value: control siRNA with cell strech


title: siCont_8_2


title: healthy control, 1 (miRNA)

value: whole blood


title: si5a_0_1

value: Wnt5a siRNA without cell strech


title: si5a_0_2


title: si5a_0_3


title: healthy control, 5 (miRNA)


title: ST22 [RNA-seq]


title: siCont_0_3

value: control siRNA without cell strech


title: siCont_0_2


title: heart CKO 4 weeks after TAC operation 41

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina RTA 1.18.64 software was used for base calling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.1.1 in combination with Bowtie2.
The number of fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 100000000.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: heart

value: Wnt5a floxed with Myh6-Cre/Esr 1

value: TAC operation


title: heart control 2 weeks after TAC operation 32

value: Wnt5a floxed


title: siCont_0_1


title: heart CKO 2 weeks after TAC operation 31


title: heart CKO at the end of tamoxifen treatment 24

value: no operation


title: heart control at the end of tamoxifen treatment 22


title: heart control at the end of tamoxifen treatment 23


title: heart CKO at the end of tamoxifen treatment 21


title: heart CKO 2 weeks after sham operation 15

value: sham operation


title: heart control 2 weeks after sham operation 16


title: heart CKO 2 weeks after TAC operation 13


title: heart control 2 weeks after sham operation 12


title: heart control 2 weeks after TAC operation 11


title: heart CKO 4 weeks after sham operation 8


title: heart control 4 weeks after sham operation 7


title: heart control 4 weeks after sham operation 6


title: heart CKO 4 weeks after TAC operation 3


title: heart control 4 weeks after TAC operation 2


title: heart control 4 weeks after TAC operation 1


title: H3K27Ac_+_BT-549

status: Public on Jul 14 2023

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101+101 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Illumina-TruSeq Adapter Trimming was performed on ChIP-seq reads, using cutadapt v2.7, discarding reads left with < 30 bp.
ChIP-seq reads were aligned to the UCSC hg19 genome using Bowtie2 version 2.3.5.1.
bigWig files were generated using the bamCoverage software of deepTools package.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
ChIP experiments were performed using the SimpleChIP Enzymatic Chromatin IP kit (9003, Cell Signaling Technologies), according to the manufacturer’s instructions. The antibodies used for ChIP were anti-H3K4me3 (9751), anti-H3K27c (8173), anti-Smad2 (5339), and anti-c-Jun (9165), which were purchased from Cell Signaling Technologies.
ChIP-seq libraries were prepared using the KAPA HyperPrep Kit.

value: Triple-negative breast cancer cell

value: TGF-beta (+,24h)


title: H3K27Ac_-_BT-549

value: TGF-beta (-)


title: healthy control, 83m (mRNA)

value: control

value: healthy


title: heart CKO 4 weeks after sham operation 4


title: Smad3_+_MCF10A

value: Normal human breast epithelial cell


title: c-Jun_-_MCF10A


title: JunB_+_MCF10A


title: Smad3_-_MCF10A


title: siCont_8_1

value: cardiomyocyte

value: Wistar


title: Smad2_+_MCF10A


title: JunB_-_MCF10A


title: c-Jun_+_MCF10A


title: H3K27Ac_+_MCF10A


title: heart CKO 2 weeks after sham operation 14


title: Smad2_-_MCF10A


title: H3K27Ac_-_MCF10A


title: H3K4me3_-_MCF10A


title: H3K4me3_+_MCF10A


title: WTf_middle_colon_epi

description:
GA37187
primary cells

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10
Supplementary files format and content: *.FPKM.txt: Tab-delimited text files include FPKM values for each sample.

source_name: middle colon

extract_protocol:
Total RNA was extracted from cells with a miRNeasy Micro Kit (Qiagen) following the manufacturer’s instruction.
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).

value: middle colon

value: epithelial cells

value: wild-type

value: female

value: no treatment


title: WTf_proximal_colon_epi

description:
GA37186
primary cells

source_name: proximal colon

value: proximal colon


title: WTm_distal_colon_epi

description:
GA37185
primary cells

source_name: distal colon

value: distal colon

value: male


title: WTf_distal_colon_epi

description:
GA37188
primary cells


title: WTm_middle_colon_epi

description:
GA37184
primary cells


title: WTm_proximal_colon_epi

description:
GA37183
primary cells


title: B3gnt7KO_female_colon_epi

description:
GA31758
primary cells

value: colon


title: B3galt5mut_female_colon_epi

description:
GA31756
primary cells


title: B3gnt7KO_male_colon_epi

description:
GA31757
primary cells


title: CD4+CD25-YFP+_rep1

status: Public on Jul 13 2023

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.1.1 in combination with Bowtie2.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 5000000.
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

extract_protocol: Total RNA was extracted from cells with a miRNeasy Mini kit (Qiagen) according to the manufacturer’s protocol. Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio, Mountain View, CA) according to the manufacturer’s instructions. An Illumina library was prepared using a Nextera DNA Library Preparation Kit (Illumina, San Diego, CA) according to SMARTer kit instructions.

value: spleen

value: Foxp3-Cre/Tbx21-Flp/VeDTR(LF) mice


title: St6galnac6KO_female_colon_epi

description:
GA31754
primary cells


title: CD4+CD25+YFP+_rep3


title: CD4+CD25+YFP-_rep3


title: WT_female_colon_epi

description:
GA31752
primary cells


title: CD4+CD25+YFP-_rep2


title: CD4+CD25-YFP-_rep3


title: B3galt5mut_male_colon_epi

description:
GA31755
primary cells


title: α-CD3/α-CD28-stimulated_YFP+ Treg cells_rep2

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.1.1 in combination with Bowtie2.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 5000000.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: α-CD3/α-CD28-stimulated_YFP+ Treg cells

extract_protocol:
Total RNA was extracted from cells with a miRNeasy Mini kit (Qiagen) according to the manufacturer’s protocol.
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio, Mountain View, CA) according to the manufacturer’s instructions. An Illumina library was prepared using a Nextera DNA Library Preparation Kit (Illumina, San Diego, CA) according to SMARTer kit instructions.


title: α-CD3/α-CD28-stimulated_YFP+ Treg cells_rep1


title: WT_male_colon_epi

description:
GA31751
primary cells


title: St6galnac6KO_male_colon_epi

description:
GA31753
primary cells


title: CD4+CD25-YFP+_rep2


title: CD4+CD25-YFP+_rep3


title: CD4+CD25-YFP-_rep2


title: CD4+CD25-YFP-_rep1


title: unstimulated_YFP- Treg cells_rep2

source_name: unstimulated_YFP- Treg cells


title: CD4+CD25+YFP+_rep1


title: unstimulated_YFP+ Treg cells_rep3

source_name: unstimulated_YFP+ Treg cells


title: α-CD3/α-CD28-stimulated_YFP+ Treg cells_rep3


title: CD4+CD25+YFP-_rep1


title: α-CD3/α-CD28-stimulated_YFP- Treg cells_rep3

source_name: α-CD3/α-CD28-stimulated_YFP- Treg cells


title: unstimulated_YFP+ Treg cells_rep1


title: α-CD3/α-CD28-stimulated_YFP- Treg cells_rep2


title: YFP- Treg cells_rep3

source_name: YFP- CD4+ CD25+ T cells


title: YFP+ Treg cells_rep1

source_name: YFP+ CD4+ CD25+ T cells


title: α-CD3/α-CD28-stimulated_YFP- Treg cells_rep1


title: unstimulated_YFP+ Treg cells_rep2


title: unstimulated_YFP- Treg cells_rep1


title: CD4+CD25+YFP+_rep2

source_name: spleen


title: mst2D epe1-deg,+TN 120hrs H3K9me3 , rep2

status: Public on Jul 11 2023

city: Waltham

first: Ajay

last: Larkin

state: MA

address: 415 South St

department: MCB

country: USA

institute: Brandeis University

data_processing:
sequences were trimmed with Trimmomatic, aligned with BWA, and normalized by SES using Deeptools BamCompare to input
Assembly: ASM294v2.29
Supplementary files format and content: bedgraph files

organism: Schizosaccharomyces pombe

source_name: mst2D epe1-deg 120hr H3K9me3 rep2

growth_protocol: EMMC, grown to log phase at 32C

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. Cells were lysed with bead beating.
ChIPseq libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina. 1Ng of DNA was used as starting material

treatment_protocol: +TN cultures were treated with 15mM thiamine and 500mM 1-napthaleneacetic acid

value: +TN


title: YFP- Treg cells_rep2


title: YFP+ Treg cells_rep3


title: unstimulated_YFP- Treg cells_rep3


title: YFP- Treg cells_rep1


title: mst2D epe1-deg,+TN 96hrs input , rep1

source_name: mst2D epe1-deg 96hr input rep1


title: mst2D epe1-deg,+TN 96hrs input , rep2

source_name: mst2D epe1-deg 96hr input rep2


title: mst2D epe1-deg,+TN 96hrs H3K9me3 , rep2

source_name: mst2D epe1-deg 96hr H3K9me3 rep2


title: mst2D epe1-deg,+TN 96hrs H3K9me3 , rep1

source_name: mst2D epe1-deg 96hr H3K9me3 rep1


title: mst2D epe1-deg,+TN 120hrs H3K9me3 , rep1

source_name: mst2D epe1-deg 120hr H3K9me3 rep1


title: mst2D epe1-deg,+TN 48hrs input , rep2

source_name: mst2D epe1-deg 48hr input rep2


title: mst2D epe1-deg,+TN 72hrs H3K9me3 , rep2

source_name: mst2D epe1-deg 72hr H3K9me3 rep2


title: mst2D epe1-deg,+TN 72hrs input , rep1

source_name: mst2D epe1-deg 72hr input rep1


title: YFP+ Treg cells_rep2


title: mst2D epe1-deg,+TN 48hrs input , rep1

source_name: mst2D epe1-deg 48hr input rep1


title: mst2D epe1-deg,+TN 72hrs input , rep2

source_name: mst2D epe1-deg 72hr input rep2


title: mst2D epe1-deg,+TN 24hrs input , rep2

source_name: mst2D epe1-deg 24hr input rep2


title: mst2D epe1-deg,+TN 48hrs H3K9me3 , rep1

source_name: mst2D epe1-deg 48hr H3K9me3 rep1


title: mst2D epe1-deg,+TN 72hrs H3K9me3 , rep1

source_name: mst2D epe1-deg 72hr H3K9me3 rep1


title: mst2D epe1-deg,+TN 120hrs input , rep1

source_name: mst2D epe1-deg 120hr input rep1


title: mst2D epe1-deg,+TN 24hrs H3K9me3 , rep1

source_name: mst2D epe1-deg 24hr H3K9me3 rep1


title: mst2D epe1-deg,-TN, input rep2

source_name: mst2D epe1-deg 0hr input rep2


title: mst2D epe1-deg,+TN 48hrs H3K9me3 , rep2

source_name: mst2D epe1-deg 48hr H3K9me3 rep2


title: mst2D epe1-deg,-TN, H3K9me3 rep1

source_name: mst2D epe1-deg 0hr H3K9me3 rep1


title: mst2D epe1-deg,-TN, input rep1

source_name: mst2D epe1-deg 0hr input rep1


title: input,DMSO,rep3

status: Public on Jul 02 2023

city: ShangHai

first: Jialun

last: Li

address: NO. 500 Dongchuan Road, Minhang distinct

country: China

institute: WuHu Hospital, East China Normal University

data_processing:
ChIP-seq raw reads were trimmed by Trim Galore v.0.6.5 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adapter sequences and poor-quality nucleotides.
The trimmed reads were mapped to the human genome (assembly hg38) using Bowtie v.2.4.556 with default parameters. The output SAM files were converted to binary (BAM) format. All BAM files were sorted and indexed using samtools v.1.7
Samtools was also used to additionally remove nonuniquely mapped reads, as well as reads with a sequencing quality score q < 20
PCR duplicates were removed using Picard Tools MarkDuplicates
BigWig files were generated using deeptools bamCoverage58 with --bs 60 and –normalize Using RPKM options.
Peak calling was performed using MACS v.2.2.759 with default parameters for Ksu, H3K23su, and H3K4me3 except for ‘-g hs -p 0.05 --nomodel --keep-dup all’. For H3K27ac data, MACS2 was run using the following parameters ‘-g hs -p 0.05 --nomodel --broad --broad-cutoff 0.1 --keep-dup all’. From the resulting peaks, those located in ENCODE black listed regions and mitochondrial DNA were filtered out, as were peaks that did not meet either the significance threshold of q-value < 0.01 for narrow peak calling or the significance threshold of q-value < 0.001 for broad peak calling.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: HeLa

growth_protocol: HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Gibco) supplemented with 10% FBS, 100 U/ml penicillin, and 100 mg/ml streptomycin in 5% CO2 at 37 °C.

extract_protocol:
The proteins and RNA in the Input and ChIP samples are enzymatically digested and the DNA is further purified by phenol–chloroform extraction and ethanol precipitation. The DNA was dissolve in ddH2O.
For ChIP-seq analysis, a total amount of 50 ng DNA per sample was used as input material for library construction. Sequencing libraries were generated using NEBNext Ultra DNA Library Prep Kit from Illumina (NEB,USA) by following manufacturer's recommendations and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using HiSeq Rapid Duo cBot Sample Loading Kit (Illumia) according to the manufacturer's instructions.

treatment_protocol: HeLa cells were treated with 1 μM TSA  for 12 h.

value: HeLa

value: DMSO


title: input,DMSO,rep2


title: input,TSA,rep3

value: TSA


title: input,TSA,rep2


title: mst2D epe1-deg,+TN 24hrs input , rep1

source_name: mst2D epe1-deg 24hr input rep1


title: input,TSA,rep1


title: H3K4me3,DMSO,rep2


title: H3K4me3,DMSO,rep3


title: H3K4me3,TSA,rep3


title: H3K4me3,DMSO,rep1


title: H3K4me3,TSA,rep2


title: H3K4me3,TSA,rep1


title: mst2D epe1-deg,+TN 24hrs H3K9me3 , rep2

source_name: mst2D epe1-deg 24hr H3K9me3 rep2


title: H3K27ac,DMSO,rep2


title: H3K27ac,DMSO,rep1


title: H3K23su,DMSO,rep3


title: H3K23su,DMSO,rep2


title: mst2D epe1-deg,+TN 120hrs input , rep2

source_name: mst2D epe1-deg 120hr input rep2


title: mst2D epe1-deg,-TN, H3K9me3 rep2

source_name: mst2D epe1-deg 0hr H3K9me3 rep2


title: H3K27ac,TSA,rep2


title: H3K23su,DMSO,rep1


title: H3K23su,TSA,rep3


title: input,DMSO,rep1


title: H3K23su,TSA,rep1


title: su,TSA,rep3

value: Ksu


title: su,DMSO,rep1


title: su,TSA,rep2


title: su,DMSO,rep3


title: su,TSA,rep1


title: H3K23su,TSA,rep2


title: su,DMSO,rep2


title: 5KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 84h

status: Public on Jun 30 2023

city: Kanagawa

first: Satoru

last: Morimoto

address: 3－25－10, Tonomachi, Kawasaki-ku, Kawasaki-shi

department: Keio Regenerative Medicine Research Center (KRM)

institute: Keio University

description: SMART-seq

data_processing:
Quality Control of the sequences was performed by fastp (version 0.23.2).
Read counts were calculated by salmon (version 1.7.0), and the read count data outputs by salmon were processed by tximport (version 1.22.0).
The processed data were subjected to Transcripts Per Million (TPM) normalization among groups.

extract_protocol:
RNA was harvested using Rneasy Micro Kit (Qiagen). 0.2 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Nextera XT DNA Library Prep Kit following manufacturer's protocols.

value: WT

value: ROPI

tag: time


title: 30KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 84h

description: SMART-seq


title: H3K27ac,DMSO,rep3


title: 3KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 84h

description: SMART-seq


title: 2KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 84h

description: SMART-seq


title: H3K27ac,TSA,rep3


title: 8KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 84h

description: SMART-seq


title: 28KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 84h

description: SMART-seq


title: 26KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 84h

description: SMART-seq


title: H3K27ac,TSA,rep1


title: 24KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 84h

description: SMART-seq


title: 29KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 84h

description: SMART-seq


title: 14KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 84h

description: SMART-seq


title: 17KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 84h

description: SMART-seq


title: 12KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 84h

description: SMART-seq


title: 18KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 84h

description: SMART-seq


title: 23KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 84h

description: SMART-seq


title: 20KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 84h

description: SMART-seq


title: 13KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 84h

description: SMART-seq


title: 22KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 84h

description: SMART-seq


title: 6KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 84h

description: SMART-seq


title: 10KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 84h

description: SMART-seq


title: 11KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 84h

description: SMART-seq


title: 5KALS, iPSC-derived motor neurons from patient with ALS, non, 84h

description: SMART-seq

value: non


title: 3KALS, iPSC-derived motor neurons from patient with ALS, non, 84h

description: SMART-seq


title: 8KALS, iPSC-derived motor neurons from patient with ALS, non, 84h

description: SMART-seq


title: 30KALS, iPSC-derived motor neurons from patient with ALS, non, 84h

description: SMART-seq


title: 29KALS, iPSC-derived motor neurons from patient with ALS, non, 84h

description: SMART-seq


title: 26KALS, iPSC-derived motor neurons from patient with ALS, non, 84h

description: SMART-seq


title: 23KALS, iPSC-derived motor neurons from patient with ALS, non, 84h

description: SMART-seq


title: 24KALS, iPSC-derived motor neurons from patient with ALS, non, 84h

description: SMART-seq


title: 22KALS, iPSC-derived motor neurons from patient with ALS, non, 84h

description: SMART-seq


title: 20KALS, iPSC-derived motor neurons from patient with ALS, non, 84h

description: SMART-seq


title: 28KALS, iPSC-derived motor neurons from patient with ALS, non, 84h

description: SMART-seq


title: 18KALS, iPSC-derived motor neurons from patient with ALS, non, 84h

description: SMART-seq


title: 6KALS, iPSC-derived motor neurons from patient with ALS, non, 84h

description: SMART-seq


title: 14KALS, iPSC-derived motor neurons from patient with ALS, non, 84h

description: SMART-seq


title: 17KALS, iPSC-derived motor neurons from patient with ALS, non, 84h

description: SMART-seq


title: 13KALS, iPSC-derived motor neurons from patient with ALS, non, 84h

description: SMART-seq


title: 12KALS, iPSC-derived motor neurons from patient with ALS, non, 84h

description: SMART-seq


title: 2KALS, iPSC-derived motor neurons from patient with ALS, non, 84h

description: SMART-seq


title: 8KALS, iPSC-derived motor neurons from patient with ALS, non, 72h

description: SMART-seq


title: 10KALS, iPSC-derived motor neurons from patient with ALS, non, 84h

description: SMART-seq


title: 30KALS, iPSC-derived motor neurons from patient with ALS, non, 72h

description: SMART-seq


title: 2KALS, iPSC-derived motor neurons from patient with ALS, non, 72h

description: SMART-seq


title: 6KALS, iPSC-derived motor neurons from patient with ALS, non, 72h

description: SMART-seq


title: 5KALS, iPSC-derived motor neurons from patient with ALS, non, 72h

description: SMART-seq


title: 28KALS, iPSC-derived motor neurons from patient with ALS, non, 72h

description: SMART-seq


title: 29KALS, iPSC-derived motor neurons from patient with ALS, non, 72h

description: SMART-seq


title: 3KALS, iPSC-derived motor neurons from patient with ALS, non, 72h

description: SMART-seq


title: 23KALS, iPSC-derived motor neurons from patient with ALS, non, 72h

description: SMART-seq


title: 14KALS, iPSC-derived motor neurons from patient with ALS, non, 72h

description: SMART-seq


title: 12KALS, iPSC-derived motor neurons from patient with ALS, non, 72h

description: SMART-seq


title: 24KALS, iPSC-derived motor neurons from patient with ALS, non, 72h

description: SMART-seq


title: 20KALS, iPSC-derived motor neurons from patient with ALS, non, 72h

description: SMART-seq


title: 17KALS, iPSC-derived motor neurons from patient with ALS, non, 72h

description: SMART-seq


title: 5KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 6h

description: SMART-seq


title: 11KALS, iPSC-derived motor neurons from patient with ALS, non, 84h

description: SMART-seq


title: 10KALS, iPSC-derived motor neurons from patient with ALS, non, 72h

description: SMART-seq


title: 18KALS, iPSC-derived motor neurons from patient with ALS, non, 72h

description: SMART-seq


title: 13KALS, iPSC-derived motor neurons from patient with ALS, non, 72h

description: SMART-seq


title: 3KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 6h

description: SMART-seq


title: 11KALS, iPSC-derived motor neurons from patient with ALS, non, 72h

description: SMART-seq


title: 29KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 6h

description: SMART-seq


title: 8KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 6h

description: SMART-seq


title: 6KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 6h

description: SMART-seq


title: 23KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 6h

description: SMART-seq


title: 22KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 6h

description: SMART-seq


title: 30KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 6h

description: SMART-seq


title: 18KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 6h

description: SMART-seq


title: 2KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 6h

description: SMART-seq


title: 26KALS, iPSC-derived motor neurons from patient with ALS, non, 72h

description: SMART-seq


title: 26KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 6h

description: SMART-seq


title: 28KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 6h

description: SMART-seq


title: 14KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 6h

description: SMART-seq


title: 13KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 6h

description: SMART-seq


title: 17KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 6h

description: SMART-seq


title: 20KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 6h

description: SMART-seq


title: 10KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 6h

description: SMART-seq


title: 24KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 6h

description: SMART-seq


title: 11KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 6h

description: SMART-seq


title: 22KALS, iPSC-derived motor neurons from patient with ALS, non, 72h

description: SMART-seq


title: 6KALS, iPSC-derived motor neurons from patient with ALS, non, 60h

description: SMART-seq


title: 5KALS, iPSC-derived motor neurons from patient with ALS, non, 60h

description: SMART-seq


title: 30KALS, iPSC-derived motor neurons from patient with ALS, non, 60h

description: SMART-seq


title: 29KALS, iPSC-derived motor neurons from patient with ALS, non, 60h

description: SMART-seq


title: 28KALS, iPSC-derived motor neurons from patient with ALS, non, 60h

description: SMART-seq


title: 8KALS, iPSC-derived motor neurons from patient with ALS, non, 60h

description: SMART-seq


title: 3KALS, iPSC-derived motor neurons from patient with ALS, non, 60h

description: SMART-seq


title: 2KALS, iPSC-derived motor neurons from patient with ALS, non, 60h

description: SMART-seq


title: 22KALS, iPSC-derived motor neurons from patient with ALS, non, 60h

description: SMART-seq


title: 23KALS, iPSC-derived motor neurons from patient with ALS, non, 60h

description: SMART-seq


title: 26KALS, iPSC-derived motor neurons from patient with ALS, non, 60h

description: SMART-seq


title: 20KALS, iPSC-derived motor neurons from patient with ALS, non, 60h

description: SMART-seq


title: 18KALS, iPSC-derived motor neurons from patient with ALS, non, 60h

description: SMART-seq


title: 12KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 6h

description: SMART-seq


title: 14KALS, iPSC-derived motor neurons from patient with ALS, non, 60h

description: SMART-seq


title: 17KALS, iPSC-derived motor neurons from patient with ALS, non, 60h

description: SMART-seq


title: 12KALS, iPSC-derived motor neurons from patient with ALS, non, 60h

description: SMART-seq


title: 13KALS, iPSC-derived motor neurons from patient with ALS, non, 60h

description: SMART-seq


title: 10KALS, iPSC-derived motor neurons from patient with ALS, non, 60h

description: SMART-seq


title: 11KALS, iPSC-derived motor neurons from patient with ALS, non, 60h

description: SMART-seq


title: 8KALS, iPSC-derived motor neurons from patient with ALS, non, 48h

description: SMART-seq


title: 6KALS, iPSC-derived motor neurons from patient with ALS, non, 48h

description: SMART-seq


title: 5KALS, iPSC-derived motor neurons from patient with ALS, non, 48h

description: SMART-seq


title: 30KALS, iPSC-derived motor neurons from patient with ALS, non, 48h

description: SMART-seq


title: 3KALS, iPSC-derived motor neurons from patient with ALS, non, 48h

description: SMART-seq


title: 29KALS, iPSC-derived motor neurons from patient with ALS, non, 48h

description: SMART-seq


title: 28KALS, iPSC-derived motor neurons from patient with ALS, non, 48h

description: SMART-seq


title: 2KALS, iPSC-derived motor neurons from patient with ALS, non, 48h

description: SMART-seq


title: 26KALS, iPSC-derived motor neurons from patient with ALS, non, 48h

description: SMART-seq


title: 24KALS, iPSC-derived motor neurons from patient with ALS, non, 60h

description: SMART-seq


title: 23KALS, iPSC-derived motor neurons from patient with ALS, non, 48h

description: SMART-seq


title: 22KALS, iPSC-derived motor neurons from patient with ALS, non, 48h

description: SMART-seq


title: 20KALS, iPSC-derived motor neurons from patient with ALS, non, 48h

description: SMART-seq


title: 24KALS, iPSC-derived motor neurons from patient with ALS, non, 48h

description: SMART-seq


title: 13KALS, iPSC-derived motor neurons from patient with ALS, non, 48h

description: SMART-seq


title: 14KALS, iPSC-derived motor neurons from patient with ALS, non, 48h

description: SMART-seq


title: 17KALS, iPSC-derived motor neurons from patient with ALS, non, 48h

description: SMART-seq


title: 10KALS, iPSC-derived motor neurons from patient with ALS, non, 48h

description: SMART-seq


title: 11KALS, iPSC-derived motor neurons from patient with ALS, non, 48h

description: SMART-seq


title: 18KALS, iPSC-derived motor neurons from patient with ALS, non, 48h

description: SMART-seq


title: 8KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 36h

description: SMART-seq


title: 5KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 36h

description: SMART-seq


title: 2KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 36h

description: SMART-seq


title: 6KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 36h

description: SMART-seq


title: 30KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 36h

description: SMART-seq


title: 3KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 36h

description: SMART-seq


title: 26KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 36h

description: SMART-seq


title: 29KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 36h

description: SMART-seq


title: 28KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 36h

description: SMART-seq


title: 24KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 36h

description: SMART-seq


title: 23KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 36h

description: SMART-seq


title: 22KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 36h

description: SMART-seq


title: 14KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 36h

description: SMART-seq


title: 17KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 36h

description: SMART-seq


title: 18KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 36h

description: SMART-seq


title: 12KALS, iPSC-derived motor neurons from patient with ALS, non, 48h

description: SMART-seq


title: 11KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 36h

description: SMART-seq


title: 10KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 36h

description: SMART-seq


title: 12KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 36h

description: SMART-seq


title: 3KALS, iPSC-derived motor neurons from patient with ALS, non, 36h

description: SMART-seq


title: 30KALS, iPSC-derived motor neurons from patient with ALS, non, 36h

description: SMART-seq


title: 13KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 36h

description: SMART-seq


title: 5KALS, iPSC-derived motor neurons from patient with ALS, non, 36h

description: SMART-seq


title: 6KALS, iPSC-derived motor neurons from patient with ALS, non, 36h

description: SMART-seq


title: 29KALS, iPSC-derived motor neurons from patient with ALS, non, 36h

description: SMART-seq


title: 8KALS, iPSC-derived motor neurons from patient with ALS, non, 36h

description: SMART-seq


title: 2KALS, iPSC-derived motor neurons from patient with ALS, non, 36h

description: SMART-seq


title: 26KALS, iPSC-derived motor neurons from patient with ALS, non, 36h

description: SMART-seq


title: 28KALS, iPSC-derived motor neurons from patient with ALS, non, 36h

description: SMART-seq


title: 23KALS, iPSC-derived motor neurons from patient with ALS, non, 36h

description: SMART-seq


title: 22KALS, iPSC-derived motor neurons from patient with ALS, non, 36h

description: SMART-seq


title: 18KALS, iPSC-derived motor neurons from patient with ALS, non, 36h

description: SMART-seq


title: 17KALS, iPSC-derived motor neurons from patient with ALS, non, 36h

description: SMART-seq


title: 13KALS, iPSC-derived motor neurons from patient with ALS, non, 36h

description: SMART-seq


title: 14KALS, iPSC-derived motor neurons from patient with ALS, non, 36h

description: SMART-seq


title: 11KALS, iPSC-derived motor neurons from patient with ALS, non, 36h

description: SMART-seq


title: 20KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 36h

description: SMART-seq


title: 12KALS, iPSC-derived motor neurons from patient with ALS, non, 36h

description: SMART-seq


title: 8KALS, iPSC-derived motor neurons from patient with ALS, non, 24h

description: SMART-seq


title: 10KALS, iPSC-derived motor neurons from patient with ALS, non, 36h

description: SMART-seq


title: 3KALS, iPSC-derived motor neurons from patient with ALS, non, 24h

description: SMART-seq


title: 6KALS, iPSC-derived motor neurons from patient with ALS, non, 24h

description: SMART-seq


title: 30KALS, iPSC-derived motor neurons from patient with ALS, non, 24h

description: SMART-seq


title: 2KALS, iPSC-derived motor neurons from patient with ALS, non, 24h

description: SMART-seq


title: 5KALS, iPSC-derived motor neurons from patient with ALS, non, 24h

description: SMART-seq


title: 29KALS, iPSC-derived motor neurons from patient with ALS, non, 24h

description: SMART-seq


title: 28KALS, iPSC-derived motor neurons from patient with ALS, non, 24h

description: SMART-seq


title: 24KALS, iPSC-derived motor neurons from patient with ALS, non, 24h

description: SMART-seq


title: 17KALS, iPSC-derived motor neurons from patient with ALS, non, 24h

description: SMART-seq


title: 26KALS, iPSC-derived motor neurons from patient with ALS, non, 24h

description: SMART-seq


title: 18KALS, iPSC-derived motor neurons from patient with ALS, non, 24h

description: SMART-seq


title: 23KALS, iPSC-derived motor neurons from patient with ALS, non, 24h

description: SMART-seq


title: 14KALS, iPSC-derived motor neurons from patient with ALS, non, 24h

description: SMART-seq


title: 24KALS, iPSC-derived motor neurons from patient with ALS, non, 36h

description: SMART-seq


title: 20KALS, iPSC-derived motor neurons from patient with ALS, non, 36h

description: SMART-seq


title: 11KALS, iPSC-derived motor neurons from patient with ALS, non, 24h

description: SMART-seq


title: 10KALS, iPSC-derived motor neurons from patient with ALS, non, 24h

description: SMART-seq


title: 12KALS, iPSC-derived motor neurons from patient with ALS, non, 24h

description: SMART-seq


title: 8KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 12h

description: SMART-seq


title: 6KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 12h

description: SMART-seq


title: 29KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 12h

description: SMART-seq


title: 3KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 12h

description: SMART-seq


title: 30KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 12h

description: SMART-seq


title: 2KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 12h

description: SMART-seq


title: 28KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 12h

description: SMART-seq


title: 5KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 12h

description: SMART-seq


title: 22KALS, iPSC-derived motor neurons from patient with ALS, non, 24h

description: SMART-seq


title: 22KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 12h

description: SMART-seq


title: 18KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 12h

description: SMART-seq


title: 20KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 12h

description: SMART-seq


title: 20KALS, iPSC-derived motor neurons from patient with ALS, non, 24h

description: SMART-seq


title: 11KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 12h

description: SMART-seq


title: 12KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 12h

description: SMART-seq


title: 24KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 12h

description: SMART-seq


title: 14KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 12h

description: SMART-seq


title: 10KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 12h

description: SMART-seq


title: 13KALS, iPSC-derived motor neurons from patient with ALS, non, 24h

description: SMART-seq


title: 8KALS, iPSC-derived motor neurons from patient with ALS, non, 12h

description: SMART-seq


title: 3KALS, iPSC-derived motor neurons from patient with ALS, non, 12h

description: SMART-seq


title: 5KALS, iPSC-derived motor neurons from patient with ALS, non, 12h

description: SMART-seq


title: 23KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 12h

description: SMART-seq


title: 13KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 12h

description: SMART-seq


title: 30KALS, iPSC-derived motor neurons from patient with ALS, non, 12h

description: SMART-seq


title: 2KALS, iPSC-derived motor neurons from patient with ALS, non, 12h

description: SMART-seq


title: 28KALS, iPSC-derived motor neurons from patient with ALS, non, 12h

description: SMART-seq


title: 6KALS, iPSC-derived motor neurons from patient with ALS, non, 12h

description: SMART-seq


title: 26KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 12h

description: SMART-seq


title: 23KALS, iPSC-derived motor neurons from patient with ALS, non, 12h

description: SMART-seq


title: 26KALS, iPSC-derived motor neurons from patient with ALS, non, 12h

description: SMART-seq


title: 24KALS, iPSC-derived motor neurons from patient with ALS, non, 12h

description: SMART-seq


title: 22KALS, iPSC-derived motor neurons from patient with ALS, non, 12h

description: SMART-seq


title: 20KALS, iPSC-derived motor neurons from patient with ALS, non, 12h

description: SMART-seq


title: 18KALS, iPSC-derived motor neurons from patient with ALS, non, 12h

description: SMART-seq


title: 17KALS, iPSC-derived motor neurons from patient with ALS, non, 12h

description: SMART-seq


title: 14KALS, iPSC-derived motor neurons from patient with ALS, non, 12h

description: SMART-seq


title: 13KALS, iPSC-derived motor neurons from patient with ALS, non, 12h

description: SMART-seq


title: 12KALS, iPSC-derived motor neurons from patient with ALS, non, 12h

description: SMART-seq


title: 11KALS, iPSC-derived motor neurons from patient with ALS, non, 12h

description: SMART-seq


title: 17KALS, iPSC-derived motor neurons from patient with ALS, ROPI, 12h

description: SMART-seq


title: 10KALS, iPSC-derived motor neurons from patient with ALS, non, 12h

description: SMART-seq


title: 8KALS, iPSC-derived motor neurons from patient with ALS, non, 0h

description: SMART-seq


title: 6KALS, iPSC-derived motor neurons from patient with ALS, non, 0h

description: SMART-seq


title: 3KALS, iPSC-derived motor neurons from patient with ALS, non, 0h

description: SMART-seq


title: 29KALS, iPSC-derived motor neurons from patient with ALS, non, 12h

description: SMART-seq


title: 26KALS, iPSC-derived motor neurons from patient with ALS, non, 0h

description: SMART-seq


title: 5KALS, iPSC-derived motor neurons from patient with ALS, non, 0h

description: SMART-seq


title: 29KALS, iPSC-derived motor neurons from patient with ALS, non, 0h

description: SMART-seq


title: 30KALS, iPSC-derived motor neurons from patient with ALS, non, 0h

description: SMART-seq


title: 23KALS, iPSC-derived motor neurons from patient with ALS, non, 0h

description: SMART-seq


title: 2KALS, iPSC-derived motor neurons from patient with ALS, non, 0h

description: SMART-seq


title: 17KALS, iPSC-derived motor neurons from patient with ALS, non, 0h

description: SMART-seq


title: 18KALS, iPSC-derived motor neurons from patient with ALS, non, 0h

description: SMART-seq


title: 28KALS, iPSC-derived motor neurons from patient with ALS, non, 0h

description: SMART-seq


title: 20KALS, iPSC-derived motor neurons from patient with ALS, non, 0h

description: SMART-seq


title: 22KALS, iPSC-derived motor neurons from patient with ALS, non, 0h

description: SMART-seq


title: 13KALS, iPSC-derived motor neurons from patient with ALS, non, 0h

description: SMART-seq


title: 11KALS, iPSC-derived motor neurons from patient with ALS, non, 0h

description: SMART-seq


title: 14KALS, iPSC-derived motor neurons from patient with ALS, non, 0h

description: SMART-seq


title: 10KALS, iPSC-derived motor neurons from patient with ALS, non, 0h

description: SMART-seq


title: H3k27me3_TaDRIM-Seq -rep2

status: Public on Jun 08 2023

city: Wuhan

first: guoting

last: chen

address: 1 Shizishan Street, Hongshan District

institute: National Key Laboratory of Crop Genetic Improvement

data_processing:
Quality control was performed using FastQC and Cutadapt
Merge the reads was performed using flash
RNA reads were aligned to the genome by HIAST2 and the non-aligned and multi-aligned reads were extracted and aligned to the genome by BOWTIE2
The DNA was marked with the given anchor using BEDTools intersect and the RNA marked the annotation genes (mRNA, lncRNA, snoRNA, snRNA, and microRNA) using HTSeq
Assembly: Download the genome from http://rice.hzau.edu.cn/ and https://www.gencodegenes.org/human/
Supplementary files format and content: The bedpe files provide processed RNA-DNA interaction data.
Library strategy: TaDRIM-Seq

organism: Oryza sativa Indica Group

source_name: mature leaf

extract_protocol:
Approximately1×106- 1×107 crosslinked cells were used per replicate. Cell nuclei were isolated in 1 mL lysis buffer (10mM Tris pH 7.5, 10mM NaCl, 0.2% NP40, 1×protease inhibitors, 0.2 U/μl RiboLock RNase) (Thermo Fisher), and incubated for 10min on ice followed by centrifugation for 3min at 2500g and 4°C. The nuclei were washed twice with 300µl 1×wash buffer A (20mM HEPES pH 7.6, 150mM NaCl, 0.5mM Spermidine, 1×protease inhibitors, 0.2U/μl RiboLock RNase) (Thermo Fisher), and nuclei were collected by centrifugation for 3min at 2500g and 4 °C. Nuclei were then resuspended in Antibody buffer (495μl 1×wash buffer A, 5μl 5% digitonin, 2μl 0.5M EDTA, 1.6μl 30%BSA, 10μg antibody (H3K4me3, Abcam, ab8580)), and incubated at 4°C for 2h with rotation. Nuclei were pelleted for 3 min at 2500g and washed five times with 300μl 1×wash buffer A, resuspended 500µl 1×transposase incubation buffer (20mM HEPES pH 7.6, 300mM NaCl, 0.5mM Spermidine, 0.01% digitonin, 1×protease inhibitors, 0.2U/μl RiboLock RNase) (Thermo Fisher), followed by adding 5μl TTE Mix, and incubated at 4°C for 1h with rotation. Nuclei were collected and washed five times with 300µl 1×transposase incubation buffer and resuspended in tagmentation buffer (500µl 1×transposase incubation buffer, 5µl 1M MgCl2), and incubated at 37°C for 1h. Next, 500µl of 40mM EDTA (Thermo Fisher) was added to stop the reaction. The isolated nuclei were washed twice with 500µl 1×PBS (Thermo Fisher) and then incubated in 200µl permeabilization buffer (190µl nuclease-free water, 10µl 10% SDS) (Thermo Fisher) at 62°C for 10min, and immediately quenched the SDS reaction by adding add 580μl of nuclease-free water and 100μl of 10% (vol/vol) Triton X-100 (Sigma-aldrich), and incubated at 37°C for 15min with rotation.The isolated nuclei were washed twice with 500µl 1×wash buffer B (20mM Tris-HCl, pH 7.5, 10mM MgCl2 and 0.2% Tween 20) and resuspended in 500µl 1× CutSmart buffer (NEB), followed by adding 1.6µl RNase If (NEB) with dilution tenfold in 1× PBS, and incubated at 37°C for 3min with rotation followed by incubation for 5min on ice. Nuclei were collected by centrifugation, then resuspended by 400µl PNK solution containing 1×T4 PNK reaction buffer, 1mM ATP, 1U/μl RiboLock RNase and 1U/μl T4 PNK (Thermo Fisher) at 37°C for 40min with rotation. The specific bridge linker was designed containing 5ʹ phosphorylation [5Phos] and Internal Biotin dT [ibiodT] chemical modifications. The forward strand is: 5′-[5APP]CCTCGATAC/iBIOdT/TGAGCTGAC-3′, and reverse strand is 5′-[5Phos]GTCAGC/iBIOdT/CAAGTATCGAG-3′. The 5′App ends of forward strand was treated by using a DNA 5′ Adenylation Kit (NEB). The isolated nuclei were washed twice with 500µl 1×wash buffer B and resuspended in 400µl of RNA ligation solution (1×T4 RNA ligase reaction buffer, 1U/μl RiboLock RNase, 10U/μl T4 RNA Ligase 2 truncated, 1.5pmol/μl bridge linker, 15% (w/v) PEG 8000, 0.1% Triton X-100) (NEB), and incubated overnight at 16 °C with rotation. The nuclei were pelleted by centrifugation, resuspended in 400 μl reverse transcription solution (1×MMLV buffer, 0.5mM dNTP, 8U/μl MMLV (RNase H-), 1U/μl RiboLock RNase) (Promega), and then incubated at 42 °C for 1 h. The isolated nuclei were washed five times with 500μl 1×wash buffer B, resuspended in T4 DNA ligation solution (1×DNA ligase reaction buffer with 10mM ATP, 4U/μl T4 DNA ligase, 0.1% (vol/vol) Triton X-100 and 0.1 mg/mLBSA) (NEB), incubated overnight at 16 °C with rotation. The isolated nuclei were resuspended in proteinase K solution (50 mM Tris-HCl, pH 7.5, 1% SDS, 100mM NaCl, 1mM EDTA and 1mg/mL proteinase K) at 65 °C for 3h with shaking at 800 rpm. RNA/DNA complex was extracted and dissolved in nuclease-free water (Thermo Fisher). The purified RNA/DNA complexes were incubated with gap-filling solution (10×NEBuffer r2.1,1mM dNTP and 0.18U/μl T4 DNA polymerase) (NEB) at room temperature for 40min to repair the pG-Tn5 transposition gap, followed by second-strand cDNA synthesis.
DNA-cDNA complexes were converted to DNA library according to the TruePrep DNA Library Prep Kit for Illumina (Vazyme, cat. no. TD501). The fragments containing biotinylated bridge-linker were enriched by M280 beads (Thermo Fisher) before PCR, and enriched library DNA is size-selected by using AMPure XP beads (Beckman), and sequenced (2×150 bp) using Illumina Hiseq X-Ten (Annoroad Gene Technology).

tag: cultivar

value: Minghui 63

value: mature leaf


title: H3_TaDRIM-Seq -rep2


title: H3_TaDRIM-Seq -rep1


title: H3k27me3_TaDRIM-Seq -rep1


title: H3k9ac_TaDRIM-Seq -rep2


title: CTCF_TaDRIM-Seq -rep1


title: 24KALS, iPSC-derived motor neurons from patient with ALS, non, 0h

description: SMART-seq


title: H3k4me3_TaDRIM-Seq -rep1


title: CTCF_TaDRIM-Seq -rep2


title: H3k4me3_TaDRIM-Seq -rep2


title: Chole-3

status: Public on May 29 2023

data_processing:
Sequencing was performed on HiSeq 3000 or NovaSeq 6000 platform in a 100+100 or 101+101 base paired-end mode.
Illumina RTA 2.7.7 or RTA 3.4.4 software was used for base calling.
Generated reads were input into the BD WTA Rhapsody Analysis Pipeline Version 1.8 or BD Rhapsody™ WTA Analysis Pipeline (Revision 4) (https://www.sevenbridges.com/bdgenomics/) for UMI counting for each cell(index)-gene combination.
Assembly: GRCh38
Supplementary files format and content: comma-delimited text files including UMI count for each cell(index)-gene combination

molecule: polyA RNA

source_name: Cholesteatoma

extract_protocol:
Single-cell RNA-seq analysis was conducted using BD Rhapsody Single-Cell Analysis System (BD BioScience) following the manufacture’s protocol. In short, the single cell suspension was loaded into a BD Rhapsody cartridge with >200,000 microwells and single cell capture was achieved by random distribution and gravity precipitation. The bead library was loaded into the microwell cartridge to saturation so that a bead was paired with a cell in a microwell. The cells were lysed in the microwell cartridge to hybridize mRNA molecules onto barcoded capture oligos on the beads. These beads were retrieved from the microwell cartridge into a single tube for the subsequent steps of cDNA synthesis, ExoI digestion and multiplex-PCR based library construction.
For library construction, we performed Whole transcriptome analysis alpha protocol (BD Rhapsody).

value: Cholesteatoma

value: CD45-negative cells


title: Caco2_DMSO_Rep2

status: Public on Jun 01 2023

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: wild type cells treatd with DMSO

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC mm9 using bowtie/1.1.2.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg38 using STAR/2.5.2.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were nonstranded, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Assembly: mm9, hg38
Supplementary files format and content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

source_name: Caco2 colorectal cancer cell line

growth_protocol: Mouse ES cells were maintained serum free neurobasal+DMEM/F12 media supplemented with 2i+LIF; for colorectal cancer cells, RKO, HCT116, SW1417 were cultured in DMEM+10%FBS, DLD1 were cultured in RPM-1640 + 10% FBS, HT55 and Caco2 were cultured in DMEM+20% FBS

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

treatment_protocol: Cells were treated with DMSO or 1 uM LTX for 24 hours.

value: Caco2 colorectal cancer cell line

tag: passages

value: Low passages (6-10)

value: wild type


title: Chole-2


title: Skin-1

source_name: Skin

value: Skin


title: 12KALS, iPSC-derived motor neurons from patient with ALS, non, 0h

description: SMART-seq


title: Skin-3


title: 22m_SPF_biol rep 2

status: Public on May 25 2023

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: brain

extract_protocol:
Young and old GF and SPF mice (young GF, 2 months, N = 2; young SPF, 2 months, N   = 2; old GF, 22 months, N = 2; old SPF, 22 months) were anaesthetized by intraperitoneal injection of three anaesthetic agents and heparin and transcardially perfused with ice-cold HBSS containing heparin. The brains were cut in sagittal midlines and the cerebral hemispheres were roughly minced by scissors, followed by digestion according to the standard protocol of Neural tissue dissociation kits (P). The brain homogenate was filtered through a 70 µm cell strainer, and cell debris was removed by centrifugation according to the standard protocol of Debris Removal Solution. The cells in HBSS with 1% BSA were then treated on ice with CD16/32 FcR-blocking reagent for 10 minutes, followed by 15 minutes of staining with fluorescence-conjugated antibodies. The following antibodies were used (all antibodies were purchased from BioLegend): Fluorescein isothiocyanate (FITC)-conjugated anti-Cd45 (cat#: 103108) and allophycocyanin (APC)-conjugated anti-Cd11b (cat#: 101212). Before sorting, cells were filtered through a 40 µm cell strainer and stained with propidium iodide (PI). PI-negative, Cd45-low, and Cd11b-positive cells were sorted into 1.5 ml Protein LoBind Tubes containing 1% BSA in HBSS and then centrifuged. After removal of the supernatant, the remaining pellet was lysed and total RNA was isolated according to the standard protocol of the RNeasy Micro Kit.
Full-length cDNA was prepared using a SMART-Seq HT Kit (Takara Bio, Japan) according to the manufacturer's instructions. According to the SMARTer kit instructions, an Illumina library was then prepared using a NexteraXT DNA Library Preparation Kit (Illumina).

value: brain

tag: condition

value: SPF

tag: age


title: 2m_GF_biol rep 2

value: GF


title: Skin-2


title: Chole-1


title: 2m_GF_biol rep 1


title: 2m_SPF_biol rep 2


title: 22m_GF_biol rep 1


title: 2m_SPF_biol rep 1


title: EHU-W3

status: Public on May 17 2023

data_processing:
Sequencing was performed on DNBSEQ-G400 platform in 28+50-base paired-end mode.
Raw sequencing data for the sample was converted to a matrix of expression using Space Ranger version: 2.0.0 (10X Genomics).
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcode
Supplementary files format and content: features.tsv.gz: list of gene ID
Supplementary files format and content: matrix.mtx.gz: non-zero gene expresion raw UMI count data in Matrix Market Exchange Formats
Supplementary files format and content: tissue_positions.csv: list of spatial barcode and the cordinate specifying spot
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: tissue_hires_image.png: image of tissue

source_name: prostatic cancer

extract_protocol:
The gene expressions of human prostatic cancer slide were detected by Visium CytAssist and 10x Visium Spatial Gene Expression Slide & Reagents Kit.
RNA libraries were prepared by using 10x Visium spatial protocols and standard MGI protocols.

value: prostatic cancer

tag: disease state

value: NEPC pT4N1M0 and ARPC pT2aN0M0, Gleason score of 4+4

value: de novo NEPC and ARPC

value: male

value: robot-assisted laparoscopic cystectomy/prostatectomy with pelvic lymphadenectomy


title: XLA, T, cell-2, 5DE

status: Public on May 12 2023

description: matrix.csv.gz

data_processing:
bcl2fastq v2.20.0.422
CellRanger software (v6.0.0) (10X Genomics) (default parameters) GRCh38 genome
Scanpy(v1.8.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: Normalized count matrix for all cells from all samples in matrix.csv.gz. Genes in Genes.csv. Metadata and cell id in meta_data.csv. UMAP coords in UMAP.coords.tsv.gz.

source_name: PBMC

growth_protocol: Human PBMCs were isolated and cryo-preserved until they were thawed and used in stimulations.

extract_protocol:
Chromium Next GEM Single Cell 5′ Library (10x Genomics)
Chromium Single Cell V(D)J Enrichment Kit, Human T Cell

treatment_protocol: Human PBMCs were stimulated with SARS-CoV-2 ligands and sorted before applied to sc-RNA and -TCR analysis.

value: T cell

value: SARS-CoV-2 peptides, 12 days stimulation

tag: sample


title: XLA, T, cell-1, TCR


title: XLA, T, cell-2, TCR


title: XLA, T, cell-2, CITE

data_processing:
Library strategy: CITE-Seq
bcl2fastq v2.20.0.422
CellRanger software (v6.0.0) (10X Genomics) (default parameters) GRCh38 genome
Scanpy(v1.8.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: Normalized count matrix for all cells from all samples in matrix.csv.gz. Genes in Genes.csv. Metadata and cell id in meta_data.csv. UMAP coords in UMAP.coords.tsv.gz.

molecule: protein


title: H3k9ac_TaDRIM-Seq -rep1

value: Minghui 63

value: mature leaf


title: XLA, T, cell-1, 5DE

description: matrix.csv.gz


title: RpoB, ptChIP, Night, Rep1

status: Public on May 10 2023

city: Coyoacan

first: V Miguel

last: Palomar

state: Mexico City

address: Circuito Exterior SN

department: Biochemistry

country: Mexico

institute: School of Chemistry, UNAM

data_processing:
Reads were adapter trimmed using Trim-galore v0.4.1
Mapping was performed using Bowtie2 v2.2.8.9 with normal paired reads and no errors were allowed
Read counts on defined genomic regions were determined using bedtools v.2.25.0
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: Genome coverage per nucleotide is included for all the datasets in txt format

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: Seeds were stratified in darkness at 4ºC for 48 hours, and for fourteen days-old plants, they grown on soil at 22ºC under white LED light (100 umol m-2 s-1) in 16h/8h day/night Cycle.

extract_protocol:
Five grams of rosette leaves were harvested and rinsed 3 times with ultra-pure water to eliminate soil debris and homogenized in chloroplast enrichment buffer (0.33 M Sorbitol, 30 mM HEPES-KOH (pH 7.5), 0.001% beta-mercaptoethanol) using a blender. The homogenate was filtered through two layers of miracloth, and the flow-through was centrifuged at 1500 g for 5 minutes at 4ºC. The pelleted chloroplasts were resuspended in 1 ml of chloroplast enrichment buffer. Chloroplasts were crosslinked with 4 % Formaldehyde for 4 h
Sequencing libraries were prepared as reported (Bowman, et al. 2013, BMC Genomics, 14:466).

treatment_protocol: Day-treated plants were exposed to reported illumination cycle and collected 2 hours after light treatment. Night treated plants were exposed to total darkness for 24 h prior sample collection

value: Leaf

tag: ecotype

tag: organelle

value: Chloroplast

value: Night

value: a-RpoB (PhytoAB Cat.:PHY1239 Lot:9321A5)


title: Chloroplast, ATAC, Nucleoid, Rep11

data_processing:
Reads were adapter trimmed using Trim-galore v0.4.1
Mapping was performed using Bowtie2 v2.2.8.9 with normal paired reads and no errors were allowed
Insertion site counts on defined genomic regions were determined using bedtools v.2.25.0
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: Genome coverage per nucleotide is included for all the datasets in txt format

extract_protocol:
Five grams of rosette leaves were harvested and rinsed 3 times with ultra-pure water to eliminate soil debris and homogenized in chloroplast enrichment buffer (0.33 M Sorbitol, 30 mM HEPES-KOH (pH 7.5), 0.001% beta-mercaptoethanol) using a blender. The homogenate was filtered through two layers of miracloth, and the flow-through was centrifuged at 1500 g for 5 minutes at 4ºC. The pelleted chloroplasts were resuspended in 1 ml of chloroplast enrichment buffer. Chloroplasts were crosslinked with 4 % Formaldehyde for 4 h
Sequencing libraries were prepared with the Nextera Library-prep kit (Illumina)

tag: genotype

value: wild type

tag: fraction

value: Nucleoid


title: Chloroplast, ATAC, Nucleoid, Rep10

tag: tissue


title: 22m_SPF_biol rep 1

value: brain

tag: strain

value: SPF

value: WT


title: Chloroplast, ATAC, Naked, Rep11

value: Naked


title: Chloroplast, ATAC, Nucleoid, Rep9


title: 22m_GF_biol rep 2

value: GF


title: SHSY_DMSO

status: Public on May 03 2023

data_processing:
Sequencing was performed on HiSeq 2500 platform in a 75-base single-end mode.
Illumina RTA 1.18.64 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffnorm v2.2.1.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

extract_protocol:
Total RNA was extracted from cells with a miRNeasy kit (Qiagen) following the manufacturer’s instruction.
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).

value: Cell line

tag: cell line

tag: cell type

value: Undifferentiated

value: Wild type

tag: treatment

value: DMSO


title: Chloroplast, ATAC, Naked, Rep10


title: Chloroplast, ATAC, Naked, Rep9


title: SB_RA

source_name: BoDV-1-infected SH-SY5Y

value: Differentiated

value: RA


title: MRC5_miR_nor_48h_P-2

status: Public on Apr 26 2023

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: cell line

extract_protocol:
Total RNA was extracted from cells with a RNeasy kit (Qiagen) following the manufacturer’s instruction.
Library preparation was performed using the TruSeq Stranded mRNA sample prep kit (Illumina, San Diego, CA), according to the manufacturer’s instructions.

value: cell line

value: normal

value: no


title: SHSY_RA


title: MRC5_miR_nor_48h_miR-1

value: miRs


title: MRC5_miR_nor_48h_miR-2


title: wild_old_drug_normal_1

data_processing:
Sequencing was performed on an MGI DNBSEQ-G400RS platform in a 100+100-base paired-end mode.
The DNBSEQ control software (ver.1.0.8.208) operated base calling analysis software and delivered raw sequencing data.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: colorectal

extract_protocol:
Total RNA was extracted from cells with a miRNeasy Mini kit (Qiagen) following the manufacturer’s instruction.
Library preparation was performed using the TruSeq Stranded mRNA sample prep kit (Illumina, San Diego, CA), according to the manufacturer’s instructions.

value: colorectal

value: AOM/DSS


title: XLA, T, cell-1, CITE

value: T cell

value: SARS-CoV-2 peptides, 12 days stimulation


title: MRC5_miR_nor_48h_P-1

value: WT


title: wild_old_drug_tumor_1

value: tumor


title: wild_young_drug_normal_2


title: wild_old_drug_normal_2


title: wild_young_drug_tumor_1


title: wild_young_drug_tumor_3


title: wild_young_drug_tumor_2


title: 8_homo_ko_drug_normal_2


title: RpoB, input, Night, Rep1

value: Leaf

value: Chloroplast

value: wild type

value: Night

tag: chip antibody


title: 8_homo_ko_drug_normal_1


title: 8_hetero_ko_drug_normal_1


title: 8_homo_ko_drug_tumor_3


title: 8_homo_ko_drug_tumor_2


title: SB_DMSO

value: Cell line

value: Undifferentiated

value: Wild type

value: DMSO


title: 8_hetero_ko_drug_tumor_2


title: 8_hetero_ko_drug_tumor_1


title: 8_hetero_ko_drug_normal_2

value: normal


title: 8_hetero_ko_drug_tumor_3


title: 1_hetero_ko_drug_normal_2


title: wild_young_drug_normal_1


title: 1_hetero_ko_drug_tumor_2


title: 1_hetero_ko_drug_tumor_3


title: wild_young_drug_tumor_4


title: 1_hetero_ko_drug_normal_1


title: GL261-HRE-UnaG

status: Public on Mar 31 2023

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Single cell samples were processed using CellRanger pipeline to obtain the counts matrix.
Clustering analysis of scRNA-seq data was performed with the Seurat software package on the R platform (Stuart et al., 2019).
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text files

source_name: Brain

extract_protocol:
Animals were euthanized, brain tissue containing the main tumor bulk was dissected on ice, and a tissue piece of approximately 3 mm edge length was diced with scalpel blades and dissociated into single cell suspension using papain digestion (Miltenyi Neural Tissue Dissociation Kit (P) 130-092-628). The cell suspension was pelleted and resuspended in 7 ml of HBSS (without Ca/Mg), mixed with 1.2 ml of fetal bovine serum (FBS) and 3.6 ml of 100% Percoll (GE Healthcare). The Percoll cell suspension was overlaid with 1 ml of 10% FBS in DMEM and spun at 800g for 15 min, and pellet was collected in a new 15 ml tube and resuspended in 0.5 ml of FACS buffer ((Hibernate-E low fluorescence (BrainBits) with 0.2% BSA and 20 μg/ml DNase (Worthington)).
Red blood cells (RBCs) were lysed by incubating cells with RBC lysis buffer (BioLegend) for 15 min at room temperature; cells were washed and resuspended in FACS buffer. The final cell suspension was submitted for single cell sequencing with the 10X Genomics system at the Mount Sinai Genomics core facility (using ~10,000 viable cells from the sample).

value: Hypoxia

tag: tissue/cell type

value: brain carrying intracranial GBM transplants


title: 1_hetero_ko_drug_tumor_1

value: colorectal


title: inguinal LNs, CreERT2Commd3flox/flox

data_processing:
Libraries were sequenced on an Illumina Novaseq 6000 in a 28+91 bp (or 26+90 bp) paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Converting from base call files into FASTQ files was performed using bcl2fastq v2.20.
Raw FASTQ files were input into the cellranger count pipeline (Cell Ranger v.6.0.0, 10x Genomics) for alignment to the mm10 genome, UMI collapsing, and UMI counting for each gene-cell (barcode) combination.
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited text files include raw counts for all cells detected

source_name: Inguinal lymph nodes of NP-CGG-immunized mice

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller, and cDNAs with UMIs were generated at single-cell level.
Single-cell RNA library construction was processed through the 10x Genomics Chromium Controller following the protocol outlined in the Chromium Single Cell 5' Reagent Kits v2 User Guide.

value: inguinal lymph nodes

value: CD45+ cells

value: Tamoxifen


title: Panc-1 cells with ZsGreen– 48h_0Gy rep1

status: Public on Mar 29 2023

data_processing:
Sequencing was performed on HiSeq 2500 platform in a 75-base single-end mode.
Illumina RTA 1.18.64 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff v2.2.1 with parameter -max-bundle-frags 100000000.
Assembly: hg19
Supplementary files format and content: *_FPKM.txt: Tab-delimited text files include FPKM values for each sample.

source_name: Panc-1 cells with ZsGreen–

extract_protocol:
Total RNAs were extracted using miRNeasy Micro kit (Qiagen) according to the manufacturer’s instructions.
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).

value: Panc-1 with ZsGreen-


title: inguinal LNs, CreERT2Commd3flox/+


title: inguinal LNs, Celastrol

value: WT

value: Celastrol


title: inguinal LNs, C170A_Vehicle

value: Vehicle


title: Panc-1 cells with ZsGreen– 48h_4Gy rep1


title: Panc-1 cells with ZsGreen– 48h_4Gy rep2


title: 8_homo_ko_drug_tumor_1

value: tumor

value: AOM/DSS


title: Panc-1 cells with ZsGreen– 30h_4Gy rep2


title: Panc-1 cells with ZsGreen++ 48h_0Gy rep2

source_name: Panc-1 cells with ZsGreen++

value: Panc-1 with ZsGreen++


title: Panc-1 cells with ZsGreen– 30h_4Gy rep1


title: Panc-1 cells with ZsGreen++ 30h_4Gy rep2


title: Panc-1 cells with ZsGreen++ 48h_0Gy rep1


title: Panc-1 cells with ZsGreen++ 48h_4Gy rep2


title: Panc-1 cells with ZsGreen++ 48h_4Gy rep1


title: inguinal LNs, C170A_Celastrol


title: Control myocardial tissue day3, rep2

status: Public on Mar 26 2023

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101+101 base paired-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: hiPSCs derived cardiac tissue

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).

value: hiPSCs derived cardiac tissue

value: cardiomyocytes

value: no treatment day3


title: Control myocardial tissue day3, rep1


title: inguinal LNs, Vehicle


title: Panc-1 cells with ZsGreen++ 30h_4Gy rep1


title: Control myocardial tissue day3, rep3


title: ONO-1301 myocardial tissue day3, rep3

value: ONO-1301 addition day3


title: Panc-1 cells with ZsGreen– 48h_0Gy rep2


title: A005_GEX

status: Public on Mar 01 2023

city: Hamburg

first: Yu

last: Zhao

address: Falkenried 94

department: Institute of Medical Systems Biology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

library_source: transcriptomic single cell

data_processing:
10x Genomics raw sequencing data were processed using CellRanger software (version 5.0.0, 10x Genomics, Pleasanton, CA) and the human genome GRCh38-2020-A release as the reference (function cellranger count). The matrices of cells and the unique molecular identifier (UMI) count were obtained and further processed by the R package Seurat (version 4.0.1)
To remove potential doublets, cutoff values for number of expressed genes (nGene) were determined for samples following visual inspection of the distribution of nGene and nUMI for each cell. The cells with higher nGene values were excluded. We further removed low-quality cells with high mitochondrial genes of all detected genes
Assembly: GRCh38-2020-A and mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample (linked to the corresponding *_GEX sample records)

source_name: kidney and blood mixded

growth_protocol: For single cell suspension kidneys were dissected and incubated for 40 min at 37°C in RPMI medium (including 0.01 M HEPES; 0.5 mL filtered FBS and 0.4µg/ mL DNase and 8 µg/ mL collagenase D). The samples were homogenized using a gentleMACS (Miltenyi Biotec).

extract_protocol:
Cells were loaded on a 10x Chromium single cell instrument.
All steps were performed according to standard protocol of the Chromium single cell 5’ v2 kit to generate high-quality cDNA libraries.

value: kidney and blood mixded

tag: disease

value: ANCA-GN

tag: patient id


title: A006_GEX


title: A008_GEX


title: A007_GEX


title: A004_GEX


title: ONO-1301 myocardial tissue day3, rep2


title: A003_GEX


title: Patient_day27_Healthy_cohort2_cohort3, BCR-derived cDNA

status: Public on Feb 20 2023

description: BCR V(D)J segments

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 28+90 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were input into the cellranger pipeline (Cell Ranger v.6.0.0, 10x Genomics) for UMI counting for each gene (or tag sequence)-cell (barcode) combination and B cell and T cell receptor repertoire profiling.
Assembly: GRCh38 and refdata-cellranger-vdj-GRCh38-alts-ensembl-4.0.0
Supplementary files format and content: genematrix.csv: comma-delimited text files including raw counts for all cells detected
Supplementary files format and content: airr_rearrangement.tsv: tab-delimited text file including detected clonotypes for each cell (barcode)
Supplementary files format and content: clonotypes.csv: comma-delimited text file including the BCR or TCR clonotype information
Supplementary files format and content: surface_protein.csv: comma-delimited text file including barcodes associated with each hashtag ID
Supplementary files format and content: Hashtag-condition.csv: comma-delimited text file including condition/treatment information for each hashtag

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller, and cDNAs with UMIs were generated at single-cell level.
The single cell libraries were prepared following the protocol outlined in the Chromium Single Cell 5' Reagent Kits v2 User Guide.

value: PBMC

value: multiplexed sample:healthy and covid


title: Patient_day27_Healthy_cohort2_cohort3, HTO-derived cDNA

description: Hashtag-derived oligonucleotide (HTO)

library_source: other


title: Patient_day27_Healthy_cohort2_cohort3, TCR-derived cDNA

description: TCR V(D)J segments


title: Patient_day27_Healthy_cohort2_cohort3, mRNA-derived cDNA

description: poly A RNA


title: A001_GEX


title: Patient_day0_day3_Healthy_cohort1, HTO-derived cDNA

description: Hashtag-derived oligonucleotide (HTO)


title: Patient_day0_day3_Healthy_cohort1, mRNA-derived cDNA

description: poly A RNA


title: Patient_day0_day3_Healthy_cohort1, TCR-derived cDNA

description: TCR V(D)J segments


title: Patient_day0_day3_Healthy_cohort1, BCR-derived cDNA

description: BCR V(D)J segments


title: ONO-1301 myocardial tissue day3, rep1


title: DTR

status: Public on Feb 14 2023

source_name: Omentum

value: Omentum

value: DT

tag: time

value: 5 days

value: DTR


title: DTR scRNA-Seq

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 28+90 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were input into the cellranger count pipeline (cellranger-6.0.0, 10x Genomics) for alignment to the mm10 genome, UMI collapsing, and UMI counting for each gene-cell (barcode) combination.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: matrix.mtx: gene expresion matrix of gene and cell barcode in the Matrix Market file format
Supplementary files format and content: barcodes.tsv: list of cell barcode corresponding to the matrix.mtx
Supplementary files format and content: features.tsv: list of gene information corresponding to the matrix.mtx


title: WT scRNA-Seq

value: WT


title: WT


title: P5

data_processing:
Sequencing was performed on NextSeq500 System in a 76-base single-end mode.
NextSeq Control Software 2.0 was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat2 v2.0.7.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks 2.1.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

extract_protocol:
Total RNA was harvested using RNeasy micro kit with DNase treatment (Qiagen) following the manufacturer’s instruction.
RNA libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina.

value: stromal fraction P5


title: P4

value: stromal fraction P4


title: A002_GEX


title: P6

value: stromal fraction P6


title: P2

value: stromal fraction P2