title: patient 16

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.15 BeadChip   (Illumina)


title: ChIP input, N2, rep 4

status: Public on Nov 01 2024

type: SRA

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: New Jersey

address: 604 Allison Road

department: Molecular Biology and Biochemistry

country: USA

institute: Rutgers University

library_source: genomic

data_processing:
Genomic alignment was performed by using Bowtie 1.2.3
bigwig files were calculated using the "bamCoverage" tool with "--binSize 10 --normalizeUsing RPKM " parameters
Assembly: WS235(ce11)
Supplementary files format and content: bigwig files

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: C. elegans were cultured on NGM plates with OP50 at 20ºC.

extract_protocol:
Briefly, grind of approximately 5000 adult worms was corsslinked and then sonicated to 200-500bp.  Immunoprecipitation was performed using the following antibodies: anti-H3K23me3 (61500, Active Motif), anti-H3K9me3 (ab8898, Abcam).  The pulled-down complexes were reversed crosslinked by proteinase K digestion and then purified by phenol chloroform extraction.
The yielded DNA was used to construct barcoded ChIP-seq libraries using the KAPA Hyper Pre Kit (Roche) according to the manufacturer’s instruction.
standard linker ligation-based DNA library

tag: tissue

value: whole animal

tag: age

value: young adults

tag: genotype

value: N2 (WT)


title: ChIP input, N2, rep 3


title: Pol II ChIP-seq, set-21(red109);set-32(red11) anti-f15d4.5+c38d9.2  piRNAi, rep 2

description:
standard linker ligation-based DNA library
SG0522_lib37
SG0522_lib37

tag: cell line


title: Caco-2 site 30 rep 2 conc1

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

description:
cell lysate
h6.h6.30.a01
30.2.A01

library_source: transcriptomic

data_processing:
Reads were aligned using STAR alignment on Qiagen's online analysis portal RAP version 1.0
match score 1, mismatch cost 2, discard short reads (<15), insertion and deletion cost 3, length and similarity fraction 0.8
Raw counts were logCPM normalized and filtered for low abundance (4) and variance (15).
Normalized counts were analyzed for differential expression using Limma.
Assembly: for human GRCh38.noalt.106, for rainbow trout USDA_OmykA_1.1.105
Supplementary files format and content: count files are provided as .txt files

molecule: total RNA

organism: Homo sapiens

growth_protocol: from ms

extract_protocol:
cells were lysed in Qiagen's proprietary lysis buffer and used directly for library preparation
ultraplex 3' transcriptome library preparation following Qiagen's UPXome protocol

treatment_protocol: cells were exposed to extract of interest 24 hours after seeding at 35,000 cells per well

tag: site

tag: treatment


title: ChIP input, set-21(red109), rep 2


title: Pol II ChIP-seq, set-21(red109);set-32(red11) anti-f15d4.5+c38d9.2 piRNAi, rep 1

description:
standard linker ligation-based DNA library
SG0522_lib36
SG0522_lib36


title: Pol II ChIP-seq, set-21(red109);set-32(red11) control piRNAi, rep 2

description:
standard linker ligation-based DNA library
SG0522_lib35
SG0522_lib35


title: patient 15

type: genomic

city: fuzhou

first: Jianhui

last: Guo

address: 20 Chazhong Road

country: China

institute: First Affiliated Hospital of Fujian Medical University

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.14 BeadChip   (Illumina)

hyb_protocol: see illumina infinium LCG assay protocal on manufacturer's web site

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing:
Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip (Illumina).
Genotype: AA,AB,BB,or NC (no call)

label: C-Bio and A-DNP

source_name: CHB

label_protocol: DNA was purified in triplicate from an aliquot of blood preserved in each anticoagulant using the Gentra Puregene Blood Kit  using the Gentra Puregene Blood Kit. T

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using QIAamp DNA Mini Kit.

treatment_protocol: Patients were treated with Peg-IFNα for at least 48 weeks and subsequently observed until 72 weeks

tag: efficacy of peg-ifnα

value: complete response

tag: gender

value: male

value: Peg-IFNα


title: ChIP input, set-32(red11), rep 2


title: Caco-2 site 30 rep 2 conc2

description:
cell lysate
h6.h6.30.b01
30.2.B01


title: patient 12

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.11 BeadChip   (Illumina)


title: Caco-2 site 30 rep 2 conc4

description:
cell lysate
h6.h6.30.d01
30.2.D01


title: Caco-2 site 30 rep 1 conc8

description:
cell lysate
h1.h1.30.h01
30.1.H01


title: patient 13

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.12 BeadChip   (Illumina)

value: suboptimal response


title: patient 14

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.13 BeadChip   (Illumina)


title: Pol II ChIP-seq, set-21(red109);set-32(red11) control piRNAi, rep 1

description:
standard linker ligation-based DNA library
SG0522_lib34
SG0522_lib34


title: Pol II ChIP-seq, hrde-1 (tm1200) anti-f15d4.5+c38d9.2  piRNAi, rep 2

description:
standard linker ligation-based DNA library
SG0522_lib31
SG0522_lib31


title: patient 10

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.9 BeadChip   (Illumina)


title: Caco-2 site 30 rep 1 conc6

description:
cell lysate
h1.h1.30.f01
30.1.F01


title: Pol II ChIP-seq, hrde-1 (tm1200) anti-f15d4.5+c38d9.2 piRNAi, rep 1

description:
standard linker ligation-based DNA library
SG0522_lib30
SG0522_lib30


title: patient 11

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.10 BeadChip   (Illumina)


title: Caco-2 site 30 rep 1 conc4

description:
cell lysate
h1.h1.30.d01
30.1.D01


title: Pol II ChIP-seq, hrde-1 (tm1200), rep 2

description:
standard linker ligation-based DNA library
SG0323_lib24
SG0323_lib24


title: patient 7

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.6 BeadChip   (Illumina)


title: Caco-2 site 30 rep 1 conc3

description:
cell lysate
h1.h1.30.c01
30.1.C01


title: Pol II ChIP-seq, hrde-1 (tm1200) control piRNAi, rep 1

description:
standard linker ligation-based DNA library
SG0522_lib28
SG0522_lib28


title: Pol II ChIP-seq, set-21(red109), set-32(red11), rep 1

description:
standard linker ligation-based DNA library
SG0323_lib25
SG0323_lib25


title: patient 6

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.5 BeadChip   (Illumina)


title: patient 8

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.7 BeadChip   (Illumina)

value: female


title: Pol II ChIP-seq, hrde-1 (tm1200) control piRNAi, rep 2

description:
standard linker ligation-based DNA library
SG0522_lib29
SG0522_lib29


title: Caco-2 site 30 rep 1 conc5

description:
cell lysate
h1.h1.30.e01
30.1.E01


title: Caco-2 site 30 rep 2 conc3

description:
cell lysate
h6.h6.30.c01
30.2.C01


title: Pol II ChIP-seq, N2, rep 1

description:
standard linker ligation-based DNA library
SG0323_lib21
SG0323_lib21


title: Caco-2 site 30 rep 1 conc7

description:
cell lysate
h1.h1.30.g01
30.1.G01


title: Caco-2 site 30 rep 1 conc2

description:
cell lysate
h1.h1.30.b01
30.1.B01


title: Whole-genome bisulfite sequencing of adult tree shrew, female4, Prefrontal Cortex

city: Santa Barbara

first: Soojin

last: Yi

state: California

address: UC Santa Barbara

department: EEMB

institute: University of California, Santa Barbara

data_processing:
Quailty and Adapter trimming using TrimGalore v0.6.7
Mapping to the tree shrew reference genome (TS_3.0) from the tree shrewDB, using Bismark v0.24.0
Deduplication using Bismark
We generated cytosine report files using Bismark methylation extractor with --bedGraph --cytosine_report --CX_context options
Assembly: KIZ version 3: TS_3.0
Supplementary files format and content: Bismark genome-wide cytosine report output. <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>

organism: Tupaia belangeri

source_name: prefrontal cortex

extract_protocol:
Genomic DNA was extracted from Prefrontal Cortex tissues by phenol-chloroform extraction and ethanol precipitation.
The extracted genomic DNA was quantified using Qubit fluorometer, and the 200ng of gDNA containing 1% unmethylated Lambda DNA was then randomly fragmented into 300bp small fragments using the Covaris LE220R ultrasonic fragmentation instrument. These small fragments were then subjected to terminal repair and adenylation before being fitted with methylated adapters. The bisulfite treatment step was performed using the EZ DNA Methylation-Gold kit (Zymo Research) following the manufacturer’s instructions. The resulting single-stranded DNA was PCR amplified and the PCR products were purified. Similarly, libraries obtained were quantified using Qubit fluorometer and their size distribution was analyzed by Agilent BioAnalyzer (Agilent). Paired-end sequencing was performed using an Illumina NovaSeq6000 according to Illumina-provided protocols.

value: prefrontal cortex


title: Caco-2 site 30 rep 1 conc1

description:
cell lysate
h1.h1.30.a01
30.1.A01


title: patient 5

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.4 BeadChip   (Illumina)


title: Pol II ChIP-seq, N2, rep 2

description:
standard linker ligation-based DNA library
SG0323_lib33
SG0323_lib33


title: H3K9me3 ChIP-seq, N2, rep 2

description:
standard linker ligation-based DNA library
SG0923_lib59
SG0923_lib59


title: Caco-2 site 20 rep 3 conc8

description:
cell lysate
h13.h13.20.h11
20.3.H11


title: H3K9me3 ChIP-seq, hrde-1 (tm1200), rep 2

description:
standard linker ligation-based DNA library
SG0923_lib61
SG0923_lib61


title: Whole-genome bisulfite sequencing of adult tree shrew, female3, Prefrontal Cortex


title: patient 9

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.8 BeadChip   (Illumina)


title: Pol II ChIP-seq, hrde-1 (tm1200), rep 1

description:
standard linker ligation-based DNA library
SG0323_lib23
SG0323_lib23


title: Pol II ChIP-seq, set-21(red109), set-32(red11), rep 2

description:
standard linker ligation-based DNA library
SG0323_lib26
SG0323_lib26


title: patient 4

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.3 BeadChip   (Illumina)


title: H3K9me3 ChIP-seq, N2, rep 1

description:
standard linker ligation-based DNA library
SG0923_lib58
SG0923_lib58


title: Whole-genome bisulfite sequencing of adult tree shrew, female1, Prefrontal Cortex


title: patient 3

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.2 BeadChip   (Illumina)


title: Caco-2 site 20 rep 3 conc6

description:
cell lysate
h13.h13.20.f11
20.3.F11


title: H3K9me3 ChIP-seq, met-2(n4256) set-25(n5021), rep 2

description:
standard linker ligation-based DNA library
SG0923_lib57
SG0923_lib57


title: Caco-2 site 20 rep 3 conc7

description:
cell lysate
h13.h13.20.g11
20.3.G11


title: Whole-genome bisulfite sequencing of adult tree shrew, male5, Prefrontal Cortex


title: patient 1

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip   (Illumina)


title: H3K9me3 ChIP-seq, met-2(n4256) set-25(n5021), rep 1

description:
standard linker ligation-based DNA library
SG0923_lib56
SG0923_lib56


title: H3K9me3 ChIP-seq, hrde-1 (tm1200), rep 1

description:
standard linker ligation-based DNA library
SG0923_lib60
SG0923_lib60


title: Whole-genome bisulfite sequencing of adult tree shrew, male4, Prefrontal Cortex


title: Caco-2 site 20 rep 3 conc5

description:
cell lysate
h13.h13.20.e11
20.3.E11


title: H3K9me3 ChIP-seq, set-21(red109); set-32(red11), rep 2

description:
standard linker ligation-based DNA library
SG0923_lib55
SG0923_lib55


title: Caco-2 site 20 rep 3 conc4

description:
cell lysate
h13.h13.20.d11
20.3.D11


title: H3K9me3 ChIP-seq, set-21(red109); set-32(red11), rep 1

description:
standard linker ligation-based DNA library
SG0923_lib54
SG0923_lib54


title: deltacoaX pMV coaX sample 4

city: New York

first: Shoshanna

middle: Celia

last: Kahne

state: NY

address: 430 E 29th Street, Lab 324 C-D

department: Microbiology

institute: New York University Grossman School of Medicine

data_processing:
Reads were mapped to the H37Rv genome (RefSeq identifier GCF_000195955.2 with socAB annotation added as previously described (Limon et al. 2023)) using Bowtie2 v2.4.1 and sorted using samtools v1.13. Aligned read counts for each gene were extracted using the featureCounts command in Subread v2.0.1.
Assembly: GCF_000195955.2
Supplementary files format and content: featureCounts.tsv - tab separated table of read counts per gene

organism: Mycobacterium tuberculosis

extract_protocol:
R. A. Festa et al., A novel copper-responsive regulon in Mycobacterium tuberculosis. Mol Microbiol 79, 133-148 (2011).
Ribozero plus

value: deltacoaX pMV coaX


title: H3K23me3 ChIP-seq, set-21(ok2320) set-32 (red11)

description:
standard linker ligation-based DNA library
SG0420_lib28
SG0420_lib28


title: deltacoaX pMV coaX sample 3


title: Caco-2 site 20 rep 3 conc3

description:
cell lysate
h13.h13.20.c11
20.3.C11


title: Whole-genome bisulfite sequencing of adult tree shrew, male1, Prefrontal Cortex


title: RNA sequencing of adult tree shrew, female4, Prefrontal Cortex

data_processing:
RNA-seq reads to the tree shrew reference genome (TS_3.0) using HISAT2 v2.2.1 with the--dtaoption. The reference annotation information (TS_3.0) were embedded in the genome index using HISAT2 –ss and –exon options
Transcripts were then assembled for each sample using StringTie v2.2.1 and an updated GTF annotation is generated and included novel transcripts using the -merge flag. This process was guided by the reference GTF annotation using the StringTie -G flag.
Gene abundance information files are generated using the StringTie -eB and -A options
Assembly: KIZ version 3: TS_3.0
Supplementary files format and content: Gene abundances in tab-delimited format. <Gene ID> <Gene Name><Reference><Strand><Start>  <End><Coverage><FPKM><TPM>

extract_protocol:
Total RNA was extracted from PFC tissues using TRIzol Reagent, and the integrity of RNA was assessed using Agilent 2100 bioanalyzer.
The library preparation began with total RNA as the initial template. Specifically, mRNA with PolyA tails was enriched from total RNA using Oligo(dT) magnetic beads. The resulting mRNA was then randomly fragmented by divalent cations in fragmentation buffer. The first strand cDNA was synthesized in the M-MuLV reverse transcriptase system using the fragmented mRNA. The second strand cDNA was subsequently synthesized in the DNA polymerase I system using dNTPs. The obtained double-stranded cDNA was purified, end repaired, and then poly-A tails and sequencing adaptors were ligated. AMPure XP beads were used to screen for cDNA fragments within the size range of 370-420bp followed by PCR amplification and product purification. Library quality assessment was performed on the Agilent Bioanalyzer 2100 system, while cluster generation took place on the cBot Cluster Generation System. Finally, library preparations were sequenced on an Illumina Novaseq platform generating paired-end reads of 150 bp each.


title: deltacoaX pMV coaX sample 2


title: H3K23me3 ChIP-seq, set-21(red109)

description:
standard linker ligation-based DNA library
SG0421_lib20
SG0421_lib20


title: Caco-2 site 20 rep 2 conc8

description:
cell lysate
h9.h9.20.h11
20.2.H11


title: Caco-2 site 20 rep 3 conc2

description:
cell lysate
h13.h13.20.b11
20.3.B11


title: patient 2

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.1 BeadChip   (Illumina)


title: Caco-2 site 20 rep 3 conc1

description:
cell lysate
h13.h13.20.a11
20.3.A11


title: H3K23me3 ChIP-seq, set-21(ok2320)

description:
standard linker ligation-based DNA library
SG0420_lib27
SG0420_lib27


title: RNA sequencing of adult tree shrew, female1, Prefrontal Cortex


title: RNA sequencing of adult tree shrew, male4, Prefrontal Cortex


title: Caco-2 site 20 rep 2 conc6

description:
cell lysate
h9.h9.20.f11
20.2.F11


title: deltacoaX pMV ev sample 2

value: deltacoaX pMV ev


title: RNA sequencing of adult tree shrew, male1, Prefrontal Cortex


title: deltacoaX pMV ev sample 4


title: deltacoaX pMV ev sample 3


title: H3K23me3 ChIP-seq, set-32(red11)

description:
standard linker ligation-based DNA library
SG0420_lib26
SG0420_lib26


title: deltacoaX pMV coaX sample 1


title: Caco-2 site 20 rep 2 conc5

description:
cell lysate
h9.h9.20.e11
20.2.E11


title: H3K23me3 ChIP-seq, hrde-1 (tm1200), rep 1

description:
standard linker ligation-based DNA library
SG0923_lib52
SG0923_lib52


title: Male-2

city: Guangzhou

first: Jinbao

state: Guangdong

address: No. 1023, Shatai South Road

department: Department of Pathogen Biology, School of Public Health

institute: Southern Medical University

data_processing:
Trimmomatic-0.30
Short Oligonucleotide Analysis Package 2 (SOAP2)
Assembly: GCF_006496715.1_Aalbo_primary.1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Aedes albopictus

source_name: whole body

extract_protocol:
Total RNA was isolated using TRIzol® reagent (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer's instructions. The purity and concentration of the total RNA samples were determined using a 2100 Bioanalyzer (Agilent) and ND-2000 instrument (NanoDrop Technologies), respectively.
Small RNAs were purified from isolated total RNA using 15% denaturing polyacrylamide gel electrophoresis (urea PAGE), and RNA oligonucleotide adaptors were sequentially ligated to the 3' and 5' ends of small RNA by T4 RNA ligase (Takara, Dalian, China).

value: whole body

tag: Sex

value: Male


title: Male-3


title: deltacoaX pMV ev sample 1


title: Caco-2 site 20 rep 2 conc7

description:
cell lysate
h9.h9.20.g11
20.2.G11


title: Caco-2 site 20 rep 2 conc3

description:
cell lysate
h9.h9.20.c11
20.2.C11


title: H3K23me3 ChIP-seq, N2, rep 2

description:
standard linker ligation-based DNA library
SG0923_lib51
SG0923_lib51


title: RNA sequencing of adult tree shrew, male5, Prefrontal Cortex


title: Caco-2 site 20 rep 2 conc1

description:
cell lysate
h9.h9.20.a11
20.2.A11


title: Caco-2 site 20 rep 2 conc2

description:
cell lysate
h9.h9.20.b11
20.2.B11


title: H37Rv pMV ev sample 3

value: H37Rv pMV ev


title: H37Rv pMV ev sample 2


title: Caco-2 site 20 rep 1 conc8

description:
cell lysate
h4.h4.20.h11
20.1.H11


title: H37Rv pMV ev sample 1


title: H3K23me3 ChIP-seq, hrde-1 (tm1200), rep 2

description:
standard linker ligation-based DNA library
SG0923_lib53
SG0923_lib53


title: H3K23me3 ChIP-seq, met-2(n4256) set-25(n5021), rep 1

description:
standard linker ligation-based DNA library
SG0923_lib48
SG0923_lib48


title: Female-3

value: Female


title: Female-2


title: H3K23me3 ChIP-seq, set-21(red109); set-32(red11), rep 2

description:
standard linker ligation-based DNA library
SG0923_lib47
SG0923_lib47


title: H3K23me3 ChIP-seq, set-21(red109); set-32(red11), rep 1

description:
standard linker ligation-based DNA library
SG0923_lib46
SG0923_lib46


title: PDB, B05, bio rep 2

city: Beijing

first: Daoxin

last: Xie

address: School of Life Sciences, Room 407, Renhuan Building, Tsinghua University

institute: Tsinghua University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence to give the clean reads
The quality-checked clean reads were mapped to B. cinerea genome using Bowtie2
The read count for each gene was determined by RSEM
The expression of genes was calculated as FPKM values
Assembly: GCA_000143535.4
Supplementary files format and content: Excel files include FPKM values for each Sample

organism: Botrytis cinerea

source_name: hyphae

growth_protocol: B. cinerea was grown on PDA medium (Potato Dextrose Agar medium, BD) at 22℃.

extract_protocol:
RNA was extrated with Transzol (TransGen Biotech, ET101-01)
mRNA was enriched using Oligo d(T) beads and fragmentated. cDNAs were synthesized using random hexamers. The resulting cDNAs were ligated with adaptors and ampliified by PCR to give the cDNA libraries.

treatment_protocol: Conidiospores were collected from B. cinerea plates and diluted to 1×106 conidiospores/mL in PDB medium (Potato Dextrose Broth, BD). The spores suspension was cultured in vitro or sprayed on Arabidopsis leaves for 24 hours.

value: hyphae

value: WT

tag: strain

value: Botrytis cinerea cultured in PDB medium for 24 hour


title: Male-1


title: H37Rv pMV ev sample 4


title: Caco-2 site 20 rep 1 conc7

description:
cell lysate
h4.h4.20.g11
20.1.G11


title: PDB, B05, bio rep 1


title: H3K23me3 ChIP-seq, N2, rep 1

description:
standard linker ligation-based DNA library
SG0923_lib50
SG0923_lib50

value: whole animal

value: young adults


title: IyerS_RNA034_23

city: Pittsburgh

first: Smita

last: Iyer

state: Pennsylvania

address: 3550 Terrace Street

department: Pathology

institute: University of Pittsburgh School of Medicine

description: FFPE Spatial Transcriptome sequencing

data_processing:
Raw sequencing data was processed using Nanostring's GeoMx DSP Control Center Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode) Library strategy: Spatial Transcriptomics
Assembly: N/A, sequencing of synthetic tags and aligment to whitelist of RTS IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform
Supplementary files format and content: dcc

organism: Macaca mulatta

source_name: Brain-Prefrontal Cortex

extract_protocol:
5um sections were cut from Paraformaldehyde-Fixed Paraffin-Embedded slides. Samples were incubated with either DNA-oligo barcoded RNA-ISH probes or antibodies which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Spatial transcriptome sequencing libraries were prepared with Nanostring reagents according to manufacturer's specifications

treatment_protocol: rhesus macaques were infected intravenousely with SIVmac251

value: Brain-Prefrontal Cortex

value: IgG


title: Caco-2 site 20 rep 1 conc6

description:
cell lysate
h4.h4.20.f11
20.1.F11


title: IyerS_RNA034_22

description: FFPE Spatial Transcriptome sequencing


title: ChIP Input, hrde-1 (tm1200), rep 2

description:
standard linker ligation-based DNA library
SG0923_lib45
SG0923_lib45


title: IyerS_RNA034_24

description: FFPE Spatial Transcriptome sequencing


title: H3K23me3 ChIP-seq, met-2(n4256) set-25(n5021), rep 2

description:
standard linker ligation-based DNA library
SG0923_lib49
SG0923_lib49


title: Caco-2 site 20 rep 1 conc5

description:
cell lysate
h4.h4.20.e11
20.1.E11


title: Female-1


title: Col-0, B05, bio rep 2

value: Botrytis cinerea infection on Arabidopsis leaves for 24 hour


title: Caco-2 site 20 rep 1 conc4

description:
cell lysate
h4.h4.20.d11
20.1.D11


title: ChIP Input, hrde-1 (tm1200), rep1

description:
standard linker ligation-based DNA library
SG0923_lib44
SG0923_lib44


title: IyerS_RNA034_21

description: FFPE Spatial Transcriptome sequencing


title: Col-0, B05, bio rep 1


title: Caco-2 site 20 rep 1 conc3

description:
cell lysate
h4.h4.20.c11
20.1.C11


title: IyerS_RNA034_20

description: FFPE Spatial Transcriptome sequencing


title: primed_GFP_RFP_2

city: Houston

first: Florencia

last: Levin

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description: ATAC-Seq

data_processing:
Raw sequencing reads were mapped to the human reference genome (GRCh38) using Bowtie2 (version 2.2.8), followed by peak calling with software MACS2 (version 2.2.9.1). Differentially accessible peaks were performed using R package csaw (version 1.28.0)55 and were defined as peaks with p < 0.05 and log2 fold change > 1.5.
Quality control (QC) metrics were collected to determine library complexity, signal to noise ratios, and reproducibility according to the current ENCODE QC standards.
Assembly: GRCh38
Supplementary files format and content: Bigwig files containing peaks for each of the samples

source_name: Primed ES cells

extract_protocol:
Cells were lysed (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.2 % IGEPAL CA-630) and nuclei were extracted Transposition was performed, DNA was isolated, PCR-amplified, and size-selected."
Other

value: Primed ES cells

value: mTeSR1 medium


title: Caco-2 site 20 rep 1 conc2

description:
cell lysate
h4.h4.20.b11
20.1.B11


title: IyerS_RNA034_19

description: FFPE Spatial Transcriptome sequencing


title: ChIP Input, N2, rep 1

description:
standard linker ligation-based DNA library
SG0923_lib42
SG0923_lib42

value: N2 (WT)


title: ChIP Input, met-2(n4256) set-25(n5021), rep 2

description:
standard linker ligation-based DNA library
SG0923_lib41
SG0923_lib41


title: IyerS_RNA034_18

description: FFPE Spatial Transcriptome sequencing


title: primed_GFP_2

description: ATAC-Seq


title: IyerS_RNA034_17

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 20 rep 1 conc1

description:
cell lysate
h4.h4.20.a11
20.1.A11


title: Caco-2 site 16 rep 3 conc7

description:
cell lysate
h12.h12.16.g08
16.3.G08


title: primed_GFP_RFP_1

description: ATAC-Seq


title: primed_GFP_1

description: ATAC-Seq


title: ChIP Input, N2, rep 2

description:
standard linker ligation-based DNA library
SG0923_lib43
SG0923_lib43


title: ChIP Input, met-2(n4256) set-25(n5021), rep 1

description:
standard linker ligation-based DNA library
SG0923_lib40
SG0923_lib40


title: Caco-2 site 16 rep 3 conc8

description:
cell lysate
h12.h12.16.h08
16.3.H08


title: ChIP Input, set-21(red109);set-32(red11), rep 2

description:
standard linker ligation-based DNA library
SG0923_lib38
SG0923_lib38


title: Caco-2 site 16 rep 3 conc6

description:
cell lysate
h12.h12.16.f08
16.3.F08


title: ChIP Input, set-21(red109)

description:
standard linker ligation-based DNA library
SG0421_lib18
SG0421_lib18


title: HCT 116 Cas9 #1A

city: Dresden

first: Alexander

middle: Arthur

last: Wurm

address: Fetscherstrasse 74

country: Germany

institute: NCT Dresden

data_processing:
Quality control assessment of raw reads was performed using FastQC, followed by Trimmomatic trimming to remove low-quality sequences. The trimmed reads were then aligned to the reference genome using STAR version 2.7.9a. To facilitate the mapping process, a genome reference index was constructed using either GRCh37.fa (hg19) or GRCh38.108.gtf (hg38) as the reference.
Supplementary files format and content: Excel file includes unfiltered normalized raw counts for all genes for each Sample

extract_protocol:
Total RNA from cell lines was isolated using RNAeasy mini kit (Qiagen)
RNA sequencing libraries were prepared using the Stranded mRNA Prep, Ligation Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Briefly, mRNA was purified from 1 µg total RNA using oligo(dT) beads, poly(A)+ RNA was fragmented to 150 bp and converted into cDNA, and cDNA fragments were end-repaired, adenylated on the 3’ end, adapter-ligated, and amplified with 12 cycles of PCR. The final libraries were validated using a Qubit 2.0 Fluorometer (Life Technologies) and a Bioanalyzer 2100 system. All barcoded libraries were pooled and sequenced 2x75bp paired-end on an Illumina NextSeq550 platform to obtain a minimum of 10 Mio reads per sample.

tag: cell type

value: colon cancer


title: HCT 116 Cas9 #1C


title: HCT 116 Cas9 #1B


title: IyerS_RNA034_15

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 16 rep 3 conc5

description:
cell lysate
h12.h12.16.e08
16.3.E08


title: IyerS_RNA034_14

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 16 rep 3 conc4

description:
cell lysate
h12.h12.16.d08
16.3.D08


title: ChIP Input, set-21(ok2320);set-32 (red11)

description:
standard linker ligation-based DNA library
SG0420_lib34
SG0420_lib34


title: IyerS_RNA034_13

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA034_12

description: FFPE Spatial Transcriptome sequencing


title: ChIP Input, set-32(red11)

description:
KAPA Hyper Pre Kit (Roche)
SG0420_lib32
SG0420_lib32


title: Caco-2 site 16 rep 3 conc3

description:
cell lysate
h12.h12.16.c08
16.3.C08


title: HCT 116 Cas9 Luc C

value: control


title: HCT 116 Cas9 Luc B


title: ChIP Input, set-21(red109);set-32(red11), rep 1

description:
standard linker ligation-based DNA library
SG0421_lib19
SG0421_lib19


title: IyerS_RNA034_16

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA034_11

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA034_10

description: FFPE Spatial Transcriptome sequencing


title: sRNA-seq, set-21(red109);set-32(red11) anti-f15d4.5+c38d9.2 piRNAi, rep 1

description:
ligation-based small RNA library construction
SG0522_lib7

data_processing:
Genomic alignment was performed by using Bowtie 1.2.3
bigwig files were calculated using the "bamCoverage" tool with "--binSize 10 --normalizeUsing RPKM --filterRNAstrand forward (or reverse)" parameters
Assembly: WS235(ce11)
Supplementary files format and content: bigwig files

extract_protocol:
Small RNA was extracted using mirVana miRNA isolation kit (ThermoFisher).
The small RNA libraries were constructed using a 5’ - monophosphate independent, 3’ and 5’ linker ligation-based methods.
ligation-based strategy

tag: molecule type

value: small RNA


title: Caco-2 site 16 rep 3 conc1

description:
cell lysate
h12.h12.16.a08
16.3.A08


title: HCT 116 Cas9 Luc A


title: sRNA-seq, set-21(red109);set-32(red11) anti-f15d4.5+c38d9.2  piRNAi, rep 2

description:
ligation-based small RNA library construction
SG0522_lib8


title: No Template Control 3

description: FFPE Spatial Transcriptome sequencing

organism: blank sample


title: IyerS_RNA034_9

description: FFPE Spatial Transcriptome sequencing


title: ChIP Input, set-21(ok2320)

description:
standard linker ligation-based DNA library
SG0420_lib33
SG0420_lib33


title: IyerS_RNA034_8

description: FFPE Spatial Transcriptome sequencing


title: No Template Control 1

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 16 rep 2 conc8

description:
cell lysate
h8.h8.16.h09
16.2.H09


title: sRNA-seq, hrde-1 (tm1200) anti-f15d4.5+c38d9.2 piRNAi, rep 1

description:
ligation-based small RNA library construction
SG0522_lib5


title: IyerS_RNA034_7

description: FFPE Spatial Transcriptome sequencing


title: sRNA-seq, hrde-1 (tm1200) anti-f15d4.5+c38d9.2  piRNAi, rep 2

description:
ligation-based small RNA library construction
SG0522_lib6


title: IgG_rabbit_1, CS031014

city: ROCKVILLE

first: Vassiliki

last: Saloura

state: MARYLAND

address: 11705 STONEWOOD LN

department: TGMB

institute: NCI

description: IgG control

data_processing:
Basecalls were performed using bcl2fastq v2.20 for NextSeq output.
CUT&RUN-Seq reads were trimmed for adaptor sequence/low quality sequence using Cutadapt 1.18 with parameter options --nextseq-trim=2 --trim-n -n 5 -O 5 -q 10,10 -m 35:35
Trimmed sequence reads were mapped to hg38 genome using  Bowtie 2-2.4.2
Peaks were called using GoPeak v1.0.0 with the significance cut-off q-value 0.05.
E. coli Spike-in normalized bigwig files were generated using bedtool 2.30.0 genomecov function and ucsc 407 bedGraphToBigWig function
Assembly: hg38
Supplementary files format and content: bigwig, tab delimited peak call bed files except for input sample
Library strategy: CUT&RUN

extract_protocol:
Cells were obtained freshly from the cell culture dishes with trypsinization, and were counted to have 500,000 cells per reaction.
Libraries were constructed according to SWIFT Accel-NGS 2S Plus DNA lib prep kit

value: head and neck squamous cell carcinoma


title: Caco-2 site 16 rep 2 conc6

description:
cell lysate
h8.h8.16.f09
16.2.F09


title: Caco-2 site 16 rep 2 conc7

description:
cell lysate
h8.h8.16.g09
16.2.G09


title: 53_H3K4me3_3, CS031014

description: SMYD3 KO

source_name: SMYD3 KO HN-6

value: SMYD3 KO HN-6


title: Caco-2 site 16 rep 2 conc5

description:
cell lysate
h8.h8.16.e09
16.2.E09


title: sRNA-seq, set-21(red109);set-32(red11) control piRNAi, rep 1

description:
ligation-based small RNA library construction
SG0522_lib3


title: 53_H3K4me3_2, CS031014

description: SMYD3 KO


title: Caco-2 site 16 rep 3 conc2

description:
cell lysate
h12.h12.16.b08
16.3.B08


title: sRNA-seq, hrde-1 (tm1200) control piRNAi, rep 1

description:
ligation-based small RNA library construction
SG0522_lib1

value: hrde-1 (tm1200) control piRNAi,


title: sRNA-seq, hrde-1 (tm1200) control piRNAi, rep 2

description:
ligation-based small RNA library construction
SG0522_lib2


title: Caco-2 site 16 rep 2 conc4

description:
cell lysate
h8.h8.16.d09
16.2.D09


title: Caco-2 site 16 rep 2 conc3

description:
cell lysate
h8.h8.16.c09
16.2.C09


title: IyerS_RNA034_4

description: FFPE Spatial Transcriptome sequencing


title: HN6_H3K4me3_3, CS031014

description: control


title: HN6_H3K4me3_2, CS031014

description: control


title: IyerS_RNA034_2

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 16 rep 2 conc1

description:
cell lysate
h8.h8.16.a09
16.2.A09


title: 53_no_INFB_SMYD3_3, CS031308

description: SMYD3 KO


title: Caco-2 site 16 rep 2 conc2

description:
cell lysate
h8.h8.16.b09
16.2.B09


title: IyerS_RNA034_6

description: FFPE Spatial Transcriptome sequencing


title: sRNA-seq, set-21(red109);set-32(red11) control piRNAi, rep 2

description:
ligation-based small RNA library construction
SG0522_lib4


title: IyerS_RNA034_1

description: FFPE Spatial Transcriptome sequencing


title: sRNA-seq, set-32(red11), rep 1

description:
ligation-based small RNA library construction
SG0720_lib2


title: sRNA-seq, set-21(ok2320), rep 2

description:
ligation-based small RNA library construction
SG0720_lib7


title: IyerS_RNA034_3

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 16 rep 1 conc8

description:
cell lysate
h3.h3.16.h08
16.1.H09


title: IyerS_RNA033_24

description: FFPE Spatial Transcriptome sequencing

source_name: Brain-Hippocampus

value: Brain-Hippocampus


title: IyerS_RNA034_5

description: FFPE Spatial Transcriptome sequencing


title: sRNA-seq, set-21(ok2320), rep 1

description:
ligation-based small RNA library construction
SG0720_lib3


title: HN6_no_INFB_SMYD3_3, CS031308

description: control


title: 53_no_INFB_SMYD3_2, CS031308

description: SMYD3 KO


title: HN6_no_INFB_SMYD3_1, CS031308

description: control


title: Caco-2 site 16 rep 1 conc7

description:
cell lysate
h3.h3.16.g09
16.1.G09


title: IyerS_RNA033_23

description: FFPE Spatial Transcriptome sequencing


title: sRNA-seq, set-21(ok2320);set-32(red11), rep 2

description:
ligation-based small RNA library construction
SG0720_lib8


title: sRNA-seq, set-32(red11), rep 2

description:
ligation-based small RNA library construction
SG0720_lib6


title: IyerS_RNA033_22

description: FFPE Spatial Transcriptome sequencing


title: Hela-siDKC1-2Days-rp2

city: Chicago

first: Chuan

last: He

state: IL

address: 929 E 57th St

department: Chemistry Department

institute: University of Chicago

data_processing:
Only R1 reads of paired-end reads were processed for 18S Ψ site detection. The R1 reads were processed by following customed shell script called “mapping.sh”. Briefly, 3’ end of R1 was trimmed by cutadapt (version 4.8), with following parameters “-j 15 -m 40 --max-n=0 -u 6 -e 0.15 -q 20 --discard-untrimmed --nextseq-trim=20 -a AGATCGGAAGAGCACACGTCTG”. The trimmed reads were mapped to Ψ/U loci sequences by STAR mapping software (version 2.7.9a) with setting “--outFilterMatchNmin 39” to minimize multiple mapping ratio. Software samtools (1.16.1-39-g1250b01) was used to calculate read number mapped to each Ψ/U locus.
Only R1 reads were included for this study.
Assembly: customed fasta covering different U/Ψ loci
Supplementary files format and content: txt files for BIHINDseq which cover loci name and read number
Library strategy: BIHIND-seq

source_name: Cervical cancer cell line

growth_protocol: Hela was cultured in DMEM medium (Gibco, 11995073) containing 10% FBS (Gibco, 26140079) and 1% penicillin-streptomycin (Gibco, 15140122) at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted by TRIzol reagent (ThermoFisher Scientific, 15596026) according to the manufacturer’s instructions.
BS Treatment: 5~10 µL Total RNA, polyA-RNA, or synthesized RNA oligos were mixed with 50 µL BS reagent (prepared by mixing 270 mg Na2SO3 and 34 mg NaHSO3 in 850 μL RNase-free water). Incubate at 70 oC for 3 hours. Then added 95~90 µL water to dilute the sample and used EZ RNA Methylation Kit (Zymo, R5001) for purification. Briefly, added 250 μL RNA Binding buffer and 400 μL EtOH. Mixed well and kept it on ice for 30 min to achieve the best recovery. Then the mixture was transferred to a spin IC column and centrifuged at 12000xg for 1 min. The column was washed with 50 μL RNA wash buffer once. Added 40 μL RNA desulphonation buffer and incubated at room temperature for 1 h. Centrifuged the column at 12000xg for 1 min. The column was washed with 50 μL RNA wash buffer once. BS-treated RNA was eluted with 10 μL water.  Library preparation: 1.5 μg BS-treated/Untreated total RNA were mixed with up-probes and down-probes (30 fmol each). The RNA and probes in total volume of 10 μL were annealed in 1X annealing buffer (10 mM Tris-HCl, pH 7.5, 50 mM NaCl, 1 mM EDTA) by incubating mixture at a temperature gradient: 90 °C for 1 min, 80 °C for 1 min, 70 °C for 1min, 60 °C for 1 min, 50 °C for 1 min, 40 °C for 5 min and hold on 35 °C. Subsequently, a 10 μl of mixture containing 0.8 U Bst 2.0 DNA polymerase (NEB, M0537S), 0.2 nmol dATP in 2X CutSmart buffer was added to the former mixture. The reaction mixture was incubated at 45 °C for 30 min. Then another 10 μL of mixture containing 15% PEG8000, 1.5 nmol ATP, 2.5 U SplintR Ligase (NEB, M0375S) in 1X CutSmart buffer was added and mixed well. The whole mixture was incubated at 25 °C for 20 min. 20 μL water was added to dilute the reaction mixture. Ligated product was purified by Zymo RNA Clean & Concentrator-5 and eluted with 15 μL water. The eluted product was added with 7.5 μL water, 2.5 μL Unique Dual Index (NEB, E6442S) and 25 μL LongAmp Taq 2X Master Mix (2X) (NEB, M0287S). PCR was run at the following condition: 94 °C, 30 s; (94 °C, 15 s; 62 °C, 30 s; 70 °C, 15 s)×C cycles (C=12 for Untreated samples, C=14 for BS-treated samples); 70 °C, 5 min; 4 °C, hold-on. PCR product was purified by running 2.5% agarose TBE gel and recovered by Qiagen MinElute Gel Extraction Kit. The libraries were pooled in equal molarities and sequenced on one lane of an Illumina NextSeq 2000 platform. Around 0.5 M reads were acquired for each library.

treatment_protocol: Transient knockdown of DKC1 was performed by siRNAs. In brief, Hela cell (60% confluent) was transfected with siCtrl (Qiagen, 1027310) and siDKC1 (Qiagen, SI03080616) using Lipofectamine™ RNAiMAX Transfection Reagent (ThermoFisher Scientific, 13778075). Cells were harvested 48 h post-transfection.

value: Cervical cancer cell line

value: Hela

value: Cervical cancer cells

value: Non-treatment


title: Caco-2 site 16 rep 1 conc6

description:
cell lysate
h3.h3.16.f09
16.1.F09


title: Hela-siCtrl-2Days-rp2


title: IyerS_RNA033_21

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 16 rep 1 conc5

description:
cell lysate
h3.h3.16.e09
16.1.E09


title: sRNA-seq, set-21(ok2320);set-32(red11), rep 1

description:
ligation-based small RNA library construction
SG0720_lib4

value: whole animal

value: young adults


title: Caco-2 site 16 rep 1 conc3

description:
cell lysate
h3.h3.16.c09
16.1.C09


title: sRNA-seq, N2, rep 2

description:
ligation-based small RNA library construction
SG0720_lib5


title: RNA-seq, set-21(red109)

extract_protocol:
RNA was extracted by using TRIZOL, phenol, and chloroform. DNase I was used to remove DNA. rRNA was depleted using anti-rRNA DNA oligoes and RNase H.
For RNA ligation-based strategy, RNA-seq library was prepared using the protocol described in Ni. et. al. 2014 (PMID: 25534009). For SMARTer Stranded Total RNA-Seq strategy, RNA libraries were made by using the SMARTer Stranded Total RNA-Seq Kit (Takara).
RNA ligation-based strategy and SMARTer Stranded Total RNA-Seq strategy

tag: library type

value: SMARTer Stranded Total RNA-Seq


title: Hela-siDKC1-2Days-BS-rp2

value: Bisulfite Treatment


title: IyerS_RNA033_20

description: FFPE Spatial Transcriptome sequencing

value: IgG


title: Caco-2 site 16 rep 1 conc4

description:
cell lysate
h3.h3.16.d09
16.1.D09


title: IyerS_RNA033_19

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA033_18

description: FFPE Spatial Transcriptome sequencing


title: sRNA-seq, N2, rep 1

description:
ligation-based small RNA library construction
SG0720_lib1

value: N2 (WT)


title: Caco-2 site 16 rep 1 conc2

description:
cell lysate
h3.h3.16.b09
16.1.B09


title: Hela-siCtrl-2Days-BS-rp2


title: IyerS_RNA033_17

description: FFPE Spatial Transcriptome sequencing


title: Hela-siDKC1-2Days-rp1


title: RNA-seq, hrde-1 (tm1200), rep2


title: Hela-siCtrl-2Days-rp1


title: Caco-2 site 16 rep 1 conc1

description:
cell lysate
h3.h3.16.a09
16.1.A09


title: Caco-2 site 8 rep 3 conc8

description:
cell lysate
h11.h11.8.h04
8.3.H04


title: RNA-seq, hrde-1 (tm1200), rep1


title: Hela-siDKC1-2Days-BS-rp1


title: IyerS_RNA033_16

description: FFPE Spatial Transcriptome sequencing


title: RNA-seq, WT, rep 4


title: Hela-siCtrl-2Days-BS-rp1


title: Caco-2 site 20 rep 2 conc4

description:
cell lysate
h9.h9.20.d11
20.2.D11


title: IyerS_RNA033_15

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 8 rep 3 conc7

description:
cell lysate
h11.h11.8.g04
8.3.G04


title: Caco-2 site 8 rep 3 conc6

description:
cell lysate
h11.h11.8.f04
8.3.F04


title: RNA-seq, WT, rep 3


title: S119

city: Davis

first: Barbara

last: Blanco-Ulate

address: One Shields Ave

department: Plant Sciences

institute: University of California Davis

data_processing:
Quality and adapter trimming were done with Trimmomatic 0.33 with the parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Bowtie2 2.3.4 was used to map the reads to a combined transcriptome of Rhizopus stolonifer and each of the fruit hosts with the following options: --end-to-end --sensitive --no-unal -q -t -p 20
Read counts were extracted form the Bowtie2 alignments using the script sam2counts.py v.0.91
Assembly: Rhizopus stolonifer BLUCD01v1, Solanum licopersicum build SL4.0 with ITAG 4.0 annotations, Vitis vinifera PN40024, Fragaria x ananassa Camarosa v1.0.a1, Prunus salicina Zhongli No. 6 v1.0
Supplementary files format and content: Processed data file contains read counts per sample, with each sample being listed on one column from column B-AZ, and transcript IDs being listed on column A
Supplementary files format and content: -

organism: Solanum lycopersicum

source_name: Tomato

extract_protocol:
RNA was extracted from 1 g of ground tissue as described in Blanco-Ulate et al. (2013). Culture media-grown samples and resulting libraries were obtained from Petrasch et al. (2019) (GEO accession GSE122555).
Libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina, CA).

value: Tomato

tag: agent

value: Rhizopus stolonifer

tag: time point

value: (hours_post_inoculation)  48


title: IyerS_RNA033_14

description: FFPE Spatial Transcriptome sequencing


title: S118


title: RNA-seq, set-21(ok2320), rep1

value: RNA ligation-based


title: Caco-2 site 8 rep 3 conc5

description:
cell lysate
h11.h11.8.e04
8.3.E04


title: IyerS_RNA033_13

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 8 rep 3 conc4

description:
cell lysate
h11.h11.8.d04
8.3.D04


title: RNA-seq, set-32(red11), rep 2


title: S117


title: S116

value: (hours_post_inoculation)  24


title: IyerS_RNA033_12

description: FFPE Spatial Transcriptome sequencing


title: RNA-seq, set-32(red11), rep 1


title: Caco-2 site 8 rep 3 conc2

description:
cell lysate
h11.h11.8.b04
8.3.B04


title: Caco-2 site 8 rep 3 conc3

description:
cell lysate
h11.h11.8.c04
8.3.C04


title: RNA-seq, set-21(ok2320), rep2


title: S115


title: IyerS_RNA033_9

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 8 rep 3 conc1

description:
cell lysate
h11.h11.8.a04
8.3.A04


title: IyerS_RNA033_10

description: FFPE Spatial Transcriptome sequencing


title: RNA sequencing of adult tree shrew, female3, Prefrontal Cortex

value: prefrontal cortex


title: S114


title: Caco-2 site 8 rep 2 conc7

description:
cell lysate
h7.h7.8.g04
8.2.G04


title: Caco-2 site 8 rep 2 conc8

description:
cell lysate
h7.h7.8.h04
8.2.H04


title: S113

value: (hours_post_inoculation)  12


title: IyerS_RNA033_8

description: FFPE Spatial Transcriptome sequencing

value: Brain-Hippocampus


title: RNA-seq, set-21(ok2320); set-32 (red11), rep1


title: Caco-2 site 8 rep 2 conc6

description:
cell lysate
h7.h7.8.f04
8.2.F04


title: RNA-seq, WT, rep 2


title: S111


title: IyerS_RNA033_6

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA033_7

description: FFPE Spatial Transcriptome sequencing


title: S110

value: (hours_post_inoculation)  6


title: Caco-2 site 8 rep 2 conc4

description:
cell lysate
h7.h7.8.d04
8.2.D04


title: RNA-seq, WT,  rep 1


title: IyerS_RNA033_11

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA033_5

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 8 rep 2 conc5

description:
cell lysate
h7.h7.8.e04
8.2.E04


title: HeLa_IMP1_iCLIP_tech_replicate_2

city: London

first: Pierre

last: Klein

address: Gower Street

department: Institute of Structural and Molecular Biology

country: United Kingdom

institute: University College London

data_processing:
iCLIP reads from the HeLa samples and IgG control were processed using the iMaps webserver (https://imaps.genialis.com/iclip), with the following steps: demultiplexing using sequencing barcodes, UMI identification, adapter trimming, pre-mapping to rRNAs and tRNAs, alignment to genome using Spliced Transcripts Alignment to a Reference (STAR)50, cross-link sites assignment, peak calling using Paraclu51. Significant cross-link sites were identified using the ‘iCount peaks’ tool, while peaks were defined by clustering the significant cross-link sites using default parameters. Summary files based on cross-link events on gene type, biotype, and gene region were generated. The percentage of total counts for each genomic region was calculated using the cross-link counts obtained from the merged replicates and normalised to each genomic length. FastQC 0.11.5, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/, PCR duplication ratio, quality of sequencing and alignment statistics were performed on each individual samples. All samples showed a high number of uniquely mapped reads (on average 2.2E+06) with low PCR duplicate ratio (1.57 to 1.74). Cross-link or peak bed files from replicates were merged using iMaps group function.
Peaks were then called using iMAPS default parameters, and the output bed/bedgraph files were used for further analysis. The human GRCh38 genome build and GENCODE version 36 annotation were used.
Correlation between replicates was assessed using the multibamSummary function from DeepTools v3.5.552, with default parameters. Scatterplots were generated with the plotCorrelation function using Spearman method and the option removeOutliers.
Assembly: GRCh38 human genome
Supplementary files format and content: Bed file containing crosslink sites
Supplementary files format and content: Bedgraph file containing peaks
Library strategy: iCLIP

source_name: HeLa

growth_protocol: HeLa cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% foetal bovine serum (FBS) and 1% penicillin–streptomycin, in a 5% CO2 incubator at 37°C. Cells were routinely tested for mycoplasma contamination.

extract_protocol:
iCLIP was performed using a previously reported protocol48 (see also Supplementary Figure 11a) which was adapted as described below. Briefly, three HeLa cell biological replicates in 10 cm dish (80% confluency) were cross-linked at 150 mJ/cm2 in a Stratalinker 2400 at 254 nm and then lysed in 1 mL of 50 mM Tris-HCl, pH 7.4, 100 mM NaCl, 1% Igepal CA-630 (Sigma I8896), 0.1% SDS, 0.5% sodium deoxycholate. 0.8 U of RNase I (Thermo Scientific, EN0602) and 4 μL of Turbo DNase I (Ambion, AM223) were added to 1 mg (protein content) of lysate for RNA fragmentation and DNA digestion respectively. Samples were incubated with 5 μg of anti-IMP1 (Rabbit anti-IMP1 (MBL, RN007P) or 5 μg of anti-IgG (Proteintech 30000-0-AP) antibodies, and coupled to Protein G beads (Dynal), rotating on a wheel at 4°C overnight.
Pre-adenylated infrared dye-labelled IRL3 adaptor (IRdye-800CW-DBCO (LI-COR, cat# 929-50000)49 with sequence /5rApp/AG ATC GGA AGA GCG GTT CAG AAA AAA AAA AAA /iAzideN/AA AAA AAA AAA A/3Bio/ was ligated to RNA. The protein-RNA complexes were then separated by SDS-PAGE29, blotted onto nitrocellulose membrane and visualised with an Odyssey scanning system (LI-COR). The desired region (determined from the RNAse gradient experiment in S11c) was excised from the membrane in small pieces and RNA was released using proteinase K (Roche, 03115828001) digestion and incubation at 60 min at 50°C. For RNase gradient experiment, 0.4, 0.8 or 2.5 U of RNase I (Thermo Scientific, EN0602) and 4 μL of Turbo DNase I (Ambion, AM223) were added to 1 mg (protein content) of lysate for RNA. Phenol-Chloroform precipitation was performed to recover RNA. Reverse transcription was performed using Superscript IV Reverse Transcriptase (Life Technologies), using primers containing Unique Molecular Identifier barcodes to allow multiplexing. cDNA molecules were purified using AMPure XP beads (Beckman-Coulter, USA), circularised using Circligase II (Epicenter), and purified using AMPure XP beads (Beckman). After PCR amplification, libraries were size-selected by gel-purification and size distribution was assessed using a2400 Bioanalyser (Agilent). QuBit dsDNA HS Assay (ThermoFisher Scientifics) was used to quantify libraries. The same quantity of cDNA for each sample in the library was sequenced as single end100bp reads on Illumina HiSeq 4000.

value: HeLa

value: epithelial cell

tag: antibody


title: S112


title: Caco-2 site 8 rep 2 conc2

description:
cell lysate
h7.h7.8.b04
8.2.B04


title: HeLa_IgG_iCLIP_tech_replicate_3


title: S109


title: IyerS_RNA033_4

description: FFPE Spatial Transcriptome sequencing


title: RNA-seq, set-21(ok2320); set-32 (red11), rep2

value: whole animal


title: Caco-2 site 8 rep 2 conc3

description:
cell lysate
h7.h7.8.c04
8.2.C04


title: HeLa_IMP1_iCLIP_tech_replicate_3


title: IyerS_RNA033_3

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA033_2

description: FFPE Spatial Transcriptome sequencing


title: A10c

city: Kraków

first: Alicja

last: Wierzbicka

address: ul. Sarego 2

country: Poland

institute: National Research Institute of Animal Produstion

data_processing:
Quality control (fastQC)
Filtration of low quality reads (phred quality <20). Minimal length of reads set to 35. Removal of adaptors (Flexbar)
Mapping with default options (Tophat)
Counting reads to Ensembl GTF version 95 intervals (htseq-count) and differential expresion calculated with the use of Deseq2
Assembly: Sscrofa11.1
Supplementary files format and content: fastq and csv

organism: Sus scrofa domesticus

source_name: jejunum

extract_protocol:
Collected tissues were stored at -80°C. RNA was isolated using PureLink™ RNA Mini Kit (Invitrogen, USA).
Collibri™ 3' mRNA Library Prep Kit for Illumina™ Systems (Thermofisher Scientific) with 500ng/ul total RNA was used to construct sequencing libraries.

value: jejunum

value: control group


title: S108


title: ST02, STZ, HFD

city: Vienna

first: Emmanuel

middle: Dauda

last: Dixon

state: Vienna

address: Waehringer Guertel 18-20,

department: Dept. of Internal Medicine III

country: Austria

institute: Medical University of Vienna

data_processing:
STAR universal alignment tool to map reads directly to a reference genome via the utilization of a pre-generated index of the reference. The reference consists of sequences in FASTA format.
The reads were provided in a text file in the FASTQ format and aligned by the STAR aligner tool. The results of this alignment are the aligned reads in SAM or binary SAM (BAM) format. The STAR source code and binaries are available at the following link: https://github.com/alexdobin/STAR/releases.
The aligned reads were subjected to quality control using the RSEQC Quality Control package. Documentation and the sources of the scripts are available at http://rseqc.sourceforge.net/.
Assembly: mmu_GRCm38.101_ERCC_SIRV
Supplementary files format and content: The reads were provided in a text file in the FASTQ format
Supplementary files format and content: The results of this alignment are the aligned reads in SAM or binary SAM (BAM) format.

organism: Mus musculus

source_name: Liver

extract_protocol:
RNA was isolated from frozen liver tissue from the left lobe using Qiagen RNeasy Mini Kit (Qiagen, Hilden, Germany). To ensure complete DNA removal, which is necessary for the downstream RNA sequencing, we used an RNase-Free DNase kit (Qiagen, Germany). RNA concentrations and purity were determined by NanoDrop 1000 Spectrophotometer (Thermo Fisher, USA).
In total, nine RNA samples extracted from the left lobe section of the livers of the STAM, STAM + ATGLi, and noSTZ + NC mice were sent to Lexogen at the Vienna Biocentre Core Facility (Vienna, Austria) for library preparation using the Lexogen’s QuanSeq 3’ mRNA-Seq kit to generate Illumina-compactible libraries from polyadenylated RNA. The prepared libraries were then sequenced on the Illumina HiSeq 4000 (Illumina, Inc., San Diego, USA) platform to generate approximately 13 million reads per sample.

value: Liver

value: No streptozotocin and Atglistatin


title: C30g

source_name: colon

value: colon

value: 10000 IU of cholecalciferol


title: ST03, STZ, HFD


title: ST01, STZ, HFD


title: IyerS_RNA032_23

description: FFPE Spatial Transcriptome sequencing

value: Brain-Prefrontal Cortex

value: IgG


title: IyerS_RNA033_1

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 8 rep 2 conc1

description:
cell lysate
h7.h7.8.a04
8.2.A04

data_processing:
Reads were aligned using STAR alignment on Qiagen's online analysis portal RAP version 1.0
match score 1, mismatch cost 2, discard short reads (<15), insertion and deletion cost 3, length and similarity fraction 0.8
Raw counts were logCPM normalized and filtered for low abundance (4) and variance (15).
Normalized counts were analyzed for differential expression using Limma.
Assembly: for human GRCh38.noalt.106, for rainbow trout USDA_OmykA_1.1.105
Supplementary files format and content: count files are provided as .txt files

extract_protocol:
cells were lysed in Qiagen's proprietary lysis buffer and used directly for library preparation
ultraplex 3' transcriptome library preparation following Qiagen's UPXome protocol


title: C26g


title: Caco-2 site 8 rep 1 conc8

description:
cell lysate
h2.h2.8.h04
8.1.H04


title: IyerS_RNA032_22

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 8 rep 1 conc7

description:
cell lysate
h2.h2.8.g04
8.1.G04


title: C27g


title: N09, noSTZ, chow, control

value: Streptozotocin


title: N08, noSTZ, chow, control


title: Caco-2 site 8 rep 1 conc6

description:
cell lysate
h2.h2.8.f04
8.1.F04


title: HeLa_IMP1_iCLIP_tech_replicate_1


title: C21g


title: C13g


title: IyerS_RNA032_21

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA032_20

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 8 rep 1 conc3

description:
cell lysate
h2.h2.8.c04
8.1.C04


title: IyerS_RNA032_19

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 8 rep 1 conc5

description:
cell lysate
h2.h2.8.e04
8.1.E04


title: C20g


title: Caco-2 site 8 rep 1 conc4

description:
cell lysate
h2.h2.8.d04
8.1.D04


title: N07, noSTZ, chow, control


title: C8g


title: IyerS_RNA032_18

description: FFPE Spatial Transcriptome sequencing


title: C2g


title: IyerS_RNA032_16

description: FFPE Spatial Transcriptome sequencing


title: C7g


title: Caco-2 site 8 rep 1 conc1

description:
cell lysate
h2.h2.8.a04
8.1.A04


title: Caco-2 site 8 rep 1 conc2

description:
cell lysate
h2.h2.8.b04
8.1.B04


title: AT05, STZ, HFD, Atglistatin-treated

value: Streptozotocin + Atglistatin


title: IyerS_RNA032_17

description: FFPE Spatial Transcriptome sequencing


title: AT04, STZ, HFD, Atglistatin-treated


title: OE3

data_processing:
HISAT
Bowtie2
Assembly: GCF_006496715.1_Aalbo_primary.1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: ovaries

extract_protocol:
Total RNA was isolated using TRIzol® reagent (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer's instructions. The purity and concentration of the total RNA samples were determined using a 2100 Bioanalyzer (Agilent) and ND-2000 instrument (NanoDrop Technologies), respectively.
RNA libraries for RNA-seg were prepared using MGIEasy RNA Library Kit following manufacturer's protocols

value: ovaries

value: Aalpi18529 overexpression


title: Whole kidney P2 control

first: Dennis

last: Kostka

state: PA

department: Developmental Biology

institute: University of Pittsburgh

data_processing:
Cellranger v 2.2.0 (10X Genomics)
Cell filtering, QC and normalization (DropletUtils, scds, scater, scran)
Genome_build: mm10
Supplementary_files_format_and_content: mtx, csv, txt; genes, barcodes, metadata, counts, log-counts

molecule: polyA RNA

source_name: control

extract_protocol:
We harvested 1 kidney from C57BL/6J control and DM_Exp mice at P2 and generated single cell suspensions using 0.05% trypsin at 37°C for 10 minutes. Kidneys were mechanically dissociated with pipetting at 5 and 10 min. 3% fetal calf serum (FCS) in PBS was added to halt the trypsin. The cell suspension was filtered using a 40 μm filter and pelleted. The cells were resuspended in 90% FCS in DMSO and frozen.
Single-cell library preparation and sequencing was performed by GENEWIZ Inc. using the 10X Genomics Inc. Chromium 3’ Single Cell v2 library preparation kit
scRNA-seq

value: whole kidney

tag: developmental stage


title: Caco-2 site 7 rep 3 conc8

description:
cell lysate
h11.h11.7.h06
7.3.H06


title: Caco-2 site 7 rep 3 conc7

description:
cell lysate
h11.h11.7.g06
7.3.G06


title: AT06, STZ, HFD, Atglistatin-treated

tag: tissue


title: B29g

value: 5000 IU of cholecalciferol


title: IyerS_RNA032_14

description: FFPE Spatial Transcriptome sequencing


title: B25g


title: Caco-2 site 7 rep 3 conc6

description:
cell lysate
h11.h11.7.f06
7.3.F06


title: OE1


title: Caco-2 site 7 rep 3 conc5

description:
cell lysate
h11.h11.7.e06
7.3.E06


title: OE2


title: B24g


title: Caco-2 site 7 rep 3 conc4

description:
cell lysate
h11.h11.7.d06
7.3.D06


title: IyerS_RNA032_12

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA032_10

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 7 rep 3 conc3

description:
cell lysate
h11.h11.7.c06
7.3.C06


title: IyerS_RNA032_11

description: FFPE Spatial Transcriptome sequencing


title: B18g


title: C1g


title: IyerS_RNA032_15

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 7 rep 3 conc2

description:
cell lysate
h11.h11.7.b06
7.3.B06


title: Caco-2 site 7 rep 3 conc1

description:
cell lysate
h11.h11.7.a06
7.3.A06


title: NC1

value: control


title: HUVECs, si-METTL3_3

city: Tianjin

first: xiaoxiao

last: Yang

state: Tianjin

address: 22 Qixiangtai Road, Heping District

institute: Tianjin Medical University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (v0.38). Trimmed sequence reads were mapped to the reference genome (GENCODE v38 GRCh38) using hisat2 (v2.2.1).
GRCh38

source_name: HUVECs

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) and the concentration and integrity of total RNA were measured by Qubit RNA HS Assay and Agilent 2113 Bioanalyzer (Agilent Technology), respectively.
RNA-Seq libraries were directly constructed using the KAPA RNA HyperPrep Kit (KAPA Biosystems) following the manufacturer’s instructions.

value: HUVECs

value: Human umbilical vein endothelial cells

value: Treated by siRNA of METTL3


title: NC3

last: Gu


title: IyerS_RNA032_13

description: FFPE Spatial Transcriptome sequencing


title: B15g


title: IyerS_RNA032_8

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA032_7

description: FFPE Spatial Transcriptome sequencing


title: B19g


title: B12g


title: B11g


title: B6g


title: HUVECs, si-METTL3_2

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) and the concentration and integrity of total RNA were measured by Qubit RNA HS Assay and Agilent 2112 Bioanalyzer (Agilent Technology), respectively.
RNA-Seq libraries were directly constructed using the KAPA RNA HyperPrep Kit (KAPA Biosystems) following the manufacturer’s instructions.


title: HUVECs, si-NC_3

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) and the concentration and integrity of total RNA were measured by Qubit RNA HS Assay and Agilent 2110 Bioanalyzer (Agilent Technology), respectively.
RNA-Seq libraries were directly constructed using the KAPA RNA HyperPrep Kit (KAPA Biosystems) following the manufacturer’s instructions.

value: Treated by siRNA of control


title: IyerS_RNA032_6

description: FFPE Spatial Transcriptome sequencing

extract_protocol:
5um sections were cut from Paraformaldehyde-Fixed Paraffin-Embedded slides. Samples were incubated with either DNA-oligo barcoded RNA-ISH probes or antibodies which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Spatial transcriptome sequencing libraries were prepared with Nanostring reagents according to manufacturer's specifications


title: Caco-2 site 7 rep 2 conc7

first: Niladri

last: Basu

institute: McGill University

description:
cell lysate
h7.h7.7.g06
7.2.G06


title: Caco-2 site 7 rep 2 conc8

description:
cell lysate
h7.h7.7.h06
7.2.H06


title: Caco-2 site 7 rep 2 conc6

description:
cell lysate
h7.h7.7.f06
7.2.F06


title: B5g


title: IyerS_RNA032_5

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA032_9

description: FFPE Spatial Transcriptome sequencing


title: HUVECs, si-NC_1

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) and the concentration and integrity of total RNA were measured by Qubit RNA HS Assay and Agilent 2108 Bioanalyzer (Agilent Technology), respectively.
RNA-Seq libraries were directly constructed using the KAPA RNA HyperPrep Kit (KAPA Biosystems) following the manufacturer’s instructions.


title: Caco-2 site 7 rep 2 conc4

description:
cell lysate
h7.h7.7.d06
7.2.D06


title: HUVECs, si-METTL3_1

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) and the concentration and integrity of total RNA were measured by Qubit RNA HS Assay and Agilent 2111 Bioanalyzer (Agilent Technology), respectively.
RNA-Seq libraries were directly constructed using the KAPA RNA HyperPrep Kit (KAPA Biosystems) following the manufacturer’s instructions.


title: IyerS_RNA032_4

description: FFPE Spatial Transcriptome sequencing


title: A23g

value: control group


title: Caco-2 site 7 rep 2 conc5

description:
cell lysate
h7.h7.7.e06
7.2.E06


title: IyerS_RNA032_3

description: FFPE Spatial Transcriptome sequencing


title: NC2


title: Caco-2 site 7 rep 2 conc3

description:
cell lysate
h7.h7.7.c06
7.2.C06


title: A22g


title: 3815_HC

city: Boston

first: Ivan

last: Zanoni

address: 1 Blackfan Circle

institute: Boston Children's Hospital and Harvard Medical School

data_processing:
Sequencing, read alignment, de-multiplexing, quality control and normalization was performed using an Ion S5 system (A27212; Ion Torrent, Torrent Suite software v5.12.1).
Expression results were obtained using Transcriptome Analysis Console (Thermo Fisher Scientific) using the settings: array type: hg19_Ampliseq_Transcriptome_21K_v1, analysis type: expression (gene), genome version: hg19 (Homo sapiens), annotation: hg19_AmpliSeq_Transcriptome_21K_v1.transcript, comparison: Healthy controls vs inflamed biopsy samples. The results were filtered to drop ERCC controls and retain only expressed genes (average log expression value greater than 1.5, determined upon inspection of the bimodal expression distribution). Log fold changes and FDR-adjusted p-values were used for downstream analyses. Volcano plots were generated using R (v4.4) with the package EnhancedVolcano (v1.22.0). PCA was performed using Python (v3.11) with the package scikit-learn (v1.5) on log expression values, without scaling. GSEA on the MSigDB Hallmark geneset collection was performed using the blitzGSEA package80 (v1.3.44), with genes ranked by the product of log fold change and log p-value, each min-max scaled to ensure equal contribution to the product.
Assembly: hg19
Supplementary files format and content: csv file includes log expression values across genes for all samples. It also contains columns for avg expression in the inflamed and the uninflamed conditions as well as their SD, fold change, p value, fdr p-value.

source_name: Sigmoid Colon

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini Kit according to the manufacturer's protocol.
50ng RNA (isolated from colonic biopsies) was reverse-transcribed to cDNA using SuperScript VILO cDNA Synthesis Kit (11754-05; Invitrogen). Barcoded libraries were prepared using the Ion AmpliSeq Transcriptome Human Gene Expression Kit (A26325; Thermo Fisher Scientific) as per the manufacturer’s protocol.

value: Sigmoid Colon


title: IyerS_RNA032_2

description: FFPE Spatial Transcriptome sequencing


title: 3802_CD

source_name: Descending Colon

value: Descending Colon


title: 3831_HC


title: A17g

value: colon


title: IyerS_RNA032_1

description: FFPE Spatial Transcriptome sequencing

value: Brain-Prefrontal Cortex


title: Caco-2 site 7 rep 2 conc1

city: Sainte-Anne-de-Bellevue

address: 21,1111 Lakeshore Blvd, Apt #2

description:
cell lysate
h7.h7.7.a06
7.2.A06


title: A16g


title: 3692_HC


title: 3687_HC


title: Caco-2 site 7 rep 1 conc7

description:
cell lysate
h2.h2.7.g06
7.1.G06


title: Caco-2 site 7 rep 1 conc8

description:
cell lysate
h2.h2.7.h06
7.1.H06


title: IyerS_RNA031_24

description: FFPE Spatial Transcriptome sequencing

value: Brain-Hippocampus

value: IgG


title: A10g


title: A28g


title: HUVECs, si-NC_2

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) and the concentration and integrity of total RNA were measured by Qubit RNA HS Assay and Agilent 2109 Bioanalyzer (Agilent Technology), respectively.
RNA-Seq libraries were directly constructed using the KAPA RNA HyperPrep Kit (KAPA Biosystems) following the manufacturer’s instructions.


title: IyerS_RNA031_23

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 7 rep 1 conc6

description:
cell lysate
h2.h2.7.f06
7.1.F06


title: Caco-2 site 7 rep 1 conc5

description:
cell lysate
h2.h2.7.e06
7.1.E06


title: 3685_UC


title: A9g


title: IyerS_RNA031_22

description: FFPE Spatial Transcriptome sequencing


title: 3598_HC


title: IyerS_RNA031_21

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA031_20

description: FFPE Spatial Transcriptome sequencing


title: A4g


title: Caco-2 site 7 rep 1 conc4

description:
cell lysate
h2.h2.7.d06
7.1.D06


title: A3g


title: Caco-2 site 7 rep 2 conc2

description:
cell lysate
h7.h7.7.b06
7.2.B06


title: IyerS_RNA031_19

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA031_18

description: FFPE Spatial Transcriptome sequencing


title: A14g


title: C8c

value: jejunum

value: 10000 IU of cholecalciferol


title: 3500_UC


title: Caco-2 site 7 rep 1 conc2

description:
cell lysate
h2.h2.7.b06
7.1.B06


title: Caco-2 site 7 rep 1 conc1

description:
cell lysate
h2.h2.7.a06
7.1.A06


title: C7c


title: IyerS_RNA031_16

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA031_17

description: FFPE Spatial Transcriptome sequencing


title: 3340_UC


title: Caco-2 site 5 rep 3 conc8

description:
cell lysate
h13.h13.5.h10
5.3.H10


title: C27c


title: 3321_CD


title: IyerS_RNA031_15

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 5 rep 3 conc7

description:
cell lysate
h13.h13.5.g10
5.3.G10


title: IyerS_RNA031_14

description: FFPE Spatial Transcriptome sequencing


title: 1434_CD


title: 3574_HC


title: Caco-2 site 5 rep 3 conc6

description:
cell lysate
h13.h13.5.f10
5.3.F10


title: C26c


title: C21c


title: Caco-2 site 7 rep 1 conc3

description:
cell lysate
h2.h2.7.c06
7.1.C06


title: 656_UC


title: 3394_UC


title: C20c


title: IyerS_RNA031_12

description: FFPE Spatial Transcriptome sequencing


title: C2c


title: Caco-2 site 5 rep 3 conc4

description:
cell lysate
h13.h13.5.d10
5.3.D10


title: IyerS_RNA031_13

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 5 rep 3 conc3

description:
cell lysate
h13.h13.5.c10
5.3.C10


title: C1c


title: IyerS_RNA031_10

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 5 rep 3 conc2

description:
cell lysate
h13.h13.5.b10
5.3.B10


title: 2366_CD


title: C30c


title: IyerS_RNA031_11

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA031_9

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 5 rep 3 conc1

description:
cell lysate
h13.h13.5.a10
5.3.A10


title: IyerS_RNA031_8

description: FFPE Spatial Transcriptome sequencing


title: B6c


title: Caco-2 site 5 rep 2 conc8

description:
cell lysate
h9.h9.5.h10
5.2.H10


title: B5c


title: IyerS_RNA031_7

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 5 rep 3 conc5

description:
cell lysate
h13.h13.5.e10
5.3.E10


title: H651

type: RNA

city: Washington

first: Nikki

last: Posnack

state: DC

address: 111 Michigan Avenue, NW

institute: Children's National Research Institute

hyb_protocol: Overnight 16 hours at 45 degrees celcius

data_processing: Transcriptome Analysis Console (Applied Biosystems)

label: biotin

source_name: Right atrial tissue

label_protocol: GeneChip WT Plus Reagent kit

growth_protocol: Fresh cardiac tissue removed during surgery

extract_protocol: RNeasy fibrous tissue kit

tag: age group

value: Adolescent/Young Adult


title: H655

value: Infant


title: Caco-2 site 5 rep 2 conc7

description:
cell lysate
h9.h9.5.g10.
5.2.G10


title: B24c

value: 5000 IU of cholecalciferol


title: H663


title: H596

value: School Age


title: H603

value: Toddler/Pre School


title: Caco-2 site 5 rep 2 conc6

description:
cell lysate
h9.h9.5.f10
5.2.F10


title: IyerS_RNA031_6

description: FFPE Spatial Transcriptome sequencing


title: H578


title: B18c


title: B19c


title: IyerS_RNA031_5

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 5 rep 2 conc4

description:
cell lysate
h9.h9.5.d10
5.2.D10


title: B15c


title: IyerS_RNA031_4

description: FFPE Spatial Transcriptome sequencing


title: H576


title: IyerS_RNA031_3

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 5 rep 2 conc3

description:
cell lysate
h9.h9.5.c10
5.2.C10


title: B12c


title: H572

value: Neonate


title: B29c


title: Caco-2 site 5 rep 2 conc2

description:
cell lysate
h9.h9.5.b10
5.2.B10


title: IyerS_RNA031_1

description: FFPE Spatial Transcriptome sequencing


title: B11c


title: H544


title: IyerS_RNA031_2

description: FFPE Spatial Transcriptome sequencing


title: A9c


title: Caco-2 site 5 rep 2 conc5

description:
cell lysate
h9.h9.5.e10
5.2.E10


title: A4c


title: IyerS_RNA030_22

description: FFPE Spatial Transcriptome sequencing


title: H542


title: Caco-2 site 5 rep 1 conc8

description:
cell lysate
h4.h4.5.h10
5.1.H10


title: Caco-2 site 5 rep 1 conc7

description:
cell lysate
h4.h4.5.g10
5.1.G10


title: IyerS_RNA030_23

description: FFPE Spatial Transcriptome sequencing


title: A3c


title: H528


title: H526


title: A28c


title: IyerS_RNA030_20

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA030_21

description: FFPE Spatial Transcriptome sequencing


title: H575


title: Caco-2 site 5 rep 1 conc6

description:
cell lysate
h4.h4.5.f10
5.1.F10


title: A23c


title: Caco-2 site 5 rep 2 conc1

description:
cell lysate
h9.h9.5.a10
5.2.A10


title: H523


title: H521


title: A22c


title: IyerS_RNA030_19

description: FFPE Spatial Transcriptome sequencing


title: H514


title: Caco-2 site 5 rep 1 conc4

description:
cell lysate
h4.h4.5.d10
5.1.D10


title: A17c


title: IyerS_RNA030_17

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA030_18

description: FFPE Spatial Transcriptome sequencing


title: A16c


title: Caco-2 site 5 rep 1 conc3

description:
cell lysate
h4.h4.5.c10
5.1.C10


title: Caco-2 site 5 rep 1 conc5

description:
cell lysate
h4.h4.5.e10
5.1.E10


title: Caco-2 site 5 rep 1 conc1

description:
cell lysate
h4.h4.5.a10
5.1.A10


title: Caco-2 site 3 rep 3 conc8

description:
cell lysate
h11.h11.3.h05
3.3.H05


title: Caco-2 site 5 rep 1 conc2

description:
cell lysate
h4.h4.5.b10
5.1.B10


title: H506


title: IyerS_RNA030_16

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA030_15

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 3 rep 3 conc7

description:
cell lysate
h11.h11.3.g05
3.3.G05


title: IyerS_RNA030_14

description: FFPE Spatial Transcriptome sequencing


title: H504


title: A14c


title: IyerS_RNA030_12

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA030_13

description: FFPE Spatial Transcriptome sequencing


title: H497


title: Caco-2 site 3 rep 3 conc6

description:
cell lysate
h11.h11.3.f05
3.3.F05


title: Caco-2 site 3 rep 3 conc5

description:
cell lysate
h11.h11.3.e05
3.3.E05


title: SUP-M2 CELLS TREATED BY ALKi, Triple 3

city: Philadelphia

first: Wasik

middle: A

last: Mariusz

address: 422 Curie Blvd

institute: University of Pennsylvania

description: Gene Expression data from ALK+ TCL lines

hyb_protocol: according to the manufacturer’s instructions as found in GeneChip Expression Analysis Technical Manual, P/N 702232 Rev. 2

data_processing: Microarray data were normalized using the MAS5 algorithm and analyzed using Partek GS (Partek). Differentially expressed genes were identified using ANOVA

label: Biotin

source_name: Huna T-lymphoblast

label_protocol: 3ug of input total RNA were amplified and labeled using the Affymetrix 1-cycle kit

growth_protocol: Cells were cultured at 37 °C and 5% CO2 in RPMI medium 1640, supplemented with 2-mM L-glutamine, 10% heat-inactivated FBS (FBS), 1% penicillin/streptomycin mixture and, where applicable, 200 units of IL-2 (Bender MedSystems)

extract_protocol: total RNA was isolated using a TRIZOL and Qiagen Rneasy protocols

treatment_protocol: The ALK+TCL Sudhl-1 cell line was treated in triplicates with the ALK inhibitor, CEP-14083, or the compound's solvent for 6 h

value: SUP-M2 cells

value: ALKi


title: H507

value: infant


title: IyerS_RNA030_11

description: FFPE Spatial Transcriptome sequencing

data_processing:
Raw sequencing data was processed using Nanostring's GeoMx DSP Control Center Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode) Library strategy: Spatial Transcriptomics
Assembly: N/A, sequencing of synthetic tags and aligment to whitelist of RTS IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform
Supplementary files format and content: dcc

source_name: Brain-Prefrontal Cortex


title: IyerS_RNA030_10

description: FFPE Spatial Transcriptome sequencing


title: SUP-M2 CELLS TREATED BY ALKi, Triple 1

scan_protocol: according to the manufacturer’s instructions as found in GeneChip Expression Analysis Technical Manual, P/N 702232 Rev. 2


title: H489


title: H501


title: IyerS_RNA030_9

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 3 rep 3 conc3

description:
cell lysate
h11.h11.3.c05
3.3.C05


title: H502


title: Caco-2 site 3 rep 3 conc2

description:
cell lysate
h11.h11.3.b05
3.3.B05


title: Caco-2 site 3 rep 3 conc1

description:
cell lysate
h11.h11.3.a05
3.3.A05


title: IyerS_RNA030_8

description: FFPE Spatial Transcriptome sequencing


title: SUP-M2 CELLS, Triple 3

value: control


title: Caco-2 site 3 rep 3 conc4

description:
cell lysate
h11.h11.3.d05
3.3.D05


title: SUP-M2 CELLS TREATED BY ALKi, Triple 2


title: H486


title: IyerS_RNA030_7

description: FFPE Spatial Transcriptome sequencing


title: H471


title: H447


title: H443


title: Caco-2 site 3 rep 2 conc8

description:
cell lysate
h7.h7.3.h05
3.2.H05


title: IyerS_RNA030_6

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 3 rep 2 conc7

description:
cell lysate
h7.h7.3.g05
3.2.G05


title: IyerS_RNA030_5

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 3 rep 2 conc6

description:
cell lysate
h7.h7.3.f05
3.2.F05


title: H435


title: H409


title: H408


title: Caco-2 site 3 rep 2 conc5

description:
cell lysate
h7.h7.3.e05
3.2.E05


title: H406


title: SUP-M2 CELLS, Triple 1


title: SUDHL1 CELLS TREATED BY ALKi, Triple 3

value: SUDHL1 cells


title: SUDHL1 CELLS TREATED BY ALKi, Triple 2


title: SUP-M2 CELLS, Triple 2


title: IyerS_RNA030_4

description: FFPE Spatial Transcriptome sequencing


title: SUDHL1 CELLS TREATED BY ALKi, Triple 1


title: SUDHL1 CELLS, Triple 3


title: IyerS_RNA030_3

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 3 rep 2 conc4

description:
cell lysate
h7.h7.3.d05
3.2.D05


title: IyerS_RNA030_1

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA030_2

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 3 rep 2 conc3

description:
cell lysate
h7.h7.3.c05
3.2.C05


title: H400


title: SUDHL1 CELLS, Triple 2


title: Caco-2 site 3 rep 2 conc1

description:
cell lysate
h7.h7.3.a05
3.2.A05


title: IyerS_RNA029_24

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA029_23

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA029_22

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 3 rep 1 conc7

description:
cell lysate
h2.h2.3.g05
3.1.G05


title: Caco-2 site 3 rep 1 conc8

description:
cell lysate
h2.h2.3.h05
3.1.H05


title: Caco-2 site 3 rep 2 conc2

description:
cell lysate
h7.h7.3.b05
3.2.B05


title: H396


title: H382


title: Caco-2 site 3 rep 1 conc6

description:
cell lysate
h2.h2.3.f05
3.1.F05


title: H371


title: SUDHL1 CELLS, Triple 1


title: H373


title: H379


title: H398


title: Caco-2 site 3 rep 1 conc5

description:
cell lysate
h2.h2.3.e05
3.1.E05


title: IyerS_RNA029_20

description: FFPE Spatial Transcriptome sequencing


title: NA2 CELLS TREATED BY ALKi, Triple 2

value: NA2 cells


title: NA2 CELLS TREATED BY ALKi, Triple 1


title: IyerS_RNA029_21

description: FFPE Spatial Transcriptome sequencing


title: NA2 CELLS TREATED BY ALKi, Triple 3


title: NA2 CELLS, Triple 2


title: H370


title: NA2 CELLS, Triple 1


title: Caco-2 site 3 rep 1 conc4

description:
cell lysate
h2.h2.3.d05
3.1.D05


title: H364


title: H351


title: NA1 CELLS TREATED BY ALKi, Triple 3

value: NA1 cells


title: NA2 CELLS, Triple 3


title: NA1 CELLS TREATED BY ALKi, Triple 2


title: IyerS_RNA029_18

description: FFPE Spatial Transcriptome sequencing

value: Brain-Hippocampus


title: Caco-2 site 3 rep 1 conc3

description:
cell lysate
h2.h2.3.c05
3.1.C05


title: IyerS_RNA029_17

description: FFPE Spatial Transcriptome sequencing

value: IgG


title: IyerS_RNA029_19

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 2 rep 3 conc8

description:
cell lysate
h12.h12.2.h07
2.3.H07


title: Caco-2 site 3 rep 1 conc1

description:
cell lysate
h2.h2.3.a05
3.1.A05


title: Caco-2 site 2 rep 3 conc7

description:
cell lysate
h12.h12.2.g07
2.3.G07


title: IyerS_RNA029_15

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA029_14

description: FFPE Spatial Transcriptome sequencing


title: ABE,NTC,day21, scRNA-seq

city: Shanghai

first: Leilei

last: Wu

address: RD215 FuTe south

institute: Epigenic Therapeutics, Inc

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The scRNA-seq reads were aligned to the GRCh38 reference genome and quantified using cellranger count (10× Genomics, v7.1.0). A filtered and qualified feature matrix was generated (provide process data), which only included barcodes with unique molecular identifier (UMI) counts surpassing the threshold for cell detection. The raw expression matrix was processed using the scanpy packages in Python. A total of 217,033 cells were detected initially. After cellranger, applying quality control metrics (total counts <50,000, mitochondrial ratio <10, and detected gene numbers between 500 and 8,000), 209,469 cells remained for further analysis. The qualified raw count data was log-normalized per cell with a size factor of 10,000. The top 3,000 genes with the highest variations across all cells were selected as "highly variable genes". A subset of the expression matrix was extracted and scaled using these highly variable genes. Principal component analysis (PCA) was then applied to derive meaningful features from the scaled data. The elbow point in the variance ratio distributions of PCA was used to select fifty principal components for computing the neighboring cluster graph. To further reduce dimensionality, Uniform Manifold Approximation Projection (UMAP) with the leiden algorithm was applied (resolution = 1.2). For ABE8.8, a total of 19 clusters were obtained and visualized using UMAP. We removed cluster 13 based on the marker genes specifically expressed in MT-related genes. For high-fidelity ABE, a total of 19 clusters were obtained and visualized using UMAP. Next, we performed differential expression analysis in each cluster using the Wilcoxon rank sum-test method. The top differentially expressed genes in each cluster, as determined by ranking, were defined as marker genes and used for subsequent cell type annotations.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMC

extract_protocol:
Cryopreserved PBMCs were then retrieved from a liquid nitrogen tank, thawed in a 37°C water bath, and transferred into the cabinet after removing any remaining ice clumps. The outer surface of the container was sterilized with 5% ethanol, dried, and transferred into the cabinet. The cells were then transferred into 9 mL of T cell medium and centrifuged at 400g for 5 minutes at room temperature. After discarding the supernatant, the cells were resuspended in 5 mL of medium and counted using a ThermoFisher Attune NxT flow cytometer. Subsequently, the cells were seeded at a density of 1e6 cells/mL in plates or culture flasks. After 6 hours of PBMC revival, CD3/28 dynabeads were added for activation. Following 3 days of cell activation, the activation beads were removed using a magnet and the culture was continued for 24 hours. For electroporation, 24-well plates were prepared by adding 900 μL of PBMC complete medium per well and incubating at 37°C for 10 minutes. The Lonza 4D Nucleofector System with the P3 Primary Cell 4D kit was used, following the kit instructions for electroporation. Each electroporation reaction consisted of 1E6 cells, 1.2 pmol of EPIREG mRNA, and 40 pmol of sgRNA for each target gene. Immediately after electroporation, 100 μL of cell-free medium was added to each well, followed by a 1-hour incubation at 37°C. The cells were then transferred to 24-well plates for further culture.
The cell suspension was loaded into Chromium microfluidic chips with 3' (v2 or v3, depending on the project) chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries were constructed using reagents from a Chromium Single Cell 3' v2 (v2 or v3, depending on the project) reagent kit (10X Genomics) according to the manufacturer's instructions. Sequencing was performed with Illumina (HiSeq 2000 or NovaSeq, depending on the project) according to the manufacturer's instructions (Illumina). The same library construction process was used in Huh7 cells.

value: blood

value: human T cells


title: ABE,B2M,day21, scRNA-seq

description: 10X Genomics


title: H346


title: H344


title: IyerS_RNA029_13

last: Iyer

description: FFPE Spatial Transcriptome sequencing


title: H340


title: H334

value: Adolescent/Young Adult


title: Caco-2 site 2 rep 3 conc6

description:
cell lysate
h12.h12.2.f07
2.3.F07


title: H298


title: Donor_79_CCR5+

city: Saint Louis

first: Hongbo

last: Gao

state: MO

address: 425 S Euclid Ave

institute: Washington university in St. Louis

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a (Dobin et al., 2013). Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5 (Liao et al., 2014). Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2 (Wang et al., 2012). Counts were first filtered by removing genes where greater than half of the samples had Counts per million (cpm) values less than 1 using python version 3.8.5. Raw counts for the genes that passed filtering were passed into DESeq2 v. 1.28.1 using R v. 4.0.0 for differential expression. DESeq2 normalized read counts were used to calculate transcripts per million reads (TPMs).
Assembly: Ensembl release 76
Supplementary files format and content: Tab-delimited text file containing DQSeq2 normalized TPM values for each sample

growth_protocol: CD4+ T cells were purified from the buffy coat of uninfected donors by Ficoll gradient separation followed by negative selection with MojoSort™ Human CD4 T Cell Isolation Kit (Biolegend). Purified CD4+ T cells (106 cells/mL) were cultured in RPMI 1640 medium supplemented with 10% FCS, penicillin (100 unit/mL) and streptomycin (100 µg/mL).

extract_protocol:
CCR5+ and CCR5- CD4+ T cells were sorted, and total RNA was extracted using Direct-zol RNA kit (Zymo Research). The cDNA library was prepared using strand-specific RNA-sequencing protocols. Samples were prepared according to library kit manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To generate activated cells, CD4+ T cells were stimulated with plate-bound anti-CD3 and anti-CD28 antibodies at 1μg/mL (BioLegend) for 3 days in the presence of 20 ng/mL IL-2. Stimulated CD4+ T cells were cultured with 20 ng/mL IL-2 for 6 days.

value: PBMC

value: CD4+ T Cells


title: IyerS_RNA029_12

first: Smita

institute: University of Pittsburgh School of Medicine

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA029_16

description: FFPE Spatial Transcriptome sequencing


title: NA1 CELLS, Triple 2


title: Caco-2 site 3 rep 1 conc2

description:
cell lysate
h2.h2.3.b05
3.1.B05


title: NA1 CELLS TREATED BY ALKi, Triple 1


title: Caco-2 site 2 rep 3 conc5

description:
cell lysate
h12.h12.2.e07
2.3.E07


title: NA1 CELLS, Triple 1


title: H296


title: Caco-2 site 2 rep 3 conc4

description:
cell lysate
h12.h12.2.d07
2.3.D07


title: Donor_77_CCR5+


title: NA1 CELLS, Triple 3


title: H295

value: Infant


title: Caco-2 site 2 rep 3 conc3

description:
cell lysate
h12.h12.2.c07
2.3.C07


title: IyerS_RNA029_9

description: FFPE Spatial Transcriptome sequencing


title: Donor_77_CCR5-


title: IyerS_RNA029_10

description: FFPE Spatial Transcriptome sequencing


title: H292


title: IyerS_RNA029_8

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 2 rep 3 conc2

description:
cell lysate
h12.h12.2.b07
2.3.B07


title: Caco-2 site 2 rep 3 conc1

description:
cell lysate
h12.h12.2.a07
2.3.A07


title: IyerS_RNA029_7

description: FFPE Spatial Transcriptome sequencing


title: Donor_76_CCR5+


title: Donor_76_CCR5-


title: H269


title: H278


title: Donor_79_CCR5-


title: Caco-2 site 2 rep 2 conc8

description:
cell lysate
h8.h8.2.h07
2.2.H07


title: Donor_68_CCR5+


title: IyerS_RNA029_11

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA029_6

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 2 rep 2 conc7

description:
cell lysate
h8.h8.2.g07
2.2.G07


title: Donor_68_CCR5-


title: Caco-2 site 2 rep 2 conc6

description:
cell lysate
h8.h8.2.f07
2.2.F07


title: H268


title: IyerS_RNA029_5

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA029_4

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 2 rep 2 conc5

description:
cell lysate
h8.h8.2.e07
2.2.E07


title: H253


title: H256


title: U2OS_30μM_AMTB

city: shanghhai

first: yujie

last: liu

address: fengyang road 415

institute: 上海长征医院

data_processing:
Quality control; Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC
content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Osteosarcoma cell line

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

value: treated with 30 uM AMTB for 24 hours


title: U2OS_Ctrl

value: untreated


title: H235


title: IyerS_RNA029_3

city: Pittsburgh

address: 3550 Terrace Street

description: FFPE Spatial Transcriptome sequencing

source_name: Brain-Hippocampus


title: H215


title: IyerS_RNA029_2

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 2 rep 2 conc3

description:
cell lysate
h8.h8.2.c07
2.2.C07


title: Caco-2 site 2 rep 2 conc4

description:
cell lysate
h8.h8.2.d07
2.2.D07


title: IyerS_RNA029_1

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 2 rep 2 conc2

description:
cell lysate
h8.h8.2.b07
2.2.B07


title: IyerS_RNA028_23

description: FFPE Spatial Transcriptome sequencing

value: Brain-Prefrontal Cortex


title: Caco-2 site 2 rep 2 conc1

description:
cell lysate
h8.h8.2.a07
2.2.A07


title: H243


title: H212


title: H210


title: IyerS_RNA028_22

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA028_20

description: FFPE Spatial Transcriptome sequencing


title: Caco-2 site 2 rep 1 conc8

description:
cell lysate
h3.h3.2.h08
2.1.H08


title: Caco-2 site 2 rep 1 conc7

description:
cell lysate
h3.h3.2.g08
2.1.G08


title: IyerS_RNA028_21

description: FFPE Spatial Transcriptome sequencing


title: H206

value: School Age


title: Caco-2 site 2 rep 1 conc6

description:
cell lysate
h3.h3.2.f08
2.1.F08


title: Caco-2 site 2 rep 1 conc5

description:
cell lysate
h3.h3.2.e08
2.1.E08


title: B16-HSV3

city: 上海

first: 玮玮

last: 代

state: 上海

address: 徐汇区东安路131号

institute: 复旦大学

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: B16 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

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 for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: B16 cells were treated with 0.1MOIHSV for 12h

value: melanoma cell lines

tag: genotype

value: WT

value: B16 cells were infected with HSV for 12 hr


title: IyerS_RNA028_18

description: FFPE Spatial Transcriptome sequencing


title: H202

value: Toddler/Pre School


title: IyerS_RNA028_19

description: FFPE Spatial Transcriptome sequencing


title: H207


title: H208