title: 2705-XX-88

description: Library name: 2705-XX-88


title: HP1714601_I21

status: Public on Aug 22 2025

type: SRA

city: Huddinge

first: Ping

last: Chen

address: Alfred Nobels allé 8

department: Department of Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were de-multiplexed and converted into fastq format for each cell by using Illumina bcl2fastq with default setting.
Reads were aligned to human genome hg38 using the STAR aligner.
Uniquely aligned reads mapping to the RefSeq gene annotations were used for gene expression estimates at reads per kilobase transcript and million mapped reads (RPKMs) using rpkmforgenes.
Low quality cells were excluded from downstream analysis when they failed to meet the following criteria for retaining cells: 1) >= 50,000 sequence reads; 2) >= 40% of reads uniquely aligned to the genome; 3) >= 40% of these reads mapping to RefSeq annotated exons; and 4) >= 1000 genes with RPKM >= 1. In addition, doublets detected by Scrublet were further removed.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each single cell …

molecule: total RNA

organism: Homo sapiens

source_name: Human pancreatic islet single cells

extract_protocol: The reverse-transcribed cDNA from single cells was amplified followed by tagmentation and a standard index PCR. The single cell libraries were prepared according to Smart-seq2 protocol. The sequencing was performed on HISEQ 3000 (IIlumina).

tag: tissue

value: Pancreatic islets

tag: disease state

value: Healthy


title: HP1605601T2D_M13


title: 2705-XX-87

city: San Diego

first: Kellen

last: Cavagnero

state: California

address: 9500 Gilman Dr

country: USA

institute: Univeristy of California, San Diego

description: Library name: 2705-XX-87

library_source: transcriptomic

data_processing:
Reads were mapped to the GRCh38 reference genome using STAR. Count matrices were generated using HTSeq. Differential expression analysis was performed using DESeq2.
Assembly: hg19
Supplementary files format and content: count matrix

source_name: skin

extract_protocol:
Samples were incubated in an optimized lysis buffer, which contains proteinase K, to release RNA from the sample sections. This was followed by an incubation at a higher temperature to partially reverse formalin crosslinking of the released nucleic acids and improve RNA yield and quality. This was followed by DNase treatment that was optimized to eliminate all genomic DNA, including very small DNA fragments. The lysate was then mixed with Buffer RBC, and ethanol was added to provide appropriate binding conditions for RNA. The sample was then applied to an RNeasy MinElute spin column, where the total RNA bound to the membrane and contaminants were effectively washed away. RNA was then eluted in 30µl of RNase-free water.
Libraries were generated using NovaSeq.

value: skin

tag: cell type

value: skin cells

tag: treatment


title: 2705-XX-86

description: Library name: 2705-XX-86


title: 2705-XX-83

description: Library name: 2705-XX-83


title: 2705-XX-85

description: Library name: 2705-XX-85


title: 2705-XX-84

description: Library name: 2705-XX-84


title: HP1606401T2D_Tn5_M2


title: HP1525401_P13


title: 2705-XX-82

description: Library name: 2705-XX-82


title: HP1601201T2D_H10


title: 8911-JF

description: Library name: 8911-JF

data_processing:
Reads were mapped to the GRCh38 reference genome and count matrices were generated using CellRanger with default parameters. Downstream processing, and analysis was done using Seurat.
Assembly: hg38
Supplementary files format and content: count matrix

molecule: nuclear RNA

extract_protocol:
Samples were incubated in an optimized lysis buffer, which contains proteinase K, to release RNA from the sample sections. This was followed by an incubation at a higher temperature to partially reverse formalin crosslinking of the released nucleic acids and improve RNA yield and quality. This was followed by DNase treatment that was optimized to eliminate all genomic DNA, including very small DNA fragments. The lysate was then mixed with Buffer RBC, and ethanol was added to provide appropriate binding conditions for RNA. The sample was then applied to an RNeasy MinElute spin column, where the total RNA bound to the membrane and contaminants were effectively washed away. RNA was then eluted in 30µl of RNase-free water.
10X Genomics Flex FFPE protocol and were subjected to 28x91bp of sequencing according to the manufacturer’s protocol (Illumina NovaSeq). Library prep and next-generation sequencing was carried out in the Advanced Genomics Core at the University of Michigan


title: HP1602301T2D_A15


title: 2705-XX-81

description: Library name: 2705-XX-81


title: 2705-XX-79

description: Library name: 2705-XX-79


title: HP1711701T2D_L15


title: 2705-XX-89

description: Library name: 2705-XX-89


title: 2705-XX-77

description: Library name: 2705-XX-77


title: 2705-XX-78

description: Library name: 2705-XX-78


title: HP1525401_M19


title: HP1714601_I24


title: 2705-XX-80

description: Library name: 2705-XX-80


title: HP1714601_O20


title: 2705-XX-76

description: Library name: 2705-XX-76


title: HP1605601T2D_B8


title: HP1606401T2D_Tn5_E12


title: HP1605601T2D_A5


title: HP1714601_J3


title: 2705-XX-75

description: Library name: 2705-XX-75


title: HP1525901_F2


title: 2705-XX-73

description: Library name: 2705-XX-73


title: 2705-XX-113

description: Library name: 2705-XX-113


title: HP1711701T2D_C11


title: 2705-XX-112

description: Library name: 2705-XX-112


title: HP1606401T2D_Tn5_C18


title: 2705-XX-111

description: Library name: 2705-XX-111


title: HP1602301T2D_E7


title: 2705-XX-110

description: Library name: 2705-XX-110


title: HP1602301T2D_F16


title: HP1605601T2D_C10


title: 2705-XX-104

description: Library name: 2705-XX-104


title: 2705-XX-109

description: Library name: 2705-XX-109


title: HP1714601_C15


title: 2705-XX-102

description: Library name: 2705-XX-102


title: HP1606401T2D_Tn5_E9


title: HP1606401T2D_Tn5_O12


title: 2705-XX-103

description: Library name: 2705-XX-103


title: 2393-XX-98

description: Library name: 2393-XX-98


title: 2705-XX-101

description: Library name: 2705-XX-101


title: 2705-XX-74

description: Library name: 2705-XX-74


title: HP1606401T2D_Tn5_E18


title: HP1606401T2D_Tn5_D7


title: 2705-XX-100

description: Library name: 2705-XX-100


title: HP1525901_I5


title: 2393-XX-93

description: Library name: 2393-XX-93


title: HP1711001_J23


title: HP1711001_I2


title: 2393-XX-95

description: Library name: 2393-XX-95


title: 2393-XX-92

description: Library name: 2393-XX-92


title: HP1605601T2D_E15


title: HP1601201T2D_G22


title: HP1714601_O21


title: 2393-XX-91

description: Library name: 2393-XX-91


title: HP1601201T2D_I23


title: 2393-XX-89

description: Library name: 2393-XX-89


title: 2393-XX-90

description: Library name: 2393-XX-90


title: 2393-XX-88

description: Library name: 2393-XX-88


title: HP1714601_N16


title: 2393-XX-87

description: Library name: 2393-XX-87


title: HP1525401_I21


title: 2393-XX-86

description: Library name: 2393-XX-86


title: 2393-XX-85

description: Library name: 2393-XX-85


title: HP1601201T2D_B1


title: 2393-XX-84

description: Library name: 2393-XX-84


title: HP1525401_I19


title: HP1525901_E12


title: HP1711001_P16


title: HP1605601T2D_H6


title: 2393-XX-83

description: Library name: 2393-XX-83


title: HP1711001_G15


title: 2393-XX-80

description: Library name: 2393-XX-80


title: 2393-XX-82

description: Library name: 2393-XX-82


title: HP1601201T2D_I17


title: HP1606401T2D_Tn5_L10


title: 2393-XX-79

description: Library name: 2393-XX-79


title: HP1714601_E8


title: HP1602301T2D_F7


title: 2393-XX-78

description: Library name: 2393-XX-78


title: HP1525401_B18


title: 2393-XX-77

description: Library name: 2393-XX-77


title: 2393-XX-76

description: Library name: 2393-XX-76


title: 2393-XX-75

description: Library name: 2393-XX-75


title: HP1711701T2D_D20


title: HP1711001_B9


title: 2393-XX-74

description: Library name: 2393-XX-74


title: HP1711701T2D_K12


title: 2393-XX-73

description: Library name: 2393-XX-73


title: HP1714601_B7


title: 2393-XX-71

description: Library name: 2393-XX-71


title: HP1525901_P5


title: 2393-XX-72

description: Library name: 2393-XX-72


title: 2393-XX-81

description: Library name: 2393-XX-81


title: 2393-XX-69

description: Library name: 2393-XX-69


title: HP1714601_J24


title: 2393-XX-68

description: Library name: 2393-XX-68


title: 2393-XX-67

description: Library name: 2393-XX-67


title: HP1711001_I14


title: 2393-XX-70

description: Library name: 2393-XX-70


title: HP1601201T2D_E9


title: 2393-XX-66

description: Library name: 2393-XX-66


title: 2393-XX-63

description: Library name: 2393-XX-63


title: HP1606401T2D_Tn5_N11


title: HP1602301T2D_I6


title: 2393-XX-62

description: Library name: 2393-XX-62


title: HP1525401_N23


title: 2393-XX-61

description: Library name: 2393-XX-61


title: HP1601201T2D_J11


title: HP1711001_K9


title: 2393-XX-60

description: Library name: 2393-XX-60


title: HP1606401T2D_Tn5_M18


title: 2393-XX-57

description: Library name: 2393-XX-57


title: HP1711701T2D_O4


title: HP1711701T2D_C20


title: 2393-XX-56

description: Library name: 2393-XX-56


title: HP1714601_A1


title: 2393-XX-55

description: Library name: 2393-XX-55


title: 2393-XX-54

description: Library name: 2393-XX-54


title: HP1525401_E23


title: 2393-XX-53

description: Library name: 2393-XX-53


title: HP1602301T2D_M23


title: HP1525901_E6


title: HP1711701T2D_H24


title: 2393-XX-52

description: Library name: 2393-XX-52


title: 2393-XX-39

description: Library name: 2393-XX-39


title: 2393-XX-34

description: Library name: 2393-XX-34


title: HP1605601T2D_G9


title: HP1525401_H12


title: HP1602301T2D_P22


title: 2393-XX-157

description: Library name: 2393-XX-157


title: 2393-XX-58

description: Library name: 2393-XX-58


title: HP1601201T2D_P11


title: 2393-XX-32

description: Library name: 2393-XX-32


title: 2393-XX-23

description: Library name: 2393-XX-23


title: 2393-XX-140

description: Library name: 2393-XX-140


title: HP1711001_F4


title: HP1602301T2D_A20


title: HP1602301T2D_N6


title: 2393-XX-141

description: Library name: 2393-XX-141


title: HP1711701T2D_B2


title: HP1605601T2D_F6


title: HP1605601T2D_G1


title: 2393-XX-138

description: Library name: 2393-XX-138


title: 2393-XX-137

description: Library name: 2393-XX-137


title: 2393-XX-136

description: Library name: 2393-XX-136


title: HP1711001_H8


title: HP1605601T2D_L15


title: 2393-XX-134

description: Library name: 2393-XX-134


title: 2393-XX-135

description: Library name: 2393-XX-135


title: HP1714601_N2


title: 2393-XX-133

description: Library name: 2393-XX-133


title: 2393-XX-132

description: Library name: 2393-XX-132


title: HP1711701T2D_K22


title: 2393-XX-130

description: Library name: 2393-XX-130


title: HP1602301T2D_C1


title: 2393-XX-127

description: Library name: 2393-XX-127


title: 2393-XX-128

description: Library name: 2393-XX-128


title: HP1714601_H17


title: 2393-XX-125

description: Library name: 2393-XX-125


title: 2393-XX-126

description: Library name: 2393-XX-126


title: HP1711701T2D_M2


title: HP1711701T2D_K23


title: HP1525401_B7


title: 2393-XX-123

description: Library name: 2393-XX-123


title: HP1714601_I8


title: 2393-XX-121

description: Library name: 2393-XX-121


title: 2393-XX-119

description: Library name: 2393-XX-119


title: 2393-XX-129

description: Library name: 2393-XX-129


title: HP1601201T2D_K8


title: HP1602301T2D_H2


title: 2393-XX-117

description: Library name: 2393-XX-117


title: HP1601201T2D_I20


title: HP1714601_G20


title: HP1711701T2D_A6


title: 2393-XX-116

description: Library name: 2393-XX-116


title: 2393-XX-115

description: Library name: 2393-XX-115


title: HP1711701T2D_D2


title: 2393-XX-114

description: Library name: 2393-XX-114


title: HP1601201T2D_B16


title: HP1714601_B16


title: HP1714601_K3


title: HP1711001_K6


title: 2393-XX-112

description: Library name: 2393-XX-112


title: HP1605601T2D_O4


title: HP1525901_E15


title: 2393-XX-124

description: Library name: 2393-XX-124


title: 2393-XX-131

description: Library name: 2393-XX-131


title: 2393-XX-111

description: Library name: 2393-XX-111


title: HP1525401_F19


title: HP1714601_H12


title: 2393-XX-110

description: Library name: 2393-XX-110


title: HP1525901_G17


title: 2393-XX-109

description: Library name: 2393-XX-109


title: HP1605601T2D_E16


title: HP1711001_B15


title: 2393-XX-108

description: Library name: 2393-XX-108


title: Oxidized guanines, WT U2OS, GSK-3484862, Biol Rep3

city: Zurich

first: Shana

last: Sturla

address: Schmelzbergstrasse 9

department: Department of Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

description: Library name: OG_U2OS_GSK-3484862_Rep3

library_source: genomic

data_processing:
After demultiplexing of sequencing data, each sample was represented by a fastq.gz file containing 101-nucleotide-long genomic reads. The quality of the raw sequencing data was checked via FastQC version 0.12.1. Low-quality reads and adapter-containing reads were removed via trimmomatic version 0.39. We retained only those reads that contained a validation code (VC). The first 17 nucleotides corresponding to VC and randomized index code (RIC) were clipped from the read sequences and appended to the read names via the tool extract of umi_tools toolkit version 1.1.4. In case of samples from cells, reads were mapped to human reference genome GRCh38 via bowtie2 version 2.5.1, using pre-built bowtie2 index from https://genome-idx.s3.amazonaws.com/bt/GRCh38_noalt_as.zip, and applying otherwise standard settings. In case of samples originating from plasmids, we built bowtie2 indexes for three plasmids, namely, i) input plasmid (vector), ii) plasmid with triple 8-oxoG insert, 8-oxoG represented by G, and iii) plasmid with triple U insert, U represented by T (triple insert explained in the article's Extended Data Fig. 2g); the plasmid sequences were flanked by 100 nucleotides to mimic circular structure in read alignment; these indexes were used to map reads via bowtie2 2.5.1. Read duplicates were removed by the tool dedup of umi_tools toolkit version 1.1.4, grouping reads with the same code sequence stored in the read name (method=unique). Samtools version 1.17 were employed to sort, index and generate statistics of bam files. bedtools2 version 2.31.0 were used to retrieve the coordinates of mapped and deduplicated reads and extract the sequence context of DNA modifications from the reference genome. Each read represented one unit of DNA-modification signal, which we positioned at the nucleotide of the 5’ end of the read. Since a read was the reverse complement of the DNA fragment captured in the method employing MoDIS, the strand of the nucleotide bearing the signal was changed to the opposite one. We implemented the described DNA-modification-signal positioning via custom scripts in Python version 3.11.6 [GCC 12.2.0] with modules numpy version 1.25.2, pandas version 2.2.2 and biopython version 1.83.
Library strategy: click-code-seq
Assembly: GRCh38
Supplementary files format and content: In the provided sample-specific tsv-files, each line reflects one DNA modification revealed by one mapped read. The tsv-files contain the following columns: 1) the chromosome, 2) the 0-based coordinate, 3) the strand, 4) the nucleotide bearing the signal, 5) MAPQ score of the read.

molecule: genomic DNA

growth_protocol: HAP1 cells (RRID:CVCL_Y019, Horizon Discovery) were cultivated in Iscove's Modified Dulbecco's Medium supplemented with 10% fetal bovine serum (Gibco) and 1% penicillin-streptomycin (Gibco). U2OS cells (RRID:CVCL_0042) were cultivated in McCoy‘s general cell culture medium, modified with high glucose, L-glutamate, bacto-peptone and phenol red, and lacking sodium pyruvate and HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) (McCoy‘s 5A, Gibco 16600082), supplemented with 10% fetal bovine serum (Gibco) and 1% penicillin-streptomycin (Gibco). 10 mL of cell culture medium was supplemented by 4 μL GSK-3484862 (MedChemExpress, 10 mM dissolved in DMSO) (final concentration 4 μM). Control medium was prepared by adding 4 μL of DMSO to 10 mL of cell culture medium. The treatment and control media were filtered with a sterile syringe filter (0.22 μm) and added to the cells, followed by 72-h incubation at 37 °C, 5% CO2, 3% O2, with the treatment and control media being refreshed after every 24 hours. In case of plasmid samples: plasmids containing site-specific 8-oxoG and uracil were constructed by inserting double-stranded oligonucleotides into a 4.7-Kbp plasmid vector via a restriction-ligation strategy. The plasmid pEGFP-W, derived from pEGFP-N1 (Addgene, Catalog Number 6085-1), was purified from BL21 (DE3) E. coli (NEB) using a Qiagen plasmid maxi prep kit (Qiagen, USA) and digested with BamHI-HF (NEB) and HindIII-HF (NEB) restriction enzymes, generating sticky ends for subsequent ligation.

extract_protocol:
In case of HAP1 and U2OS, cells were harvested by removing the medium, washing once with 10 mL DPBS followed by addition of 1 mL 0.25% Trypsin EDTA solution (Gibco). After an incubation of 5 min at 37°C, 9 mL medium was added, cells resuspended and transferred to a Falcon centrifugal tube. Cells were centrifuged (4°C, 0.3 rcf, 5 min) and the supernatant removed. gDNA was extracted from  cell pellets using the Monarch Genomic DNA Extraction Kit following the manufacturer’s instructions. In order to avoid artefactual oxidation, DPBS used in the cell pellet resuspension  was supplemented with 1 mM deferoxamine and 50 µM n-tert-butyl-α-phenylnitrone. In case of the plasmid samples, the input plasmid vector pEGFP-W, derived from pEGFP-N1 (Addgene, Catalog Number 6085-1), was purified from BL21 (DE3) E. coli (NEB) using a Qiagen plasmid maxi prep kit (Qiagen, USA).
To minimize artefactual damage, samples were inverted or flicked, instead of pipette mixing, until the CuAAC step. For DNA oxidation mapping, gDNA was eluted in H2O supplemented with 500 µM 8-hydroxyquinoline (HQ; Sigma) after extraction and purification. Undesired background modifications were blocked by adding 1 µL ENDOIV (NEB, 10 U/µL) and 500 µM 8-HQ to 5 µg of gDNA, freshly extracted from HAP1 pellets, in 1x ThermoPol Buffer (NEB) in a final volume of 20 µL, and incubating the mixture for 20 min at 37°C. 2.5 µL ddNTP mix (Jena Biosciences, 2.5 mM), 0.5 µL 10x ThermoPol Buffer, 1.8 µL of 8-HQ (500 µM) and 0.2 µL Therminator IX (NEB, 10 U/µL) were added, followed by a 10 min incubation at 60°C. 25 µL 8-HQ (500 µM) and 80 µL Pronex® beads were added for purification with an elution volume of 25 µL. To label oxidative modifications, 1 µL FPG (NEB, 8 U/µL), 1 µL ENDOIV (NEB, 10 U/µL) and 3 µL 10x NEBuffer 2 (NEB) were added for a final volume of 30 µL; the reaction mixture was incubated for 1 h at 37°C, immediately followed by adding 3.5 µL prop-dGTP (Jena Biosciences, 2.5 mM), 0.5 µL 10x NEBuffer 2 (NEB), 0.8 µL 8-HQ (500 µM) and 0.2 µL Therminator IX (NEB 10 U/µL) for 10-min incubation at 60°C. As for the plasmid DNA, each modified plasmid was separately spiked into 2 µg of the original pEGFP-W plasmid and subjected to these same initial steps. In the case of the uracil-modified plasmid, UDG (NEB, 5 U/µL) was used instead of FPG to excise the uracil base, and prop-dTTP (Jena Biosciences, 2.5 mM) was used instead of prop-dGTP. Two control samples containing 2 µg of unmodified pEGFP-W plasmid were processed under identical conditions with either FPG and prop-dGTP or UDG and prop-dTTP. Steps for mapping either AP sites or oxidative damage, both for gDNA and plasmid DNA, are identical from this point onwards. DNA was purified using Pronex® Magnetic Beads (Promega) with a sample:bead ratio of 50:80 and using an elution volume of 50 µL with Buffer EB. Sonication of DNA was performed using a Q800R2 sonicator (QSonica) with the following settings: 4°C, 20% amplitude, pulse 15 s on, 5 s off, total 5 min for gDNA and 4 min for plasmid DNA. The resulting DNA fragments were analyzed on a Tapestation 2200 using a High Sensitivity D100 ScreenTape (Agilent Technologies). DNA was purified using Pronex® beads with a sample:beads ratio of 1:2 and 50 µL elution volume. Samples were quantified using a Quantus™ Fluorometer. For adapter ligation, NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB) was utilized using either 1 µg of gDNA or the remaining plasmid DNA and the pre-annealed NEB adapter (NEB_P7, NEB_P5, 15 µM; Supplementary Table 1). The manufacturer’s instruction was followed without performing the USER enzyme step. The sample was purified using Pronex® beads in sample:beads ratio 1:2 and elution in 50 µL Buffer EB. Successful adapter ligation was checked on an Agilent TapeStation with a High Sensitivity D100 ScreenTape. The sample volume was then condensed to 6 µL using a vacuum concentrator. To denature DNA, the sample was heated to 95°C for 2 min and rapidly cooled on ice. CuAAC reaction was performed using 2 µL MoDIS (100 µM equimolar mixture of MoDIS_1 and MoDIS_2; Supplementary Table 1), 4 µL DMSO, 2 µL premixed CuSO4:THPTA (THPTA from Lumiprobe; 20 mM Cu2+ and 200 mM THPTA) and 2 µL sodium phosphate buffer (1 M, pH 7.0). The reaction was started by adding 2 µL sodium ascorbate (400 mM in H2O, freshly prepared) and incubated for 60 min at 37°C. Purification was done using Pronex® beads in a sample:beads ratio 1:2 and 30 µL elution volume. Biotin enrichment of sample DNA was performed using Dynabeads™ MyOne™ Streptavidin C1 (ThermoFisher). First, B&W buffer was prepared according to the manufacturer’s protocol including 0.05 % Tween™ 20. Then, 15 µL Dynabeads™ were transferred to a fresh tube, washed three times with 200 µL 1x B&W buffer and resuspended in 30 µL 2x B&W buffer. The DNA sample was denatured by heating to 95°C for 2 min and rapid cooling on ice. Then, 30 µL sample was mixed with 30 µL of the prepared Dynabeads™ and rotated for 15 min at RT. Afterwards, the Dynabeads™ were washed 3x with 1x B&W buffer by resuspending the beads, 3 min rotation and 1 min pelleting on a magnetic rack. A final wash was performed with Buffer EB and Dynabeads™ were resuspended in 20 µL Buffer EB. To amplify the biotin-enriched material, a PCR was performed by adding 5 µL 10x ThermoPol buffer, 5 µL dNTP mix (NEB, 2 mM), 1 µL MgSO4 (100 mM), 1 µL ex_UMI (10 µM; Supplementary Table 1), 1 µL Pr_P7 (10 µM; Supplementary Table 1) and 0.5 µL Vent (exo-) DNA Polymerase (NEB 2 U/µL). The PCR program comprised an initial denaturation step (95°C, 120 s), followed by 5 cycles of denaturation (95°C, 20 s), annealing (59°C, 20 s) and elongation (72°C, 60 s) and a final elongation step (72°C, 300 s). The sample was purified with Pronex® beads in a sample:beads ratio 1:2 and an elution volume of 30 µL. Final library amplification and indexing was performed by adding 25 µL NEBNext® Ultra™ II Q5® Master Mix (NEB), 2.5 µL i5_Index (10 µM; Supplementary Table 1) and 2.5 µL i7_Index (10 µM; Supplementary Table 1) to 20 µL sample. The PCR program comprised an initial denaturation step (98°C, 30 s), 10 cycles of denaturation (98°C, 10 s), annealing (68°C, 30 s) and elongation (72°C, 20 s), and a final elongation step (72°C, 120 s). The same PCR setup can be used for a precedent qPCR by adding a qPCR dye as Evagreen (Biotium) to test for successful sample amplification. The PCR sample was purified with the Pronex® beads dual size selection protocol using an initial sample:beads ratio of 1:1, followed by a sample:beads ratio of 0.5:1 to exclude fragments longer than 1000 bp and shorter than 250 bp. The final sample concentration was adjusted to a concentration of 4 ng/µL and sequenced on an Illumina NovaSeq 6000.

treatment_protocol: In case of DNMT1 inhibition experiment: 10 mL of cell culture medium was supplemented by 4 μL GSK-3484862 (MedChemExpress, 10 mM dissolved in DMSO) (final concentration 4 μM); control medium was prepared by adding 4 μL of DMSO to 10 mL of cell culture medium. In case of plasmid samples, 8-oxoG-inserted plasmid was mixed with the input vecor, and the mixture was treated with FPG to recognize oxidized guanines (as in the DNMT1-inhbition samples within the click-code-seq protocol). For the uracil-modified plasmid, UDG (NEB, 5 U/µL) was used instead of FPG to excise the uracil base. Two control samples containing 2 µg of unmodified pEGFP-W plasmid were processed under identical conditions with either FPG or UDG.

tag: cell line

tag: genotype

value: wild type


title: HP1711701T2D_B22


title: Oxidized guanines, WT U2OS, GSK-3484862, Biol Rep2

description: Library name: OG_U2OS_GSK-3484862_Rep2


title: Oxidized guanines, WT U2OS, DMSO, Biol Rep3

description: Library name: OG_U2OS_DMSO_Rep3

value: DMSO


title: HP1601201T2D_J24


title: Oxidized guanines, WT U2OS, GSK-3484862, Biol Rep1

description: Library name: OG_U2OS_GSK-3484862_Rep1


title: HP1714601_G16


title: Oxidized guanines, WT U2OS, DMSO, Biol Rep2

description: Library name: OG_U2OS_DMSO_Rep2


title: 2393-XX-113

description: Library name: 2393-XX-113


title: Oxidized guanines, WT U2OS, DMSO, Biol Rep1

description: Library name: OG_U2OS_DMSO_Rep1


title: HP1714601_E7


title: Oxidized guanines, WT HAP1, GSK-3484862, Biol Rep2

description: Library name: OG_HAP1_GSK-3484862_Rep2


title: HP1602301T2D_F12


title: Oxidized guanines, WT HAP1, GSK-3484862, Biol Rep1

description: Library name: OG_HAP1_GSK-3484862_Rep1


title: HP1602301T2D_K21


title: Oxidized guanines, WT HAP1, DMSO, Biol Rep2

description: Library name: OG_HAP1_DMSO_Rep2


title: Oxidized guanines, WT HAP1, DMSO, Biol Rep3

description: Library name: OG_HAP1_DMSO_Rep3


title: HP1605601T2D_D5


title: HP1711001_A17


title: Oxidized guanines, WT HAP1, DMSO, Biol Rep1

description: Library name: OG_HAP1_DMSO_Rep1


title: MDA-HepG2 JQ1_3

city: Chengdu

first: Yumei

last: Wang

address: 1166 LiuTai

country: China

institute: Chengdu University of TCM

description:
Library name: sample12
Gene expression data from HepG2 cells treated with JQ1

data_processing:
The clean data obtained from bulk RNA-seq were aligned to the reference genome (GRCh38) using Hisat2, and reads corresponding to each gene were quantified using HTSeq.
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

source_name: cell line

growth_protocol: MDA-MB-231and HepG2 cells were cultured in RPMI1640 medium (Gibco, C11875500BT, USA). All mediums were supplemented with 10% fetal calf serum (ExCell, FSP500, China) and 100 units/ml streptomycin and penicillin. All cells were cultured at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA extraction was carried out using the RNA isolator Total RNA Extraction Reagent (Vazyme, R401-01, China) in accordance with the manufacturer's instructions.
Sequencing libraries were prepared using TruSeq Stranded Total RNA Library Prep Human kits (Illumina 20020596)

treatment_protocol: MDA-MB-231 and HepG2 cells were treated with 0.1% DMSO or 10 μM JQ1 for 24 hours.

value: cell line

value: tumor cells

value: WT


title: HP1711701T2D_L5


title: HP1711701T2D_M17


title: MDA-HepG2 JQ1_1

description:
Library name: sample10
Gene expression data from HepG2 cells treated with JQ1


title: HP1605601T2D_P21


title: HP1711001_B7


title: HP1605601T2D_K21


title: MDA-MB-231JQ1_2

description:
Library name: sample5
Gene expression data from MDA-MB-231 cells treated with JQ1


title: HP1525901_M20


title: MDA-MB-231JQ1_3

description:
Library name: sample6
Gene expression data from MDA-MB-231 cells treated with JQ1


title: HP1601201T2D_C16


title: MDA-HepG2 Control_1

description:
Library name: sample7
Gene expression data from HepG2 cells treated with DMSO


title: HP1602301T2D_O2


title: Oxidized guanines, WT HAP1, GSK-3484862, Biol Rep3

description: Library name: OG_HAP1_GSK-3484862_Rep3


title: HP1605601T2D_H22


title: HP1602301T2D_J5


title: HP1525901_B19


title: HP1525401_L5


title: MDA-MB-231JQ1_1

description:
Library name: sample4
Gene expression data from MDA-MB-231 cells treated with JQ1


title: MDA-MB-231 Control_2

description:
Library name: sample2
Gene expression data from MDA-MB-231 cells treated with DMSO


title: HP1714601_K21


title: MDA-MB-231 Control_1

description:
Library name: sample1
Gene expression data from MDA-MB-231 cells treated with DMSO


title: HP1714601_J13


title: MDA-MB-231 Control_3

description:
Library name: sample3
Gene expression data from MDA-MB-231 cells treated with DMSO


title: HP1602301T2D_B8


title: MDA-HepG2 JQ1_2

description:
Library name: sample11
Gene expression data from HepG2 cells treated with JQ1


title: WES of STA-ET-1 (p54)

city: Essen

first: Maximilian

last: Kerkhoff

address: Hufelandstrasse 55

department: Pediatrics III

country: Germany

institute: University Hospital Essen

description: Library name: STA-ET-1 p54 wxs

data_processing:
Raw data was processed by using the snakemake pipeline “varlociraptor”. We utilized a single sample germline scenario (due to the lack of normal control) and treated every sample independently for variant calling. For more information, please see varlociraptor documentation.
Assembly: GRCh38
Supplementary files format and content: tsv files with variants and mutations in coding and non-coding sequences. Output from varlociraptor pipeline.

growth_protocol: Cells were grown in DMEM (high glucose, pyruvate)+ 10% FBS in rat collagen (6mg/mL) coated T25 flasks in a ratio of 6000 cells/cm^2 for 96h

extract_protocol:
Cells got a media exchange after 48h, were washed after 96h with 1xPBS and then harvested in 200µL Buffer T1 for DNA extraction
Library construction was performed with the kits SureSelect XT HS 2 and SureSelect Human All Exon V7 according to the manufacturers instructions

value: Ewing sarcoma

tag: batch


title: WES of SK-N-MC (p15)

description: Library name: SK-N-MC p15 wxs

source_name: SK-N-MC

value: SK-N-MC


title: HP1711001_D12


title: HP1606401T2D_Tn5_F17


title: MDA-HepG2 Control_3

description:
Library name: sample9
Gene expression data from HepG2 cells treated with DMSO


title: MDA-HepG2 Control_2

description:
Library name: sample8
Gene expression data from HepG2 cells treated with DMSO


title: HP1605601T2D_G20


title: WES of C-ES-Y (p55)

description: Library name: C-ES-Y p55 wxs

source_name: C-ES-Y

value: C-ES-Y


title: HP1605601T2D_E11


title: HP1714601_O12


title: WES of C-ES-P (p17)

description: Library name: C-ES-P p17 wxs

source_name: C-ES-P

value: C-ES-P


title: WES of C-ES-Y (p10)

description: Library name: C-ES-Y p10 wxs


title: HP1602301T2D_E20


title: HP1601201T2D_P9


title: WES of C-ES-M (p53)

description: Library name: C-ES-M p53 wxs

source_name: C-ES-M

value: C-ES-M


title: WES of C-ES-M (p11)

description: Library name: C-ES-M p11 wxs


title: HP1525401_A2


title: HP1605601T2D_B23


title: HP1605601T2D_B15


title: WGS of SK-N-MC (p15)

description: Library name: SK-N-MC p15 wgs

data_processing:
Raw data was preprocessed using the snakemake pipeline “varlociraptor” until the function “apply_bqsr” to generate bam files. For further info see varlociraptor documentation
Bam files were used as input for the copy number variation analysis pipelines “cnvkit” to generate cns files. For further info, see cnvkit documentation
Assembly: GRCh38
Supplementary files format and content: cns file (see cnvkit documentation)
Supplementary files format and content: cnr file (see cnvkit documentation)

extract_protocol:
Cells got a media exchange after 48h, were washed after 96h with 1xPBS and then harvested in 200µL Buffer T1 for DNA extraction
Library construction was performed with the kit SureSelect XT HS 2 according to the manufacturers instructions


title: HP1525401_C11


title: WES of C-ES-I (p53)

description: Library name: C-ES-I p53 wxs

source_name: C-ES-I

value: C-ES-I


title: HP1711001_L24


title: WGS of STA-ET-1 (p22)

description: Library name: STA-ET-1 p22 wgs


title: HP1606401T2D_Tn5_H19


title: WES of STA-ET-1 (p22)

description: Library name: STA-ET-1 p22 wxs


title: WGS of C-ES-Y (p55)

description: Library name: C-ES-Y p55 wgs


title: HP1525401_F4


title: HP1711701T2D_E8


title: WGS of C-ES-Y (p10)

description: Library name: C-ES-Y p10 wgs


title: WGS of C-ES-P (p54)

description: Library name: C-ES-P p54 wgs


title: HP1711701T2D_H14


title: WGS of C-ES-P (p17)

description: Library name: C-ES-P p17 wgs


title: HP1525901_I7


title: HP1525401_D23


title: WES of C-ES-P (p54)

description: Library name: C-ES-P p54 wxs


title: HP1711001_E9


title: WGS of C-ES-M (p53)

description: Library name: C-ES-M p53 wgs


title: WGS of C-ES-M (p11)

description: Library name: C-ES-M p11 wgs


title: HP1602301T2D_F15


title: HP1711001_P20


title: HP1601201T2D_I24


title: WES of C-ES-I (p13)

description: Library name: C-ES-I p13 wxs


title: WGS of STA-ET-1 (p54)

description: Library name: STA-ET-1 p54 wgs


title: WGS of C-ES-I (p13)

description: Library name: C-ES-I p13 wgs


title: 230112-7-3_N

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

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

description: Library name: GA51950

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 151+151-base paired-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: blood

extract_protocol:
Total RNA was extracted from cells with a miRNeasy Micro kit (Qiagen) following the manufacturer’s instruction.
Full-length cDNA was prepared using a SMART-Seq HT Kit (Takara Bio, Japan). According to the SMART-Seq kit instructions, an Illumina library was then prepared using a NexteraXT DNA Library Preparation Kit (Illumina).

value: blood

value: pbmc

tag: type


title: HP1606401T2D_Tn5_A3

value: Pancreatic islets


title: 230112-6-3_N

description: Library name: GA51947


title: HP1714601_C12

value: Healthy


title: HP1602301T2D_J23


title: 230112-7-1_C

description: Library name: GA51948

value: classical


title: 230112-7-2_I

description: Library name: GA51949

value: intermediate


title: 230112-6-2_I

description: Library name: GA51946


title: HP1711701T2D_E23


title: HP1711001_O16


title: HP1606401T2D_Tn5_O15


title: HP1601201T2D_M18


title: 230112-5-3_N

description: Library name: GA51944


title: 230112-5-2_I

description: Library name: GA51943


title: HP1601201T2D_M7


title: 230112-6-1_C

description: Library name: GA51945


title: HP1711701T2D_L16


title: 230112-3-3_N

description: Library name: GA51941


title: WGS of C-ES-I (p53)

description: Library name: C-ES-I p53 wgs


title: HP1602301T2D_A5


title: 230112-3-2_I

description: Library name: GA51940


title: 230112-3-1_C

description: Library name: GA51939


title: HP1711701T2D_N5


title: 230112-2-3_N

description: Library name: GA51938


title: 230112-2-2_I

description: Library name: GA51937


title: HP1525901_M11


title: HP1711001_I11


title: HP1606401T2D_Tn5_G19


title: HP1601201T2D_G20


title: 230112-1-2_I

description: Library name: GA51934


title: HP1605601T2D_I13


title: 230112-1-1_C

description: Library name: GA51933


title: 230112-1-3_N

description: Library name: GA51935


title: HP1602301T2D_C19


title: HP1605601T2D_P13


title: 230112-5-1_C

description: Library name: GA51942


title: HP1711001_J3


title: HP1601201T2D_I4


title: HP1606401T2D_Tn5_H20


title: 221014-3-3_CD14

description: Library name: GA46981


title: 221014-4-1_CD4

description: Library name: GA46982


title: 221014-4-3_CD14

description: Library name: GA46984


title: HP1525401_L16


title: 221014-3-2_CD8

description: Library name: GA46980


title: HP1601201T2D_D12


title: 230112-2-1_C

description: Library name: GA51936


title: mESC, H3K9me3, Rep1

city: Rochester

first: Patrick

middle: J

last: Murphy

state: New York

address: 601 Elmwood Avenue

department: Biomedical Genetics and Genomics

institute: University of Rochester

description:
Library name: H3K9me3_rep1_mESC
mESC, H3K9me3, Rep1

data_processing:
cutAdapt was used on all raw fastq files, and then each was mapped with bowtie2 using mm10.
PICARD MergeSamFiles was used to convert files to BAM files, and PICARD MarkDuplicates was used to remove duplicate reads.
bigWig files were made with deeptools BAMcoverage  --normalizeUsing RPKM --binSize 10 --extendReads 100.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

organism: Mus musculus

source_name: mouse embyronic stem cell

growth_protocol: mESCs were purchased from ATCC (cat. #SCRC-1002) and cultured on mitomycin C-inactivated MEFs at 37°C. Mitomycin C-inactivated MEFs were grown on 0.1% gelatin-coated plates for 1 day prior to mESC seeding.  mESCs were grown in KO DMEM supplemented with 15% KO Serum Replacement, 1% Gluta-MAX, 1% NEAA, 0.1% LIF, and 0.1% β-mercaptoethanol.

extract_protocol:
mESCs were harvested with trypsin and processed using the standard CUT&Tag (Kaya-Okur et al. Nat. Comm. 2019. and https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3) protocol.
Libraries were prepared for sequencing using standard CUT&Tag (Kaya-Okur et al. Nat. Comm. 2019. and https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3) protocols. i5 and i7 sequencing adaptors were added to isolated DNA via PCR.

value: mouse embyronic stem cell


title: mESC, H3K9me3, Rep2

description:
Library name: H3K9me3_rep2_mESC
mESC, H3K9me3, Rep2


title: mESC, H3K9me3, Rep3

description:
Library name: H3K9me3_rep3_mESC
mESC, H3K9me3, Rep3


title: HP1711001_J14


title: HP1525401_G19


title: 221014-2-2_CD8

description: Library name: GA46977


title: MDA-MB-231, Shikonin 3

city: Xi'an

first: wen

last: liu

address: New temple Road num 1

institute: Tangdu Hospital of Air Force Medical University

data_processing:
Raw data (raw reads) in fastg format were processed by fastp software. In this step, clean data (clean reads) is obtained by removing the read data containing the adapter
Hisat2 v2.0.5 was used as the index of the reference genome, and the reference genome was aligned with Hisat2 v2.0.5
The reads number of each gene was concont using featurests v1.5.0-p3. FPKM was then calculated for each gene based on the length of the gene and the number of reads mapped to the gene
Differential expression analysis of two coiditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (.20.0).
The clusterProfiler R package was used to perform Gene Ontology (GO) enrichment analysis of differentially expressed genes
Assembly: hg38
Supplementary files format and content: baseMean,log2FoldChange

growth_protocol: MDA-MB-231 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% Penicillin-Streptomycin Solution and incubator environment was 37°C, 5% CO2, 95% O2

extract_protocol:
Total RNA was extracted with chloroform, and isopropanol and washed with 95% ethanol
RNA-seq libraries were prepared using the NEBNext Ultra RNA Library Preparation kit for illumina according to the manufacturer's protocol

treatment_protocol: MDA-MB-231 cells were treated with 0.5μm shikonin for 24h, then collected cells and dissolved in Trizol

value: triple-negative breast cancer cells

value: shikonin


title: MDA-MB-231, Shikonin 2


title: HP1525901_I13


title: 221014-3-1_CD4

description: Library name: GA46979


title: MDA-MB-231, Shikonin 1


title: MDA-MB-231, Control 3


title: HP1711001_C1


title: 221014-1-3_CD14

description: Library name: GA46975


title: MDA-MB-231, Control 2


title: 221014-4-2_CD8

description: Library name: GA46983


title: MDA-MB-231, Control 1


title: 221014-1-2_CD8

description: Library name: GA46974


title: HP1711001_D10


title: CD11b_2331_Control

city: Lille cedex

first: David

last: Blum

address: 1, Place de Verdun

country: France

institute: Inserm UMR-S1172

description:
Library name: DDBM319
S21058_RawReadCounts_microglie.txt

data_processing:
Image analysis and base calling were performed using RTA and bcl2fastq.
Reads were preprocessed in order to remove adapter, polyA and low-quality sequences (Phred quality score below 20). After this preprocessing, reads shorter than 40 bases were discarded for further analysis. These preprocessing steps were performed using cutadapt version 1.10. Reads were mapped onto the mm10 assembly of Mus musculus genome using STAR version 2.5.3. Gene expression quantification was performed from uniquely aligned reads using htseq-count version 0.6.1p1, with annotations from Ensembl version 102 and “union” mode.
Assembly: mm10
Supplementary files format and content: Tab-separated text file with raw read counts per Ensembl Gene.

molecule: polyA RNA

source_name: Hippocampus

extract_protocol:
mRNAs from microgli-enriched suspensions were extracted using CD11b-magnetic microbeads following astrocyte enrichement after ACSA2 magnetic microbeads
Full length cDNAs were generated from 500 pg to 1ng of total RNA using SMART-SeqX v4 UltraX Low Input RNA Kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq-Amp polymerase. 600 pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, USA) followed by 12 cycles of library amplification. Following purification with SPRIselect beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.

value: Hippocampus

value: Microglie


title: CD11b_2329_Control

description:
Library name: DDBM317
S21058_RawReadCounts_microglie.txt


title: 221014-1-1_CD4

description: Library name: GA46973


title: CD11b_2328_Control

description:
Library name: DDBM316
S21058_RawReadCounts_microglie.txt


title: 221014-2-3_CD14

description: Library name: GA46978


title: CD11b_2347_A2AR

description:
Library name: DDBM325
S21058_RawReadCounts_microglie.txt


title: HP1601201T2D_J22


title: CD11b_2343_A2AR

description:
Library name: DDBM321
S21058_RawReadCounts_microglie.txt


title: HEK-293 cells, LINC00324 1xpA, clone 1

city: Toronto

first: Philipp

last: Maass

state: Ontario

address: 686 Bay St

department: Genetics and Genome Biology

country: Canada

institute: The Hospital for Sick Children

description: Library name: Sample 5

data_processing:
We aligned reads to hg38 using STAR aligner, version 2.7.0.63
We used FeatureCounts to count reads aligning to genes in GENCODE v41 (human).64
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: kidney; embryo

growth_protocol: See methods of this paper, and Maass et al Nat Gen 2015.

extract_protocol:
We extracted total RNA from cells using the phenol-chloroform extraction method according to standard protocols.
For RNA-sequencing, we depleted rRNA with the RiboZero rRNA removal kit (Illumina), and prepared RNAseq libraries using the TruSeq RNA Library Prep kit v2 (Illumina).

value: kidney; embryo

value: embryonic kidney cells

value: LINC00324 polya signal insertion


title: 313_A2A

extract_protocol:
mRNAs from astrocyte-enriched suspensions were extracted as described previously (Batiuk et al., 2017).
Full length cDNAs were generated from 500 pg to 1ng of total RNA using SMART-SeqX v4 UltraX Low Input RNA Kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq-Amp polymerase. 600 pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, USA) followed by 12 cycles of library amplification. Following purification with SPRIselect beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.

value: Astrocytes


title: HEK-293 cells, LINC02042 KO, clone 2

description: Library name: Sample 4

value: LINC02042 knockout


title: HEK-293 cells, LINC02042 KO, clone 1

description: Library name: Sample 3


title: 310_A2A


title: 309_A2A


title: HP1601201T2D_B15


title: 307_GFP


title: HP1602301T2D_L1


title: HEK-293 cells, LINC01970 KO, clone 2

description: Library name: Sample 2

value: LINC01970 knockout


title: 306_GFP


title: HEK-293 cells, LINC01970 KO, clone 1

description: Library name: Sample 1


title: 221014-2-1_CD4

description: Library name: GA46976

value: blood


title: 303_GFP


title: HP1711001_F10


title: primary MSCs, female, rep 2, 14d

description:
MSC.GENCODEv41.counts.gene.consensus.txt
MSC.GENCODEv41.RPKM.gene.consensus.txt
MSC_F_rep2_14d

source_name: lipoaspirates

value: lipoaspirates

value: mesenchymal stem cells

value: chondrogenic differentiation


title: CD11b_2344_A2AR

description:
Library name: DDBM322
S21058_RawReadCounts_microglie.txt


title: HP1605601T2D_E21

value: Pancreatic islets


title: HP1525401_C8

value: Healthy


title: HP1711701T2D_O23


title: primary MSCs, female, rep 2, 7d

description:
MSC.GENCODEv41.counts.gene.consensus.txt
MSC.GENCODEv41.RPKM.gene.consensus.txt
MSC_F_rep2_7d


title: HP1711001_M9


title: primary MSCs, female, rep 2, 3d

description:
MSC.GENCODEv41.counts.gene.consensus.txt
MSC.GENCODEv41.RPKM.gene.consensus.txt
MSC_F_rep2_3d


title: primary MSCs, female, rep 2, 1d

description:
MSC.GENCODEv41.counts.gene.consensus.txt
MSC.GENCODEv41.RPKM.gene.consensus.txt
MSC_F_rep2_1d


title: primary MSCs, female, rep 2, 0d

description:
MSC.GENCODEv41.counts.gene.consensus.txt
MSC.GENCODEv41.RPKM.gene.consensus.txt
MSC_F_rep2_0d


title: 954 siID3-2

city: Chicago

first: Han

last: Peng

state: IL

address: 303 E Chicago Ave, Ward 9-120

institute: Feinberg School of Medicine, Northwestern University

data_processing:
follow the protocol from manufacturer
Assembly: hg38
Supplementary files format and content: excel

extract_protocol:
HLECs were transfected with a 20 nM siRNA pool against ID3 (Invitrogen, Carlsbad, CA, USA) or nontarget control (Invitrogen, Carlsbad, CA, USA) as previously described for 3 days. Then, cells were processed for total RNA isolation using miRNeasy kit (Qiagen, Hilden, Germany). Expression profiling was conducted using a Next-Generation Sequencing platform at Northwestern University Center for Genetic Medicine core. Gene differential expression profiles obtained from RNA-seq analysis were subjected to gene ontology analysis using DAVID.
follow the instructions from manufacturer


title: HP1714601_H23


title: 132 siID3-1


title: primary MSCs, female, rep 1, 14d

description:
MSC.GENCODEv41.counts.gene.consensus.txt
MSC.GENCODEv41.RPKM.gene.consensus.txt
MSC_F_rep1_14d


title: 16160 sicontrol3


title: primary MSCs, female, rep 1, 7d

description:
MSC.GENCODEv41.counts.gene.consensus.txt
MSC.GENCODEv41.RPKM.gene.consensus.txt
MSC_F_rep1_7d


title: primary MSCs, female, rep 1, 3d

description:
MSC.GENCODEv41.counts.gene.consensus.txt
MSC.GENCODEv41.RPKM.gene.consensus.txt
MSC_F_rep1_3d


title: HP1601201T2D_J3


title: primary MSCs, female, rep 1, 1d

description:
MSC.GENCODEv41.counts.gene.consensus.txt
MSC.GENCODEv41.RPKM.gene.consensus.txt
MSC_F_rep1_1d


title: HP1714601_D20


title: primary MSCs, female, rep 1, 0d

description:
MSC.GENCODEv41.counts.gene.consensus.txt
MSC.GENCODEv41.RPKM.gene.consensus.txt
MSC_F_rep1_0d


title: primary MSCs, male, rep 2, 14d

description:
MSC.GENCODEv41.counts.gene.consensus.txt
MSC.GENCODEv41.RPKM.gene.consensus.txt
MSC_M_rep2_14d


title: HP1525401_A3


title: 954 sicontrol2


title: primary MSCs, male, rep 2, 7d

description:
MSC.GENCODEv41.counts.gene.consensus.txt
MSC.GENCODEv41.RPKM.gene.consensus.txt
MSC_M_rep2_7d


title: HP1602301T2D_J21


title: primary MSCs, male, rep 2, 3d

description:
MSC.GENCODEv41.counts.gene.consensus.txt
MSC.GENCODEv41.RPKM.gene.consensus.txt
MSC_M_rep2_3d


title: HEK-293 cells, ENSG00000287264 KO, clone 2

description:
HEK.GENCODEv41.counts.gene.consensus.txt
HEK.GENCODEv41.RPKM.gene.consensus.txt
HEK.GENCODEv41.counts.transcript.consensus.txt
HEK.GENCODEv41.RPKM.transcript.consensus.txt
HEK293_ENSG00000287264_KO_c2

value: ENSG00000287264 knockout


title: primary MSCs, male, rep 2, 1d

description:
MSC.GENCODEv41.counts.gene.consensus.txt
MSC.GENCODEv41.RPKM.gene.consensus.txt
MSC_M_rep2_1d


title: 132 sicontrol1


title: primary MSCs, male, rep 2, 0d

description:
MSC.GENCODEv41.counts.gene.consensus.txt
MSC.GENCODEv41.RPKM.gene.consensus.txt
MSC_M_rep2_0d


title: primary MSCs, male, rep 1, 14d

description:
MSC.GENCODEv41.counts.gene.consensus.txt
MSC.GENCODEv41.RPKM.gene.consensus.txt
MSC_M_rep1_14d


title: primary MSCs, male, rep 1, 3d

description:
MSC.GENCODEv41.counts.gene.consensus.txt
MSC.GENCODEv41.RPKM.gene.consensus.txt
MSC_M_rep1_3d


title: HP1525401_G24


title: HEK-293 cells, ENSG00000284607 KO, clone 2

description:
HEK.GENCODEv41.counts.gene.consensus.txt
HEK.GENCODEv41.RPKM.gene.consensus.txt
HEK.GENCODEv41.counts.transcript.consensus.txt
HEK.GENCODEv41.RPKM.transcript.consensus.txt
HEK293_ENSG00000284607_KO_c2

value: ENSG00000284607 knockout


title: HP1711001_L22


title: 16160 siID3-3


title: primary MSCs, male, rep 1, 1d

description:
MSC.GENCODEv41.counts.gene.consensus.txt
MSC.GENCODEv41.RPKM.gene.consensus.txt
MSC_M_rep1_1d


title: primary MSCs, male, rep 1, 7d

description:
MSC.GENCODEv41.counts.gene.consensus.txt
MSC.GENCODEv41.RPKM.gene.consensus.txt
MSC_M_rep1_7d


title: HP1601201T2D_D4


title: primary MSCs, male, rep 1, 0d

description:
MSC.GENCODEv41.counts.gene.consensus.txt
MSC.GENCODEv41.RPKM.gene.consensus.txt
MSC_M_rep1_0d


title: HP1714601_C2


title: HEK-293 cells, LINC01962 KO, clone 2

description:
HEK.GENCODEv41.counts.gene.consensus.txt
HEK.GENCODEv41.RPKM.gene.consensus.txt
HEK.GENCODEv41.counts.transcript.consensus.txt
HEK.GENCODEv41.RPKM.transcript.consensus.txt
HEK293_LINC01962_KO_c2

value: LINC01962 knockout


title: HP1525901_C2


title: HP1711001_B6


title: Rep2_unsorted

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Sequencing reads were first processed by requiring the presence of flanking upstream (GTGGAAAGGACGAAACACCG) and downstream (GTTTT) sequences flanking a 20nt region using a custom Perl script.
These 20nt regions were tallied, and then queried against sgRNA sequences present in the Gecko v2 “A” or “B” libraries.
Per-sgRNA Reads Per Million (RPM) were calculated by adding a pseudocount of 1 read and normalizing against the sum of all sequenced reads that contained an exact sequence match to a sgRNA sequence in the queried library.
Genome_build: n/a
Supplementary_files_format_and_content: Processed files contain read counts (zero-mismatch only) for each sgRNA in a tab-delimited text file

source_name: 293T cells

extract_protocol:
gDNA was isolated using the DNeasy Blood and Tissue Kit (Qiagen), including RNAse A treatment. gDNA was quantified by TapeStation 2200 (Agilent), and then fragmented by sonication (either Q800R2 Sonicator (Qsonica) or Bioruptor Plus (Diagenode)) to 800-1000bp fragments. After gDNA was denatured, 10% of biotinylated probes (by mass; e.g. 10 μg probes for 100 μg gDNA)  were pre-coupled to Streptavidin beads (ThermoFisher) using the manufacturer recommended protocol, and were then hybridized to vector-containing gDNA fragments in 1× LiCl/Urea Buffer (the final 1× Buffer contains 25 mM Tris pH 7.4, 5 mM EDTA, 400 mM LiCl, 0.1% NP40, 0.1% SDS, 0.1% sodium deoxycholate, 1M urea) for 3 hours at 60ºC. After hybridization, beads were rinsed with 1× LiCl/Urea Buffer at 45ºC for 2-3 minutes. sgRNA-containing gDNA fragments were eluted by digesting RNA probes with Ambion® RNase Cocktail™ (ThermoFisher) and by degrading RNA with NaOH (Sigma). gDNA fragments were purified using the DNA Clean & Concentrator-5 kit (Zymo Research).
Purified gDNA fragments were then PCR amplified (NEBNext Ultra II Q5, NEB) with FLI1F and FLIR primers in PCR1 (denaturation at 98ºC for 30 seconds, followed by 6-9 cycles of denaturation at 98ºC for 12 seconds, annealing at 69ºC for 60 seconds, and extension at 72ºC for 30 seconds, followed by a final elongation at 72ºC for 60 seconds). PCR1 products were purified using AMPure XP beads at 1.6× ratio by volume and manufacturer protocol. After purification, PCR2 was performed with NEBNext Ultra II Q5 (NEB) using standard Illumina indexed primers (e.g. D501 and D701) as follows: denaturation at 98ºC for 30 seconds, followed by 7-8 cycles of denaturation at 98ºC for 10 seconds and annealing and elongation at 72ºC for 40 seconds, followed by a final elongation at 72ºC for 60 seconds). PCR2 products were purified using AMPure XP beads at 1.3× ratio by volume and manufacturer protocol. Libraries were quantified by Tapestation 2200 (Agilent) and sequenced on the HiSeq 2500 or 4000 platforms (Illumina). As these libraries contain identical sequences upstream of the variable sgRNA region, pools submitted for sequencing contained at most 20% FLI-seq libraries, with the remainder of the pool containing high-diversity samples (e.g. standard RNA-seq).
Other: pooled CRISPR

treatment_protocol: Samples were transduced with lentivirus containing either Gecko V2 "A" or "B" library, selected, and grown for a number of days as indicated.

value: 293T cells

tag: facs sorted population

tag: sgrna coverage

tag: infection replicate

tag: transduced with lentivirus containing library

value: Gecko v2 A

tag: technical replicate

value: A


title: Rep1_Cy5high

value: Cy5-labeled DPANP - high fluorescence


title: Rep2_Cy5low

value: Cy5-labeled DPANP - low fluorescence


title: Rep2_Cy5high


title: Rep1_Cy5low


title: HEK-293 cells, LINC01962 KO, clone 1

description:
HEK.GENCODEv41.counts.gene.consensus.txt
HEK.GENCODEv41.RPKM.gene.consensus.txt
HEK.GENCODEv41.counts.transcript.consensus.txt
HEK.GENCODEv41.RPKM.transcript.consensus.txt
HEK293_LINC01962_KO_c1

value: kidney; embryo

value: embryonic kidney cells


title: Rep1_unsorted


title: HEK-293 cells, ENSG00000287264 KO, clone 1

description:
HEK.GENCODEv41.counts.gene.consensus.txt
HEK.GENCODEv41.RPKM.gene.consensus.txt
HEK.GENCODEv41.counts.transcript.consensus.txt
HEK.GENCODEv41.RPKM.transcript.consensus.txt
HEK293_ENSG00000287264_KO_c1


title: HEK-293 cells, LINC00324 KO, clone 2, passage 2

description:
HEK.GENCODEv41.counts.gene.consensus.txt
HEK.GENCODEv41.RPKM.gene.consensus.txt
HEK.GENCODEv41.counts.transcript.consensus.txt
HEK.GENCODEv41.RPKM.transcript.consensus.txt
HEK293_LINC00324_KO_c2_p2

value: LINC00324 knockout


title: GeckoB1_12x_Bio1Tech2

description: SupplementaryTable1_GeckoB_Replication.txt

value: Gecko v2 B

value: B


title: HP1602301T2D_N18


title: HEK-293 cells, LINC00324 KO, clone 1, passage 3

description:
HEK.GENCODEv41.counts.gene.consensus.txt
HEK.GENCODEv41.RPKM.gene.consensus.txt
HEK.GENCODEv41.counts.transcript.consensus.txt
HEK.GENCODEv41.RPKM.transcript.consensus.txt
HEK293_LINC00324_KO_c1_p3


title: HEK-293 cells, LINC00324 KO, clone 2, passage 1

description:
HEK.GENCODEv41.counts.gene.consensus.txt
HEK.GENCODEv41.RPKM.gene.consensus.txt
HEK.GENCODEv41.counts.transcript.consensus.txt
HEK.GENCODEv41.RPKM.transcript.consensus.txt
HEK293_LINC00324_KO_c2_p1


title: GeckoB1_12x_Bio1Tech1


title: HP1714601_N4


title: GeckoB1_25x_Bio1Tech2


title: GeckoB1_12x_Bio2


title: GeckoB1_25x_Bio2


title: HEK-293 cells, LINC00324 KO, clone 1, passage 2

description:
HEK.GENCODEv41.counts.gene.consensus.txt
HEK.GENCODEv41.RPKM.gene.consensus.txt
HEK.GENCODEv41.counts.transcript.consensus.txt
HEK.GENCODEv41.RPKM.transcript.consensus.txt
HEK293_LINC00324_KO_c1_p2


title: HP1525401_A9


title: GeckoB1_25x_Bio1Tech1


title: GeckoB1_17x_Bio2


title: GeckoB1_35x_Bio1Tech2


title: HEK-293 cells, ENSG00000284607 KO, clone 1

description:
HEK.GENCODEv41.counts.gene.consensus.txt
HEK.GENCODEv41.RPKM.gene.consensus.txt
HEK.GENCODEv41.counts.transcript.consensus.txt
HEK.GENCODEv41.RPKM.transcript.consensus.txt
HEK293_ENSG00000284607_KO_c1


title: HP1601201T2D_F24


title: Library

city: London

first: Komila

last: Zakirova

state: ON

address: 790 Commissioners Road E

department: Pathology and Laboratory Medicine

institute: Western University

description:
Library name: Sample13
Library

library_source: other

data_processing:
Pooled preparation containing all barcoded samples was sequenced using an Illumina NextSeq 550 75-cycle High-Output kit. Raw reads were mapped and count tables analyzed using TRACS software (v1.1.3)
Assembly: GRCh38/hg38 Human GeCKO v2 library A+B reference sgRNA sequences
Supplementary files format and content: Plain Text Document with read counts for each condition
Library strategy: CRISPR Screen

molecule: other

source_name: Other

growth_protocol: OVCAR8 cells were maintained in DMEM/F12 media supplemented with 10% fetal bovine serum (FBS) and 1% pen-strep-glutamine in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Genomic DNA was extracted from cell pellets using the QIAamp DNA Blood Maxi Kit (Qiagen #51194). Guide RNA inserts were amplified by PCR using NEBNext Q5 Ultra Master Mix (NEB #MO544), and barcodes were attached for sample identification. PCR amplicons were gel-purified using the Monarch DNA Gel Extraction Kit (NEB #T1020), then quantified with Qubit (Invitrogen) and pooled prior to high-throughput sequencing.
CRISPR library comprised a total of 17,840 sgRNAs, with 6 sgRNAs per gene from the 2,740 genes. Guide sequences were derived from the human GeCKOv2 lentiviral library (Sanjana et al., 2014), along with non-targeting control sgRNAs for Luc, EGFP, and LacZ genes.

value: Other

value: Plasmid DNA

value: Plasmid library

value: CRISPR Lentiviral Library


title: GeckoB1_35x_Bio2


title: GeckoB1_50x_Bio1Tech2


title: SPH_Cas9-negative_replicate_2

description:
Library name: Sample11
SPH_Cas9-negative_replicate_2

source_name: Ovarian

value: Ovarian

value: High-grade serous carcinoma

value: Spheroid Cas9-non-expressing cells


title: HP1525401_H8

value: Pancreatic islets

value: Healthy


title: GeckoB1_35x_Bio1Tech1

value: 293T cells

value: A


title: HP1711001_P7


title: HEK-293 cells, WT, clone 1, passage 2

description:
HEK.GENCODEv41.counts.gene.consensus.txt
HEK.GENCODEv41.RPKM.gene.consensus.txt
HEK.GENCODEv41.counts.transcript.consensus.txt
HEK.GENCODEv41.RPKM.transcript.consensus.txt
HEK293_WT_c1_p2

value: WT


title: HEK-293 cells, WT, clone 1, passage 3

description:
HEK.GENCODEv41.counts.gene.consensus.txt
HEK.GENCODEv41.RPKM.gene.consensus.txt
HEK.GENCODEv41.counts.transcript.consensus.txt
HEK.GENCODEv41.RPKM.transcript.consensus.txt
HEK293_WT_c1_p3

value: kidney; embryo


title: SPH_Cas9-negative_replicate_3

description:
Library name: Sample12
SPH_Cas9-negative_replicate_3


title: HP1711001_C17


title: SPH_Cas9-negative_replicate_1

description:
Library name: Sample10
SPH_Cas9-negative_replicate_1


title: HEK-293 cells, WT, clone 1, passage 1

description:
HEK.GENCODEv41.counts.gene.consensus.txt
HEK.GENCODEv41.RPKM.gene.consensus.txt
HEK.GENCODEv41.counts.transcript.consensus.txt
HEK.GENCODEv41.RPKM.transcript.consensus.txt
HEK293_WT_c1_p1

value: embryonic kidney cells


title: HP1605601T2D_L23


title: ADH_Cas9-negative_replicate_3

description:
Library name: Sample9
ADH_Cas9-negative_replicate_3

value: Adherent Cas9-non-expressing cells


title: GeckoB1_50x_Bio1Tech1

value: Gecko v2 B


title: C-28/I2 chondrocytes, LINC00324 KO, clone 2, passage 2

description:
C28.GENCODEv41.counts.gene.consensus.txt
C28.GENCODEv41.RPKM.gene.consensus.txt
C28I2_LINC00324_KO_c2_p2

source_name: cartilage

value: cartilage

value: chondrocytes

value: LINC00324 knockout


title: HEK-293 cells, LINC00324 KO, clone 1, passage 1

description:
HEK.GENCODEv41.counts.gene.consensus.txt
HEK.GENCODEv41.RPKM.gene.consensus.txt
HEK.GENCODEv41.counts.transcript.consensus.txt
HEK.GENCODEv41.RPKM.transcript.consensus.txt
HEK293_LINC00324_KO_c1_p1


title: ADH_Cas9-negative_replicate_2

description:
Library name: Sample8
ADH_Cas9-negative_replicate_2


title: HP1714601_D17

source_name: Human pancreatic islet single cells


title: GeckoB1_70x_Bio1Tech2

value: B


title: C-28/I2 chondrocytes, LINC00324 KO, clone 1, passage 3

description:
C28.GENCODEv41.counts.gene.consensus.txt
C28.GENCODEv41.RPKM.gene.consensus.txt
C28I2_LINC00324_KO_c1_p3


title: GeckoB1_50x_Bio2


title: HP1711001_D5


title: GeckoB1_70x_Bio2


title: HP1714601_D9


title: C-28/I2 chondrocytes, LINC00324 KO, clone 2, passage 1

description:
C28.GENCODEv41.counts.gene.consensus.txt
C28.GENCODEv41.RPKM.gene.consensus.txt
C28I2_LINC00324_KO_c2_p1


title: ADH_Cas9-negative_replicate_1

description:
Library name: Sample7
ADH_Cas9-negative_replicate_1

value: CRISPR Lentiviral Library


title: C-28/I2 chondrocytes, LINC00324 KO, clone 1, passage 2

description:
C28.GENCODEv41.counts.gene.consensus.txt
C28.GENCODEv41.RPKM.gene.consensus.txt
C28I2_LINC00324_KO_c1_p2


title: SPH_Cas9-positive_replicate_3

description:
Library name: Sample6
SPH_Cas9-positive_replicate_3

value: Ovarian

value: Spheroid Cas9-expressing cells


title: HP1714601_F13


title: C-28/I2 chondrocytes, LINC00324 KO, clone 1, passage 1

description:
C28.GENCODEv41.counts.gene.consensus.txt
C28.GENCODEv41.RPKM.gene.consensus.txt
C28I2_LINC00324_KO_c1_p1


title: C-28/I2 chondrocytes, WT, clone 1, passage 3

description:
C28.GENCODEv41.counts.gene.consensus.txt
C28.GENCODEv41.RPKM.gene.consensus.txt
C28I2_WT_c1_p3


title: HP1606401T2D_Tn5_E2


title: SPH_Cas9-positive_replicate_2

description:
Library name: Sample5
SPH_Cas9-positive_replicate_2

value: High-grade serous carcinoma


title: HP1602301T2D_M13

value: Pancreatic islets


title: GeckoB1_100x_Bio1Tech2

description: SupplementaryTable1_GeckoB_Replication.txt


title: C-28/I2 chondrocytes, WT, clone 1, passage 2

description:
C28.GENCODEv41.counts.gene.consensus.txt
C28.GENCODEv41.RPKM.gene.consensus.txt
C28I2_WT_c1_p2


title: GeckoB1_100x_Bio2


title: HP1714601_J16

value: Healthy


title: GeckoB1_100x_Bio1Tech1

value: 293T cells


title: C-28/I2 chondrocytes, WT, clone 1, passage 1

description:
C28.GENCODEv41.counts.gene.consensus.txt
C28.GENCODEv41.RPKM.gene.consensus.txt
C28I2_WT_c1_p1


title: GeckoB1_200x_Bio1Tech2


title: ADH_Cas9-positive_replicate_1

description:
Library name: Sample1
ADH_Cas9-positive_replicate_1

value: Adherent Cas9-expressing cells


title: HP1606401T2D_Tn5_M24


title: NCI-H358 cells, 30nM selumetinib, 24 hours, rep4

city: Berkeley

first: Paul

last: Severson

address: 91 Bolivar Dr.

institute: Plexxikon Inc

data_processing:
Reads were trimmed for quality and to remove adapter sequences using fastp version 0.23.4
Trimmed reads were then quantified with salmon (v1.10.1) using the hg38 transcriptome index with full decoy sequences downloaded from RefGenie
The R package tximeta was used to calculate offsets, annotate (ensembl 97) and summarize expression to the gene level
The cpm function from the edgeR package was used to calculate log counts per million reads using offsets and a prior count of 2
Assembly: hg38
Supplementary files format and content: gene level Log2 counts per million reads using offsets and a prior count of 2

source_name: Lung

extract_protocol:
Cells were lysed in RLT bufer with added B-mercaptoethanol. Lysates were then disrupted using qiashredder columns and RNA isolated with Rneasy plus reagents. RNA samples were eluted in RNAse free water.
Poly-A enrichment followed by library prep with KAPA biosystems stranded RNAseq library prep kit

value: Lung

value: epithelial

value: lung cancer cell line

value: 30nM selumetinib, 24 hours


title: GeckoB1_200x_Bio2

value: Gecko v2 B

value: A


title: GeckoB1_200x_Bio1Tech1


title: ADH_Cas9-positive_replicate_2

description:
Library name: Sample2
ADH_Cas9-positive_replicate_2


title: HP1606401T2D_Tn5_B18

extract_protocol: The reverse-transcribed cDNA from single cells was amplified followed by tagmentation and a standard index PCR. The single cell libraries were prepared according to Smart-seq2 protocol. The sequencing was performed on HISEQ 3000 (IIlumina).


title: NCI-H358 cells, 30nM selumetinib, 24 hours, rep2


title: Aged MuSC 2 IgG

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

description: Library name: Aged_rep2_IgG

data_processing:
FastQ files were generated with bcl2fastq/2.20.0. Paired-end reads were processed using CutRunTools/20200629 with minor modifications. Adapter sequences and low-quality bases were trimmed using Trimmomatic/0.39. Trimmed reads were aligned to mm10 mouse genome using Bowtie/2-2.5.3. Duplicate reads were marked using Picard/2.27.3and removed using Samtools/1.9
Assembly: mm10
Supplementary files format and content: bw
Library strategy: CUT&Run

source_name: Mouse muscle

extract_protocol:
MuSCs were crosslinked with 0.1% formaldehyde for 2 minutes at room temperature.
CUT&RUN was conducted using the CUT&RUN Assay kit from Cell Signaling Technology. MuSCs were crosslinked with 0.1% formaldehyde for 2 minutes at room temperature. For each reaction, 130,000 MuSCs were gently resuspended in 100uL of the supplied Wash Buffer, while 30,000 MuSCs were used as Input. MuSCs were bound to Concanavalin- A beads, and incubated overnight with the following antibodies. The enzyme pAG-MNase was added to the suspension, incubated at 4°C for 1 hour, then activated by adding 3 μL of cold Calcium Chloride to each tube and rotated at 4°C for 30 more minutes. Samples were resuspended with the STOP buffer provided by the kit and kept at 37°C for 10 min to release the DNA fragments into the solution. The final DNA was isolated using spin columns, and resuspended to 3 nM for NGS-library generation. The final libraries were diluted to 3 nM and sequenced on an Illumina NextSeq 2000 using the following setting: R1: 50 cycles, R2: 50 cycles, i7: 8 cycles.

treatment_protocol: TA muscles of adult and aged mice were injured with Notexin and FACS-isolated at 3 dpi. Cells were fixed and processed for library preparation.

value: Mouse muscle

value: MuSCs

value: WT

tag: age

value: Aged

value: 3 days post Notexin muscle injury


title: HP1606401T2D_Tn5_M14

data_processing:
Raw sequencing data were de-multiplexed and converted into fastq format for each cell by using Illumina bcl2fastq with default setting.
Reads were aligned to human genome hg38 using the STAR aligner.
Uniquely aligned reads mapping to the RefSeq gene annotations were used for gene expression estimates at reads per kilobase transcript and million mapped reads (RPKMs) using rpkmforgenes.
Low quality cells were excluded from downstream analysis when they failed to meet the following criteria for retaining cells: 1) >= 50,000 sequence reads; 2) >= 40% of reads uniquely aligned to the genome; 3) >= 40% of these reads mapping to RefSeq annotated exons; and 4) >= 1000 genes with RPKM >= 1. In addition, doublets detected by Scrublet were further removed.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each single cell …


title: NCI-H358 cells, 30nM selumetinib, 24 hours, rep3


title: HP1601201T2D_F18


title: NCI-H358 cells, 30nM selumetinib, 24 hours, rep1


title: Ppp4r2a_KD_R3

city: Kansas City

first: Ariel

middle: Alejandro

last: Bazzini

state: Missouri

institute: Stowers Institute for Medical Research

description: instrument model: Singular Genomics G4 sequencer

data_processing:
sgdemux 1.2.0 was run to demultiplex reads for all libraries and generate FASTQ files.
Assembly: danrer11
Supplementary files format and content: tab-delimited txt file includes raw counts for each Sample

organism: Danio rerio

source_name: whole embryo

extract_protocol:
Total RNA then was extracted using Direct-zol RNA Miniprep Kit (#R2050, Zymo Research) following manufacturer’s instructions.
Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, Cat. No. E7760L), t

value: whole embryo

value: 4 hpf

value: Knockdown


title: GeckoB1_70x_Bio1Tech1


title: SPH_Cas9-positive_replicate_1

description:
Library name: Sample4
SPH_Cas9-positive_replicate_1

value: Ovarian

value: High-grade serous carcinoma

value: CRISPR Lentiviral Library

value: Spheroid Cas9-expressing cells


title: HP1711001_A20

value: Pancreatic islets

value: Healthy


title: NCI-H358 cells, 1uM dabrafenib & 30nM selumetinib, 24 hours, rep4

value: Lung

value: epithelial

value: lung cancer cell line


title: Ppp4r2a_KD_R2


title: Aged MuSC 1 IgG

description: Library name: Aged_rep1_IgG

value: Mouse muscle


title: HP1601201T2D_J1


title: Aged MuSC 1 H3K27Me

description: Library name: Aged_rep1_K27Me3

value: MuSCs


title: ADH_Cas9-positive_replicate_3

description:
Library name: Sample3
ADH_Cas9-positive_replicate_3

value: Adherent Cas9-expressing cells


title: Ppp4r2a_KD_R1


title: Adult MuSC 2 H3K27Me

description: Library name: Adult_rep2_K27Me3

value: WT

value: Adult


title: NCI-H358 cells, 1uM dabrafenib & 30nM selumetinib, 24 hours, rep3


title: Ppp4r2a_Cas13d_control_R3

value: whole embryo

value: Cas13d Control


title: Adult MuSC 2 IgG

description: Library name: Adult_rep2_IgG

value: 3 days post Notexin muscle injury


title: HP1601201T2D_E23


title: NCI-H358 cells, 1uM dabrafenib & 30nM selumetinib, 24 hours, rep2


title: HP1711001_B2


title: Ppp4r2a_Cas13d_control_R2

value: 4 hpf


title: NCI-H358 cells, 1uM dabrafenib & 30nM selumetinib, 24 hours, rep1


title: Adult MuSC 1 IgG

description: Library name: Adult_rep1_IgG


title: Adult MuSC 1 H3K27Me

description: Library name: Adult_rep1_K27Me3


title: Aged MuSC 2 H3K27Me

description: Library name: Aged_rep2_K27Me3

value: Aged


title: HP1525901_P15


title: Ppp4r2a_Cas13d_control_R1


title: NCI-H358 cells, 1uM dabrafenib, 24 hours, rep4

value: 1uM dabrafenib, 24 hours


title: HP1711701T2D_E3


title: Phf10_KD_R3

value: Knockdown


title: Phf10_KD_R2


title: NCI-H358 cells, 1uM dabrafenib, 24 hours, rep2


title: NCI-H358 cells, 1uM dabrafenib, 24 hours, rep3


title: HP1606401T2D_Tn5_L16

value: Pancreatic islets


title: Phf10_KD_R1


title: NCI-H358 cells, 1uM dabrafenib, 24 hours, rep1


title: Phf10_Cas13d_control_R3


title: HP1602301T2D_J13


title: Tumor_anti-PTB_6

city: Wuhan

first: Dong

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Raw reads were first discarded if containing more than 2-N bases, then reads were processed by clipping adaptor, removing low quality bases, and discarding too short reads (less than 16nt). FASTX-Toolkit (Version 0.0.13) was used to get the clean reads.
After that, clean reads were aligned to the human-hg19 genome by tophat2 (Kim et al., 2013). Aligned reads with more than one genome location were discarded due to their ambiguous location.
Uniquely localized reads were used to calculate reads number and RPKM value (RPKM represents reads per kilobase and per million) for each gene according to reads and genes genome location. Other statistical results, such as gene coverage and depth, reads distribution around start codon and stop codon, were also obtained.
After getting the Expression level of all genes in all samples, differentially expressed genes were analyzed by using edgeR(Robinson et al., 2010), one of R packages. 0.01 p-value and 2 fold change were set as the threshold to define DEGs.
Alternative splicing events (ASEs) in the RNA-Seq samples and the regulated alternative splicing events (RASEs) between tumor and normal were detected and quantified by in house AS method called ABLas.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited MS Excel files including RPKM values for each Sample ...

source_name: cervical cancer

extract_protocol:
Total RNA was extracted from tissue or cell samples by using TRIzol Reagent (Ambion) following the manufacturer’s instructions. RQ1 DNase (promega) was added to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% Agarose gel electrophoresis.
For each sample, 10 μg of total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo (dT)-conjugated magnetic beads (invitrogen) before used for directional RNA-seq library preparation. Purified mRNAs were ion fragmented at 95 ℃ followed by end repair and 5' adaptor ligation. Then mRNA reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified. And products corresponding to 200-500 bps were purified, quantified and stored at -80 ℃ before sequencing. Illumina NextSeq 500 platform was used to generating paired-end, 150-bp reads.

value: tumor tissue

value: anti-PTB


title: Tumor_anti-PKM2_5


title: Tumor_anti-PKM2_3


title: Phf10_Cas13d_control_R1


title: NCI-H358 cells, DMSO, 24 hours, rep2

value: Lung

value: epithelial

value: DMSO, 24 hours


title: Tumor_anti-PTB_4


title: HP1605601T2D_M20

city: Huddinge

first: Ping

institute: Karolinska Institutet


title: Tumor_anti-PKM2_8


title: HP1602301T2D_J2


title: Tumor_anti-PTB_5


title: Yeast-sin3D-C

city: New Orleans

first: Tina

middle: M

last: O'Grady

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

data_processing:
Reads were mapped to the S. cerevisiae R64-1-1 transcriptome (Ensembl cDNA release 97) and quantified using Salmon v0.8.2
Assembly: S. cerevisiae R64-1-1
Supplementary files format and content: Salmon quant.sf file: read counts and TPM per transcript

organism: Saccharomyces cerevisiae

growth_protocol: Cells were cultured under non-selective conditions using yeast extract-peptone-dextrose (YPD) at 30°C.

extract_protocol:
Invitrogen RiboPure RNA Purification Kit
Illumina TruSeq stranded mRNA

treatment_protocol: Cells were grown up to OD(600 nm) ~0.5 in 0.8-1 ml YPD, then incubated for 2 h with 50 µM E6R, 20 µM TSA, or 0.7% DMSO, then centrifuged to remove supernatant. Pellets were frozen on dry ice before RNA extraction.

tag: genetic information

value: MATa leu2-3,112 trp1-901 his3-200 ura3-52 ade2-101 gal4Δ gal80Δ SPAL10::URA3@ura3 GAL1::LacZ can1R cyh2R pdr5::HIS3 snq2::KanMX sin3Δ::NatMX

value: 0.7% DMSO


title: Tumor_NC_7

last: Chen

value: WT


title: NCI-H358 cells, DMSO, 24 hours, rep1

value: lung cancer cell line


title: HP1711701T2D_E2

address: Alfred Nobels allé 8


title: Tumor_NC_6


title: NCI-H358 cells, 30nM selumetinib, 4 hours, rep4

value: 30nM selumetinib, 4 hours


title: HP1601201T2D_K16


title: HP1601201T2D_M24


title: NCI-H358 cells, 30nM selumetinib, 4 hours, rep3


title: NCI-H358 cells, DMSO, 24 hours, rep4


title: HP1602301T2D_G17


title: Yeast-rpd3D-C

value: MATa leu2-3,112 trp1-901 his3-200 ura3-52 ade2-101 gal4Δ gal80Δ SPAL10::URA3@ura3 GAL1::LacZ can1R cyh2R pdr5::HIS3 snq2::KanMX rpd3Δ::NatMX


title: NCI-H358 cells, 30nM selumetinib, 4 hours, rep2


title: Yeast-sin3D-A


title: Tumor_NC_5


title: HP1605601T2D_N14


title: H3K4me3_dKDM-ifKO_3,ChIP

city: San Juan de Alicante

first: Sergio

last: Niñerola

state: Alicante

address: Avenida Santiago Ramon y Cajal, s/n

department: Molecular Neurobiology and Neuropathology

country: Spain

institute: CSIC-Instituto de Neurociencias de Alicante

description: Library name: D3KO_3

data_processing:
Reads obtained were aligned to the mouse genome (mm10) using Bowtie2 (v 2.3.4.3; (Langmead and Salzberg, 2012). For posterior analysis, only reads with mapq > 30 were selected. For data processing, Samtools v1.9 (Li et al., 2009), Bedtools v2.27.1 (Quinlan and Hall, 2010), and DeepTools v3.5.0 (Ramirez et al., 2016)were used. To generate BigWigs Deeptools was used to normalize reads by reads per genomic content.
Assembly: mm10
Supplementary files format and content: Bigwig

extract_protocol:
Nuclei from hippocampal cells were extracted in a dounce homogenizer as explained for the FANS method (see above). For H3K4me3 (07-473, Millipore), nuclei were fixed in 1% formaldehyde for 10 min at room temperature, and fixation was blocked with 0.1 M glycine for 5 min. The nuclei pellet was resuspended in SDS lysis buffer (containing, in mM: SDS 1%, EDTA 10, Tris 50; pH 8) and sonicated in a Bioruptor Pico (Diagenode) for 12 cycles of 15 s with 30 s off. Samples were centrifuged for 6 min at 13000 rpm at room temperature and the supernatants were kept in LoBind Eppendorf tubes. 10% of the samples were saved for quality control analysis (DNA concentration measurement and visualization of smir DNA in an electrophoresis gel) and the rest was diluted in ChIP Dilution buffer (containing, in mM: SDS 0.01%, Triton X-100 1.1%, EDTA 1.2, Tris-HCl 16.7, NaCl 167; pH 8). 5% of the sample was saved as Input and the rest incubated overnight at 4°C with the Dynabeads (Invitrogen) bound to the antibody. Samples were rinsed with several washes, 5 minutes each, as follows: 2x in RIPA-150 buffer (containing, in mM: Tris-HCl 50, NaCl 150, EDTA 1, SDS 0.1%, Triton X-100 1%, and sodium deoxycholate 0.1%; pH 8), 2x in RIPA-500 buffer (containing, in mM: Tris-HCl 50, NaCl 500, EDTA 1, SDS 0.1%,  Triton X-100 1%, sodium deoxycholate 0.1%; pH 8), 2x in RIPA LiCl buffer (containing, in mM: Tris-HCl 50, EDTA 1, NP-40 1%, sodium deosycholate 0.7%, LiCl2 500), and 2x in TE buffer (containing, in mM: Tris-HCl 10, pH 8.0, EDTA 1; pH 8.0). Samples were diluted in Elution buffer (containing, in mM: Tris-HCl 10, 5 mM EDTA, NaCl 300, SDS 0.5%; pH 8) and incubated with 1 μL of RNase A 10 mg/mL (Fermentas) overnight at 65°C in agitation to reverse crosslink. Samples were then placed on a magnetic rack, allowing beads to clump. Supernatants were transferred to new tubes and incubated with 2 μL of Proteinase K 20 mg/mL (Thermo Scientific) for 4 h at 55°C, in agitation. Quality controls and Inputs were also incubated with RNase A and Proteinase K. Finally, DNA was precipitated using phenol-chloroform-isoamil alcohol.
ChIP-seq

value: Hippocampus

value: ifKO

value: TMX


title: Yeast-rpd3D-B


title: NCI-H358 cells, 30nM selumetinib, 4 hours, rep1


title: NCI-H358 cells, DMSO, 24 hours, rep3


title: Phf10_Cas13d_control_R2

value: whole embryo

value: 4 hpf

value: Cas13d Control


title: Yeast-rpd3D-A


title: HP1602301T2D_D7

value: Pancreatic islets


title: HP1601201T2D_E7


title: HP1714601_K24

value: Healthy


title: H3K4me3_dKDM-ifKO_1,ChIP

description: Library name: D3KO_1


title: NCI-H358 cells, 1uM dabrafenib & 30nM selumetinib, 4 hours, rep4

value: Lung


title: Yeast-sin3D-B


title: NCI-H358 cells, 1uM dabrafenib & 30nM selumetinib, 4 hours, rep3

value: epithelial


title: H3K4me3_dKDM-WT_2,ChIP

description: Library name: D3WT_2


title: H3K4me3_dKDM-ifKO_2,ChIP

description: Library name: D3KO_2


title: Yeast-DMSO-C

value: Wild-type

value: MATa leu2-3,112 trp1-901 his3-200 ura3-52 ade2-101 gal4Δ gal80Δ SPAL10::URA3@ura3 GAL1::LacZ can1R cyh2R pdr5::HIS3 snq2::KanMX


title: Yeast-DMSO-B

value: 0.7% DMSO


title: NCI-H358 cells, 1uM dabrafenib & 30nM selumetinib, 4 hours, rep2


title: HP1601201T2D_I6


title: HP1711701T2D_F17


title: Yeast-DMSO-A


title: NCI-H358 cells, 1uM dabrafenib & 30nM selumetinib, 4 hours, rep1


title: DKDM_3,RNA

description: Library name: DKDM_KO_3

data_processing:
Adapters were trimmed using cutadapt (v1.18;  and reads longer than 25bp were selected. The reads obtained were aligned to the GRCm38.89 mouse genome (mm10) using HISAT2 (Kim et al., 2015a), and reads with mapq > 30 and that mapped to nuclear chromosomes were quantified with HTSeq (v0.11.1;  Anders et al., 2015)
Assembly: mm10
Supplementary files format and content: Tab-delimited file with raw counts for each Sample

extract_protocol:
Working in RNase-free conditions, mice were sacrificed by cervical dislocation and brain was immediately extracted followed by hippocampi dissection. Hippocampi were placed in SafeLock Eppendorf tubes together with TRI Reagent (Sigma-Aldrich) and zirconium oxide beads 0,5 mm of diameter (Next Advance, ZrOB05). Samples were homogenized in a Bullet blender Storm 24 for 3 minutes. Chloroform was added to each sample and vigorously mixed by vortex. After 3 minutes of incubation, samples were centrifuged for 15 minutes at 12000 x g at 4°C. The aqueous phase was transferred to a new Eppendorf tube and was mixed with isopropanol. For improved visualization of the nucleic acid, 10 μg of RNase-free glycogen was added to the samples. After 30 minutes of room temperature, samples were centrifugated for 1 hour at 12000 x g at 4°C. Supernatant was discarded and pellet washed in 75% ethanol and was allowed to air dry for 15 minutes. Finally, the pellet was resuspended in RNase-free water. To eliminate genomic DNA, samples were treated with RNase-free DNase I (Qiagen) for 30 minutes at 25°C. RNA was precipitated with phenol-chloroform-isoamil alcohol (Sigma-Aldrich). The supernatant was discarded, and the pellet washed with 80% ethanol. The RNA pellet was air-dried for 15 minutes and dissolved in RNase-free water.
Poly A RNA


title: NCI-H358 cells, 1uM dabrafenib, 4 hours, rep4

value: 1uM dabrafenib, 4 hours


title: DKDM_2,RNA

description: Library name: DKDM_KO_2


title: Yeast-E6R-B


title: DKDM_1,RNA

description: Library name: DKDM_KO_1


title: NCI-H358 cells, 1uM dabrafenib, 4 hours, rep3

value: lung cancer cell line


title: Yeast-E6R-A


title: NCI-H358 cells, 1uM dabrafenib, 4 hours, rep2


title: dKDM_wt_3,RNA

description: Library name: dKDM_wt_3

value: WT


title: HP1711001_B14


title: dKDM_wt_2,RNA

description: Library name: dKDM_wt_2


title: NCI-H358 cells, 1uM dabrafenib, 4 hours, rep1


title: HP1711001_A12


title: Yeast-TSA-B

value: 20 μM TSA (0.7% DMSO)


title: dKDM_wt_1,RNA

description: Library name: dKDM_wt_1

value: Hippocampus


title: HP1711001_K23


title: Yeast-TSA-C


title: Yeast-TSA-A


title: NCI-H358 cells, DMSO, 4 hours, rep4

value: DMSO, 4 hours


title: H3K4me3_dKDM-WT_1,ChIP

description: Library name: D3WT_1

value: TMX


title: NCI-H358 cells, DMSO, 4 hours, rep3


title: miR430_rescue_6h_mRescue_R2

description: Library name: miR430_rescue_6h_mRescue_R2

data_processing:
Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and bcl-convert-3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files.
Assembly: Danrer11
Supplementary files format and content: tab-delimited txt file includes raw counts for each Sample

extract_protocol:
Total RNA then was extracted using Direct-zol RNA Miniprep Kit (#R2050, Zymo Research) following manufacturer’s instructions.
Libraries were made according to the manufacturer’s directions for the TruSeq Stranded mRNA Library Prep Kit (Illumina, Cat. No. 20020594),

value: whole embryo

value: 6 hpf

value: Knockdown


title: NCI-H358 cells, DMSO, 4 hours, rep2


title: miR430_rescue_6h_mRescue_R1

description: Library name: miR430_rescue_6h_mRescue_R1


title: HP1602301T2D_F17

value: Pancreatic islets


title: HP1606401T2D_Tn5_H6


title: E6-INPUT-2

data_processing:
ChIP-seq reads were mapped to the yeast S. cerevisiae genome (R64-1-1) with bwa v.0.7.8-r455 using the mem algorithm.
Bigwig files were generated using deeptools.
Peaks were called with MACS2 using input sequencing data as a control.
Assembly: S. cerevisiae R64-1-1
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: JOY116 (sin3Δ) yeast cells transformed with the YEplac181-Sin3-(HA)3 plasmid were cultured in liquid SC-LEU, until OD600 nm ~0.7.

extract_protocol:
After overnight incubation, phenol-chloroform extractions and EtOH precipitations were conducted to purify ChIP-DNA. The ChIP-DNA was eluted in a total volume of 200 μL double-distilled water.
ChIP-seq libraries were prepared using Swift S2 Acel reagents on a Beckman Coulter Biomek i7 liquid handling platform from approximately 1 ng of DNA according to manufacturer’s protocol and 14 cycles of PCR amplification.

treatment_protocol: DMSO (0.6% of total volume), 400 μM E6, or 400 μM TSA was added to 2x10^9 yeast cells, and the resulting suspensions were incubated for 2 h at 30°C (200 rpm), and subsequently treated with 1% formaldehyde for 20 min at 4°C for cross-linking. Then, 125 mM glycine was applied for 5 min at room temperature to quench cross-linking. Yeast cells were centrifuged (10 min at 1,000 g), and the resulting pellets were washed twice with 50 mL ice-cold PBS. Yeast pellets were resuspended in 500 μL of ChIP lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, and yeast protease inhibitors). Next, 500 μL of the yeast suspensions in lysis buffer were mixed with 500 μL of zirconia beads in a screw-top microcentrifuge tube. For cell lysis, the tubes were vortexed at maximum speed for 15 min at 4°C. Cell lysates were collected by punching a hole on the bottom of the screw-cap tube, with a sterile needle, and centrifuging the lysates into new Eppendorf tubes. Then, 300 μL of lysates were added into 1.5 mL Bioruptor Pico microtubes with caps (Diagenode, cat#C30010016), and subsequent sonication was conducted with a Bioruptor Pico sonication device, in the following conditions: 30 s/3 cycles on, and 30 s/3 cycles off, at 4°C. The sonicated lysates were cleared by 30 min centrifugation at maximum speed at 4°C. The resulting cleared lysates with sheared chromatin were saved, snap freezed, and stored at -80°C until used. Next, 10 μL cleared lysates were reverse-cross linked overnight at 65°C in the presence of proteinase K. Phenol-chloroform extractions and EtOH precipitations were then applied to purify the sheared DNA. DNA agarose gel running and DNA concentration measurements with a NanoDrop spectrophotometer were finally conducted to assess the size and yield of the sheared DNA, respectively. For the pull-downs, 25 μg of sheared chromatin from each sample were diluted (1:10) in ice-cold dilution buffer (1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8, 150 mM NaCl, and yeast protease inhibitors), and mixed with 10 μg ChIP-grade anti-HA (Abcam, Cambridge, MA, USA, cat#ab9110)68, or isotype control anti-IgG (Abcam, Cambridge, MA, USA, cat#ab171870) antibodies. Then, 50 μL of pre-washed Dynabeads Protein G for Immunoprecipitation (ThermoFisher, cat#10003D) were added to each individual sample. Chromatin immunoprecipitation was performed by incubating samples at 4°C overnight, under gentle shaking (300 rpm). Then, the Dynabeads were washed three times with 1 mL ice-cold wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8, 150 mM NaCl), and once with 1 mL ice-cold final wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA pH 8, 20 mM Tris-HCl pH 8, 500 mM NaCl), using a magnetic rack. DNA was eluted with 120 μL elution buffer (1% SDS, 100 mM NaHCO3), by incubating samples at 30°C for 15 min. For input, 10 μL of sheared cell lysates were added to 110 μL of elution buffer. Then, 4 μL proteinase K were added to the eluted DNA or inputs, and reverse-cross linking was achieved by incubating samples overnight at 65°C.

value: transformed with YEplac181-Sin3-(HA)3 plasmid

value: MATa leu2-3,112 trp1-901 his3-200 ura3-52 ade2-101 gal4Δ gal80Δ SPAL10::URA3@ura3 GAL1::LacZ can1R cyh2R pdr5::HIS3 snq2::KanMX sin3Δ::NatMX (2μ LEU2 SIN3-3xHA)


title: HP1525901_E1

value: Healthy


title: E6-INPUT-1


title: NCI-H358 cells, DMSO, 4 hours, rep1

value: Lung

value: epithelial


title: Yeast-E6R-C

value: Wild-type

value: MATa leu2-3,112 trp1-901 his3-200 ura3-52 ade2-101 gal4Δ gal80Δ SPAL10::URA3@ura3 GAL1::LacZ can1R cyh2R pdr5::HIS3 snq2::KanMX


title: HP1606401T2D_Tn5_N12


title: Bckdk_KD_6h_mRescue_R2

description: Library name: Bckdk_KD_6h_mRescue_R2


title: HP1601201T2D_O13


title: RKO cells, shControl, biol rep3

city: Suzhou

first: Xiaoqin

last: Yang

state: Jiangsu

address: NO. 199 Renai Road

institute: Soochow University

data_processing:
All libraries were sequenced on the Illumina NovaSeq 6000 instrument, and 150 bp paired-end reads were generated.
Sequencing reads were aligned back to the human genome (version: hg38) by TopHat 2 software.
Read count extraction was performed using GFOLD software.
The expression matrix of all samples was subjected to the Bayesian workflow for differential gene modeling based on the “edgeR” (V3.38.1) and “limma” (V3.52.2) R packages.
hg38
tab-delimited text files include reads count for each Sample

source_name: mouse colon cancer tissue

growth_protocol: RKO cell lines stably expressing TRIM21-specific shRNA (shRNA/TRIM21) or scrambled shRNA control (shRNA/Control) were constructed using a lentiviral shRNA technique. The cells were infected with the lentivirus, and 36 h later, cells were selected using 5 μg/ml puromycin for 2–3 weeks.

extract_protocol:
Total RNA was isolated from the colorectal cancer cells using Trizol reagent (Invitrogen; ThermoFisher) according to the manufacturer’s instructions. Then, the ribosomal RNA was depleted from the Trizol-harvested total RNA with the GenSeq rRNA Removal Kit (GenSeq, Inc.) by adhering to its operation guideline.
Next, RNA-seq libraries (with each treatment in triplicate) were constructed with the GenSeq Low Input RNA Library Prep Kit (GenSeq, Inc.) following the manual specifications.

value: RKO

value: a poorly differentiated colon carcinoma cell line

value: scrambled shRNA control (shRNA/Control) using a lentiviral shRNA technique


title: Bckdk_KD_6h_mRescue_R1

description: Library name: Bckdk_KD_6h_mRescue_R1


title: E6-SINHA-2


title: HP1605601T2D_O2


title: E6-SINHA-1


title: HP1711001_H11


title: RKO cells, shControl, biol rep2

value: WT


title: Cas13d_alone_6h_mRescue_R2

description: Library name: Cas13d_alone_6h_mRescue_R2

value: Cas13d Control


title: HP1602301T2D_P16


title: RKO cells, shControl, biol rep1


title: Cas13d_alone_6h_mRescue_R1

description: Library name: Cas13d_alone_6h_mRescue_R1


title: TSA-INPUT-1

value: 400 μM TSA (0.6% DMSO)


title: RKO cells, shTRIM21, biol rep3

value: TRIM21 knockdown

value: TRIM21-specific shRNA (shRNA/TRIM21) using a lentiviral shRNA technique


title: RFP_KD_4h_non_targeting_R3

description: Library name: RFP_KD_4h_non_targeting_R3

value: whole embryo

value: 4 hpf

value: Knockdown


title: TSA-INPUT-2

value: transformed with YEplac181-Sin3-(HA)3 plasmid

value: MATa leu2-3,112 trp1-901 his3-200 ura3-52 ade2-101 gal4Δ gal80Δ SPAL10::URA3@ura3 GAL1::LacZ can1R cyh2R pdr5::HIS3 snq2::KanMX sin3Δ::NatMX (2μ LEU2 SIN3-3xHA)


title: HP1602301T2D_L5

value: Pancreatic islets


title: RKO cells, shTRIM21, biol rep2


title: HP1711701T2D_L22


title: TSA-SIN3HA-1


title: RKO cells, shTRIM21, biol rep1


title: RFP_KD_4h_non_targeting_R1

description: Library name: RFP_KD_4h_non_targeting_R1


title: TSA-SIN3HA-2


title: HP1714601_M16

value: Healthy


title: HP1714601_B18


title: DMSO-INPUT-2

value: 0.6% DMSO


title: HP1711701T2D_F16


title: hESC(H1) FXR1-IP rep2

city: Beijing

first: Zhongyang

address: No.5, Dongdan Santiao, Dongcheng District

institute: School of Basic Medicine, Peking Union Medical College (PUMC)

description:
sample36
eCLIP-seq of FXR1 in H1 cell line
ip.r2.norm.neg.bw
ip.r2.norm.pos.bw
FXR1-all.peak.bed

data_processing:
(Sample 33-36) For eCLIP-seq: Raw reads with distinct inline barcodes were demultiplexed and the 10-mer random sequence was appended to the reads name in bam file.
Cutadapt was used to trimming low quality reads and adapter sequence.
Reads were aligned with the sequence of human repetitive elements in the RepBase database by STAR to remove the repetitive reads and obtain the cleaned reads.
Cleaned reads were then mapped to human genome using STAR. Removing PCR duplicate reads based on sharing identical random sequence. Two biological replicates were merged by SAMtools.
Peaks calling and downstream data analysis were performed by clipper. Peaks normalization by “Peak_input_normalization_wrapper.pl” tools. The eCLIP-seq peaks were filtered by P-value < 10e-3 and fold change > 2.
Assembly: GRCh38.83
Supplementary files format and content: bw file, peak text file

growth_protocol: Human ESC line H1 was maintained in mTeSR1 on matrigel-coated plates.

extract_protocol:
The RNA bonded by FXR1 was purified by RNA Clean & Concentrator-5 kit (ZYMO).
Libraries were prepared for high-throughput sequencing using standard Illumina protocols.
eCLIP-Seq

treatment_protocol: About 10^8 hESCs were  UV crosslinked. RNA-FXR1 complexes were captured with RNase A digestion and anti-FXR1 antibody immunoprecipitation.

value: human embryonic stem cells

tag: rip antibody

value: anti-FXR1 antibody

tag: fraction

value: IP


title: DMSO-INPUT-1


title: hESC(H1) FXR1-IP rep1

description:
sample35
eCLIP-seq of FXR1 in H1 cell line
ip.r2.norm.neg.bw
ip.r2.norm.pos.bw
FXR1-all.peak.bed


title: GFP_KD_4h_non_targeting_R2

description: Library name: GFP_KD_4h_non_targeting_R2

tag: tissue


title: GFP_KD_4h_non_targeting_R3

description: Library name: GFP_KD_4h_non_targeting_R3


title: DMSO-SIN3HA-2


title: GFP_KD_4h_non_targeting_R1

description: Library name: GFP_KD_4h_non_targeting_R1


title: hESC(H1) input rep1

description:
sample33
eCLIP-seq input in H1 cell line
input.r2.norm.neg.bw
input.r2.norm.pos.bw
FXR1-all.peak.bed

value: input


title: HP1711001_F8

tag: disease state


title: HP1602301T2D_H1


title: Cas13d_4h_alone_non_targeting_R3

description: Library name: Cas13d_4h_alone_non_targeting_R3


title: HP1602301T2D_I21


title: RFP_KD_4h_non_targeting_R2

description: Library name: RFP_KD_4h_non_targeting_R2


title: DMSO-SIN3HA-1


title: hESC(H1) FXR1-OE input rep2, Day4

description:
sample32
Poly(A)+ RNA-seq after FXR1 overexpression in H1 cell line

data_processing:
(Sample 13-32) For RNA-seq data of hESC differentiation into mesoderm, all reads were aligned to human genome using STAR with the parameter "--outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outBAMsortingThreadN 5".
Uniquely mapped reads were retained for calculating gene counts by FeatureCounts.
The nucleo-cytoplasmic ratio of gene was conducted using DESeq2 and differential gene N/C ratio analysis was conducted using DESeq2 with the P-value < 0.05 and |log2 (Fold change)| > log2 (1.2).
Assembly: GRCh38.83
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
The collected cells and components were subjected to RNA extraction using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: H1 hESCs were transfected in mTesR1 medium with the addition of 4 µg/ml (working concentration) polybrene and concentrated viral particles (NC, FXR1 OE).  After 48-72 hours, hESCs were induced to differentiate into the mesoderm using differentiation medium containing BMP4 and bFGF for 0, 2, and 4 days.  The cytoplasmic and nuclear cell fractions of hESCs were separated using NE-PER nuclear and cytoplasmic extraction reagents (Thermo Fisher).

tag: cell type

value: FXR1 overexpression

value: hESC differentiation into mesoderm

tag: time

value: Day 4