title: T24A

tag: patient

tag: tissue type

tag: sample type

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: 28-08-0005-6_post_0

status: Public on Dec 18 2024

type: SRA

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

country: USA

institute: Benaroya Research Institute

library_source: transcriptomic

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads. The FASTQs were aligned to the University of California Santa Cruz (UCSC) Human genome assembly version 38.91, using STAR v.2.4.2a. Duplicate filtering, QC and metrics analysis was performed using the Picard 1.134 family of tools[ref]. For quality control, samples were kept that had human aligned counts > 250,0001 million mapped reads and median coefficient of variation (CV) coverage < 0.956. Genes were filtered to include those that had a trimmed mean of M values (TMM) normalization count of at least 1.20.8 in at least 23 samples and further filtered for only protein coding genes. Normalized counts were transformed to log2 counts per million mapped reads along with observations level weights using voomWithQualityWeights from the limma R package version 3.5.1.(Ritchie ME et al. Nucleic Acids Res. 2015;20;43(7):e47) Sequencing was performed in 3 sample batches and a batch correction was done using limma removeBatcheffects.
Differentially expressed genes were then coassociated into modules using weighted gene correlation network analysis (WGCNA)
Assembly: GRCh38
Supplementary files format and content: csv file voom normalized counts

molecule: total RNA

organism: Homo sapiens

source_name: nasal lavage sample

extract_protocol:
Total RNA was isolated from pre- and post NAC nasal lavage samples.  Cell pellets were collected in RNAprotect Saliva Reagent (Qiagen) with extraction using the RNeasy MinElute spin column (Qiagen) following the manufacturer’s protocol. Total RNA was isolated from nasal cell pellets in RNAprotect Saliva Reagent (Qiagen). Samples were centrifuged for 10 minutes at 10,000g, supernatant was removed, and the cell pellet was resuspended in 350μl RLT Buffer + 1% beta mercaptoethanol. The sample was vortexed for 1-2 seconds, sonicated for 30 seconds, spun through a Qiashredder column (Qiagen) and then extracted using the RNeasy MinElute spin column (Qiagen) following the manufacturer’s protocol. RNA quality was assessed using RNA electrophoresis (Agilent) and NanoDrop 1000 (NanoDrop Products, Thermo Fisher Scientific).
Sequencing libraries were constructed from total RNA using SMART-Seq v4 Ultra Low Input RNA Kit (Takara) and clustered onto a flowcell using a cBOT amplification system with a HiSeq SR v4 Cluster Kit (Illumina)

tag: participant id

tag: Sex

value: Male

tag: treatment

value: Placebo

tag: age

tag: month

tag: nac

value: post

tag: tnss

tag: tsneez

tag: dose

tag: batch

tag: pct reads

tag: median cv

tag: tissue

value: nasal lavage sample


title: 28-03-0025-1_post_12

value: SCIT


title: control, R13055

city: New York City

first: Michael

middle: S

last: Breen

state: NY

address: 1468 Madison Ave

department: Depts. of Psychiatry, Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw RNA sequences were aligned to the hg38 reference genome from Ensembl via the STAR algorithm.
Quality control checks, including assessments of GC content, duplication rates, gene body coverage, and library complexity, were carried out using RSeQC30 and Picard tools (https://broadinstitute.github.io/picard/). Gene expression levels were quantified with featureCounts and the resulting expression matrix was curated to retain genes present in at least one-third of our sample set. This matrix was then normalized through the VOOM method.
Assembly: hg38
Supplementary files format and content: Raw count data were generated with featureCounts and are provided as a separate matrix.

source_name: Caudate

extract_protocol:
Total RNA was extracted from all tissue samples using AllPrep DNA/RNA Mini Kit (Qiagen Cat No./ID: 80204).
Paired-end strand-specific sequencing libraries were prepared from 300ng total RNA using the TruSeq Stranded Total RNA Library Preparation kit with Ribo-Zero Gold ribosomal RNA depletion which removes rRNA and mtRNA. The libraries were then sequenced on an Illumina HiSeq 3000 at the Promega Sequencing Facility, producing a median of 46.9 million reads per sample.

value: Caudate

tag: cell type

value: Postmortem brain tissue

value: M

tag: group/disease

value: control

tag: rin


title: N24

city: Oxford

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

description:
Freshbiopsies.rds
Freshbiopsies_epithelial_reclustered.rds
Freshbiopsies_endothelial_ccRCC_and_normal_reclustered.rds
Freshbiopsies_pericytes_ccRCC_and_normal_reclustered.rds
Freshbiopsies_macrophages_ccRCC_and_normal_reclustered.rds
Freshbiopsies_Tcells_ccRCC_and_normal_reclustered.rds

library_source: transcriptomic single cell

data_processing:
Demultiplexing of sequencing results, barcode processing, read alignment, and UMI counting were performed using the Illumina 10x Cell Ranger analysis pipeline v6.1.1 with default parameters. Raw reads for each sample were aligned to GRCh38 reference genome, refdata-gex-GRCh38-2020-A.tar.gz, which was provided by 10X Genomics, using Cell Ranger. Cell hashing was used to pool cultured samples. Cells with detected genes < 500, fraction of mitochondrially-encoded reads > 0.5, or detected genes > 3x median for each sample as well as Scrublet73 predicted doublets (expected doublet rate 0.095) were removed. The threshold for mitochondrially-encoded reads was used to allow for the high mitochondrial content in renal tubular epithelial cells and was consistent with an observed bimodal distribution and with previous scRNA-seq analysis of renal tissue. For the pooled, hash tagged, cultured cells, a previously described hashing-based doublet detection strategy, implemented in HTODemux78 was employed to identify doublets.
Assembly: GRCh38
Supplementary files format and content: Seurat objects in rds format

molecule: polyA RNA

source_name: Kidney

growth_protocol: Cultured cells were maintained in growth medium in a humidified incubator or hypoxia chamber with 5%CO2 at 37degreesC.

extract_protocol:
For primary cultures, cells were detached using TrypleExpress and labelled with TotalSeq-A ‘hashtag’ antibodies (Biolegend) prior to analysis. For freshly-biopsied samples, single cell suspensions were generated using MACS Tumor Dissociation Kit enzymes in addition to Collagenase II, DNase I and trypsin prior to analysis.
10x Genomics 3' GEX v3.1

treatment_protocol: For physoxia and hypoxia conditions, an 'In Vivo2 400' Hypoxia Work Station (Ruskinn Technology) was used to obtain the desired ambient oxygen concentration. For PT2385 (Belzutifan) treatments, cells were treated with 1uM drug in growth medium, or DMSO (vehicle only control) for 16 hours.

tag: patient

value: Patient 24

value: Kidney

tag: tissue type

value: Background normal kidney

tag: sample type

value: Freshly-dissociated biopsy

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: control, R13151

tag: Sex


title: control, R13045


title: 28-03-0025-1_pre_12

tag: participant id

tag: treatment

tag: age

tag: month

tag: nac

value: pre

tag: tnss

tag: tsneez

tag: dose

tag: batch


title: T23C

description:
Freshbiopsies.rds
Freshbiopsies_epithelial_reclustered.rds
Freshbiopsies_epithelial_T23_RO_reclustered.rds

tag: patient

value: Patient 23

tag: tissue

tag: tissue type

value: Oncocytoma tumor

tag: sample type


title: 28-03-0025-1_post_0

tag: pct reads

tag: median cv


title: control, R13033

tag: cell type

tag: group/disease

tag: rin


title: 28-07-0019-7_post_0

tag: participant id

tag: Sex

value: Female

tag: treatment


title: T23A

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: 28-07-0019-7_pre_0

tag: age

tag: month

tag: nac

tag: tnss

tag: tsneez

tag: dose

tag: batch

tag: tissue


title: 28-03-0023-5_post_12

tag: participant id

value: Male

tag: pct reads

tag: median cv


title: 28-07-0016-9_pre_0

tag: Sex

tag: treatment


title: control, R12976

tag: cell type

tag: group/disease

tag: rin


title: T23B

tag: patient

tag: tissue type

tag: sample type

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: control, R13124

tag: tissue


title: control, R4075

source_name: DLPFC

value: DLPFC


title: 28-07-0016-9_post_0

tag: participant id

tag: age

tag: month

tag: nac

value: post

tag: tnss

tag: tsneez

tag: dose

tag: batch

tag: pct reads


title: OCD, R5594

tag: cell type

tag: Sex

tag: group/disease

value: OCD

tag: rin


title: 28-07-0014-4_post_0

tag: treatment

value: SCIT

tag: median cv

value: nasal lavage sample


title: T22E

description:
Freshbiopsies.rds
Freshbiopsies_epithelial_reclustered.rds
Freshbiopsies_epithelial_T22_pRCC_reclustered.rds

tag: patient

value: Patient 22

tag: tissue type

value: pRCC tumor

tag: sample type

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: control, R4047

tag: tissue

value: Postmortem brain tissue

value: M

value: control


title: N23

value: Kidney

value: Background normal kidney


title: 28-03-0023-5_pre_12

tag: participant id

tag: age

tag: month

tag: nac

value: pre

tag: tnss

tag: tsneez

tag: dose

tag: batch

tag: pct reads


title: T22D

tag: patient

tag: tissue type

tag: sample type

value: Freshly-dissociated biopsy


title: 28-07-0014-4_pre_0

tag: Sex

tag: treatment

tag: median cv


title: 28-08-0005-6_pre_0

value: Placebo


title: CEA_scRNAseq_1

city: New York

last: Gildea

state: New York

address: 550 1st avenue

institute: NYU Langone Health

description: 10x Genomics

data_processing:
Cell Ranger (10x Genomics, v2.1.1 or v3.1.0) was used to performalignment (GRCh38, Ensembl 93), filtering, barcode counting and UMI counting of sequencing reads from fastq files.
Assembly: GRCh38
Supplementary files format and content: Tab -separated values files and matrix files

source_name: carotid plaque

extract_protocol:
Briefly, plaques were washed, minced and digested in DMEM supplemented with 10% vol/vol FBS, 1 mg ml−1 collagenase type IV (Sigma, C5138) and 0.3 mg ml–1 DNase I (Sigma, DN25), hyaluronidase (Sigma, H3506), collagenase type XI (Sigma, C7657) and collagenase type II (Sigma, C6885) in a gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec) set to 0–25 rpm in five spin cycles at 37 °C for 40 min. Digested specimens were sequentially filtered through 70-μm and 40-μm cell strainers (Fisher Scientific, 22363547 and 22363548, respectively), then centrifuged at 300 g for 8 min. Dead cells were removed using an EasySep Dead Cell Removal (Annexin V) kit (StemCell Technologies, 17899) and then a leukocyte enrichment assay was carried out using an EasySep Release Human CD45 positive selection kit (StemCell Technologies, 100-0105), following the manufacturers’ instructions, respectively. Live, CD45+ cells were counted using a Cellometer Auto 2000 (Nexcellom) and loaded onto the Chromium Controller (10x Genomics)
scRNA-seq libraries were prepared using the Chromium Single Cell 3’ Library v3 reagent, Gel Bead and Multiplex Kit and Chip Kit (10X Genomics; 1000268, 1000215 and 100127, respectively) according to the manufacturer’s instructions.

value: carotid plaque

tag: cell type

value: CD45+ Immune cells

tag: subject status

value: patients undergoing carotid endarterectomy


title: ED, R23672

tag: tissue

value: DLPFC

value: F

tag: group/disease

value: ED

tag: rin


title: T22C

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: 28-07-0013-3_post_0

tag: participant id

value: Female

tag: age

tag: month

tag: nac

value: post

tag: tnss

tag: tsneez

tag: dose

tag: batch

tag: pct reads

value: nasal lavage sample


title: 28-03-0009-3_post_0

tag: Sex

value: Male

tag: treatment

tag: median cv

tag: tissue


title: 28-03-0020-7_pre_12

value: SCIT


title: 28-03-0025-1_pre_0


title: 28-03-0020-7_post_12


title: T22A

tag: patient

value: Patient 22

tag: tissue type

value: pRCC tumor

tag: sample type

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment


title: ED, R3682

tag: cell type

value: Postmortem brain tissue

tag: group/disease

tag: rin


title: 28-07-0013-3_pre_0

tag: participant id

tag: age

tag: month

tag: nac

value: pre

tag: tnss

tag: tsneez


title: 28-07-0010-0_post_0

tag: Sex

tag: treatment

tag: dose

tag: batch

tag: pct reads

tag: median cv


title: control, R22675

tag: tissue

value: control


title: T22B

tag: patient

value: Kidney

tag: tissue type

tag: sample type

value: Freshly-dissociated biopsy

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: N22

value: Background normal kidney


title: 28-02-0007-2_post_12

tag: participant id

tag: age

tag: month

tag: nac

tag: tnss

tag: tsneez


title: ED, R22673

tag: cell type

tag: Sex

tag: group/disease

tag: rin


title: control, R22567

tag: tissue


title: 28-07-0010-0_pre_0

tag: treatment

tag: dose

tag: batch

tag: pct reads

tag: median cv


title: T18B

description:
Freshbiopsies.rds
Freshbiopsies_epithelial_reclustered.rds
Freshbiopsies_endothelial_ccRCC_and_normal_reclustered.rds
Freshbiopsies_pericytes_ccRCC_and_normal_reclustered.rds
Freshbiopsies_macrophages_ccRCC_and_normal_reclustered.rds
Freshbiopsies_Tcells_ccRCC_and_normal_reclustered.rds
Freshbiopsies_epithelial_T18B_ccRCC_reclustered.rds

tag: patient

value: Patient 18

tag: tissue type

value: ccRCC tumor

tag: sample type

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: 28-07-0007-9_post_0

tag: participant id

tag: Sex

value: Placebo

tag: age

tag: month

tag: nac

tag: tnss

tag: tsneez


title: T18A

description:
Freshbiopsies.rds
Freshbiopsies_epithelial_reclustered.rds
Freshbiopsies_endothelial_ccRCC_and_normal_reclustered.rds
Freshbiopsies_pericytes_ccRCC_and_normal_reclustered.rds
Freshbiopsies_macrophages_ccRCC_and_normal_reclustered.rds
Freshbiopsies_Tcells_ccRCC_and_normal_reclustered.rds
Freshbiopsies_epithelial_T18A_ccRCC_reclustered.rds

tag: tissue


title: control, R21738

value: DLPFC

tag: cell type

value: F

tag: group/disease

tag: rin


title: 28-02-0007-2_post_0

tag: treatment

value: post

tag: dose

tag: batch

tag: pct reads

tag: median cv


title: OCD, R21640

value: M

value: OCD


title: 28-02-0007-2_pre_0

value: Male

value: SCIT

value: nasal lavage sample


title: N18D

description:
Freshbiopsies.rds
Freshbiopsies_epithelial_reclustered.rds
Freshbiopsies_endothelial_ccRCC_and_normal_reclustered.rds
Freshbiopsies_pericytes_ccRCC_and_normal_reclustered.rds
Freshbiopsies_macrophages_ccRCC_and_normal_reclustered.rds
Freshbiopsies_Tcells_ccRCC_and_normal_reclustered.rds
Freshbiopsies_epithelial_N18_proximal_reclustered.rds

tag: patient

tag: tissue type

tag: sample type

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: control, R21581

tag: tissue

tag: cell type

value: Postmortem brain tissue

tag: Sex


title: N18C


title: 28-06-0005-8_post_0

tag: participant id

value: Female

tag: treatment

tag: age

tag: month

tag: nac

tag: tnss

tag: tsneez


title: 28-02-0004-7_post_12

tag: dose

tag: batch

tag: pct reads

tag: median cv


title: 28-03-0009-3_pre_0

value: pre


title: N18B

tag: patient

value: Kidney

tag: tissue type

tag: sample type

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions


title: 28-02-0004-7_pre_12

tag: participant id

tag: Sex

tag: treatment

tag: tissue


title: control, R21515

tag: cell type

tag: group/disease

value: control

tag: rin


title: 28-06-0005-8_pre_0

tag: age

tag: month

tag: nac

tag: tnss

tag: tsneez

tag: dose

tag: batch


title: control, R21361


title: N18A

tag: patient

tag: tissue type

value: Background normal kidney

tag: sample type

value: Freshly-dissociated biopsy

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: 28-02-0007-2_pre_12

tag: participant id

tag: Sex

tag: treatment

tag: pct reads

tag: median cv

tag: tissue


title: 28-05-0007-6_post_0

tag: age

tag: month

tag: nac

tag: tnss


title: E_BI07_BCR

city: Jinan

first: yuwei

last: Zhang

state: Shandong

address: No.16992 Jingshi Road

department: Pathogenobiology

country: China

institute: SDCDC

description: 10x Genomics

data_processing:
CellRanger software (10× Genomics, v.7.0.0) with the default settings was used to align the sequenced fastq files to the human reference version GRCh38 and generate a unique molecular identifier (UMI)–filtered gene and protein expression count matrix for each sample by the “Cellranger count”and "Cellranger vdj" function.
Assembly: human reference version GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMC

extract_protocol:
16,000 cells per reaction, gel beads and partitioning oil were loaded to Chromium Next GEM Chip K for gel GEM generation and barcoding on Chromium Controller (10X genomics). The GEMs were transferred to prepare GEM-RT incubation.
According to chromium next GEM single cell 5' v2 user guide(10X genomics), 50ng cDNA per sample was used to construct 5ʹ Gene Expression (GEX) and V(D)J library

tag: cell type

value: PBMC

value: BA.5.2 breakthrough infection after 3 dose BBIBP-CorV and 1 dose aerosolized Ad5-nCoV


title: 28-05-0007-6_pre_0

tag: tsneez

tag: dose

tag: batch


title: T17A-G mix PT2385

description:
Cells that were initially incompletely attached in T17 cultures (A-G) were pooled to generate the culture
Cultured.rds

tag: patient

value: Patient 17

tag: tissue type

value: ccRCC tumor

tag: sample type

value: Patient-derived primary culture

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

value: Culture treated with 1uM PT2385, 16 hours

tag: culture maintenance_conditions

value: 5%O2, Advanced DMEM/F12 1:1, 1X Glutamax, 1X anti-anti, 1X insulin-transferrin-sodium selenite, 4 ng/ml triiodo-L-thyronine, 100 ng/ml epidermal growth factor, 36 ng/ml hydrocortisone and 10% fetal bovine serum

value: anti-human 5 (AAGTATCGTTTCGCA)


title: 28-05-0006-5_post_0

tag: participant id

tag: Sex

tag: treatment

value: Placebo

value: post

tag: pct reads

tag: median cv


title: E_BI09_BCR

description: 10x Genomics


title: T17A-G mix

tag: tissue

tag: total-seq a_hashtag_oligo

value: anti-human 3 (TTCCGCCTCTCTTTG)

tag: genetic syndrome


title: E_BI02_BCR

description: 10x Genomics

tag: cell type


title: 28-07-0007-9_pre_0

value: Male

tag: age

tag: month

tag: nac

tag: tnss

tag: tsneez

tag: dose

tag: batch

value: nasal lavage sample


title: control, R21359

value: DLPFC

value: Postmortem brain tissue

value: F

tag: group/disease

tag: rin


title: ED, R20559

tag: Sex

value: ED


title: T17A-G mix DMSO

tag: patient

value: Kidney

tag: tissue type

tag: sample type

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

value: Culture treated with DMSO control, 16 hours

tag: culture maintenance_conditions

value: anti-human 4 (AGTAAGTTCAGCGTA)


title: 28-05-0005-9_post_0

tag: participant id

tag: treatment

tag: age

tag: pct reads

tag: median cv

tag: tissue


title: D_BIC03_BCR

description: 10x Genomics

tag: cell type

value: PBMC

value: SARS-Cov-2 naïve with 3 dose BBIBP-CorV and 1 dose aerosolized Ad5-nCoV


title: control, R21345

value: M

tag: group/disease

value: control


title: D_BIC02_BCR

description: 10x Genomics


title: T20AB mix

description:
Two small biopsies from different regions of T20 (A and B) were pooled to generate the culture
Cultured.rds

value: Patient 20

value: ccRCC tumor

value: Patient-derived primary culture

value: 5%O2, Advanced DMEM/F12 1:1, 1X Glutamax, 1X anti-anti, 1X insulin-transferrin-sodium selenite, 4 ng/ml triiodo-L-thyronine, 100 ng/ml epidermal growth factor, 36 ng/ml hydrocortisone and 10% fetal bovine serum

tag: total-seq a_hashtag_oligo

value: anti-human 5 (AAGTATCGTTTCGCA)

tag: genetic syndrome


title: N20 hypoxia

description: Cultured.rds

tag: patient

value: Background normal kidney

value: 16 hours

value: anti-human 3 (TTCCGCCTCTCTTTG)


title: control, R20469

value: DLPFC

value: Postmortem brain tissue

tag: Sex

value: F

tag: rin


title: ED, R20558

value: ED


title: D_BIC01_BCR

description: 10x Genomics


title: ED, R20212


title: 28-05-0004-3_post_0

value: Female

value: SCIT

tag: month

tag: nac

value: post

tag: tnss

tag: tsneez

tag: dose

tag: batch

value: nasal lavage sample


title: 28-05-0006-5_pre_0

tag: participant id

tag: treatment

value: Placebo

tag: age

value: pre


title: 28-05-0004-3_pre_0

tag: pct reads

tag: median cv

tag: tissue


title: C_YT07_BCR

description: 10x Genomics

tag: cell type

value: PBMC

value: BF.7 breakthrough infection after 3 dose inactivated vaccine


title: 28-05-0002-1_post_0

value: Male


title: N18C hypoxia

description: Cultured.rds

value: Patient 18

value: Kidney

tag: tissue type

tag: sample type

value: Patient-derived primary culture

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions

value: 5%O2, Advanced DMEM/F12 1:1, 1X Glutamax, 1X anti-anti, 1X insulin-transferrin-sodium selenite, 4 ng/ml triiodo-L-thyronine, 100 ng/ml epidermal growth factor, 36 ng/ml hydrocortisone and 10% fetal bovine serum

tag: total-seq a_hashtag_oligo

value: anti-human 5 (AAGTATCGTTTCGCA)

tag: genetic syndrome


title: C_YT02_BCR

description: 10x Genomics


title: 28-05-0002-1_pre_0

tag: Sex

tag: month

tag: nac

tag: tnss

tag: tsneez

tag: dose


title: N18C physoxia

description: Cultured.rds

tag: patient

value: Background normal kidney

value: anti-human 1 (GTCAACTCTTTAGCG)


title: B_BI06_BCR

description: 10x Genomics

tag: treatment

value: BA.5.2 breakthrough infection after 3 dose inactivated vaccine


title: N18C normoxia

description: Cultured.rds

tag: tissue

value: 16 hours

value: anti-human 4 (AGTAAGTTCAGCGTA)


title: 28-04-0026-1_post_0

tag: participant id

value: SCIT

tag: age

value: post

tag: batch

tag: pct reads

tag: median cv


title: control, R19219

value: DLPFC

tag: cell type

value: Postmortem brain tissue

value: F

tag: group/disease

value: control

tag: rin


title: control, R19938

tag: Sex


title: 28-04-0026-1_pre_0

value: Male

tag: month

value: pre

value: nasal lavage sample


title: 28-05-0005-9_pre_0

value: Placebo

tag: nac


title: N20 physoxia

description: Cultured.rds

value: Patient 20

value: Kidney

tag: tissue type

tag: sample type

value: Patient-derived primary culture

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions

value: 5%O2, Advanced DMEM/F12 1:1, 1X Glutamax, 1X anti-anti, 1X insulin-transferrin-sodium selenite, 4 ng/ml triiodo-L-thyronine, 100 ng/ml epidermal growth factor, 36 ng/ml hydrocortisone and 10% fetal bovine serum

tag: total-seq a_hashtag_oligo

tag: genetic syndrome


title: T17G

description:
Cultured.rds
Cultured_epithelial_T17_ccRCC_reclustered.rds

tag: patient

value: Patient 17

tag: tissue

value: ccRCC tumor

value: anti-human 2 (TGATGGCCTATTGGG)


title: C_YT11_BCR

description: 10x Genomics

value: PBMC

tag: treatment

value: BF.7 breakthrough infection after 3 dose inactivated vaccine


title: ED, R18928

value: DLPFC

tag: cell type

value: ED


title: B_BI03_BCR

description: 10x Genomics

value: BA.5.2 breakthrough infection after 3 dose inactivated vaccine


title: control, R18887

value: Postmortem brain tissue

value: M

tag: group/disease

value: control


title: T17F

value: anti-human 1 (GTCAACTCTTTAGCG)


title: 28-04-0012-6_post_0

tag: participant id

value: Female

value: Placebo

tag: age

value: post

tag: tnss

tag: tsneez

tag: dose

tag: batch

tag: pct reads

tag: median cv

value: nasal lavage sample


title: A_LC35_BCR

description: 10x Genomics

value: SARS-Cov-2 naïve with 3 dose inactivated vaccine


title: 28-04-0012-6_pre_0

tag: Sex

tag: month

tag: nac

value: pre


title: ED, R20155

value: F

tag: rin


title: A_LC12_BCR

description: 10x Genomics


title: T17E

tag: patient

value: Patient 17

value: Kidney

tag: tissue type

value: ccRCC tumor

tag: sample type

value: Patient-derived primary culture

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions

value: 5%O2, Advanced DMEM/F12 1:1, 1X Glutamax, 1X anti-anti, 1X insulin-transferrin-sodium selenite, 4 ng/ml triiodo-L-thyronine, 100 ng/ml epidermal growth factor, 36 ng/ml hydrocortisone and 10% fetal bovine serum

tag: total-seq a_hashtag_oligo

value: anti-human 5 (AAGTATCGTTTCGCA)

tag: genetic syndrome


title: control, R20007

tag: tissue

value: DLPFC

tag: cell type

value: Postmortem brain tissue

tag: group/disease


title: N20 normoxia

description: Cultured.rds

value: Patient 20

value: Background normal kidney

value: 16 hours

value: anti-human 2 (TGATGGCCTATTGGG)


title: 28-04-0008-1_post_0

tag: participant id

value: Male

tag: treatment

value: Placebo

tag: age

value: post

tag: tnss

tag: tsneez

tag: dose

tag: batch

tag: pct reads

tag: median cv


title: control, R18752

tag: Sex

value: control

tag: rin


title: B_BI04_BCR

description: 10x Genomics

value: PBMC

value: BA.5.2 breakthrough infection after 3 dose inactivated vaccine


title: 28-04-0008-1_pre_0

tag: month

tag: nac

value: pre

value: nasal lavage sample


title: T17D

tag: patient

value: Patient 17

value: Kidney

tag: tissue type

value: ccRCC tumor

tag: sample type

value: Patient-derived primary culture

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions

tag: total-seq a_hashtag_oligo

value: anti-human 4 (AGTAAGTTCAGCGTA)

tag: genetic syndrome


title: control, R18722

tag: tissue

value: DLPFC

tag: cell type

value: Postmortem brain tissue

value: F

tag: group/disease


title: E_BI09_TCR

description: 10x Genomics

tag: treatment

value: BA.5.2 breakthrough infection after 3 dose BBIBP-CorV and 1 dose aerosolized Ad5-nCoV


title: T17C

value: 5%O2, Advanced DMEM/F12 1:1, 1X Glutamax, 1X anti-anti, 1X insulin-transferrin-sodium selenite, 4 ng/ml triiodo-L-thyronine, 100 ng/ml epidermal growth factor, 36 ng/ml hydrocortisone and 10% fetal bovine serum

value: anti-human 3 (TTCCGCCTCTCTTTG)


title: 28-03-0024-6_post_0

tag: participant id

tag: Sex

value: Male

value: Placebo

tag: age

value: post

tag: tnss

tag: tsneez

tag: dose

tag: batch

tag: pct reads

tag: median cv


title: E_BI07_TCR

description: 10x Genomics

value: PBMC


title: ED, R18681

value: ED

tag: rin


title: T17B

tag: patient

tag: tissue type

tag: sample type

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

tag: drug treatment

tag: culture maintenance_conditions

value: anti-human 2 (TGATGGCCTATTGGG)


title: 28-03-0024-6_pre_0

tag: participant id

tag: treatment

tag: month

tag: nac

value: pre

tag: tissue

value: nasal lavage sample


title: OCD, R18660

tag: cell type

tag: Sex

tag: group/disease

value: OCD


title: T17A

value: Patient 17

value: Kidney

value: ccRCC tumor

value: Patient-derived primary culture

tag: total-seq a_hashtag_oligo

value: anti-human 1 (GTCAACTCTTTAGCG)

tag: genetic syndrome


title: 28-03-0023-5_post_0

value: SCIT

tag: age

tag: tnss

tag: tsneez

tag: dose

tag: batch

tag: pct reads

tag: median cv


title: ED, R18764

value: DLPFC

value: Postmortem brain tissue

value: F

tag: rin


title: OCD, R18642


title: E_BI02_TCR

description: 10x Genomics

tag: treatment

value: BA.5.2 breakthrough infection after 3 dose BBIBP-CorV and 1 dose aerosolized Ad5-nCoV


title: N17 hypoxia

description: Cultured.rds

tag: patient

tag: tissue type

value: Background normal kidney

tag: sample type

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia

value: 16 hours

tag: drug treatment

tag: culture maintenance_conditions

value: 5%O2, Advanced DMEM/F12 1:1, 1X Glutamax, 1X anti-anti, 1X insulin-transferrin-sodium selenite, 4 ng/ml triiodo-L-thyronine, 100 ng/ml epidermal growth factor, 36 ng/ml hydrocortisone and 10% fetal bovine serum


title: N17 physoxia

description: Cultured.rds

tag: tissue

tag: total-seq a_hashtag_oligo

value: anti-human 3 (TTCCGCCTCTCTTTG)

tag: genetic syndrome


title: 28-03-0023-5_pre_0

tag: participant id

tag: Sex

value: Male

tag: age

tag: month

tag: nac

value: pre

tag: tnss

tag: tsneez


title: D_BIC02_TCR

description: 10x Genomics

tag: cell type

value: PBMC

tag: treatment

value: SARS-Cov-2 naïve with 3 dose BBIBP-CorV and 1 dose aerosolized Ad5-nCoV


title: OCD, R18624

tag: group/disease

value: OCD

tag: rin


title: ED, R18639

value: ED


title: N17 normoxia

description: Cultured.rds

tag: patient

value: Patient 17

value: Kidney

tag: tissue type

tag: sample type

value: Patient-derived primary culture

tag: ambient o2_concentration

tag: duration of_oxygenation/hypoxia


title: D_BIC01_TCR

description: 10x Genomics


title: 28-03-0020-7_post_0

value: SCIT

value: post

tag: dose

tag: batch

tag: pct reads

tag: median cv

tag: tissue

value: nasal lavage sample


title: A_LC11_BCR

description: 10x Genomics

value: SARS-Cov-2 naïve with 3 dose inactivated vaccine


title: 28-03-0020-7_pre_0

tag: participant id

tag: Sex

tag: age

tag: month

tag: nac


title: ED, R18620

value: DLPFC

tag: cell type

value: Postmortem brain tissue

value: F

tag: group/disease


title: 28-02-0004-7_post_0

value: Female

tag: treatment

value: Placebo

tag: tnss

tag: tsneez


title: ED, R18618

tag: rin


title: C_YT11_TCR

description: 10x Genomics

value: BF.7 breakthrough infection after 3 dose inactivated vaccine


title: C_YT07_TCR

description: 10x Genomics

value: PBMC


title: 28-02-0004-7_pre_0

value: pre


title: ES-2 shMAML2, biological rep2

city: Gainesville

first: Lizi

last: Wu

state: FL

address: 2033 Mowry Road

institute: University of Florida

data_processing:
The sequencing reads were aligned to the human hg38 reference genome from UCSC using HISAT2 v2.0.4 splice-aware aligner.
Ambiguous reads mapping to multiple regions in the genome or reads with a MAPQ score of less than 10 were further filtered out.
Quantification of gene and transcript levels was performed using Partek Genomics Suite (version 7.18 Partek Inc, St. Louis MI) based on hg38 RefSeq transcripts 88 (2019-02-01).
Genes with absent read counts across all samples were excluded from subsequent analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw read counts for each sample.
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample.

source_name: human ovarian clear cell carcinoma

growth_protocol: ES2 and HEK293FT cells were maintained in Dulbecco's Modified Eagle's Medium (DMEM, Corning Cellgro) supplemented with 10% fetal bovine serum (FBS, Gibco) and 1% penicillin-streptomycin (Corning Cellgro). Cells were grown at 37°C under 5% CO2.

extract_protocol:
RNA was isolated with the Trizol Reagent (Invitrogen) and purified by the Qiagen Column with in column DNase digestion.
RNA-seq libraries (non-strand-specific, paired end) were prepared with the NEBNext® Ultra™ RNA Library Prep Kit (Illumina, San Diego, CA) and were sequenced according to the paired-end 150bp protocol using NovaSeq 6000.

treatment_protocol: ES-2 cells were transduced with pLKO.1-based lentiviruses expressing nontargeting control shRNA or shRNA targeting MAML2 for 8 hours on two consecutive days. RNA was isolated from transduced cells 96 hours after the first viral infection and subjected to RNA-seq.

value: human ovarian clear cell carcinoma

tag: cell line

value: ovarian cancer cells

value: MAML2 shRNA


title: ES-2 shCtl, biological rep2

value: non-targeting shRNA


title: 28-01-0012-8_post_0

tag: dose


title: ES-2 shMAML2, biological rep1


title: D_BIC03_TCR

description: 10x Genomics

value: SARS-Cov-2 naïve with 3 dose BBIBP-CorV and 1 dose aerosolized Ad5-nCoV


title: B_BI06_TCR

description: 10x Genomics

value: BA.5.2 breakthrough infection after 3 dose inactivated vaccine


title: ED, R18607

value: ED


title: 28-01-0012-8_pre_0

tag: batch

value: nasal lavage sample


title: control, R18580

value: control


title: ED, R18579

value: DLPFC

value: M


title: B_BI04_TCR

description: 10x Genomics


title: B_BI03_TCR

description: 10x Genomics


title: control, R18574

value: Postmortem brain tissue

value: F


title: Tibial nerves of TLA patient 3

city: Shanghai

first: Xiangyun

last: Yao

address: 600 Yishan Road

institute: Shanghai Sixth People's Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Peripheral nerves

extract_protocol:
For single-cell RNA sequencing experiments, tibial nerves from donors (4 DPN patients, 3 TLA patients) were rapidly frozen on liquid nitrogen in the operating room and stored until tissue digestion. Single-cell suspensions were generated by enzyme digestion and subjected to fluorescenceactivated cell sorting (FACS) to exclude doublets, debris, and DAPI+ dead cells.
Single-cell RNA sequencing of human injured nerves was carried out using ChromiumTM Single Cell 3' Solution (10X Genomics). Libraries were sequenced using an Illumina NovaSeq6000 platform (performed by CapitalBio Technology, Beijing). The human nerve datasets were integrated and then analyzed for clustering and t-SNE visualization using the Seurat 4.0 package.

value: Peripheral nerves

value: Nerve cell

tag: subject status

value: TLA patient


title: ES-2 shCtl, biological rep1


title: 28-01-0006-2_post_0

value: Male

value: Placebo

value: post

tag: pct reads

tag: median cv


title: Tibial nerves of TLA patient 2

description: 10x Genomics

tag: tissue


title: A_LC35_TCR

description: 10x Genomics

value: PBMC

value: SARS-Cov-2 naïve with 3 dose inactivated vaccine


title: Tibial nerves of TLA patient 1

description: 10x Genomics


title: control, R18281

tag: Sex


title: control, R18206


title: 28-08-0018-5_pre_0

tag: participant id

value: SCIT

tag: age

value: pre


title: Tibial nerves of DPN patient 4

description: 10x Genomics

value: DPN patient


title: 28-09-0027-9_post_0

value: Female

tag: month

tag: nac

value: nasal lavage sample


title: OCD, R18041

value: DLPFC

tag: cell type

tag: group/disease

value: OCD


title: C_YT02_TCR

description: 10x Genomics

tag: treatment

value: BF.7 breakthrough infection after 3 dose inactivated vaccine


title: A_LC11_TCR

description: 10x Genomics


title: 28-09-0027-9_pre_0

tag: tnss

tag: tsneez


title: Tibial nerves of DPN patient 3

description: 10x Genomics


title: OCD, R18040

value: Postmortem brain tissue

value: M

tag: rin


title: Tibial nerves of DPN patient 2

description: 10x Genomics

value: Peripheral nerves

value: Nerve cell


title: 28-09-0012-4_post_0

value: Male

tag: dose


title: 28-01-0006-2_pre_0

value: Placebo

tag: batch


title: E_BI09

description: 10x Genomics

value: BA.5.2 breakthrough infection after 3 dose BBIBP-CorV and 1 dose aerosolized Ad5-nCoV


title: E_BI07

description: 10x Genomics

value: PBMC


title: control, R18030

value: F

value: control


title: control, R18037


title: 28-09-0012-4_pre_0

value: pre


title: E_BI02

description: 10x Genomics


title: Tibial nerves of DPN patient 1

description: 10x Genomics

tag: subject status

value: DPN patient


title: 28-09-0021-2_pre_0

tag: pct reads


title: PPD.UV.24h.3

city: Lausanne

first: Paris

last: Jafari

address: Genopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

data_processing:
Data cleaning: Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011). Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1). Remaining reads were further filtered for low complexity with reaper (v. 15-065).
Reads were aligned against the GRCh38.102 genome using STAR (v. 2.5.3a). The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1) using GRCh38.102 gene annotation. Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7).
Assembly: GRCh38.102
Supplementary files format and content: tab-deliminated text files include log2 transformed normalized cpm values

source_name: Skin

growth_protocol: Cells were maintained in EpiLife™ Medium (MEPI500CA, Invitrogen) supplemented with Human Keratinocyte Growth Supplement, and Penicillin-Streptomycin 10 U/ml, in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (74104 Qiagen) manufacturer's protocol
RNA-seq libraries were prepared from 500 ng of total RNA with the Illumina TruSeq Stranded mRNA reagents (Illumina) using a unique dual indexing strategy and following the official protocol automated on a Sciclone liquid handling robot (PerkinElmer).

treatment_protocol: Cells were exposed to UVB (30mJ/cm2)

value: Skin

tag: cell line

value: NHEK

value: Epithelial keratinocyte

tag: genotype

value: PPARb knockdown

value: UV exposure

tag: time point


title: PPD.UV.24h.2

tag: tissue


title: 28-09-0017-8_post_0

tag: participant id

tag: Sex

value: Female

value: SCIT

tag: age

value: post

tag: median cv

value: nasal lavage sample


title: 28-09-0021-2_post_0

value: Male

tag: month

tag: nac


title: PPD.UV.24h.1

tag: cell type

tag: treatment


title: D_BIC02

description: 10x Genomics

value: SARS-Cov-2 naïve with 3 dose BBIBP-CorV and 1 dose aerosolized Ad5-nCoV


title: control, R18027

value: DLPFC

value: Postmortem brain tissue

value: M

tag: group/disease

tag: rin


title: D_BIC03

description: 10x Genomics

value: PBMC


title: control, R18025

value: control


title: A_LC12_TCR

description: 10x Genomics

value: SARS-Cov-2 naïve with 3 dose inactivated vaccine


title: PPD.NT.24h.3

value: Skin


title: control, R18024


title: 28-09-0017-8_pre_0

value: pre

tag: tnss

tag: tsneez

tag: dose

tag: batch


title: control, R18001


title: C_YT11

description: 10x Genomics

value: BF.7 breakthrough infection after 3 dose inactivated vaccine


title: PPD.NT.24h.2

tag: cell line

value: NHEK

value: Epithelial keratinocyte

tag: genotype

value: PPARb knockdown


title: 28-09-0009-9_post_0

value: Placebo

tag: pct reads

tag: tissue


title: control, R18000

tag: Sex


title: PPD.NT.24h.1

tag: time point


title: C_YT07

description: 10x Genomics


title: control, R17321

value: F


title: C_YT02

description: 10x Genomics


title: control, R17309


title: PPB.UV.24h.3

value: UV exposure


title: 28-09-0029-6_post_0

tag: participant id

value: Male

value: SCIT

tag: age

value: post

tag: median cv

value: nasal lavage sample


title: 28-09-0026-8_post_0

tag: month

tag: nac


title: 28-09-0029-6_pre_0

tag: treatment


title: PPB.UV.24h.2

tag: cell type


title: B_BI06

description: 10x Genomics

value: BA.5.2 breakthrough infection after 3 dose inactivated vaccine


title: PPB.UV.24h.1


title: 28-09-0011-3_post_0

value: Female

tag: tnss


title: control, R17307

value: DLPFC

value: Postmortem brain tissue

tag: group/disease

value: control

tag: rin


title: B_BI04

description: 10x Genomics

value: PBMC


title: PPB.NT.24h.3

value: Skin


title: ED, R17271

value: M

value: ED


title: A_LC35

description: 10x Genomics

value: SARS-Cov-2 naïve with 3 dose inactivated vaccine


title: D_BIC01

description: 10x Genomics

value: SARS-Cov-2 naïve with 3 dose BBIBP-CorV and 1 dose aerosolized Ad5-nCoV


title: OCD, R17237

value: OCD


title: PPB.NT.24h.2

value: NHEK

value: Epithelial keratinocyte

value: PPARb knockdown


title: B_BI03

description: 10x Genomics


title: ED, R17214

value: F


title: 28-09-0018-9_post_0

value: Male

value: SCIT

value: post

tag: tsneez

tag: dose

tag: batch

value: nasal lavage sample


title: A_LC12

description: 10x Genomics


title: PPB.NT.24h.1

tag: cell line

tag: genotype


title: 28-09-0018-9_pre_0

tag: Sex

value: pre

tag: pct reads

tag: tissue


title: control, R17190

value: DLPFC

value: Postmortem brain tissue

value: control


title: PP2.UV.24h.3

value: Skin

value: UV exposure

tag: time point


title: 28-06-0009-7_post_0

tag: participant id

value: Female

tag: age

tag: median cv


title: ED, R17181

value: M

value: ED


title: PP2.UV.24h.2

value: NHEK

tag: treatment


title: 28-06-0009-7_pre_0

tag: month

tag: nac


title: PP2.UV.24h.1

tag: cell type

value: Epithelial keratinocyte


title: control, R17109

tag: group/disease

tag: rin


title: DAP-CDF1_rep2

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

description: Protein-DNA interaction

library_source: genomic

data_processing:
2*75 bp pair-  ended reads
Adaptors were trimmed and low quality reads were filtered with Trim Galore
Alignment to genome sequence with Bowtie2
BAM files are used for peak calling with GEMv3.4, using input files as control
Assembly: ENSEMBLE Solanum tuberosum, DM 1-3-516-R44v4.03 reference genome
Supplementary files format and content: Significant peaks of protein-DNA interactions in narrowpeak fromat generated by GEMv3.4
Library strategy: DAP-seq

molecule: genomic DNA

organism: Solanum tuberosum

source_name: stolon

extract_protocol:
Genomic DNA extraacted with the CTAB method and RNase A treated
gDNA fragmented to 200 bp fragments in average and ligated a a truncated Illumina TruSeq adapter (Y adapter). gDNA library is incubated with recombinant protein expressed in E.coli, previously immobilized with Amylose beads. After binding and washing, DNA is eluted and PCR-amplified with Truseq primers, including a single index.

value: stolon

tag: protein

value: E.coli expressed


title: control, R17043


title: Hep3B IgG rep 3

city: Heidelberg

first: Moritz

last: Mall

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center (DKFZ)

description: Library name: Hep3B IgG rep 3

data_processing:
CUT&RUN data were analysed using the nf-core/cutandrun pipeline v1.0.0 with Nextflow version 21.05.0. Reads were aligned to mm10 or hg38. Software versions: bedtools (v2.30.0), bowtie2 (2.4.2), deeptools (v3.5.0), DESeq2 (v1.28.0), fastqc (v0.11.9), multiqc (v1.11), picard (v2.23.9), python (v3.8.3), samtools (v1.10), Genrich (v0.6.1)(https://github.com/jsh58/Genrich), TrimGalore (v0.6.6), ucsc (v377).
Consensus peaks were defined by running Genrich -m 30 -e chrM -r -l 5 -q 0.3.
To determine peaks containing motifs, we mapped the PROX1 binding motif (CIS-BP ID: M03445_2.00) onto mm10 or hg38, extended each resulting motif peak to a total width of 50 bp, and ran bedtools intersect -wa on the CUT&RUN consensus peaks and motif peaks, respectively.
Genes defined as direct target genes based upon CUT&RUN were determined by running Homer annotatePeaks.pl on the final peak set and filtering for genes with a peak within ±1kb of their TSS.
Assembly: mm10
Assembly: hg38
Supplementary files format and content: individual bigwig coverage files
Supplementary files format and content: Narrow peak files
Library strategy: CUT&Run

growth_protocol:
MEF: Mouse embryonic fibroblasts (MEFs) were harvested from E13.5 embryos of C57BL/6N (wild-type). Wild-type MEFs were transduced with rtTA (FUW-rtTA) and tetO-FLAG-mmProx1 (Prox1 overexpression) lentivirus in MEF medium containing 8μg/ml polybrene (Sigma) for 16 to 20h. Medium was exchanged to MEF medium containing 2μg/ml doxycycline (Sigma) to induce Prox1 overexpression (Prox1 overexpression) for two days followed by nuclei harvesting for CUT&RUN.
Liver: Mouse livers were harvested from 2 to 3-month-old wildtype C57BL/6J mice and directly processed for nuclei isolation using liver swelling buffer (10 mM Tris pH 7.5, 2 mM MgCl2, 3 mM CaCl2) with the help of a douncer. Homogenized tissue was passed through a 70 μm strainer and centrifuged (400g, 5 min, 4°C). Tissue pellets were resuspended in liver lysis buffer (10 mM Tris pH 7.5, 1% NP-40, 2 mM MgCl2, 10% Glycerol, 3 mM CaCl2) and centrifuged again. Pellets, now containing hepatocyte nuclei, were washed twice in PBS. These nuclei were processed for CUT&RUN.
Hep3B: Hep3B grown in DMEM (Invitrogen) containing 10% foetal bovine serum (Sigma), non-essential amino acids, sodium pyruvate, L-glutamine, and penicillin/streptomycin (all from Invitrogen) were transduced with pLIX-Puro-hsPROX1 (PROX1 overexpression) lentivirus. Puromycin selection was performed (2 μg/ml) for 2 days to generate stable cell lines. Medium was exchanged to growth medium containing 2 μg/ml doxycycline (Sigma) to induce PROX1 expression (PROX1 overexpression) for two days followed by nuclei harvesting for CUT&RUN.

extract_protocol:
Cells were harvested with Accutase and strained through a 70 um strainer followed by CUT&RUN processing. 250,000 cells were washed twice with wash buffer (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, and 1X Roche Complete Protease Inhibitor), then resuspended in wash buffer and added to Concanavalin-A beads (Polysciences) pre-activated in cold binding buffer (20 mM HEPES-KOH pH 7.5, 10 mM KCl, 1 mM CaCl2, and 1 mM MnCl2). The bead-cell suspension was rotated (RT, 10 min). The supernatant was removed on a magnet and the beads were resuspended in antibody buffer (0.2 mM EDTA, 0.05% w/v digitonin in wash buffer). Primary antibody (as indicated) or control (rabbit IgG) was added at 1:100 v/v, and cells were incubated on a nutator (overnight, 4°C). Beads were washed twice in digitonin-wash buffer (0.05% w/v digitonin in wash buffer), resuspended in 700 ng/mL pAG-MNase (Protein Expression and Purification Core Facility, EMBL, Heidelberg) in digitonin-wash buffer, and rotated (4°C, 1 h). pAG-MNase-loaded beads were then washed twice in digitonin-wash buffer, resuspended in digitonin-wash buffer, and placed on ice. 1 uL of 100 mM CaCl2 was added to induce chromatin digestion, and the mixture was incubated on ice (30 min). 50 uL of 2x stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% w/v digitonin, 50 ug/mL RNase A, 50 ug/mL glycogen, 0.5 ng/mL spike-in E. coli DNA) was added, and the suspension incubated at 37°C for 10 minutes to release chromatin fragments from cells.
The supernatant was subjected to phenol-chloroform extraction, and purified DNA fragments were used for library preparation with NEBNext DNA Library Prep Kit for Illumina (NEB E7645). Libraries were then sequenced (paired-end, 2x40 bp) on the NextSeq 550 platform (Illumina).

value: Hepatocellular carcinoma

tag: chip antibody

value: Rabbit IgG (Sigma 12-370)

value: PROX1 overexpression


title: 28-07-0001-2_pre_0

value: Male

value: SCIT

tag: tnss

tag: tsneez

tag: dose

tag: batch

value: nasal lavage sample


title: 28-05-0001-0_pre_0

tag: Sex

value: pre

tag: pct reads

tag: tissue


title: Hep3B IgG rep 2

description: Library name: Hep3B IgG rep 2

tag: cell line


title: ED, R15979

value: DLPFC

value: Postmortem brain tissue


title: 28-03-0002-6_post_0

tag: participant id

value: Placebo

tag: age

value: post

tag: median cv


title: PP2.NT.24h.1

value: Skin

tag: genotype

value: PPARb knockdown

tag: treatment

tag: time point


title: Hep3B IgG rep 1

description: Library name: Hep3B IgG rep 1

tag: cell type


title: control, R16377

value: M

tag: group/disease

value: control

tag: rin


title: ED, R15766

value: F

value: ED


title: 28-09-0011-3_pre_0

value: Female

tag: month

tag: nac

tag: tnss


title: PP2.NT.24h.2

value: NHEK

value: Epithelial keratinocyte


title: Hep3B Flag rep 3

description: Library name: Hep3B Flag rep 3

value: Hepatocellular carcinoma

tag: chip antibody

value: Rabbit anti-FLAG (Cell Signaling Technology 14793)

value: PROX1 overexpression


title: Ctrl.UV.24h.3

value: WT

value: UV exposure


title: PP2.NT.24h.3


title: 28-02-0002-5_pre_0

tag: Sex

value: pre

tag: tsneez

tag: dose

tag: batch

value: nasal lavage sample


title: DAP-CDF1_rep3

description: Protein-DNA interaction

tag: tissue

value: stolon

tag: protein

value: E.coli expressed


title: A_LC11

description: 10x Genomics

value: PBMC

value: SARS-Cov-2 naïve with 3 dose inactivated vaccine


title: ED, R15763

value: DLPFC

value: Postmortem brain tissue


title: ED, R15765

value: F

value: ED


title: Ctrl.UV.24h.2

value: Skin

tag: cell line

value: NHEK


title: Hep3B Flag rep 1

description: Library name: Hep3B Flag rep 1

value: Hepatocellular carcinoma


title: Ctrl.UV.24h.1

value: Epithelial keratinocyte

tag: genotype


title: ED, R15744


title: 28-02-0002-5_post_0

tag: participant id

value: Female

tag: treatment

value: Placebo

tag: age

value: post

tag: pct reads

tag: median cv


title: MOC-1 tumor, SX-682 Docetaxel, 5

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
20 mRNA-Seq samples were pooled and sequenced on NextSeq 2000 P2 using Illumina® Stranded mRNA Prep and paired-end sequencing.
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt v1.18.
Alignment with the reference genome (mm10) and the annotated transcripts using STAR v2.7.0f in 2-pass mode.
Gene expression quantification analysis was performed for all samples using RSEM v1.3.1 and the gene annotation GENCODE_M21 GTF.
Assembly: mm10 / GENCODE_M21
Supplementary files format and content: Raw counts provided in tab-delimited .txt format.

organism: Mus musculus

source_name: Tumor

growth_protocol: MOC-1 cells (4e6) were implanted subcutaneously in a 3:1 suspension of PBS and Matrigel in the flank of C57BL/6 mice (day 0). Mice were randomized based on tumor size at the start of drug treatment to equalize the average tumor volume in each group.

extract_protocol:
Total RNA from tumors was prepared using a Qiagen RNeasy Mini Kit and analyzed on an Agilent TapeStation.
RNA libraries were prepared using Illumina® Stranded mRNA Prep

treatment_protocol: Control diet feed or SX-682-containing feed (200 mg/kg body weight/day) was administered to mice starting on day 6. Docetaxel (5 mg/kg) was administered on days 6, 8, 13, 15, 21, 23. On day 26, mice were euthanized, and tumors were collected and stored in RNAlater.

value: Tumor

tag: cell type

value: WT

value: SX-682 plus docetaxel


title: control, R15580

tag: group/disease

value: control

tag: rin


title: MOC-1 tumor, SX-682 Docetaxel, 4


title: PPD.UV.06h.3

value: PPARb knockdown

value: UV exposure

tag: time point


title: ED, R15543

value: DLPFC

tag: Sex


title: Ctrl.NT.24h.2


title: ED, R15568

value: Postmortem brain tissue


title: MOC-1 tumor, SX-682 Docetaxel, 2


title: MOC-1 tumor, SX-682 Docetaxel, 3


title: 28-03-0005-4_pre_12

value: Male

value: SCIT

tag: month

tag: nac

value: pre

tag: tnss

tag: tsneez

value: nasal lavage sample


title: PPD.UV.06h.2

tag: tissue

value: Skin

value: NHEK


title: 28-10-0002-7_post_0

value: Female

tag: dose

tag: batch


title: Hep3B Flag rep 2

description: Library name: Hep3B Flag rep 2

tag: cell line

value: Hepatocellular carcinoma

tag: chip antibody

value: Rabbit anti-FLAG (Cell Signaling Technology 14793)

value: PROX1 overexpression


title: 28-03-0005-4_post_12

tag: participant id

tag: treatment

tag: age

value: post


title: 28-09-0004-2_post_12

tag: pct reads

tag: median cv


title: control, R15536

tag: cell type

value: F

tag: group/disease

tag: rin


title: 28-02-0001-9_post_0

tag: Sex

tag: month


title: Ctrl.NT.24h.1

value: Epithelial keratinocyte

tag: genotype

value: WT

tag: time point


title: 28-09-0004-2_pre_12

tag: nac

tag: tnss

tag: tsneez

tag: tissue


title: MOC-1 tumor, SX-682 Docetaxel, 1

value: Tumor

tag: cell line

value: SX-682 plus docetaxel


title: MOC-1 tumor, SX-682, 5


title: 28-02-0001-9_pre_0

tag: participant id

tag: dose

tag: batch


title: 28-07-0009-6_post_12

tag: treatment

value: Placebo

tag: age

tag: pct reads


title: control, R15510

value: DLPFC

tag: cell type

value: Postmortem brain tissue

tag: group/disease

value: control


title: control, R15529

tag: Sex

tag: rin


title: MOC-1 tumor, SX-682, 4

tag: genotype


title: Ctrl.NT.24h.3

tag: time point


title: PPD.NT.06h.3

value: PPARb knockdown


title: 28-07-0009-6_pre_12

tag: month

tag: nac

value: pre

tag: median cv

value: nasal lavage sample


title: ED, R15505

tag: tissue

value: M

value: ED


title: PPD.NT.06h.2

value: Skin

tag: cell line

value: NHEK


title: MOC-1 tumor, SX-682, 3


title: control, R15172


title: 28-07-0008-5_post_12

tag: participant id

value: Male

value: SCIT

value: post

tag: tnss

tag: tsneez


title: ED, R15163

value: F


title: MOC-1 tumor, SX-682, 1

value: Tumor

value: WT

tag: treatment


title: ED, R15140


title: PPD.NT.06h.1

value: Epithelial keratinocyte


title: PPB.UV.06h.2

value: UV exposure


title: OCD, R14986

value: DLPFC

value: Postmortem brain tissue

value: OCD


title: 28-07-0001-2_post_12

tag: age

tag: dose

tag: batch


title: MOC-1 tumor, Docetaxel, 5

tag: cell type

value: Docetaxel


title: PPD.UV.06h.1

value: PPARb knockdown


title: PPB.UV.06h.1


title: 28-07-0001-2_pre_12

tag: Sex

value: pre

tag: pct reads

value: nasal lavage sample


title: MOC-1 tumor, Docetaxel, 4

tag: genotype


title: ED, R14981

tag: group/disease

value: ED

tag: rin


title: 28-07-0005-7_post_12

value: Placebo

tag: month

tag: nac


title: MOC-1 tumor, Docetaxel, 3

tag: tissue


title: PPB.NT.06h.3

value: Skin

tag: cell line

value: NHEK

tag: time point


title: ED, R14945


title: 28-07-0005-7_pre_12

tag: participant id

value: Male

tag: tnss

tag: median cv


title: 28-07-0006-8_post_12

tag: treatment

tag: age

value: post

tag: tsneez


title: 28-07-0008-5_pre_12

value: SCIT

tag: dose

tag: batch


title: PPB.NT.06h.2

tag: cell type


title: OCD, R14924

tag: Sex

value: M


title: MOC-1 tumor, Docetaxel, 1

value: Tumor

tag: genotype

value: WT


title: MOC-1 tumor, SX-682, 2


title: PPB.UV.06h.3

value: Epithelial keratinocyte

value: UV exposure


title: PPB.NT.06h.1


title: ED, R14590

value: DLPFC

value: Postmortem brain tissue

value: F

tag: group/disease

tag: rin


title: PP2.UV.06h.3

value: PPARb knockdown


title: 28-06-0004-4_post_12

value: Female

tag: month

tag: nac

tag: pct reads

value: nasal lavage sample


title: OCD, R14567

tag: tissue

value: OCD


title: 28-06-0004-4_pre_12

tag: participant id

value: pre


title: PP2.UV.06h.2

value: Skin

tag: cell line

value: NHEK

tag: time point


title: 28-06-0003-3_post_12

value: Male

tag: treatment

value: Placebo

value: post

tag: tnss

tag: median cv


title: MOC-1 tumor, Control, 3

value: Tumor

value: Control


title: PP2.UV.06h.1

value: Epithelial keratinocyte


title: MOC-1 tumor, Control, 2

value: WT


title: ED, R14559

value: DLPFC

value: ED


title: 28-06-0010-4_post_12

tag: age

tag: tsneez

tag: dose


title: 28-06-0003-3_pre_12

tag: Sex

tag: batch


title: MOC-1 tumor, Docetaxel, 2

tag: cell type

tag: genotype

value: Docetaxel


title: MOC-1 tumor, Control, 1


title: control, R14383

value: Postmortem brain tissue

value: F

tag: group/disease

value: control

tag: rin


title: PP2.NT.06h.2

value: PPARb knockdown


title: 28-06-0010-4_pre_12

value: Female

tag: month

tag: nac

value: pre

tag: pct reads

value: nasal lavage sample


title: PP2.NT.06h.1

tag: tissue

value: Skin

tag: cell line

value: NHEK


title: control, R14374


title: 28-06-0009-7_post_12

tag: participant id

tag: treatment

value: SCIT

value: post


title: control, R14352

value: M


title: MOC-1 tumor, Control, 5

value: Tumor

value: Control


title: Ctrl.UV.06h.3

value: Epithelial keratinocyte

value: WT

value: UV exposure

tag: time point


title: 28-06-0009-7_pre_12

tag: age

tag: tnss

tag: median cv


title: OCD, R14333

value: DLPFC

value: Postmortem brain tissue

tag: Sex

value: OCD


title: OCD, R14562


title: MOC-1 tumor, Control, 4


title: Ctrl.UV.06h.2


title: 28-06-0014-3_post_12

value: Male

value: Placebo

tag: tsneez

tag: dose

tag: batch


title: PP2.NT.06h.3

tag: cell type

tag: genotype

value: PPARb knockdown


title: Ctrl.NT.06h.3


title: Ctrl.UV.06h.1


title: 28-06-0014-3_pre_12

tag: month

value: pre

value: nasal lavage sample


title: Ctrl.NT.06h.2

value: Skin

value: NHEK


title: 28-06-0001-1_post_12

value: SCIT

tag: nac

value: post


title: 28-06-0001-1_pre_12

tag: pct reads


title: ED, R13787

tag: tissue

value: M

tag: group/disease

value: ED

tag: rin


title: 28-05-0001-0_post_12

tag: participant id

value: Female

tag: treatment


title: HCT116 cells, treated, 24 hours, rep2

city: Stony Brook

first: Agnieszka

last: Bialkowska

address: 100 Nicolls Road

department: Medicine

institute: Stony Brook University

data_processing:
Data was analyzed using usegalaxy platform and R
Sample quality was checked using FASTQC and Trimmomatic
The paired-ended sequences were aligned to hg38 using HISAT2
To quantify the number of reads per gene, featureCounts was used
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: Human HCT116 cells were maintained in McCoy's 5a medium supplemented with 10% fetal bovine serum (FBS) and 1% Pencillin/Streptomycin in a humidified atmosphere at 37°C and 5% CO2

extract_protocol:
RNA was isolated using Qiagen Rneasy Mini Kit
RNA library and sequencing was performed by Novogene. mRNA library preparation (poly A enrichment) and sequencing was performed using NovaSeq PE150

treatment_protocol: HCT116 cells were trypsinized, counted, and seeded (7.5x104 cells/well) in a 6 well-plate format. After 24 hours of incubation, media was aspirated and replaced with treatment-supplemented media (0.1% DMSO or 50nM TR-107). Cells were then treated for 24 hours total, followed by total RNA extraction and quantification

tag: disease

value: colorectal cancer

tag: cell line

tag: time

value: 24 hours


title: ED, R13767

value: DLPFC

tag: Sex

value: F


title: HCT116 cells, treated, 24 hours, rep3


title: 28-10-0002-7_post_12

tag: age

tag: tnss

tag: tsneez

tag: median cv


title: HCT116 cells, treated, 24 hours, rep1


title: 28-05-0001-0_pre_12

tag: dose

tag: batch


title: control, R13813

tag: cell type

value: Postmortem brain tissue

value: control


title: control, R13750


title: HCT116 cells, control, 24 hours, rep3

value: 0.1% DMSO


title: ED, R13766


title: control, R13751


title: 28-10-0002-7_pre_12

value: Placebo

tag: month

tag: nac

tag: pct reads


title: 28-03-0009-3_pre_12

value: Male

value: pre

tag: tissue


title: control, R14330

tag: group/disease

tag: rin


title: control, R13747


title: OCD, R14324

value: OCD


title: 28-03-0003-7_post_12

tag: participant id

tag: treatment

value: nasal lavage sample


title: control, R13745


title: HCT116 cells, control, 24 hours, rep1

tag: disease

tag: cell line

tag: time


title: 28-03-0003-7_pre_12

tag: Sex

value: SCIT

tag: age

tag: tnss


title: Ctrl.NT.06h.1

value: Skin

value: NHEK

value: Epithelial keratinocyte

tag: genotype

value: WT

tag: time point


title: OCD, R13734

tag: cell type

value: M


title: 28-03-0006-0_pre_12

value: Female

tag: month

tag: tsneez

tag: dose

tag: batch

tag: median cv


title: P-T3H2-3

city: shanghai

first: sihan

last: wu

address: 上海市杨浦区翔殷路800号

institute: Naval medical university

data_processing:
The raw reads were filtered by Seqtk before mapping to genome using Hisat2 (version:2.0.4).
. The fragments of genes were counted using stringtie(v1.3.3b) followed by TMM (trimmed mean of M values) normalization
Significant differential expressed genes (DEGs) were identified as those with a False Discovery Rate (FDR) value above the threshold (Q< 0.05) and fold-change >2 using edgeR software.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Cell line

growth_protocol: Huh7 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% fetal bovine serum (FBS).

extract_protocol:
Total RNA (1.5 μg) was extracted from TRIZOL followed by library preparation according to Illumina standard instruction (VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® ).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer'sprotocols.

treatment_protocol: Huh7 cells were treated with 20μM of P-T3H2-2A or P-T3H2 for 5days.

tag: tissue

value: Cell line

value: hepatoma carcinoma cell

value: peptide P-T3H2


title: ED, R13721

value: DLPFC

value: Postmortem brain tissue

value: F

tag: group/disease

value: ED

tag: rin


title: P-T3H2-2

address: 上海市杨浦区翔殷路800号

tag: treatment


title: 28-03-0004-8_post_12

tag: participant id

value: Male

value: Placebo

tag: nac

value: post

tag: pct reads


title: OCD, R13709

tag: Sex

value: OCD


title: P-T3H2-1

address: 上海市杨浦区翔殷路800号

tag: cell line


title: 4in1_Prox1_OE day02 rep3 [ATAC-seq]

description:
4in1_GFP_4in1_Prox1_diffbind_deseq2.txt
Prox1_enriched.bed

data_processing:
Raw reads were quality-checked with fastqc (v0.11.8), trimmed with trimmomatic (v0.38), and aligned to UCSC mm10 with bowtie2 (v2.3.4.3)
Aligned reads were cleaned and base-recalibrated (to take account of Tn5 insertion biases) with samtools (v1.10) and picard (v2.18.16). Reads were filtered with bedtools (v2.27.1), samtools, and picard.
Peaks were called using macs2 (2.1.2) and coverage was calculated with deeptools (v3.1.3). Final quality checks were performed with multiqc (v1.6).
Differential peak analysis was performed with DiffBind (v3.4.11) as described in the authors’ vignette (same version).
To determine the PROX1 footprint, 11 bp-wide motif peaks (CIS-BP ID: M03445_2.00, mapped on mm10) were intersected with CUT&RUN consensus peaks, respectively, using bedtools intersect -wa. This generated peaks present in the CUT&RUN consensus peak set which contain motifs and are centered on the motif. DiffTF (v1.8) was then run using ATAC-seq bam files and the motif-centered peak set.
Assembly: mm10
Supplementary files format and content: bigwig files of coverage
Supplementary files format and content: tsv files with significantly differentially accessible regions and stats
Supplementary files format and content: bed files of significantly differentially accessible regions

source_name: Primary mouse embryonic fibroblasts

growth_protocol: Mouse embryonic fibroblasts (MEFs) were harvested from E13.5 embryos of C57BL/6N (wild-type). MEFs were transduced with indicated lentivirus in MEF medium containing 8 ug/mL polybrene (Sigma) and 2 ug/mL doxycycline (Sigma) to induce transgene expression. 1 day following transduction medium was exchanged to MEF medium containing doxycycline. On day 2, cells were harvested.

extract_protocol:
Cells on culture plates were washed twice with PBS and detached by Accutase digestion (4-6 min, RT) followed by ATAC processing. Cell suspensions were placed into an equal volume of MEF medium followed by centrifugation (500g, 5 min, 4°C) before resuspension in ice-cold PBS + 1% BSA. Cells were then strained through a 70 μm filter, centrifuged (500g, 5 min, 4°C), and 50,000 cells resuspended in 50 μL of ice-cold cell lysis buffer containing 0.1% NP-40 and 0.01% digitonin in wash buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, and 1% BSA in ddH2O) for 3-5 minutes. 1 mL of ice-cold wash buffer was then added to stop cell lysis, and nuclei were centrifuged (500g, 10 min, 4°C). 4.5 μL of each of the tagmentation oligos, Tn5_ME and Tn5-R1N, were annealed in oligo annealing buffer (10 mM Tris-HCl pH 7.5, 50 mM NaCl, and 10 mM EDTA final concentration in ddH2O) by heating at 95°C (3 min) followed by a ramp down by 1°C to 25°C. The same procedure was performed for Tn5_ME and Tn5-R2N. Tn5 was assembled with annealed oligos by combining 50 μL Tn5 (1 mg/mL stock) with 25 μL annealed Tn5_ME and Tn5-R1N and 25 μL Tn5_ME and Tn5-R2N. Nuclei were resuspended in 40 μL tagmentation buffer (38.8 mM Tris-acetate, 77.6 mM K-acetate, 11.8 Mg-acetate, 18.8% dimethylformamide, and 0.12% NP-40 in ddH2O), to which 5 μL ice-cold PBS + 1% BSA and 5 μL pre-assembled Tn5 was added. Samples were incubated on a Thermomixer (37°C, 30 min, 500 rpm) before being subjected to MinElute (Qiagen) cleanup to extract tagmented DNA.
Eluted DNA was pre-amplified with P5 and P7 primers using the NEBNext HF 2x PCR Master Mix (New England Biolabs) in a thermocycler set to 72°C (5 min), 98°C (30 sec), and 5 cycles of 98°C (10 sec), 63°C (30 sec), and 72°C (1 min). A qPCR side reaction was performed with the resulting pre-amplified libraries to determine the necessary additional cycles (5 cycles fewer than the number of cycles corresponding to ⅓ of max fluorescence) for complete amplification. After finishing amplification, 50 μL of each library was subjected to 2-sided size selection by addition of 27.5 μL (0.55x) AMPure XP beads, incubation (5 min), transfer of supernatant to new tubes, addition of 42.5 μL (1.4x) AMPure XP beads to the supernatant, incubation (5 min), three washes with 80% ethanol, and elution of DNA.

treatment_protocol: MEFs were seeded onto collagen-coated plates and transduced 1 day later with lentivirus encoding rtTA (FUW-rtTA) ± Prox1 (tetO-FLAG-mmProx1) or rtTA and 4in1 (LV.4TF) together with GFP (tetO-GFP) or Prox1 (tetO-FLAG-mmProx1) , respectively. 2 ug/ml doxycycline (Sigma) was used to induce transgene expression in growth media for 2 days.

value: Primary mouse embryonic fibroblasts

tag: genotype

tag: strain background

value: 4in1, Prox1, and rtTA overexpression


title: P-T3H2-2A-3

address: 上海市杨浦区翔殷路800号

tag: cell type

value: control peptide P-T3H2-2A


title: ED, R13701


title: HCT116 cells, control, 24 hours, rep2

tag: disease

value: colorectal cancer

value: 0.1% DMSO

tag: time

value: 24 hours


title: OCD, R13702

value: M


title: 28-02-0001-9_post_12

value: Female

value: SCIT

tag: age

tag: month

tag: tnss

tag: tsneez

tag: dose

value: nasal lavage sample


title: ED, R13675

tag: tissue

value: DLPFC

value: Postmortem brain tissue

tag: group/disease

tag: rin


title: 28-03-0002-6_post_12

tag: participant id

tag: treatment

tag: nac

tag: batch

tag: median cv


title: ED, R13660

tag: Sex

value: F

value: ED


title: 4in1_Prox1_OE day02 rep2 [ATAC-seq]

tag: cell type

tag: genotype

value: WT

tag: strain background


title: 28-03-0002-6_pre_12

value: Placebo

tag: age

value: pre

tag: pct reads


title: P-T3H2-2A-1

address: 上海市杨浦区翔殷路800号

value: Cell line

tag: cell line

value: hepatoma carcinoma cell


title: HeLa cells, SFTSV infected, Input2

city: Nanjing

first: Bingxin

last: Liu

state: Jiangsu province

address: 22 Hankou Road

department: Medical school

institute: Nanjing University

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
MeRIPseq reads were aligned to the hg38 genome using STAR.
m6A Peaks were called uing MetPeak  with the significance cut-off p-value <=0.05
Assembly: hg38, KY362310, M:KY362358, S: KY362334
Supplementary files format and content: BW

source_name: HeLa cells

extract_protocol:
Total RNA was extracted using the Trizol method (Thermo Fisher Scientific, 15596018). DNase I (Roche Diagnostics, 04716728001) treatment was performed on the total RNA to remove residual DNA. Oligo-dT was used for mRNA enrichment.RNA was fragmented using RNA Fragmentation Buffer (100 mM Tris-HCl, 100 mM ZnCl2). The reaction was terminated with EDTA, and fragmented RNA was recovered. A portion of the fragmented RNA was used as input, while the remainder was used for immunoprecipitation (IP). The IP mixture was prepared using the following components: fragmented RNA, RNasin (40 U μl–1, Promega, cat. no. N2611), RVC (200 mM, Sigma-Aldrich, cat. no. R3380), IP buffer (50 mM Tris-HCl, 750 mM NaCl, 0.5% (vol/vol) IGEPAL CA-630), and m6A-specific antibody. The mixture was incubated at 4°C for 2 hours with rotation. Protein A beads (Thermo Fisher Scientific, 10002D) were washed twice with IP buffer, then suspended in IP buffer containing BSA (0.5 mg ml-1) and incubated with rotation for 2 hours at 4°C. The beads were washed twice with IP buffer. The IP mixture and the washed protein A beads were combined and incubated at 4°C for 2 hours with rotation, followed by three washes with IP buffer. The IP-eluted RNA was then purified using RNeasy Mini Kit (QIAGEN, 74106) RLT buffer.
The Input RNA and IP RNA were subjected to library preparation using the NEBNext® Ultra™ II RNA Library Prep Kit (NEB E7770).
Me RIP-seq

value: HeLa cells

value: epithelialcell

value: infected


title: P-T3H2-2A-2

address: 上海市杨浦区翔殷路800号

value: control peptide P-T3H2-2A


title: 4in1_GFP_OE day02 rep3 [ATAC-seq]

description:
4in1_GFP_4in1_Prox1_diffbind_deseq2.txt
GFP_enriched.bed

value: Primary mouse embryonic fibroblasts

value: 4in1, GFP, and rtTA overexpression


title: control, R13628

value: control


title: 28-02-0001-9_pre_12

value: Female

value: SCIT

tag: month

tag: tnss

tag: tsneez

value: nasal lavage sample


title: control, R13622

tag: tissue

value: DLPFC

value: Postmortem brain tissue

value: M

tag: group/disease


title: 4in1_GFP_OE day02 rep1 [ATAC-seq]

value: WT


title: 28-02-0002-5_post_12

tag: participant id

value: Placebo

value: post

tag: dose


title: control, R13616

tag: rin


title: 28-02-0002-5_pre_12

tag: treatment

tag: nac

value: pre

tag: batch


title: HeLa cells, control, Input

description: HeLa-SFTSV-Mock-Input

value: HeLa cells

tag: cell type

value: unifected


title: 28-03-0004-8_pre_12

tag: Sex

value: Male

tag: median cv


title: HeLa cells, SFTSV infected, IP2

value: epithelialcell

tag: genotype

value: infected


title: 28-01-0004-6_post_12

tag: age

tag: pct reads


title: 4in1_Prox1_OE day02 rep1 [ATAC-seq]

value: Primary mouse embryonic fibroblasts

tag: strain background

value: 4in1, Prox1, and rtTA overexpression


title: 28-01-0004-6_pre_12

tag: month

tag: tnss


title: HeLa cells, SFTSV infected, IP1

tag: tissue

tag: cell line


title: OCD, R13611

value: F

tag: group/disease

value: OCD


title: control, R13614

value: control


title: Prox1_OE day02 rep2 [ATAC-seq]

value: Prox1 and rtTA overexpression


title: Prox1_OE day02 rep1 [ATAC-seq]


title: 28-11-0012-7_post_0

tag: participant id

value: Female

tag: tsneez

tag: dose

value: nasal lavage sample


title: DRBHU_WGRS

city: Beijing

first: Jiadong

last: Wang

address: 38 College Road, Haidian District

department: Department of Radiation Medicine

institute: Peking University Health Science Center

description: HeLa DDX39A-Tet-On cells, HU and 5,6-dichloro-benzimidazole 1-β-D-ribofuranoside (DRB) treatment, without replicate

data_processing:
The raw FASTQ data were processed with Trim-Galore (parameters: -q 25  --phred33 --length 35 --stringency 3).
The cleaned reads were aligned to the hg38 genome with Burrows–Wheeler Aligner (BWA) version 0.7.17-r1188, and sorted by using SAMtools version 1.17.
Duplicate reads were removed with the MarkDuplicates function of The Genome Analysis Toolkit (GATK) version v4.4.0.0-63-g7058e0c-SNAPSHOT. Sequencing reads require correction of base quality scores. To this end, the BaseRecalibrator function of GATK was used to obtain a quality score recalibration table. Subsequently, the ApplyBQSR function of GATK used this table to generate the corrected BAM files. The variant call format (VCF) files were generated with the Mutect2 function of GATK, and the parameters were set as follows: disable-read-filter, MateOnSameContigOrNoMappedMateReadFilter; af-of-alleles-not-in-resource, 0.0000025; germline-resource, was af-only-gnomad VCF files from GATK resources. We removed false-positive variants from the VCF files. The GetPileupSummaries function was used to obtain the pileup table of base counts, and this table was used by the CalculateContamination function to calculate the fraction of reads originating from cross-sample contamination. The FilterMutectCalls function was used to filter the VCF files, and only the variants with PASS status were retained.
Assembly: hg38
Supplementary files format and content: variant call format files (VCF)

source_name: HeLa cell line

growth_protocol: HeLa DDX39A-Tet-On stable cells were cultured in DMEM supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 100 μg/mL streptomycin, and incubated at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Genomic DNA was isolated using a Genomic DNA Kit (TIANGEN, DP304).
The genomic DNA was cleaved with Hieff NGS® OnePot Pro DNA Fragmentation Reagent (Yeasen, 12619ES) into fragments of approximately 250 bp, and these fragments were subsequently used for cDNA library construction with the Hieff NGS® DNA Library Prep Kit (Yeasen).

treatment_protocol: DDX39A overexpression was induced with Dox (1 µg/mL). To induce replication stress, HU (100 µM) was continuously applied. DRB (50 µM) was added for 2 hours at each cell passage to induce transcriptional inhibition-associated DNA damage under conditions of replication stress.  Cells were treated with either the individual or combined treatments for 3 weeks.

value: HeLa cell line

value: DDX39A-Tet-On stable

tag: treatment

value: HU (100 µM) was continuously applied, DRB (50 µM) was added for 2 hours at each cell passage


title: MEF day02 rep3 [ATAC-seq]

value: WT

value: rtTA overexpression


title: 28-11-0012-7_pre_0

value: Placebo

tag: nac

value: pre

tag: batch


title: 4in1_GFP_OE day02 rep2 [ATAC-seq]

tag: cell type

value: 4in1, GFP, and rtTA overexpression


title: control, R13597

value: DLPFC

value: Postmortem brain tissue

tag: Sex

tag: rin


title: HeLa cells, control, IP

description: HeLa-SFTSV-Mock-IP

value: HeLa cells

value: epithelialcell

tag: genotype

value: unifected


title: HeLa cells, SFTSV infected, Input1

value: infected


title: control, R13591

value: M

value: control


title: OCD, R13575

value: F

value: OCD


title: Prox1_OE day02 rep3 [ATAC-seq]

value: Primary mouse embryonic fibroblasts

value: Prox1 and rtTA overexpression


title: 28-07-0009-6_post_0

value: Female

tag: age

value: post

tag: pct reads

tag: median cv

value: nasal lavage sample


title: HU_WGRS

description: HeLa DDX39A-Tet-On cells, hydroxyurea (HU) treatment, without replicate

value: HeLa cell line

value: DDX39A-Tet-On stable

value: HU (100 µM) was continuously applied


title: DOXHU_WGRS

description: HeLa DDX39A-Tet-On cells, HU and doxycycline (Dox) treatment, without replicate

value: HU (100 µM) and Dox (1 µg/mL) were continuously applied


title: ctrl_WGRS

description: HeLa DDX39A-Tet-On cells, untreated, without replicate

value: untreated


title: 28-07-0009-6_pre_0

value: Placebo

tag: month

value: pre

tag: tnss


title: ED, R13568

tag: tissue

value: DLPFC

value: Postmortem brain tissue

value: ED


title: HU_IP_MRE11_rep2

description:
HeLa, treated with 4 mM HU for 6 h and incubated with MRE11 antibody, rep2
HU_vs_untreated_MRE11.narrowPeak

data_processing:
The raw reads were trimmed with Trim-galore version 0.6.10 (parameters: -q 20  --phred33 --length 20 --stringency 4).
The cleaned reads were aligned to the genome with HISAT2 version 2.2.1 (parameters: --dta-cufflinks --un-conc).
Duplicate reads were removed with Sambamba version 0.8.2, mapped reads were sorted with SAMtools version 1.17, and converted to generate bigWig files via the bamCoverage function of deepTools version 3.5.1 (parameters: --normalizeUsing CPM).
The called peaks and narrowPeak files were generated with MACS2 version 2.1.0.20150731 (parameters: -q 0.2).
Assembly: hg38
Supplementary files format and content: bigWig and narrowPeak files

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 100 μg/mL streptomycin, and incubated at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Cells were harvested by scraping, washed twice with prechilled PBS, and fixed with 1% formaldehyde at room temperature for 10 minutes, and the reaction was then quenched with 0.125 M glycine. After being washed once with PBS, the cells were lysed with buffer 1 (50 mM HEPES, pH 7.5; 140 mM NaCl; 1 mM EDTA, pH 8.0; 10% glycerol; 0.5% NP-40; 0.25% Triton X-100) and buffer 2 (200 mM NaCl; 1 mM EDTA; 0.5 mM ethylene glycol-bis (β-aminoethyl ether)-N,N,N′,N′-tetraacetic acid (EGTA); 10 mM Tris-HCl, pH 8.0) at 4°C for 10 minutes. After centrifugation, the pellets were treated with lysis buffer (1% SDS, 10 mM EDTA, pH 8.0; 50 mM Tris-HCl, pH 8.0). All the above buffers contained 1 mM PMSF (Amresco), 0.6-2 μg/mL aprotinin (TargetMol) and 1× cocktail (CWBIO). The mixtures were subjected to sonication with a Covaris M220 focused ultrasonicator for 4 minutes to obtain smeared DNA fragments of 200-500 bp. After sonication, the samples were centrifuged at 15000 rpm, and the supernatants were diluted with an equal volume of NETN buffer (20 mM Tris-HCl (pH 7.5), 500 mM NaCl, 1 mM EDTA (pH 8.0), and 0.5% NP-40). A portion of each sample was taken as input; 5 μg of an anti-DNA2 (Abcam, ab96488), or anti-MRE11 (Bethyl, A301-998A) was added to the remainder of each sample; and the samples were then incubated with rotation at 4°C overnight. Protein A (Millipore) beads were added to each sample, and the samples were incubated with rotation at 4°C for 2-3 hours. The beads were subsequently washed successively with the following buffers: one wash with low-salt buffer (0.1% SDS, 1% Triton X-100; 2 mM EDTA, pH 8.0; 20 mM Tris-HCl, pH 8.0; 150 mM NaCl); one wash with high-salt buffer (0.1% SDS, 1% Triton X-100; 2 mM EDTA, pH 8.0; 20 mM Tris-HCl, pH 8.0; 500 mM NaCl); one wash with LiCl buffer (10 mM Tris-HCl, pH 8.0; 1% sodium deoxycholate; 1% NP-40; 250 mM LiCl; 1 mM EDTA, pH 8.0); and two washes with TE buffer (10 mM Tris-HCl, pH 8.0; and 1 mM EDTA, pH 8.0). Then, the beads were incubated in 200 μL of elution buffer (10 mM Tris-HCl, 1% SDS, 1 mM EDTA) and incubated in a Thermo Mixer-Heat with vibration at 1200 rpm at 65°C overnight. Finally, the samples were incubated with 10 μg/mL RNase A at 37°C for 1 h and then with 20 μg/mL proteinase K at 55°C for 1 hour. The samples were extracted with phenol–chloroform. Then, 10 μL of glycogen (20 mg/mL), 100 μL of ammonium acetate (7.5 M), 40 μL of NaCl (5 M), and a 5x volume of ethanol were added to each supernatant and mixed, and the mixtures were incubated at -20°C overnight. The next day, the samples were centrifuged at 15000 rpm for 30 minutes at 4°C. We washed each pellet once with 75% ethanol and then centrifuged the sample and removed the supernatant. Finally, we resuspended the pellet in nuclease-free water to prepare the sample for sequencing.
The purified DNA was used NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645L) for library preparation.

treatment_protocol: First, the cells were synchronized by a double thymidine block. The cells were treated with 2 mM thymidine for 18 h, the block was released for 9 hours, and the cells were then treated again with thymidine for 18 hours. This process allowed the cells to be synchronized at the G1/S boundary, and the block was released for 1 hour. Cells were then treated with 4 mM HU for 6 h.

tag: cell line

value: Wild type

value: treated with 4 mM HU for 6 h

tag: chip antibody

value: incubated with MRE11 antibody


title: ED, R13561

value: F

tag: group/disease


title: 28-07-0008-5_post_0

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads. The FASTQs were aligned to the University of California Santa Cruz (UCSC) Human genome assembly version 38.91, using STAR v.2.4.2a. Duplicate filtering, QC and metrics analysis was performed using the Picard 1.134 family of tools[ref]. For quality control, samples were kept that had human aligned counts > 250,0001 million mapped reads and median coefficient of variation (CV) coverage < 0.956. Genes were filtered to include those that had a trimmed mean of M values (TMM) normalization count of at least 1.20.8 in at least 23 samples and further filtered for only protein coding genes. Normalized counts were transformed to log2 counts per million mapped reads along with observations level weights using voomWithQualityWeights from the limma R package version 3.5.1.(Ritchie ME et al. Nucleic Acids Res. 2015;20;43(7):e47) Sequencing was performed in 3 sample batches and a batch correction was done using limma removeBatcheffects.
Differentially expressed genes were then coassociated into modules using weighted gene correlation network analysis (WGCNA)
Assembly: GRCh38
Supplementary files format and content: csv file voom normalized counts

extract_protocol:
Total RNA was isolated from pre- and post NAC nasal lavage samples.  Cell pellets were collected in RNAprotect Saliva Reagent (Qiagen) with extraction using the RNeasy MinElute spin column (Qiagen) following the manufacturer’s protocol. Total RNA was isolated from nasal cell pellets in RNAprotect Saliva Reagent (Qiagen). Samples were centrifuged for 10 minutes at 10,000g, supernatant was removed, and the cell pellet was resuspended in 350μl RLT Buffer + 1% beta mercaptoethanol. The sample was vortexed for 1-2 seconds, sonicated for 30 seconds, spun through a Qiashredder column (Qiagen) and then extracted using the RNeasy MinElute spin column (Qiagen) following the manufacturer’s protocol. RNA quality was assessed using RNA electrophoresis (Agilent) and NanoDrop 1000 (NanoDrop Products, Thermo Fisher Scientific).
Sequencing libraries were constructed from total RNA using SMART-Seq v4 Ultra Low Input RNA Kit (Takara) and clustered onto a flowcell using a cBOT amplification system with a HiSeq SR v4 Cluster Kit (Illumina)

tag: participant id

value: Male

value: SCIT

tag: tsneez

tag: dose


title: ED, R13596

data_processing:
Raw RNA sequences were aligned to the hg38 reference genome from Ensembl via the STAR algorithm.
Quality control checks, including assessments of GC content, duplication rates, gene body coverage, and library complexity, were carried out using RSeQC30 and Picard tools (https://broadinstitute.github.io/picard/). Gene expression levels were quantified with featureCounts and the resulting expression matrix was curated to retain genes present in at least one-third of our sample set. This matrix was then normalized through the VOOM method.
Assembly: hg38
Supplementary files format and content: Raw count data were generated with featureCounts and are provided as a separate matrix.

extract_protocol:
Total RNA was extracted from all tissue samples using AllPrep DNA/RNA Mini Kit (Qiagen Cat No./ID: 80204).
Paired-end strand-specific sequencing libraries were prepared from 300ng total RNA using the TruSeq Stranded Total RNA Library Preparation kit with Ribo-Zero Gold ribosomal RNA depletion which removes rRNA and mtRNA. The libraries were then sequenced on an Illumina HiSeq 3000 at the Promega Sequencing Facility, producing a median of 46.9 million reads per sample.


title: 28-10-0002-7_pre_0

value: Female

tag: treatment

tag: nac

tag: batch

value: nasal lavage sample


title: 28-07-0008-5_pre_0

tag: Sex


title: MEF day02 rep2 [ATAC-seq]

tag: cell type

value: Primary mouse embryonic fibroblasts

tag: genotype

value: WT

tag: strain background

value: rtTA overexpression


title: HU_IP_DNA2_rep1

description:
HeLa, treated with 4 mM HU for 6 h and incubated with DNA2 antibody, rep1
HU_vs_untreated_DNA2.narrowPeak

value: HeLa cell line

value: incubated with DNA2 antibody


title: OCD, R13552

value: M

value: OCD

tag: rin


title: MEF day02 rep1 [ATAC-seq]


title: 28-06-0010-4_post_0

value: Placebo

tag: age

tag: month

value: post

tag: pct reads

tag: median cv


title: ED, R13104

tag: tissue

value: DLPFC

value: Postmortem brain tissue

value: ED


title: HU_IP_DNA2_rep2

description:
HeLa, treated with 4 mM HU for 6 h and incubated with DNA2 antibody, rep2
HU_vs_untreated_DNA2.narrowPeak

tag: cell line

value: Wild type

value: treated with 4 mM HU for 6 h

tag: chip antibody


title: 28-06-0010-4_pre_0

tag: participant id

value: pre

tag: tnss

tag: tsneez


title: Cas13d gRNA amplicon of Homo sapiens: Essentiality HAP1_D14_R2

first: Sydney

last: Hart

address: 101 AVENUE OF THE AMERICAS NEW YORK, NY

institute: New York Genome Center

description:
Library name: Essentiality_HAP1_D14_R2
EssHAP_D14_R2

data_processing:
We processed reads from pooled Cas13d screens following established pipelines4: First, reads were de-multiplexed based on Illumina i7 barcodes present in PCR2 reverse primers and custom in-read i5 barcodes, allowing for one mismatch. Reads were trimmed to the expected gRNA length by identifying known anchor sequences relative to the guide sequence. Reads were trimmed using Cutadapt (v.1.13)19 with the following parameters: -g CTGGTCGGGGTTTGAAAC -e 0.2 -O 5 --discard-untrimmed and -a TTTTTGAATTCGCTAGCT -e 0.1 -O 5 --minimum-length 15 --discard-untrimmed.
We aligned processed reads to the designed crRNA reference using bowtie (v.1.1.2)20 and allowed for up to three mismatches (parameters: -v 1 -m 3 –best -q) for Screen 1 and Screen 3. For Screen 2 (HDAC1 and HDAC2 titration), processed reads were collapsed (FASTX-Toolkit) to count perfect duplicates followed by exact string-match intersection with the reference such that only perfectly matching and unique alignments were kept. The raw gRNA counts were normalized using a median of ratio method21 and batch corrected for biological replicates using combat from the SVA R package (v.3.34.0)22 . Nonreproducible technical outliers were removed by pair-wise linear regression for each sample, collecting residuals, and taking the median value for individual gRNAs across each time point.
Assembly: GRCh38
Supplementary files format and content: comma-separated values files include raw counts for each sample.

source_name: chronic myelogenous leukemia

growth_protocol: HEK293FT (Thermo R70007) and A375 (ATCC CRL-1619) cells were cultured in D10 medium, which is Dulbecco’s Modified Eagle Medium (DMEM) with high glucose and stabilized L-glutamine (Caisson DML23) supplemented with 10% fetal bovine serum (Sigma 14009C). HAP1 (Horizon C631) cells were cultured in I10 medium: Iscove’s Modified Dulbecco’s Medium (IMDM) with L-glutamine (Caisson IML02) supplemented with 10% fetal bovine serum. All cells were incubated at 37 °C with 5% carbon dioxide.

extract_protocol:
Genomic DNA was isolated from cell pellets via a modified salting out procedure. For that, 12 ml of NK Lysis Buffer (50 mM Tris, 50 mM EDTA, 1% SDS, pH 8) and 60 µl of 20 mg/ml Proteinase K (QIAGEN 19131) were added to 80 million cells and incubated at 55 °C overnight. The next day, 6 µl of 100 mg/ml RNase A (A.G. Scientific R-2000) was added to the lysed sample, which was then inverted 25 times and incubated at 37 °C for 30 min. Samples were cooled on ice before addition of 4 ml of pre-chilled 7.5M ammonium acetate (Sigma A1542) to precipitate proteins. After adding ammonium acetate, the samples were vortexed and centrifuged at 4,000 × g for 10 minutes. After the spin, 12 ml isopropanol was added to the collected supernatant, inverted 50 times and centrifuged at 4,000 × g for 10 minutes. The supernatant was discarded, 12 ml of freshly prepared 70% ethanol was added, the tube was inverted 10 times, and then centrifuged at 4,000 × g for 10 minutes. The supernatant was discarded, and remaining ethanol was removed. After air drying for 30 minutes, 500 µl of 0.2× TE buffer (Sigma 93283) was added, the tube was incubated at 65 °C for 1 hour and at room temperature overnight to fully resuspend the DNA. The next day, the gDNA samples were vortexed briefly. The gDNA concentration was measured using a Nanodrop (Thermo).
We amplified gRNA cassettes from the genomic DNA using a two-step PCR protocol (PCR1 and PCR2). PCR1 was performed to amplify a region containing the crRNA cassette in the lentiviral genomic integrant using TaqB polymerase (Enzymatics P7250L). We performed an appropriate amount of PCR1 reactions for each gDNA sample based on library size (Screen 1: 40 reactions; Screen 2: 20 reactions; Screen 3: 48 reactions) using 10 μg gDNA per 100 μl PCR1 reaction (10 cycles). We then combined PCR1 products for the same sample together before PCR2, which was done to incorporate Illumina adaptors using Q5 polymerase (NEB M0491). We performed an appropriate number of PCR2 reactions for each sample (Screen 1: 16 reactions; Screen 2: 8 reactions; Screen 3: 24 reactions) using 5 μl unpurified PCR1 product per 50 μl reaction (18 cycles). The resulting amplicons from PCR2 (~270 bp) were pooled and then purified using SPRI beads (Beckman B23317) or gel extracted using a QiaQuick Gel Extraction kit (Qiagen 28704).

treatment_protocol: Cas13d-expressing cells were transduced with the library lentivirus through separate infection replicates by spinfection at 1000 rpm for 1 hour at 37 °C, followed by overnight incubation. After 24 hours, new media with 1 μg/ml puromycin (Invivogen ant-pr-1) was added. Puromycin selection was completed within 48 hours for all cell lines. Following puromycin selection, RfxCas13d or HfCas13d expression was induced by replenishing the growth medium containing 1 μg/ml puromycin, 5 μg/ml blasticidin and 1 μg/ml doxycycline. Cells were passaged every 2 to 4 days and split as needed, ensuring a guide representation of >1,000×. Samples with a guide abundance of 1,000-fold were harvested at day 0 and 14 days post-Cas13d induction.

value: chronic myelogenous leukemia

value: cancer cells

tag: treatment

value: doxycycline induction

value: Fitness Screen Day 14


title: Cas13d gRNA amplicon of Homo sapiens: Essentiality HAP1_D0_R2

description:
Library name: Essentiality_HAP1_D0_R2
EssHAP_D0_R2

tag: batch

value: Input Day 0


title: Cas13d gRNA amplicon of Homo sapiens: Essentiality HEK293FT_D14_R2

description:
Library name: Essentiality_HEK293FT_D14_R2
EssHEK_D14_R2

source_name: human embryonic kidney cells

value: human embryonic kidney cells

value: embryonic kidney cells


title: Cas13d gRNA amplicon of Homo sapiens: Essentiality HEK293FT_D14_R1

description:
Library name: Essentiality_HEK293FT_D14_R1
EssHEK_D14_R1


title: Cas13d gRNA amplicon of Homo sapiens: Essentiality HAP1_D0_R1

description:
Library name: Essentiality_HAP1_D0_R1
EssHAP_D0_R1


title: Cas13d gRNA amplicon of Homo sapiens: Essentiality HAP1_D14_R1

description:
Library name: Essentiality_HAP1_D14_R1
EssHAP_D14_R1


title: 28-03-0010-8_post_0

source_name: nasal lavage sample

tag: Sex

value: Female

tag: nac

tag: dose

value: nasal lavage sample


title: control, R12816

tag: cell type

value: F

tag: group/disease

value: control


title: HU_input (for DNA2_MRE11)

description: HeLa, treated with 4 mM HU for 6 h, input

value: HeLa cell line

tag: genotype


title: 28-03-0010-8_pre_0

value: Placebo

tag: age

tag: month


title: Ctrl_IP_MRE11

description: HeLa, incubated with MRE11 antibody, without replicate

value: untreated

value: incubated with MRE11 antibody


title: Cas13d gRNA amplicon of Homo sapiens: Essentiality HEK293FT_D0_R2

description:
Library name: Essentiality_HEK293FT_D0_R2
EssHEK_D0_R2


title: OCD, R13521

value: DLPFC

value: Postmortem brain tissue

value: M

value: OCD

tag: rin


title: control, R12810

tag: tissue


title: 28-03-0006-0_post_0

value: SCIT

value: post

tag: pct reads

tag: median cv


title: Cas13d gRNA amplicon of Homo sapiens: Dual Titration A375_D14_R3

description:
Library name: DualTitration_A375_D14_R3
Dual_D14_R3

source_name: malignant melanoma skin cells

value: malignant melanoma skin cells

tag: cell line

value: cancer cells

value: doxycycline induction

value: Fitness Screen Day 14


title: Ctrl_IP_IgG

description: HeLa, incubated with Rabbit IgG, without replicate

value: Wild type

tag: chip antibody

value: incubated with Rabbit IgG


title: control, R12726

value: F

value: control


title: HU_IP_MRE11_rep1

description:
HeLa, treated with 4 mM HU for 6 h and incubated with MRE11 antibody, rep1
HU_vs_untreated_MRE11.narrowPeak

value: HeLa cell line

value: treated with 4 mM HU for 6 h


title: Ctrl_IP_DNA2

description: HeLa, incubated with DNA2 antibody, without replicate

value: untreated

value: incubated with DNA2 antibody


title: control, R12719

value: DLPFC

value: Postmortem brain tissue


title: 28-03-0005-4_post_0

tag: participant id

value: Male

tag: tnss

tag: tsneez

value: nasal lavage sample


title: 28-03-0006-0_pre_0

tag: Sex

value: Female

tag: treatment

value: SCIT

value: pre

tag: batch


title: Cas13d gRNA amplicon of Homo sapiens: Dual Titration A375_D14_R2

description:
Library name: DualTitration_A375_D14_R2
Dual_D14_R2

value: malignant melanoma skin cells

tag: cell type

value: cancer cells

value: doxycycline induction


title: Ctrl_input (for DNA2_MRE11_IgG)

description: HeLa, untreated, input

value: Wild type


title: Cas13d gRNA amplicon of Homo sapiens: Dual Titration A375_D14_R1

description:
Library name: DualTitration_A375_D14_R1
Dual_D14_R1

value: Fitness Screen Day 14


title: 28-03-0005-4_pre_0

tag: nac

tag: dose


title: ED, R12698

value: M

tag: group/disease

value: ED


title: 28-09-0002-0_post_12

value: Placebo

tag: age

tag: month

value: post


title: control, R12568

tag: tissue

value: control

tag: rin


title: Cas13d gRNA amplicon of Homo sapiens: Dual Titration A375_D0_R2

description:
Library name: DualTitration_A375_D0_R2
Dual_D0_R2

tag: genotype

value: Input Day 0


title: control, R12569

value: DLPFC

value: Postmortem brain tissue

value: F


title: Cas13d gRNA amplicon of Homo sapiens: Dual Titration A375_D0_R3

description:
Library name: DualTitration_A375_D0_R3
Dual_D0_R3

tag: cell line


title: control, R12567