title: ISC 22 month (old) SMC Lane7 rep1

status: Public on Mar 14 2022

city: Clayton

first: Monika

last: Mohenska

state: VIC

address: 15 Innovation Walk

institute: Monash University

data_processing:
Single-end reads were trimmed using Trimmomatic-V0.32, to remove adaptor contamination and poor quality reads.
Trimmed reads were then aligned to reference mouse genome (mm10) using BSSeeker2 with default parameters.
Reads mapping to multiple locations were removed using sambamba-v0.5.9.
bs_seeker2-call_methylation.py module was used to call methylation levels.
DMR identification was done using HOME version 0.4 and parameters --delta 0.3 and --minc 5 (rest of parameters default).
Assembly: mm10
Supplementary files format and content: CGmap

source_name: intestinal stem cell (ISC)

extract_protocol:
The isolated small intestine was flushed with PBS and opened longitudinally. The tissue was then scraped with a glass coverslip to remove villi, cut into 5-mm pieces and washed with PBS five times (20 inversions of the tube per wash). Following incubation for 30 min at 4°C in 4mM EDTA-PBS, intestinal crypts were released from small intestinal tissue fragments by mechanically pipetting with a 10ml pipette in PBS and repeating this step twice. After centrifugation (430xg for 5 min at 4°C), the pellet was resuspended in PBS and strained using a 70-μm cell strainer (BD Biosciences). Following centrifugation (430xg for 5 min at 4°C), the collected crypts were incubated for 30 minutes at 4°C in DMEM/F12 – 10% serum (Gibco), pelleted again by centrifugation (430xg for 5 min at 4°C) and then dissociated in TrypLE Express (Invitrogen) supplemented with 10 μM Rock inhibitor (Y-27632, Abcam) and 2.5µg/ml DNAse 1 (Sigma-Aldrich) for 4 minutes at 37°C. The dissociated cells were strained using a 70-μm cell strainer and were washed twice with PBS and collected by centrifugation at 4°C at 430xg for 5 minutes. Cellularized intestinal epithelial were labelled with antibodies and ISCs isolated by FACS (SM6 strategy, CD31-/CD45-/CD24med/CD166+/CD44high/GRP78low/EPHB2high/EPCAM+).
Genomic DNA was isolated with the DNeasy Blood and Tissue Kit (QIAGEN, Cat#69504) according to manufacturer’s instructions. Libraries were prepared using NxSeq AmpFREE Low DNA Library kit (Lucigen, Cat#14000-1). Briefly, 200 ng sample genomic DNA with 0.5% (w/w) unmethylated lambda phage DNA (Thermo Fisher Scientific Cat#SD0011) was fragmented with a Covaris S220 sonicator to a mean length of 200 bp. Fragments were end-repaired, A-tailed, and ligated to methylated Illumina TruSeq adapters (BIOO Scientific, Cat#BIOO-511912) followed by bisulfite conversion using EZ DNA-methylation Direct kit (Zymo Research, Cat#D5024). Library fragments were then subjected to 5 cycles of PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems, Cat#KP-KK2801). Single-end 100 bp sequencing was performed on a HiSeq 1500.
MethylC-seq

value: intestinal stem cell (ISC)

value: WT

tag: age

value: 22 months

value: old


title: ISC 22 month (old) SMC Lane5 rep1

type: SRA

country: Australia

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell type

tag: strain

tag: genotype

tag: developmental stage


title: ISC 22 month (old) SMC Lane2 rep1


title: ISC 22 month (old) SMC Lane6 rep1


title: ISC 2 month (young) SMC Lane6 rep1

value: 2 months

value: young


title: FRA013119-003

status: Public on Mar 15 2022

city: Chicago

first: Leonid

last: Feferman

state: Illinois

address: 1737 West Polk St

department: Research Resources Center

country: USA

institute: University of Illinois at Chicago

description:
library type: single-cell (OneCellBio/InDrop)
Cells were treated for 2 weeks with 4-Hydroxytamoxifen

library_source: transcriptomic

data_processing:
Raw R2 reads were mapped to the reference transcriptome (hg38  Ensembl gene sequences, exonic only) using BWA MEM. Cell barcodes and UMIs were extracted from R1 using a custom pipeline following OneCellBio adapter design for inDrop. Unique UMI counts were summed for each gene and each unique cell barcode. Only cell barcodes with >500 counts included in the final counts table.
Assembly: hg38 Ensembl gene sequences (exonic only)
Supplementary files format and content: Cell list: Tab-delimited text of cell name (matches columns in scRNA-seq counts tables), barcode, number of genes expressed, and UMI counts. All cell barcodes are listed in this file, including those below the 500 count minimum.

molecule: polyA RNA

organism: Homo sapiens

source_name: MCF-7 cell line

growth_protocol: Before treatments, cells were routinely cultured in RPMI 1640 containing  10% fetal bovine serum, 1% penicillin–  streptomycin, 1% nonessential amino acids, 2 mmol/L L-glutamine, and 0.5 µg/ml puromycin.

extract_protocol:
Single cell encapsulation was performed using inDrop system from 1CellBio, followed by transfer to 1CellBio UV Cleavage Device to release oligo linkers from the hydrogel beads and RT reaction.
Sequencing was performed using the Illumina NextSeq 500 with the High Output Kit 75 cycles. Read format was as follows: Read1 50b, Read2 36b. Total cDNA reads output approximately 400Mb

treatment_protocol: Cell were seeded in 6 well plate 1000 cells/well and treated with 4-Hydroxytamoxifen for next 2 weeks. Treatment was refreshed each 3-4 days.

tag: cell line

tag: tissue

value: Breast

tag: treatment


title: ISC 2 month (young) SMC Lane8 rep1


title: root tip, scr3_cvi

status: Public on Mar 16 2022

city: Perth

first: Ryan

last: Lister

state: WA

address: 35 Stirling Highway

institute: The University of Western Australia

description:
root_final.rds
scr_final.rds

data_processing:
Reads were mapped using a modified version of the 10x Genomics CellRanger pipeline. Reads were mapped to a version of the Arabidopsis (TAIR10) genome with ambiguous base codes placed at SNP positions for the genotypes sequenced, as identified by the Arabidopsis 1001 genomes project.
Cells were then genotyped and cell doublets identified by performing density-based clustering on the SNP UMI counts for each genotype
The Seurat v3 R package was used for data normalization, cell filtering, batch correction, dimension reduction, and clustering.
Assembly: TAIR10
Supplementary files format and content: Processed data files are Seurat objects. The root_final.rds object contains all processed wild-type cells: the 'integrated' slot contains the integrated (genotype-corrected) data, and the 'batch_corrected' slot the batch-corrected data. The col_final.rds object contains wild-type col-0 cells only, and batch-corrected data. The scr_final.rds object contains scr-3 data, and the ms_final.rds object contains data from Col-0 cells from seedlings grown on full or half MS and processed simultaneously. The meta data of each object contains different cell annotations.

organism: Arabidopsis thaliana

source_name: root tip (~up to 3 mm) of seedlings at 6dag

growth_protocol: Seedlings were grown vertically on Murashige and Skoog basal medium with vitamins plates supplemented with 1% sucrose for 6-7 dag before root tips were collected

extract_protocol:
For each genotype, root tips were placed in 15ml of protoplasting solution [1.25% w/v cellulase, 0.3% w/v macerozyme, 0.4M D-mannitol, 20mM MES (pH 5.7), 20mM KCl, 10mM CaCl2, 0.5% w/v BSA, and 5mM β-mercaptoethanol in ultrapure water] and incubated at room temperature for 1 hour on a tube rotator. The solution was subsequently filtered through a 70μm and a 40μm cell strainer (Falcon) to separate protoplasts from undissociated tissue. Cells were centrifuged for 5 minutes at 500 x g in a swinging bucket centrifuge. The pellet was resuspended in 15ml of protoplast resuspension buffer [0.4M D-mannitol, 20mM MES (pH 5.7), 20mM KCl, 10mM CaCl2, and 0.5% w/v BSA in ultrapure water] and centrifuged at 500 x g for 5 minutes. Cells were resuspended in the protoplast resuspension buffer, and filtered through a 35μm cell strainer Snap Cap (Falcon). The final concentration was adjusted to 900-1,200 cells/μl. Protoplasts from two Arabdiopsis accessions were mixed in equimolar quantities and barcoded with a Chromium Controller (10X Genomics).
10X Genomics 3' Single Cell Gene Expression v2/v3
scRNA-seq

value: seedlings at 6dag

value: root tip

value: mix of scr-3 and Cvi cells

tag: growth medium

value: full MS (1x)


title: Day Infusion PBMC from Patient 5

status: Public on Mar 11 2022

city: Cambridge

first: Guangan

last: Hu

state: MA

address: 500 Main Street

department: Koch Institute

institute: MIT

description:
D21-10233
single cell
D21-10233_counts.csv.gz

data_processing:
Raw sequences were demultiplexed, aligned, filtered, barcode counting, unique molecular identifier (UMI) counting with Cell Ranger software v3.1 (10XGenomics) to digitalize the expression of each gene for each cell.
The outlier cells with very low number of gene features (<500), or high number of gene features as doublets (>5000),  or low total UMI (<1000) and high mitochondrial ratio (>10%) from each data set were removed.
Samples were combined based on the  identified anchors for the following integrated analysis.
Cell subpopulations were defined as described in the manuscriipt
Assembly: hg19
Supplementary files format and content: CSV files include mRNA molecule count values and single cell barcodes for each Sample

source_name: PBMC

extract_protocol:
Cryopreserved PBMC samples from patients were thawed and diluted with pre-warmed complete RPMI, and cells were centrifuged at 200 rcf (xg) for 10 min to remove dead cells. Cell pellets were resuspended in 25% Percoll solution in PBS and centrifuged at 300 rcf (xg) for 10min to further remove dead cells. Live cells were resuspended in 2%FBS PBS for single cell isolation and cDNA library construction. The relapse samples were CD34-depleted using a CD34+ positive selection kit (STEMCELL technologies), with the CD34+ cells resuspended as independent tumor samples.
10x Chromium Next GEM Single Cell 3' Kit.

value: PBMC


title: Day Infusion PBMC from Patient 1

description:
D21-10229
single cell
D21-10229_counts.csv.gz


title: ISC 2 month (young) SMC Lane4 rep1


title: Day Infusion PBMC from Patient 4

description:
D21-10232
single cell
D21-10232_counts.csv.gz


title: Day +28 PBMC from Patient 5

description:
D21-10228
single cell
D21-10228_counts.csv.gz


title: Day Infusion PBMC from Patient 3

description:
D21-10231
single cell
D21-10231_counts.csv.gz


title: Day Infusion PBMC from Patient 2

description:
D21-10230
single cell
D21-10230_counts.csv.gz


title: FRA013119-004


title: Day +28 PBMC from Patient 2

description:
D21-10225
single cell
D21-10225_counts.csv.gz


title: ISC 2 month (young) SMC Lane2 rep1


title: Day +28 PBMC from Patient 3

description:
D20-7410
single cell
D20-7410_counts.csv.gz


title: Day +60 PBMC from Patient 4

description:
D21-10227
single cell
D21-10227_counts.csv.gz


title: Day +28 PBMC from Patient 6

description:
D21-10224
single cell
D21-10224_counts.csv.gz


title: Day +28 PBMC from Patient 4

description:
D21-10226
single cell
D21-10226_counts.csv.gz


title: relapse (day +60) CD34+  from Patient 3

description:
D20-7413
single cell
D20-7413_counts.csv.gz


title: relapse (day +60) PBMC from Patient 1

description:
D20-7409
single cell
D20-7409_counts.csv.gz


title: ISC 2 month (young) SMC Lane5 rep1


title: Day +28 PBMC from Patient 1

description:
D20-7408
single cell
D20-7408_counts.csv.gz


title: ISC 2 month (young) SMC Lane1 rep1


title: PERKKO-Vector-polysome-bound-rep2

status: Public on Mar 07 2022

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

country: China

institute: Life Sciences Institute, Zhejiang University

data_processing:
Polysome-Seq was performed with biological replicates for all samples. Raw reads were trimmed to 50 bp and mapped to the human genome (hg19) using Tophat v2.1.1 with default parameters. Only uniquely mapped reads were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) using Cufflinks v2.2.1. The RNA abundance of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments) and was further normalized with the ERCC spike-in. Briefly, sequencing reads were mapped to ERCC reference to obtain the ratio of ERCC reads to human reads. Then gene abundance was normalized by multiplying the raw FPKM values by a normalization factor (normalization factor = percentage of ERCC in control polysome-free sample/percentage of ERCC in the sample). Samples prepared in different batches were normalized by the control polysome-free sample in each batch. Genes with FPKM < 1 in all samples were excluded, and for the remaining genes, all FPKM values smaller than 1 were set to 1 in subsequent analyses. The ribosome load was defined as the ratio of the proportion of an mRNA in the polysome-bound and the polysome-free pool.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of all RNA-seq samples

molecule: total RNA

source_name: HEK293 cells

growth_protocol: HEK293 cells were obtained from ATCC, and  were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) at 37°C in 5% CO2 (v/v).

extract_protocol:
Cells transfected with different plasmids  were pretreated with 100 mg/ml cycloheximide for 30 min at 37°C prior to washing with ice-cold PBS containing 100 mg/ml cycloheximide. Cells were then lysed in polysome lysis buffer (20 mM Tris-HCl (pH 7.4), 100 mM KCl, 5 mM MgCl2, 100 mg/ml cycloheximide and 1% NP40). After 20 min on ice, the lysates were centrifuged (12,000 rpm for 15 min at 4°C), and the supernatants were loaded onto 10-50% sucrose gradients and centrifuged for 15 h at 25,000 rpm and 4°C in a SW41 rotor. Separated samples were fractionated at 0.75 ml/min through an automated fractionation system that continually monitors OD254 values. An aliquot of the ribosomal fraction was used for extraction of total RNA with TRIzol reagent (Yeasen). Purified RNAs and ERCC spike-in (0.4 μl 1:1000 diluted) mixtures were used for cDNA synthesis using the Smart-seq2 method (Picelli et al., 2014). Briefly, the polyadenylated mRNAs were captured usingby the PolyT primers. After 3 min lysis at 72°C, the Smart-seq2 reverse transcription reactions were performed. After the first-strand reaction, the cDNA was amplified using a limited number of cycles (12∼14 cycles).
Sequencing libraries were constructed from 1 ng of amplified cDNA using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to the manufacturer's instructions. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform in the 150 bp paired-end mode.
Polysome-seq

treatment_protocol: A total of 7*106 cells were transfected with 5ug Vector or STING plasmid for 24 hours.

value: HEK293 cells

value: Ectopic expression of Vector

value: PERK KO


title: Day Infusion PBMC from Patient 6

description:
D21-10234
single cell
D21-10234_counts.csv.gz


title: PERKKO-STING-polysome-bound-rep2

value: Ectopic expression of STING


title: WT-STING-polysome-bound-rep1

value: Wild type


title: WT-STING-polysome-bound-rep2


title: PERKKO-STING-polysome-bound-rep1


title: PERKKO-Vector-polysome-bound-rep1


title: WT-Vector-polysome-bound-rep1


title: relapse (day +60) CD34+  from Patient 1

description:
D20-7412
single cell
D20-7412_counts.csv.gz


title: shFSCN1_2

status: Public on Mar 05 2022

city: jilin

first: Hongfei

last: cai

address: No.1 Xinmin Street, Chaoyang District, Changchun City, Jilin Province

department: Ddepartment of Thoracic Surgery

institute: The First Hospital of Jilin University

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 20 -p 16 --no-discordant. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2, FDR <= 0.05.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

growth_protocol: Eca-109 cells were cultured under standard conditions with Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, and 100 U/mL penicillin.

extract_protocol:
The RNA was treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were assessed by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of each RNA sample was further verified by 1.5% agarose gel electrophoresis.electrophoresis.
A total 1μg RNA for each sample was used for RNA-seq library preparation. PolyA mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Invitrogen, Carlsbad, CA, USA) before directional RNA-seq library preparation. The fragmented RNA were end repaired and 5' adaptor ligation. Then, reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified, amplified, and stored at -80°C until they were used for sequencing.

treatment_protocol: To knockdown FSCN1, shRNA against human FSCN1 transfection of Eca-109 cells was performed using lipofectAMINE 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. Transfected cells were harvested after 48 h for analysis.

tag: transfection


title: shFSCN1_3


title: shFSCN1_1


title: ECA_NC_3

value: shNC


title: ECA_NC_2


title: ECA_NC_1


title: WT-Vector-polysome-bound-rep2


title: ccRCC tumor  frozen_b_18

status: Public on Mar 03 2022

city: Paris

first: Maxime

last: Meylan

state: Paris

address: 15 rue de l'école de Médecine

country: France

institute: UMRS 1138 - Centre de Recherche des Cordeliers

data_processing:
Raw fatsqs were processed with SpaceRranger
Genome_build: hg38
Supplementary_files_format_and_content: matrices, images and json files

source_name: frozen ccRCC human tumor

extract_protocol:
RNA extraction with the 10X Visium protocol
Libraries preparation with illumina Truseq kit

tag: disease state

value: renal cell cancer

value: ccRCC tumor


title: ccRCC tumor  frozen_c_2


title: ccRCC tumor  frozen_c_5


title: ccRCC tumor  frozen_a_3


title: ccRCC tumor  frozen_b_13


title: ccRCC tumor  frozen_b_7


title: ccRCC tumor  frozen_a_17


title: ccRCC tumor  frozen_c_23


title: ccRCC tumor  frozen_b_1


title: ccRCC tumor  frozen_a_15


title: relapse (day +60) PBMC from Patient 3

description:
D20-7411
single cell
D20-7411_counts.csv.gz


title: ccRCC tumor  ffpe_c_51

source_name: fresh ccRCC human tumor


title: ccRCC tumor  frozen_a_1


title: ccRCC tumor  ffpe_c_7


title: ccRCC tumor  ffpe_c_21


title: ccRCC tumor  ffpe_c_39


title: ccRCC tumor  ffpe_c_36


title: ccRCC tumor  ffpe_c_20


title: ccRCC tumor  ffpe_c_4


title: ccRCC tumor  ffpe_c_2


title: Jej.IBSC 6_S12

status: Public on Feb 28 2022

city: Rochester

first: Ting

last: Wei

state: MN

address: 507 3rd St SW

institute: Mayo Clinic

description: Jej.IBSC

data_processing:
Image data and base calling were processed using the Illumina Standard Pipeline.
Fastq data were analyzed by Mayo Analysis Pipeline for RNA Sequencing (MAPRSeq v3.1.3) with STAR (2.6.1) for reads alignment to the human genome reference GRCh38 (hg38) and RSeqQC for gene expression.
After read counts and library size filtration, normalized counts and RPKM for samples were calculated by edgeR (v4.0.1) and differentially expressed genes between groups were determined
Gene set enrichment analysis (GSEA, v4.0.1) was conducted using preranked module based on gene expression ranks
Genome_build: hg38
Supplementary_files_format_and_content: Raw counts and RPKM (merged)

source_name: Jejunum

extract_protocol:
RNA extracted using Qiagen miRNeasy kit for total RNA (Cat# 217004)
Illumina NovaSeq 6000 S2 flow cell (paired-end libraries 2×50bp)

treatment_protocol: Biopsies were collected, immediately placed in Qiagen Allprotect Tissue Reagent (Cat# 76405) and flash frozen in LN2. Storage at -80°C.

value: Jejunum

value: IBS-C

tag: gender

value: F

tag: bmi


title: P053 control male 121

status: Public on Mar 02 2022

city: Jena

first: Bastian

last: Seelbinder

address: Adolf-Reichwein-Straße 23

department: Systems Biology and Bioinformatics

country: Germany

institute: Hans-Knoell-Institute Jena

data_processing:
trimmomatic v0.36; single-end mode; Illumina adapter trimming; LEADING:3; TRAILING:3; SLIDINGWINDOW:15:25; MINLEN:30
hisat2 exon-indexing of human GRCH38-109 from 2018-03-26
featureCounts as implemented in Rsubread 1.34.0
Genome_build: GRCH38-109
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with median-by-ratio normalized gene counts for every gene and every sample; MRN normalization as implemented in EBSeq and GEO2RNAseq

source_name: blood

extract_protocol:
Human blood samples were preserved in Tempus Blood RNA tubes for shipping. Library preparation was performed with the Illumina TruSeq Stranded mRNA (incl. Ribo-Zero Globin) technology, according to the manufacturer ́s protocol. After depletion of cytoplasmic and mitochondrial rRNA as well as globin mRNA using the Ribo-Zero Globin technology, included in the TruSeq® Stranded Total RNA library prep kit, the samples were quality controlled. Therefore, the RNA 6000 Pico LabChip kit was used on the 2100 Bioanalyzer (Agilent Technologies). All libraries were quantified using the highly sensitive fluorescent dye-based Qubit® ds DNA HS Assay Kit (Thermo Fisher Scientific). All single libraries were pooled into several sequencing library pools with an equal DNA amount per sample. Subsequently, the sequencing library pools were pooled separately with libraries of other projects for sequencing in several NextSeq HighOutput runs. Clustering of the library pools was performed on the NextSeq® 500 sequencing system (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ia

value: control

tag: subject

tag: timepoint

tag: Sex

value: male


title: ccRCC tumor  frozen_c_57


title: ccRCC tumor  ffpe_c_3


title: Lung_CUT_TAG_PRMK_rep1_KMT2C

status: Public on Feb 23 2022

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

description: library strategy: CUT&TAG

data_processing:
CUT-TAG:
Sequenced reads were mapped to mm10 whole genome using bowtie2
peaks were called using SEACR
RNA-Seq:
Sequenced reads were mapped to mm10 whole genome using STAR_2.6.0a
Counts were normalized by DESeq2
WGBS:
WGBS reads were aligned to the mm10 genome assembly using BS-Seeker2(v2.1.8)
Bismark was used to call methylation
Genome_build: mm10 or GRCm38
Supplementary_files_format_and_content: bigwig files
Supplementary_files_format_and_content: txt files with gene normalised by DESeq2
Supplementary_files_format_and_content: CGmap.gz files for WGBS

source_name: Lung

growth_protocol:
CUT-TAG: The PRM and PRMK mouse were developed on recipient mice after transplantation through injection into the left lobe of lung.
RNA-Seq: The PRMK mouse were developed on recipient mice after transplantation through injection into the left lobe of lung.
WGBS: The PRM and PRMK mouse were developed on recipient mice after transplantation through injection into the left lobe of lung.

extract_protocol:
CUT-TAG: PRMK lung organoids were harvested from the recipient mice.
RNA-Seq: RNA was extracted with Trizol
CUT&TAG assay was performed using NovoNGS® CUT&TAG 2.0 High-Sensitivity Kit (Novoprotein scientific Inc., Cat# N259-YH01-01A).
WGBS: After in situ transplantation, lung organoids carrying Trp53 and Rb1 mutations and Myc overexpression lead to single primary PRM in recipient mice. And lung organoids carrying Trp53 ，Rb1 and kmt2c mutations and Myc overexpression lead to single primary PRMK in recipient mice.

treatment_protocol:
RNA-Seq: Treated with SAM and Vehicle in PRMK organoids
WGBS: PRM and PRMK tumor tissue  were harvested from the recipient mice. The PRM and PRMK tumor tissue  were harvested from the recipient mice at ~3-4 mouths after transplantation.

tag: genotype/plasmids

tag: replicates

tag: antibody


title: Lung_CUT_TAG_PRMK_rep2_KMT2C

description: library strategy: CUT&TAG


title: ccRCC tumor  ffpe_c_45


title: Lung_CUT_TAG_PRM_rep2_KMT2C

description: library strategy: CUT&TAG


title: Lung_CUT_TAG_PRM_rep1_KMT2C

description: library strategy: CUT&TAG


title: ccRCC tumor  ffpe_c_34


title: Lung_CUT_TAG_PRMK_rep2_H3K4me3

description: library strategy: CUT&TAG


title: Lung_CUT_TAG_PRMK_rep2_H3K4me2

description: library strategy: CUT&TAG


title: Lung_CUT_TAG_PRM_rep1_H3K4me3

description: library strategy: CUT&TAG


title: Lung_CUT_TAG_PRMK_rep1_H3K4me2

description: library strategy: CUT&TAG


title: Lung_CUT_TAG_PRM_rep2_H3K4me2

description: library strategy: CUT&TAG


title: PRMK_RNA_seq_vehicle_rep3

description: processed data file: RNAseq5_SAM_VS_vehicle_result_all.xlsx


title: Lung_CUT_TAG_PRM_rep1_H3K4me2

description: library strategy: CUT&TAG


title: PRMK_RNA_seq_vehicle_rep1


title: PRMK_RNA_seq_vehicle_rep2


title: liver_CUT_TAG_PRM_rep1_KMT2C

description: library strategy: CUT&TAG

source_name: Liver


title: PRMK_RNA_seq_SAM_rep2


title: Lung_CUT_TAG_PRM_rep2_H3K4me3

description: library strategy: CUT&TAG


title: PRMK_RNA_seq_SAM_rep3


title: Liver_WGBS_seq_PRM_rep1


title: Lung_CUT_TAG_PRMK_rep1_H3K4me3

description: library strategy: CUT&TAG


title: PRMK_RNA_seq_SAM_rep1


title: liver_CUT_TAG_PRM_rep2_KMT2C

description: library strategy: CUT&TAG


title: G1_Citrobacter_DMSO_1_S77_L003

status: Public on Feb 03 2022

city: La Jolla

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

data_processing:
RNASeq data was processed using kallisto (version 0.45.0) and mouse genome GRCm38 Ensembl version 94 annotation (Mus_musculus.GRCm38.94.chr_patch_hapl_scaff.gtf). Gene-level TPM values and gene annotations were computed using tximport and biomaRt R package. Batch correction was performed using sva::ComBat_seq R function. Expression values were generated using log2(batch corrected counts + 1).
Genome_build: Genome assembly: GRCm38 Ensembl 94, Gene annotatiopn: Mus_musculus.GRCm38.94.chr_patch_hapl_scaff.gtf
Supplementary_files_format_and_content: tab-delimited text files include log2(batch corrected TPM+1).

source_name: Distal colon

growth_protocol: Adult C57BL/6 mice were acquired from Jackson Laboratories. All animals were maintained in an institutional animal care. Provided with standard light–dark cycle, fed with standard laboratory chow and clean drinking water.

extract_protocol:
All colon tissues were lysed using TRI-Reagent and RNA was isolated using Zymo Research: Direct-zol RNA MiniPrep Kit.
RNA sequencing libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, except modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End (PE100) to a depth of approximately 25-40 million reads per sample on an Illumina NovaSeq 6000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).

treatment_protocol: Mice were orally challenged with C. rodentium at 5 x 108 CFU in 0.1 ml of PBS. PPARa agonist (GW7647, 20 ug/kg body weight/day), PPARg agonist (Pioglitazone, 20mg/kg body weight/day), PPARa/g dual agonist (PAR5359, 1 mg/kg body weight/day) were administered via intraperitoneal route in 200 ul total volume (DMSO less than 4%).

tag: strain

value: inflammatory bowel disease

value: distal colon

tag: time

value: day 18

value: DMSO

tag: infection

value: Yes


title: Lung_CUT_TAG_PRM_rep1_IgG

description: library strategy: CUT&TAG


title: Liver_WGBS_seq_PRM_rep2


title: Melanoma [06S18034206]

status: Public on Jan 28 2022

type: genomic

city: Tampa

first: Xuefeng

last: Wang

state: FL

address: 12902 Magnolia Dr

institute: H. Lee Moffitt Cancer Center and Research Institute

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented, and hybridized to MethylationEPIC BeadArrays according to the Illumina Infinium HD Methylation Assay protocol.

scan_protocol: BeadArrays were scanned at standard settings using the Illumina iScan instrument.

data_processing: IDAT files were processed, background corrected and normalized using control probes in R using the minfi bioconductor package.

source_name: Melanoma

label_protocol: Sample labeling and staining steps were performed on the Tecan liquid handling station using the Tecan GenePaint system following the Illumina Infinium HD Methylation Assay protocol.

extract_protocol: Genomic DNA was extracted using QIAamp DNA extraction kit (QIAGEN, Valencia, CA).

tag: diagnosis

value: Melanoma

tag: tissue

value: Tumor


title: Melanoma [06S18034211]


title: Melanoma [06S18034198]


title: Melanoma [06S18031450]


title: Melanoma [06S18034208]


title: Melanoma [06S18034212]


title: iCLIP-seq of SP1, replicate S3

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

description: Extracted RNA was reverse transcribed using primer Rt13clip: /5Phos/NNTCCGNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNNCGGANN, where N are random bases.

data_processing:
Base calls were processed with bcl2fastq2 (Illumina) version 2.18.
Raw reads that consisted of 3 random positions, a 4-nt multiplexing barcode, and another 2 random positions, followed by the actual read were initially trimmed to 45 nt from the 3'-end, and duplicates were discarded.
Reads were de-multiplexed (note that they are already de-multiplexed in this GEO record), and the random positions, barcode, and 3'-bases matching Illumina adaptors were removed.
Reads shorter than 25 nt were filtered out and remaining reads trimmed to 35 nt. These steps were carried out using Trimmomatic (Bolger et al., 2014). Surviving reads were mapped to the mouse genome/transcriptome (Ensembl annotation of NCBIm37) using tophat (Trapnell et al., 2009) with default settings. To prevent false assignments of reads from repetitive regions, any reads with a mapping quality < 3 were removed from further analysis.
Sites of crosslink-induced mutation sites (CIMS) and crosslink-induced truncation sites (CITS) were derived using the CLIP Tool Kit (Shah A. et al., Bioinformatics 2017). Peaks from CITS and CIMS analyses were thresholded at a p-value (or FDR for CIMS) of 10e-10 and concatenated into one BED file.
Genome_build: hg19
Supplementary_files_format_and_content: Concatenated CIMS and CITS derived with CLIP Tool Kit, in BED format.
Supplementary_files_format_and_content: bigWig file; crosslinks were approximated as being position 1 of the read, binned to 50 nt, and normalized to counts per million.

source_name: Human embryonic kidney cells

extract_protocol:
Cells were crosslinked (0.4 J/cm2) at 254 nm with a Stratalinker 1800 prior to immunoprecipitation. Lysates generated from the crosslinked cells were treated with Turbo DNAse (Ambion) and diluted RNAse I (Ambion) for 5 minutes at 37°C to digest the genomic DNA and trim the RNA to short fragments of an optimal size range. RNA-protein complexes were immunoprecipitated using 100 μL of protein A/G Dynabeads (Life Technologies) and 5-10 μg of indicated antibodies. Following stringent high salt washes, the immunoprecipitated RNA was 3´ end dephosphorylated and a pre-adenylated adaptor was ligated at the 3´ end as described for a previously described enhanced CLIP ligation method (Van Nostrand et al., Nat. Methods 2016) for adaptor ligation. After additional washes, the immunoprecipitated RNA was 5´ end-labeled with radioactive 32P isotopes using T4 polynucleotide kinase (New England Biolabs). The immunoprecipitated complexes were separated with SDS-PAGE and transferred to a nitrocellulose membrane (Protran). For the input sample, the membrane was cut to match the size of the immunoprecipitated material. RNA was recovered by digesting proteins using proteinase K (Thermo Fisher).
RNA was reverse transcribed into cDNA using reverse transcription primers that include barcode sequences to enable multiplexing, a unique molecular identifier, and a BamHI restriction site. The cDNA was size selected (low: 70 to 85 nt, middle: 85 to 110 nt, and high: 110 to 180 nt), circularized to add the adaptor to the 5′ end, digested at the internal BamHI site, and then PCR amplified using AccuPrime SuperMix I (Thermo Fisher). The final PCR libraries were purified on PCR purification columns (QIAGEN). Eluted DNA was mixed at a ratio of 1:5:5 from the low, middle, and high fractions and submitted for sequencing.

treatment_protocol: Crosslinking (0.4 J/cm2) was done at 254 nm with a Stratalinker 1800.

tag: cell line

tag: growth protocol

value: Human embryonic kidney cells (HEK293) cells were grown in DMEM supplemented with 10% FBS, sodium pyruvate, MEM non-essential amino acids, and penicillin/streptomycin, and maintained at 37°C with 5% CO2.

tag: genotype

value: wild-type cells

value: Sp1 monoclonal antibody (SANTA CRUZ Biotechnology)


title: Size-matched input for SP1

description: Extracted RNA was reverse transcribed using primer Rt15clip: /5Phos/NNTATTNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNNGAATAN, where N are random bases.

value: no antibody used for input samples


title: Melanoma [06S18034210]


title: Melanoma [06S18031438]


title: Melanoma [06S18034202]


title: Melanoma [06S18031449]


title: Melanoma [06S18031442]


title: Melanoma [06S18034200]


title: iCLIP-seq of FIP, replicate B

description: Extracted RNA was reverse transcribed using primer Rt16clip: /5Phos/NNTTAANNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNNTTAANN, where N are random bases.

data_processing:
Base calls were processed with bcl2fastq2 (Illumina) version 2.18.
Raw reads that consisted of 3 random positions, a 4-nt multiplexing barcode, and another 2 random positions, followed by the actual read were initially trimmed to 45 nt from the 3'-end, and duplicates were discarded.
Reads were de-multiplexed (note that they are already de-multiplexed in this GEO record), and the random positions, barcode, and 3'-bases matching Illumina adaptors were removed.
Reads shorter than 25 nt were filtered out and remaining reads trimmed to 35 nt. These steps were carried out using Trimmomatic (Bolger et al., 2014). Surviving reads were mapped to the mouse genome/transcriptome (Ensembl annotation of NCBIm37) using tophat (Trapnell et al., 2009) with default settings. To prevent false assignments of reads from repetitive regions, any reads with a mapping quality < 3 were removed from further analysis.
Sites of crosslink-induced mutation sites (CIMS) and crosslink-induced truncation sites (CITS) were derived using the CLIP Tool Kit (Shah A. et al., Bioinformatics 2017). Peaks from CITS and CIMS analyses were thresholded at a p-value (or FDR for CIMS) of 10e-10 and concatenated into one BED file.
Genome_build: hg19
Supplementary_files_format_and_content: Concatenated CIMS and CITS derived with  CLIP Tool Kit, in BED format.
Supplementary_files_format_and_content: bigWig file; crosslinks were approximated as being position 1 of the read, binned to 50 nt, and normalized to counts per million.

extract_protocol:
Cells were crosslinked (0.4 J/cm2) at 254 nm with a Stratalinker 1800 prior to immunoprecipitation.  Lysates generated from the crosslinked cells were treated with Turbo DNAse (Ambion) and diluted RNAse I (Ambion) for 5 minutes at 37°C to digest the genomic DNA and trim the RNA to short fragments of an optimal size range. RNA-protein complexes were immunoprecipitated using 100 μL of protein A/G Dynabeads (Life Technologies) and 5-10 μg of indicated antibodies. Following stringent high salt washes, the immunoprecipitated RNA was 3´ end dephosphorylated and a pre-adenylated adaptor was ligated at the 3´ end as described for a previously described enhanced CLIP ligation method (Van Nostrand et al., Nat. Methods 2016) for adaptor ligation. After additional washes, the immunoprecipitated RNA was 5´ end-labeled with radioactive 32P isotopes using T4 polynucleotide kinase (New England Biolabs). The immunoprecipitated complexes were separated with SDS-PAGE and transferred to a nitrocellulose membrane (Protran). For the input sample, the membrane was cut to match the size of the immunoprecipitated material. RNA was recovered by digesting proteins using proteinase K (Thermo Fisher).
RNA was reverse transcribed into cDNA using reverse transcription primers that include barcode sequences to enable multiplexing,  a unique molecular identifier, and a BamHI restriction site. The cDNA was size selected (low: 70 to 85 nt, middle: 85 to 110 nt, and high: 110 to 180 nt), circularized to add the adaptor to the 5′ end, digested at the internal BamHI site, and then PCR amplified using AccuPrime SuperMix I (Thermo Fisher). The final PCR libraries were purified on PCR purification columns (QIAGEN).  Eluted DNA was mixed at a ratio of 1:5:5 from the low, middle, and high fractions and submitted for sequencing.

value: Fip1 Polyclonal antibody (Bethyl)


title: Input for CPSF2, CPSF7, Fip1 and CPSF160

description: Extracted RNA was reverse transcribed using primer Rt2clip: /5Phos/NNACAANNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNNTTGTNN, where N are random bases.


title: Melanoma [06S18031447]


title: iCLIP-seq of SP1, replicate S2

description: Extracted RNA was reverse transcribed using primer Rt10clip: /5Phos/NNGACCNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNNGGTCNN, where N are random bases.


title: Melanoma [06S18034203]


title: iCLIP-seq of CPSF7, replicate A

description: Extracted RNA was reverse transcribed using primer Rt6clip: /5Phos/NNCCGGNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNNCCGGNN, where N are random bases.

value: CPSF7 Polyclonal antibody (Bethyl)


title: Melanoma [06S18034199]


title: Melanoma [06S18031440]


title: iCLIP-seq of CPSF2, replicate B

description: Extracted RNA was reverse transcribed using primer Rt9clip: /5Phos/NNGCCANNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNNTGGCNN, where N are random bases.

value: CPSF2 Polyclonal antibody (Abcam)


title: iCLIP-seq of SP1, replicate E


title: Melanoma [06S18031448]


title: iCLIP-seq of CPSF2, replicate A


title: iCLIP-seq of CPSF160, replicate B

value: CPSF160 Polyclonal antibody (Abcam)


title: Melanoma [06S18034207]


title: Melanoma [06S18034201]


title: Melanoma [06S18031444]


title: Melanoma [06S18031437]


title: iCLIP-seq of GFP-NUDT21, replicate E

description: Extracted RNA was reverse transcribed using primer Rt14clip: /5Phos/NNTGCCNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNNGGCANN, where N are random bases.

value: GFP-NUDT21 was expressed in an HEK293 cell line engineered with the Flp-in system under the control of doxycyclin, and expression was induced for 48 hours prior to crosslinking.

value: GFP monoclonal antibody  (Life Technologies)


title: iCLIP-seq of GFP-NUDT21, replicate D


title: Melanoma [06S18031439]


title: Melanoma [06S18031443]


title: Melanoma [06S18031446]


title: Melanoma [06S18031445]


title: pancreatic cells for patch-seq [P2G7]

status: Public on Jan 27 2022

city: Gothenburg

first: Joan

last: Camunas-Soler

address: Medicinaregatan 9C

country: Sweden

institute: University of Gothenburg

data_processing:
Mapped to GRCh38 using STAR.
Gene counts using htseq-count.
Genome_build: GRCh38
Supplementary_files_format_and_content: pclamp_v2_counts.tab: Tab-delimited text file includes gene counts.

source_name: pancreatic islets

extract_protocol: SmartSeq2 (21X-23X PCR cycles).

value: Nondiabetic

value: Pancreatic islets

value: Male

tag: patched


title: iCLIP-seq of GFP-NUDT21, replicate B


title: pancreatic cells for patch-seq [P2G6]


title: Melanoma [06S18034204]


title: Melanoma [06S18031441]


title: pancreatic cells for patch-seq [P2G4]


title: pancreatic cells for patch-seq [P2F10]

value: Female


title: pancreatic cells for patch-seq [P2E8]

value: Yes


title: pancreatic cells for patch-seq [P2F7]


title: pancreatic cells for patch-seq [P2D7]


title: pancreatic cells for patch-seq [P2D2]


title: iCLIP-seq of CPSF7, replicate B


title: Size-matched input for NUDT21


title: pancreatic cells for patch-seq [P2D11]


title: pancreatic cells for patch-seq [O2H11]


title: pancreatic cells for patch-seq [O2G6]


title: pancreatic cells for patch-seq [P2A12]


title: pancreatic cells for patch-seq [P2A8]


title: Size-matched input for SP1, replicate A

description: Extracted RNA was reverse transcribed using primer Rt1clip: /5Phos/NNAACCNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNNGGTTNN, where N are random bases.


title: pancreatic cells for patch-seq [O2G2]


title: pancreatic cells for patch-seq [P2B4]


title: pancreatic cells for patch-seq [P2D9]


title: Melanoma [06S18034197]

value: Melanoma


title: pancreatic cells for patch-seq [O2F12]


title: pancreatic cells for patch-seq [O2C6]


title: pancreatic cells for patch-seq [O2C9]


title: pancreatic cells for patch-seq [O2E8]


title: Melanoma [06S18034209]

value: Tumor


title: pancreatic cells for patch-seq [O2A12]


title: pancreatic cells for patch-seq [O2C10]


title: pancreatic cells for patch-seq [O2D6]


title: iCLIP-seq of FIP, replicate A

value: Human embryonic kidney cells (HEK293) cells were grown in DMEM supplemented with 10% FBS, sodium pyruvate, MEM non-essential amino acids, and penicillin/streptomycin, and maintained at 37°C with 5% CO2.


title: pancreatic cells for patch-seq [N2H3]


title: pancreatic cells for patch-seq [O2B11]


title: Melanoma [06S18034205]


title: pancreatic cells for patch-seq [N2F4]


title: pancreatic cells for patch-seq [N2H12]


title: pancreatic cells for patch-seq [N2D6]


title: pancreatic cells for patch-seq [M2H4]


title: pancreatic cells for patch-seq [N2C7]


title: pancreatic cells for patch-seq [M2F6]


title: pancreatic cells for patch-seq [M2H12]


title: pancreatic cells for patch-seq [M2H11]


title: iCLIP-seq of GFP-NUDT21, replicate C


title: pancreatic cells for patch-seq [M2C5]


title: pancreatic cells for patch-seq [M2D7]


title: pancreatic cells for patch-seq [M2E2]


title: pancreatic cells for patch-seq [M2H2]


title: pancreatic cells for patch-seq [M2C10]


title: pancreatic cells for patch-seq [L2F4]


title: pancreatic cells for patch-seq [L2G10]


title: pancreatic cells for patch-seq [L2D2]


title: pancreatic cells for patch-seq [O2B2]


title: pancreatic cells for patch-seq [L2C12]


title: pancreatic cells for patch-seq [M2A9]


title: pancreatic cells for patch-seq [J2G1]


title: pancreatic cells for patch-seq [L2H1]


title: pancreatic cells for patch-seq [L2G11]


title: pancreatic cells for patch-seq [L2H4]


title: pancreatic cells for patch-seq [J2F7]


title: pancreatic cells for patch-seq [L2F12]


title: pancreatic cells for patch-seq [O2B3]


title: pancreatic cells for patch-seq [J2E2]


title: pancreatic cells for patch-seq [J2E3]


title: pancreatic cells for patch-seq [J2F5]


title: pancreatic cells for patch-seq [L2C8]


title: pancreatic cells for patch-seq [L2C9]


title: pancreatic cells for patch-seq [L2B6]


title: pancreatic cells for patch-seq [H2G11]


title: pancreatic cells for patch-seq [L2C3]


title: pancreatic cells for patch-seq [H2H11]


title: pancreatic cells for patch-seq [H2F4]


title: pancreatic cells for patch-seq [J2D1]


title: pancreatic cells for patch-seq [H2E2]


title: pancreatic cells for patch-seq [J2C10]


title: pancreatic cells for patch-seq [H2E1]


title: pancreatic cells for patch-seq [H2C1]


title: pancreatic cells for patch-seq [H2A4]


title: pancreatic cells for patch-seq [H2A2]


title: KAA_rep3

status: Public on Jan 26 2022

city: Helsinki

first: Tomi

last: Makela

address: Biomedicum 1, Haartmaninkatu 8

country: Finland

institute: University of Helsinki

data_processing:
Sequenced reads were aligned to mouse reference genome build GRCm38.p3 using STAR aligner (Dobin et al. 2013) and gene wise number of aligned reads were computed using Htseq (Anders, Pyl, and Huber 2015).
Gene wise aligned read counts were analyzed for differential gene expression analysis using limma-voom R package.
Genome_build: mouse GRCm38.p3
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung tumor

extract_protocol:
Lung tumor samples were freshly dissected and preserved in RNAlater, and RNA was extracted using RNeasy Mini Kit (QIAGEN) and treated with DNase. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
mRNA-seq libraries were prepared with the SureSelect Strand Specific RNA library prep kit (Agilent Technologies) after PolyA capture, and then sequenced by single-end 75 base pairs using the Illumina NextSeq 500 platform.

value: lung

value: LSL-Kras (G12D/+), AMPKa1 (flox/flox), AMPKa2 (flox/flox)

tag: virus (pfu)

tag: age (day) when infected

tag: sample collection time (day) after infection


title: pancreatic cells for patch-seq [H2G9]


title: pancreatic cells for patch-seq [H2G5]


title: iCLIP-seq of CPSF160, replicate A

value: wild-type cells


title: Huh7.5.1-ACE2 Cas9CRISPRa infected population screen 2.construct

status: Public on Jan 20 2022

first: John

middle: G

last: Doench

address: 75 Ames St.

department: Genetic Perturbation Platform

institute: Broad Institute

description: Supplemental_File_14_Huh7.5.1-ACE2_Act_SecondaryLibrary_Goujon.xlsx

data_processing:
Raw read counts were retrieved from sequencing data using PoolQ version 3.2.9-3.2.11
Read counts were log-normalized, then averaged across conditions if applicable
Log-fold changes were calculated relative to pDNA
Fit a natural cubic spline between the control and infected conditions and calculated residuals from this spline (anchors package)
Z-scored residuals at the guide-level (anchors package)
Averaged across guides and conditions to get gene-level average z-score (anchors package)
Applied filter based on number of guides per gene then ranked genes where a rank of 1 was assigned to the top pro-viral hit
Genome_build: NCBI GRCh38 primary assembly
Supplementary_files_format_and_content: Spreadsheets with data from each individual screen structured such as that sheet 1: gene symbols with gene-level average z-scores and ranks for each screen, sheet 2: raw read counts, sheet 3: guide-gene annotation mapping
Supplementary_files_format_and_content: Two summarized spreadsheets (Supplementary_Data_6_All_Secondary_KO_Screens_Goujon.xlsx, Supplementary_Data_7_All_Secondary_Act_Screens_Goujon.xlsx) with gene-level average z-scores and ranks for KO secondary and activation secondary screens, respectively

source_name: liver cells overexpressing ACE2

growth_protocol: Dulbecco's modified Eagle medium (DMEM) supplemented with 10% foetal bovine serum and penicillin/streptomycin, 37°C, 5%CO2

extract_protocol:
NucleoSpin Blood XL kit as per the manufacturer's instructions
For PCR amplification, gDNA was divided into 100 μL reactions such that each well had at most 10 μg of gDNA. Plasmid DNA (pDNA) was also included at a maximum of 100 pg per well. Per 96 well plate, a master mix consisted of 150 μL DNA Polymerase (Titanium Taq; Takara), 1 mL of 10x buffer, 800 μL of dNTPs (Takara), 50 μL of P5 stagger primer mix (stock at 100 μM concentration), 500 μL of DMSO, and water to bring the final volume to 4 mL. Each well consisted of 50 μL gDNA plus water, 40 μL PCR master mix, and 10 μL of a uniquely barcoded P7 primer (stock at 5 μM concentration). PCR cycling conditions were as follows: an initial 1 min at 95 °C; followed by 30 s at 94 °C, 30 s at 52.5 °C, 30 s at 72 °C, for 28 cycles; and a final 10 min extension at 72 °C. PCR primers were synthesized at Integrated DNA Technologies (IDT). PCR products were purified with Agencourt AMPure XP SPRI beads according to manufacturer’s instructions (Beckman Coulter, A63880). Prior to sequencing the sample was quantitated by qPCR and diluted to 2nM. 5 µL of the  sample was then further diluted and denatured with 5 µL 0.1N NaOH and 490 µL HT1 buffer (Illumina). Samples were sequenced on a HiSeq2500 HighOutput (Illumina) with a 5% spike-in of PhiX.

treatment_protocol: Infection with SARS-CoV-2 (BetaCoV/France/IDF0372/2020 isolate), MOI 0.005

tag: cell type

value: liver cells

value: overexpressing ACE2

tag: perturbation type

value: CRISPR activation

tag: crispr library

value: Cas9CRISPRa (CP1663)

tag: infected with sars-cov-2?

value: YES

tag: population


title: pancreatic cells for patch-seq [H2E5]

tag: Sex


title: Caco-2-ACE2 Cas9KO uninfected population screen 1.construct

description: Supplemental_File_10_Caco-2-ACE2_KO_SecondaryLibrary_Goujon.xlsx

source_name: colorectal adenocarcinoma cells overexpressing ACE2

value: colorectal adenocarcinoma cells

value: CRISPR knockout

value: Cas9KO (CP1658)

value: NO


title: pancreatic cells for patch-seq [P2H12]

value: Nondiabetic

value: Pancreatic islets

value: Female


title: Calu-3 Cas12aKO infected population screen 1.construct

description: Supplemental_File_12_Calu-3_Cas12a_KO_SecondaryLibrary_Goujon_(1).xlsx

source_name: lung adenocarcinoma cells

value: lung adenocarcinoma cells

value: control

value: Cas12aKO (CP1660)


title: pancreatic cells for patch-seq [H2F7]

value: Male

value: Yes


title: pancreatic cells for patch-seq [H2C4]


title: pancreatic cells for patch-seq [H2B8]


title: pancreatic cells for patch-seq [H2B9]


title: Calu-3 Cas12aKO uninfected population screen 1.construct


title: pancreatic cells for patch-seq [J2D6]


title: Huh7.5.1-ACE2 Cas9KO infected population screen 1.construct

description: Supplemental_File_9_Huh7.5.1-ACE2_KO_SecondaryLibrary_Goujon.xlsx

value: liver cells


title: Calu-3 Cas12aKO uninfected population screen 2.construct


title: Huh7.5.1-ACE2 Cas9KO uninfected population screen 1.construct

value: overexpressing ACE2


title: Huh7.5.1-ACE2 Cas9CRISPRa uninfected population screen 2.construct

value: CRISPR activation


title: S100A4 2

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

description:
S100A4_rep2
processed data file: Raw_counts.txt

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Reads were mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1.
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads.
Genome_build: Sscrofa11.1.96
Supplementary_files_format_and_content: Raw_counts.txt: Tab-delimited text file includes raw counts.

organism: Sus scrofa

source_name: porcine smooth muscle cells

extract_protocol:
Total RNA was extracted from treated SMCs by using the NucleoSpin kit (Macherey-Nagel).
Libraries were prepared according to Illumina's instructions using the TruSeq RNA-seq protocol.
Libraries were sequenced using single-end reads (100 nt-long) on an Illumina HiSeq4000.

treatment_protocol: SMCs between the 6th and 11th passages were plated at a density of 60 cells/mm2 in 35 mm culture dishes containing Dulbecco's modiﬁed eagle medium supplemented with 10% fetal calf serum and after 24 hours they were treated for 4 hours with 30 ng/ml of PDGF-BB, 1µg/ml of S100A4 or both together.

value: smooth muscle cells

tag: cell source

value: porcine coronary artery

tag: cell phenotype

value: differentiated/contractile

tag: sample type

value: primary cell culture

tag: treatment


title: Huh7.5.1-ACE2 Cas9CRISPRa infected population screen 1.construct

value: Cas9CRISPRa (CP1663)

value: YES


title: Huh7.5.1-ACE2 Cas9CRISPRa uninfected population screen 1.construct

value: NO


title: Huh7.5.1-ACE2 Cas9KO uninfected population screen 2.construct

value: CRISPR knockout

value: Cas9KO (CP1658)


title: Caco-2-ACE2 Cas9KO infected population screen 2.construct

value: colorectal adenocarcinoma cells


title: A549-ACE2 Cas9KO infected population screen 2.construct

description: Supplemental_File_8_A549-ACE2_KO_SecondaryLibrary_Goujon.xlsx

source_name: lung cells overexpressing ACE2

value: lung cells


title: Caco-2-ACE2 Cas9KO infected population screen 1.construct


title: Calu-3 Cas9CRISPRa infected population screen 2 1.construct

description: Supplemental_File_16_Calu-3_Act_SecondaryLibrary_Goujon.xlsx

value: lung adenocarcinoma cells

value: control


title: Caco-2-ACE2 Cas9KO uninfected population screen 2.construct


title: Calu-3 Cas12aKO infected population screen 2.construct

value: Cas12aKO (CP1660)


title: Huh7.5.1-ACE2 Cas9KO infected population screen 2.construct

value: liver cells


title: iCLIP-seq of GFP-NUDT21, replicate A

tag: cell line

value: Human embryonic kidney cells (HEK293) cells were grown in DMEM supplemented with 10% FBS, sodium pyruvate, MEM non-essential amino acids, and penicillin/streptomycin, and maintained at 37°C with 5% CO2.

value: GFP-NUDT21 was expressed in an HEK293 cell line engineered with the Flp-in system under the control of doxycyclin, and expression was induced for 48 hours prior to crosslinking.

tag: antibody

value: GFP monoclonal antibody  (Life Technologies)


title: Calu-3 Cas9CRISPRa uninfected population screen 2.construct

tag: genotype

value: CRISPR activation


title: A549-ACE2 Cas9KO infected population screen 1.construct

value: overexpressing ACE2


title: A549-ACE2 Cas9KO uninfected population screen 2.construct


title: Caco-2-ACE2 Cas9CRISPRa uninfected population screen 2.construct

description: Supplemental_File_15_Caco-2-ACE2_Act_SecondaryLibrary_Goujon.xlsx


title: Caco-2-ACE2 Cas9CRISPRa infected population screen 2.construct


title: A549-ACE2 Cas9KO uninfected population screen 1.construct


title: Calu-3 Cas9CRISPRa infected population screen 1.construct


title: Calu-3 Cas9KO uninfected population screen 2.construct

description: Supplemental_File_11_Calu-3_Cas9_KO_SecondaryLibrary_Goujon.xlsx


title: Calu-3 Cas9CRISPRa infected population screen 2 2.construct


title: Caco-2-ACE2 Cas9CRISPRa infected population screen 1.construct


title: Calu-3 Cas9CRISPRa uninfected population screen 1.construct


title: Caco-2-ACE2 Cas9CRISPRa uninfected population screen 1.construct


title: Calu-3 Cas9KO infected population screen 2.construct


title: A549-ACE2 Cas9CRISPRa infected population screen 2.construct

description: Supplemental_File_13_A549-ACE2_Act_SecondaryLibrary_Goujon.xlsx


title: Calu-3 Cas9KO infected population screen 1.construct


title: Calu-3 Cas9KO uninfected population screen 1.construct


title: A549-ACE2 Cas9CRISPRa uninfected population screen 2.construct


title: A549-ACE2 Cas9CRISPRa uninfected population screen 1.construct


title: Donor 3_RNA-seq

status: Public on Jan 15 2022

city: Durham

first: Purushothama Rao

last: Tata

email: pt93@duke.edu, tata.lab@yahoo.com

state: NC

address: 303 Research Dr., Alexander Sands Building, Room- 451, BOX 3709

department: Department of Cell Biology

institute: Duke University School of Medicine

data_processing:
FASTQ files were processed using Cell Ranger (10x Genomics) and mapped to the GRCh38 reference genome.
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell Ranger output
Supplementary_files_format_and_content: epi.sub_SAE10x3.integrated_v2.RDS: Seurat object of epithelial cells.
Supplementary_files_format_and_content: endo.sub_SAE10x3.integrated_temp_v2.RDS: Seurat object of endothelial cells.
Supplementary_files_format_and_content: immune_platelet.sub_SAE10x3.integrated_temp.RDS: Seurat object of immune cells.
Supplementary_files_format_and_content: mes.sub_SAE10x3.integrated_v2.RDS: Seurat object of mesenchymal cells.

source_name: Human lung

extract_protocol:
Human lung was micro-dissected under a dissection microscope to enrich for airways measuring less than 1 mm in their outer diameter and contiguous alveoli. The dissected pieces were placed in a dish containing DMEM/F-12 medium on ice and were longitudinally cut open. Samples were then dissociated in two steps. Step 1: samples were incubated in an enzyme cocktail containing 4 mg/ml pronase, 5 U/ml dispase, 1 mg/ml collagenease type IV and  0.33 U/ml DNase I  for 15 min at 37°C followed by rigorous pipetting for 1 min followed by another round of incubation for 15 min at 37°C. After incubation cells were centrifuged at 550 g for 10 min, supernatant was collected in a fresh 50 ml conical tube. Step 2: The cell pellet from step 1 was incubated 1 ml with TrypLE™ Select Enzyme (Thermofisher, #12563029) at 37°C for 10 min followed by rigorous pipetting for 1 min followed by another round of incubation for 10 min at 37°C. The cells were filtered through a 100 µm strainer and rinsed with 15 ml DMEM/F-12+10% FBS medium. The supernatant from step 1 and step 2 were combined and centrifuged at 550 g for 10 min. The supernatant was removed and the cell pellet was resuspended in red blood cell lysis buffer (Millipore Sigma, #11814389001 ) for 5 min, washed with DMEM/F-12 containing 10% FBS and filtered through a 40 µm strainer. Total cells were centrifuged at 550 g for 10 min at 4ºC. Cells were counted manually using Fuchs-Rosenthal hemocytometer (Incyto # DHC-F01).
Followed the protocol of 10x Genmics Chromium v3.1 chemistry for single-cell RNA-seq (3' enrichment)

tag: tissue

value: lung

value: Airway cells

tag: age

value: Adult

tag: disease state

value: Normal

value: 21 years


title: Donor 1_RNA-seq

value: 45 years


title: Donor 2_RNA-seq

extract_protocol:
Human lung was micro-dissected under a dissection microscope to enrich for airways measuring less than 1 mm in their outer diameter and contiguous alveoli. The dissected pieces were placed in a dish containing DMEM/F-12 medium on ice and were longitudinally cut open. Samples were then dissociated in two steps. Step 1: samples were incubated in an enzyme cocktail containing 4 mg/ml pronase, 5 U/ml dispase, 1 mg/ml collagenase type IV , 1X accutase, and  0.33 U/ml DNase I  for 15 min at 37°C followed by rigorous pipetting for 1 min followed by another round of incubation for 15 min at 37°C. After incubation cells were centrifuged at 550 g for 10 min, supernatant was collected in a fresh 50 ml conical tube. Step 2: The cell pellet from step 1 was incubated 1 ml with TrypLE™ Select Enzyme (Thermofisher, #12563029) at 37°C for 10 min followed by rigorous pipetting for 1 min followed by another round of incubation for 10 min at 37°C. The cells were filtered through a 100 µm strainer and rinsed with 15 ml DMEM/F-12+10% FBS medium. The supernatant from step 1 and step 2 were combined and centrifuged at 550 g for 10 min. The supernatant was removed and the cell pellet was resuspended in red blood cell lysis buffer (Millipore Sigma, #11814389001 ) for 5 min, washed with DMEM/F-12 containing 10% FBS and filtered through a 40 µm strainer. Total cells were centrifuged at 550 g for 10 min at 4ºC. Cells were counted manually using Fuchs-Rosenthal hemocytometer (Incyto # DHC-F01).
Followed the protocol of 10x Genomics Chromium v3.1 chemistry for single-cell RNA-seq (3' enrichment)

value: 20 years


title: KP day 28 mouse 5.1

city: New York

first: Dana

last: Pe'er

state: NY

address: 417 E 68th St

department: Computational and Systems Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Library strategy: Spatial transcriptomics
Library strategy: Spatial Transcriptomics (Visium)
The 10x Genomics Spaceranger mkfastq (v. 1.2.1) pipeline was utilized to demultiplex raw base call files into FASTQ format. The FASTQ files along with a microscopy brightfield image stained with hematoxylin and eosin (H&E), was used by Spaceranger count (v 1.2.1) to perform alignment to a modified mm10 genome, tissue detection, fiducial detection, and barcode/UMI counting. The modified mm10 genome contained additional sequences for the WPRE sequence of the Pro-Code-bearing transcript, to identify Pro-Code expressing spots. The pipeline used the Visium spatial barcodes to generate feature-spot matrices. Spots deemed off-tissue by visual inspection were annotated in the Loupe browser and removed from subsequent analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix with raw counts for every gene and every spot
Supplementary_files_format_and_content: Matrix with raw counts for every gene and every spot, filtered to include spots under tissue
Supplementary_files_format_and_content: High resolution tissue image
Supplementary_files_format_and_content: Scalefactors in json format
Supplementary_files_format_and_content: Table with array and pixel coordinates (tissue_positions)
Supplementary_files_format_and_content: Table with cluster annotations for each spot as detailed in the Perturb-map manuscript (spot_annotations)
Supplementary_files_format_and_content: Table with manually annotated off-tissue spots
Supplementary_files_format_and_content: *_aligned_fiducials.jpg and *_tissue_lowres_image.png files are standard outputs of the Spaceranger processing for the 10X Visium platform. They are low resolution tissue images and the aligned fiducials of the tissue images accompanying the Visium gene expression profiling.

source_name: lung

extract_protocol: Fresh frozen samples embedded in OCT were cryosectioned and 10 μm-thick sections were placed on the Visium Tissue Optimization Slides and Visium Spatial Gene Expression Slides (10x Genomics). Tissue sections were fixed in methanol and processed using the Visium Spatial Gene Expression Kit (10x Genomics), following manufacturer’s instructions. Based on the tissue optimization time course experiment, the lung tissue sections were permeabilized for 6 minutes to maximize RNA recovery. A serial section was used for Hyperion detection of the Pro-Code epitopes.

treatment_protocol: KP cells transduced with a library encoding 35 different Pro-Code/CRISPR vectors were injected (1x10^6 cells) intravenously (i.v.) in the tail vein of C57BL/6 mice or Cas9 mice (to avoid immune rejection of Cas9 expressing KP cells). Mice were sacrificed 28 days later, and the lungs were collected.

tag: strain

value: male


title: Hi-C for Patient 3

status: Public on Jan 12 2022

first: Ce

last: Gao

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT and Harvard

data_processing:
Raw data were trimmed using Homer (v4.10.3) and aligned to Human reference genome using Bowtie2 (v2.3.4.3).
TADs were determined using Homer (v4.10.3).
FIREs were called using FIREcaller (v1.10).
Significant contacts were identified using Fit-Hi-C (v2.0.7).
Genome_build: hg38

growth_protocol: The cells were not cultured.

extract_protocol:
One million cells were crosslinked in 1% formaldehyde (Sigma, F8775-25ML) for 10 min, followed by quenching with glycine (Sigma, 50046-50G). Cell nuclei were permeabilized with 0.4% sodium dodecyl sulphate (SDS) solution and chromatin was digested using 100 U of MboI (NEB, R0147L). Overhangs generated by the restriction enzyme were filled using Klenow DNA polymerase (NEB, M0210L) and a mix of dNTPs including biotin-14-dCTP (Invitrogen, 19518018). DNA fragments were then ligated using T4 DNA ligase (NEB, M0202). After reversion of crosslinking, cellular proteins were digested with Proteinase K (NEB, P8107), followed by DNA extraction using Phenol-Chloroform-Isoamyl alcohol.
The extracted DNA was subjected to digestion of contaminating RNA with RNase A (ThermoFisher, EN0531). Samples were sheared using a Covaris E220 instrument with a target size of 300-500 base pairs (140W peak incident power, each 67s, 10% duty, 200 cycles/burst) at the MGH NextSeq Core facility. Biotinylated fragments were isolated with Dynabeads MyOne Streptavidin C1 beads (Life Technologies, 65002). DNA linked to the Dynabeads was end-repaired using the End Prep Enzyme Mix and subsequently used for library construction with the NEBNext Ultra DNA Library Prep Kit for Illumina Sequencing (NEB, E7370S). Final amplification of the libraries was done in 4 parallel reactions per sample according to the following program: 98 °C for 1 min, (98 °C for 10 s, 65 °C for 75 s, ramping 1.5 °C/s) repeated 12–20 times, 65 °C for 5 min, 4 °C. The indexed samples were processed individually and double size-selected using SPRISelect beads (Beckman Coulter). Final Hi-C libraries were quantified using the Qubit dsDNA HS assay kit and a DNA HS kit on a Tapestation 4200 (Agilent). The library was then sequenced on an Illumina NextSeq 500/550 (2x80 bp paired-end; NextSeq 500/550 High Output kit v2.5-150 cycles).

treatment_protocol: The cells were not treated.

tag: cell type

value: antiretroviral therapy (ART)

tag: restriction enzyme

value: MboI


title: KP day 28 mouse 7.2


title: A549-ACE2 Cas9CRISPRa infected population screen 1.construct

value: lung cells

tag: perturbation type

tag: crispr library

value: Cas9CRISPRa (CP1663)

value: YES


title: Hi-C for Patient 1


title: TSC ZIKV exposed EVs replicate 3 [TZ3ev]

status: Public on Jan 10 2022

city: Madison

first: Thaddeus

last: Golos

state: Wisconsin

address: 1223 Capitol Court

department: WNPRC

institute: UW Madison

data_processing:
miRNA abundance estimations were done using the miARma-Seq miRNA-Seq workflow:
trimming with CutAdapt using Qiagen adapter AACTGTAGGCACCATCAAT
alignment with Bowtie1 and counting with featureCounts.
Accessions for known miRNAs from the Mmul_8.0.1 were obtained from miRbase v22 (October 2018).
Data were filtered with the edgeR filterByExpr function and statistical analysis was performed with the edgeRglm function.
Genome_build: Mmul_8.0.1 from miRbase v22 (October 2018)
Supplementary_files_format_and_content: edgeRglm_Counts files include miRNA counts by sample. edgeRglm_GENE files include fold change, p-value, likelihood ratio, and counts per million (CPM) for all the cell types analyzed by miRNA.

organism: Macaca mulatta

source_name: TSC ZIKV exposed EVs

growth_protocol: cells were grown in uninfected or ZIKV exposed conditions. Media was collected for EV isolation. Cells were collected for RNA isolation.

extract_protocol:
Total RNA was isolated from cells using an RNeasy kit (Qiagen, Cat #74104). Each EV sample was diluted in 5 volumes Qiazol and incubated for 5 mins at RT prior to freezing at -80°C until RNA extraction. The miRNeasy serum/plasma kit (Qiagen, Cat #217184) was used to isolate total RNA from EVs
Approximately 0.4 - 1 µg of total RNA were used to prepare small RNA cDNA libraries utilizing the specified protocol for the TruSeq Small RNA Sample Prep Kit (Illumina, San Diego, USA).

treatment_protocol: An MOI of 5, 10, and 5 were used to infect the TSCs, ST3Ds, and EVTs, respectively. Inoculated and mock-inoculated control TSCs were cultured for 60 hrs, while ST3Ds and EVTs were cultured for 48 and 72 hrs, respectively

value: Evs from ZIKV exposed cells

value: placenta


title: TSC ZIKV exposed EVs replicate 4 [TZ4ev]

value: female


title: KP day28 mouse 4.1


title: Hi-C for Patient 2


title: KP day 28 mouse 4.3


title: TSC control EVs replicate 3 [TC3ev]

source_name: TSC control EVs

value: EVs from control cells


title: TSC ZIKV exposed EVs replicate 1 [TZ1ev]


title: TSC control EVs replicate 4 [TC4ev]


title: TSC control EVs replicate 2 [TC2ev]


title: TSC ZIKV exposed EVs replicate 2 [TZ2ev]


title: ST3D ZIKV exposed EVs replicate 3 [SZ3ev]

source_name: ST3D ZIKV exposed EVs


title: ST3D ZIKV exposed EVs replicate 4 [SZ4ev]


title: ST3D ZIKV exposed EVs replicate 2 [SZ2ev]


title: ST3D control EVs replicate 3 [SC3ev]

source_name: ST3D control EVs


title: TSC control EVs replicate 1 [TC1ev]


title: EVT ZIKV exposed EVs replicate 4 [EZ4ev]

source_name: EVT ZIKV exposed EVs


title: ST3D ZIKV exposed EVs replicate 1 [SZ1ev]


title: EVT ZIKV exposed EVs replicate 2 [EZ2ev]


title: ST3D control EVs replicate 4 [SC4ev]


title: EVT ZIKV exposed EVs replicate 3 [EZ3ev]


title: ST3D control EVs replicate 2 [SC2ev]


title: EVT ZIKV exposed EVs replicate 1 [EZ1ev]


title: EVT control EVs replicate 3 [EC3ev]

source_name: EVT control EVs


title: EVT control EVs replicate 2 [EC2ev]


title: EVT control EVs replicate 4 [EC4ev]


title: EVT control EVs replicate 1 [EC1ev]


title: ST3D control EVs replicate 1 [SC1ev]


title: TSC ZIKV exposed cell replicate 4 [TZ4c]

source_name: TSC ZIKV exposed cell

value: ZIKV exposed


title: TSC ZIKV exposed cell replicate 3 [TZ3c]


title: TSC control cell replicate 4 [TC4c]

source_name: TSC control cell

value: control


title: TSC ZIKV exposed cell replicate 1 [TZ1c]


title: TSC control cell replicate 2 [TC2c]


title: TSC control cell replicate 1 [TC1c]


title: ST3D ZIKV exposed cell replicate 1 [SZ1c]

source_name: ST3D ZIKV exposed cell


title: ST3D ZIKV exposed cell replicate 4 [SZ4c]


title: ST3D ZIKV exposed cell replicate 3 [SZ3c]


title: ST3D control cell replicate 2 [SC2c]

source_name: ST3D control cell


title: ST3D control cell replicate 4 [SC4c]


title: ST3D ZIKV exposed cell replicate 2 [SZ2c]


title: EVT ZIKV exposed cell replicate 3 [EZ3c]

source_name: EVT ZIKV exposed cell


title: ST3D control cell replicate 3 [SC3c]


title: EVT control cell replicate 3 [EC3c]

source_name: EVT control cell


title: EVT ZIKV exposed cell replicate 4 [EZ4c]


title: EVT control cell replicate 1 [EC1c]


title: TSC ZIKV exposed cell replicate 2 [TZ2c]


title: EVT ZIKV exposed cell replicate 1 [EZ1c]


title: EVT control cell replicate 2 [EC2c]


title: EVT ZIKV exposed cell replicate 2 [EZ2c]


title: TSC control cell replicate 3 [TC3c]


title: TBRT2203_40

status: Public on Jan 09 2022

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Raw sequencing reads were aligned to the hg19 reference with the spliced gap aligner STAR, with count-based quantitation carried out via the Subread package featureCounts at the geneic levels for annotation builds.
Genome_build: hg19
Supplementary_files_format_and_content: txt format; the raw read count for each gene

source_name: Liver biopsy tissue

extract_protocol:
Total RNA was isolated from fixed tissue specimens using High Pure RNA Paraffin Kit (Roche) and quantified by qubit (Thermo Fisher). Only RNA samples with DV200 > 30% by Agilent 2100 bioanalyzer were used.
RNA-Seq libraries were prepared by using TruSeq RNA Access kit following manufacturer's protocol.
Targeting genome-wide coding regions by capture probes. Single-end read of 75bp was performed by NextSeq genome sequencer (Illumina).

value: liver

tag: timing of biopsy

value: post-treatment

tag: fibrosis improvement

value: improved


title: TBRT2203_07

value: pre-treatment


title: TBRT2203_16


title: TBRT2203_05


title: TBRT2203_24


title: TBRT2203_09


title: TBRT2203_04


title: EVT control cell replicate 4 [EC4c]

tag: Sex


title: ST3D control cell replicate 1 [SC1c]


title: TBRT2203_11


title: TBRT2203_34


title: TBRT2203_22


title: TBRT2203_39


title: TBRT2203_23


title: TBRT2203_18


title: TBRT2203_20


title: TBRT2203_31


title: TBRT2203_01


title: TBRT2203_28


title: TBRT2203_32


title: TBRT2203_33


title: TBRT2203_36


title: TBRT2203_21


title: TBRT2203_06


title: TBRT2203_02


title: TBRT2203_14


title: TBRT2203_27


title: TBRT2203_30


title: TBRT2203_35


title: TBRT2203_10


title: TBRT2203_13


title: TBRT2203_12


title: TBRT2203_03


title: TBRT2203_37


title: TBRT2203_17


title: TBRT2203_26


title: TBRT2203_29


title: TBRT2203_38


title: TBRT2203_15


title: EVT-Z3

status: Public on Jan 01 2022

data_processing:
For cell poly(A)seq data, sequencing reads were filtered to remove adaptors and primer sequences and to remove sequences with a quality score lower than 20.
The cleaned sequencing reads were aligned to the reference genome (GCF_003339765.1_Mmul _10) using the HISAT2 package. Multiple alignments with a maximum of two mismatches were allowed for each read sequence (up to 20 by default).
Transcript abundance estimation and differential expression analysis of aligned reads of individual samples were assembled using StringTie.
Transcriptomes from all samples were then merged to reconstruct a comprehensive transcriptome using a proprietary Perl script designed by LC Sciences.
Following transcriptome reconstruction, raw read counts were filtered, normalized, and differential expression determined with DESeq2 and edgeR. The glmLRT test was used for edgeR differential expression analysis
Genome_build: GCF_003339765.1_Mmul _10
Supplementary_files_format_and_content: alldata_IPA.csv contains fold change, p-value, and counts per million (CPM) for all the cell types analyzed by gene ID. The my.dge.csv file contains the normalized counts.

source_name: EVTs

growth_protocol: TSCs were differentiated into either EVTs or ST3D aggregates  TSCs were grown in 13 ml media, EVTs in 15 ml media, and ST3Ds in 10 ml media.    TSCs were differentiated to EVT by seeding into T75 flasks coated with 1 µg/ml collagen (col IV; Corning, NY, USA, Cat #354233) with 2% Matrigel (Corning, Cat # 354234) added to the EVT media. No additional Matrigel was added on day 3 when the media were changed as previously described. Growth Factor Reduced Matrigel (0.5%; Corning, Cat #354230) was added on day 6.     For ST3D culture, TSCs were plated in non-adherent T75 flasks (Thermo Fisher, Cat #174952 and Cat #156800) and cultured for 5 days total. Three days after initial plating, the media were removed, and fresh media added. For additional details on the media composition and growth conditions, please see Schmidt, et al. 2020 11.

extract_protocol:
Total RNA was isolated from cells using an RNeasy kit (Qiagen, Cat #74104) following kit recommendations with modifications. A volume of 700 µl of Qiazol was added to the cell pellet and then frozen at -80°C until RNA extraction. The protocol was followed with the same minor adaptations as with the miRNeasy kit. A 15 min DNAse treatment was performed on the column using RNase-Free DNase (Qiagen, Cat # 79254) prior to washing the column.
The poly(A) RNA cDNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Pair-end sequencing reads of 150 bp reads were generated on an Illumina NovaSeq 6000 sequencing system.

treatment_protocol: For infection of the TSCs and EVTs, one flask of cells from each line was lifted and counted just prior to infection. For TSCs and EVTs, media were aspirated, and 1 ml of inoculum was added to the flask. Cultures were incubated at 37°C and rocked gently every 15 mins for 1 hr. The inoculum was removed, and the cells were washed once with PBS followed by addition of fresh medium. The number of ST3D “cells” (at this point they are aggregates) present was based on the number of TSCs added to the flask three days prior. To infect the ST3Ds that were grown in suspension, aggregates/cells were pelleted by centrifugation at 500 x g for 3 mins, the supernatant was removed, and the cells were resuspended in 300 µl of inoculum. Aggregates were incubated in the ZIKV inoculum for 2 hrs at 37°C and gently disturbed every 30 mins. Since ST3Ds are grown in suspension, a larger volume of inoculum was used, and the length of inoculation was extended to account for this increase. Next, 2 ml of PBS was added, the cells were re-pelleted by centrifugation as above, and the supernatant was removed. A volume of 10 ml ST3D medium was added to the cells, and they were then transferred back into a T75 flask.     Once fresh media were added back for all cell types, a 500 µl aliquot was removed to serve as a baseline of initial viral titer in the culture. The aliquot was spun at 500 x g for 5 mins to remove any cellular debris and a plaque assay was conducted. For EVTs, Growth Factor Reduced Matrigel (0.5%; Corning, Cat #354230) was supplemented to the cultures after this step. EVTs were cultured for a day longer than previously reported 11 (72 hrs total) to extend the duration of ZIKV infection.

value: placental

value: Zika virus exposed


title: EVT-Z4


title: EVT-Z2


title: EVT-Z1

value: male


title: EVT-C3

value: uninfected control


title: EVT-C4


title: TBRT2203_19


title: ST3D-C2


title: ST3D-C3


title: ST3D-Z3


title: ST3D-Z2


title: ST3D-C4


title: TSC-Z2

source_name: TSCs


title: TSC-C1


title: TSC-C4


title: ST3D-Z4


title: ST3D-C1


title: TSC-C2


title: DAUDI FBXO11 knock-out cell line [DAUDI104]

status: Public on Dec 31 2021

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

description:
DAUDI104
raw_counts.txt

data_processing:
Fastq trimming with skewer v 0.2.2.
Genome alignment with STAR v 2.5.0.
Gene quantification with RSEM v 1.3.0.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: raw_counts.txt: Tab-delimited file containing counts generated with RSEM.

source_name: DAUDI FBXO11 knock-out

growth_protocol: All lymphoma cell lines were cultured in RPMI 1640 medium (Thermo Fisher Scientific, USA) supplemented with 10% fetal bovine serum (FBS), penicillin-streptomycin (100 U/ml) and L-Glutamine (2 mM).

extract_protocol:
Total RNA was isolated from BL cell lines using TRIzol solution (Life Technologies) and subjected to RNase-free DNase I set (Roche) for genomic DNA digestion. RNA samples quality was assessed by 2100 bioanalyzer. RNAs concentration was estimated by Qubit.
Sequencing libraries were prepared starting from using 100 ng total RNA using TruSeq RNA Library Prep Kit v2 (Illumina, USA) following the manufacturer indications. The qualities of the libraries were assessed by 2100 Bioanalyzer.

treatment_protocol: FBXO11 knock out BL cell lines were generated using CRISPR/Cas9 mediated gene targeting. Guides targeting the exon 4 of FBXO11 (sgRNAs #1 and #2) (5’-CCTGCTGAACAGTATCTTC-3’, 5’-CTTCTCTTACTTGCTGGAAC-3’) were designed using the CRISPR design tool at http://crispr.mit.edu and ligated into the LentiCRISPR v2 vector (Addgene plasmid #52961). Lentiviral particles were produced in HEK293T cells and viral supernatant used to transduce BL cell lines (RAJI and DAUDI), according to the protocol described above. Puromycin was added after 48 h, using the minimal toxic dose per cell line to select transduced cells. The selected cells were seeded as single colonies in 96-well plates by serial dilutions. Clonal cells from individual wells were screened by western blotting and genomic sequencing of the sgRNA target region to identify cell lines which are FBXO11 deficient. DNA fragments covering the sgRNA target region were amplified using the primers int3F (5’-GTGCAAGAGTGTCTGGAAAA-3’) and int3R (5’-AATACCACCTGGACTGACAG-3’). To confirm the bi-allelic deletion of the clones (bi-allelic KO), the PCR products were cloned and sequenced.

value: DAUDI

value: Burkitt lymphoma (BL) cell line

tag: genotype/variation

value: FBXO11 knock-out


title: TSC-C3


title: ST3D-Z1


title: TSC-Z4


title: EVT-C2


title: RAJI FBXO11 knock-out cell line [RAJI13]

description:
RAJI13
raw_counts.txt

source_name: RAJI FBXO11 knock-out

value: RAJI


title: DAUDI wt cell line [DAUDIA]

description:
DAUDIA
raw_counts.txt

source_name: DAUDI wt

value: WT


title: EVT-C1


title: RAJI FBXO11 knock-out cell line [RAJI14]

description:
RAJI14
raw_counts.txt


title: DAUDI wt cell line [DAUDIB]

description:
DAUDIB
raw_counts.txt


title: RAJI wt cell line [RAJID]

description:
RAJID
raw_counts.txt

source_name: RAJI wt


title: RAJI wt cell line [RAJIA]

description:
RAJIA
raw_counts.txt


title: RAJI wt cell line [RAJIB]

description:
RAJIB
raw_counts.txt


title: RAJI wt cell line [RAJIC]

description:
RAJIC
raw_counts.txt


title: TSC-Z1


title: TSC-Z3


title: DAUDI FBXO11 knock-out cell line [DAUDI1015]

description:
DAUDI1015
raw_counts.txt


title: RAJI FBXO11 knock-out cell line [RAJI12]

description:
RAJI12
raw_counts.txt


title: hESC_EZH2_RedChIP_rep1

status: Public on Dec 18 2021

city: Moscow

first: Alexey

middle: A.

last: Gavrilov

address: 34/5 Vavilova street

country: Russia

institute: Institute of Gene Biology of the Russian Academy of Sciences

data_processing:
For raw data processing RedClib pipeline was used (github: https://github.com/agalitsyna/RedClib)
Genome_build: hg38
Supplementary_files_format_and_content: Processed RedC data files are available as TSV files with individual mapped RNA-DNA contacts. Each row corresponds to an individual RNA-DNA contact that passed filtering steps. Columns represent information about 3' RNA, 5' RNA and DNA mapping position (chromosome, start, end, strand), CIGAR string and mapped sequence length.

source_name: Human embryonic stem cells

growth_protocol:
Human K562 cells (ATCC® CCL-243™) were cultured in RPMI supplemented with 10% FBS and penicillin/streptomycin. Normal human skin fibroblasts (female 46XX) were cultured in DMEM supplemented with 10% FBS and penicillin/streptomycin. All cells were grown at 37°C and 5% CO2 in a conventional humidified CO2 incubator.
For all hESC passaging, we used ACCUTASETM сell detachment solution (Stem Cell Technologies), Rock-inhibitor Y-27632 (Abcam), plastic surface was pre-coated with BD-MatrigelTM solution (1/40 in DMEM/F12) (BD Bioscience). The cells were cultured in mTeSR1TM medium (Stem Cell Technologies) at 37ºC in a CO2-incubator with 5% CO2 and 100% humidity.

extract_protocol: RedChIP uses custom oligos and adapters resulting in libraries ready for sequencing on the Illumina platform.

tag: cell cycle

value: asynchronous


title: K562_CTCF_RedChIP_input_rep2

source_name: chronic myelogenous leukemia immortalized cell line K562


title: Human HepG2 scrambled sample - Scr-3

status: Public on Nov 24 2021

city: Montreal

first: Julie

last: Hussin

state: QC

address: 5000, rue Bélanger

institute: Montreal Heart Institute

data_processing:
Read trimming using TrimGalore!
Mapping the human genome for which ADCY9-205 isoform (ENST00000574721.1) was removed using STAR v.2.6.1a and PCR duplicates removed for each library.
RSEM ran to get isoforms and gene count levels per library and then the two lanes were combined together.
Samples are paired
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw count for each Sample

source_name: Human HepG2 scrambled cells

extract_protocol:
Total RNA was extracted from transfected HepG2 cells using RNeasy Plus Mini Kit (Qiagen cat #74136) in accordance with the manufacturer’s recommendation.
Ribosomal RNA was depleted using NEBNext rRNA depletion kit.

treatment_protocol: The human liver hepatocellular HepG2 cell line was obtained from ATCC. Cells were cultured in EMEM Minimum essential Medium Eagle’s, supplemented with 10% fetal bovine serum (Wisent Inc). 250 000 cells in 2 ml of medium in a six-well plate were transfected using 12.5 pmol of Silencer Select siRNA against human ADCY9 (Ambion cat # 4390826 ID 1039) or Negative Control siRNA (Ambion cat #4390844) with 5 μl of Lipofectamine RNAiMAX reagent (Invitrogen cat #13778) in 500 μl Opti-MEM I reduced serum medium (Invitrogen cat # 31985) for 72h.

tag: treatment


title: K562_CTCF_RedChIP_rep2


title: hESC_EZH2_RedChIP_input_rep2


title: Human HepG2 ADCY9 knock down cells - si-1039-5

source_name: Human HepG2 ADCY9 knock down cells

value: ADCY9 knock down


title: Human HepG2 ADCY9 knock down cells - si-1039-3


title: Human HepG2 ADCY9 knock down cells - si-1039-2


title: HL60 [RNA-seq]

status: Public on Nov 25 2021

city: Guangzhou

first: Tianyuan

last: Liu

address: Shatai South Road, Baiyun District

department: Bioinformatics Department

institute: Sourthern Medical University

data_processing:
All paired-end reads from RNA-seq were trimmed for adaptor sequence using fastp with standard filtration requirements.
The hg38 reference genome (GRCh38) and gene annotation file (GTF format) were downloaded from GENCODE Release 28 (31). The reads were mapped to the hg38 genome using HISAT2 (Version 2.2.1) with default settings.
Expression levels relative to transcripts were estimated using StringTie (Version 2.1.5).
Genome_build: hg38
Supplementary_files_format_and_content: gtf file were generated with command stringtie followed by StringTie.

source_name: HL60 cell line

growth_protocol: The following cell lines were purchased from the ATCC and cultured in the corresponding medium with 10% FBS (Hyclone, Logan, Utah) at 37 ºC, 5% CO2 in a cell culture incubator. MOLM13 (DMEM), THP-1 (RPMI1640, 2-mercaptoethanol to a final concentration of 0.05 mM), HL60 (IMDM), K562 (IMDM).

extract_protocol:
Total RNA was used as the input material for RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5X).
First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally established. The library was then tested in order to ensure the quality. The library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library was detected by Agilent 2100 bioanalyzer. After insert size meet the expectation, qRT-PCR was used to accurately quantify the effective concentration (>2nM) of the library to ensure the quality of the library.

tag: cell line

value: HL60 cell line

value: leukemia cell


title: Human HepG2 scrambled sample - Scr-2

value: control


title: Shield_ctrl_H3K4me3_rep1

status: Public on Dec 29 2021

city: Beijing

first: Wei

last: Xie

address: Zhongguancun street, Haidian

department: THU-PKU Center for Life Sciences

institute: Tsinghua University

data_processing:
Library strategy: CUT&RUN
All STEM-seq datasets were mapped to the danRer7 reference genome by Bismark (Krueger and Andrews, 2011). Reads were trimmed with cutadaptor (Martin, 2011) using parameters: --minimum-length 20 --pair-filter=any. Alignments were performed with the following parameters: -N 1 -X 600 --score_min L,0,-0.6. Multi-mapped reads and PCR duplicates were removed. bismark_methylation_extractor was used to calculate the DNA methylation level.
Total RNA-seq data were firstly processed using Trim Galore! with default parameters to trim the adapter-containing and low quality reads. The filtered data were then mapped to the zebrafish reference genome (danRer7) by STAR (version: STAR_2.5.3a_modified) (Dobin et al., 2013) with the following parameters: --outSAMstrandField intronMotif --outSAMattributes All --outSAMunmapped Within --outSAMattrIHstart 0 --outWigStrand Stranded --outFilterMultimapNmax 20 --twopassMode Basic. The gene expression level was normalized to fragments per kilobase of transcript per million mapped (FPKM) values using Cufflinks (version 2.2.1) (Trapnell et al., 2012).
The scRNA-seq data were processed with Cell Ranger 3.1 for genome alignment (danRer10), transcript counting, and gene-cell-barcode matrix generation. Before the downstream analysis, cells with unique detected genes lower than <2,000 and higher than 6,000 genes were discarded, and cells with high percentage of mitochondrial genes (>5%) were removed too. Subtypes of cells were identified with Seurat 3.0 through the integrating of control and mKD embryos at dome and shield stages with setting control embryos as reference. To make the data comparable samples, we performed SCTransform normalization separately for each dataset. To further reduce the bais caused by sequencing depth of scRNA-seq and percentage of mitochondrial genes, UMI variance and percent.mt were regressed out from SCTransform normalized data matrix by linear model with negative binomial distribution.
All ChIP-seq reads were aligned to the zebrafish reference genome (danRer7) using Bowtie2 (version 2.2.2) (Langmead and Salzberg, 2012) with the parameters –t –q –N 1 –L 25. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. For downstream analysis, the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM). To visualize the STAR ChIP-seq signal in the UCSC genome browser, each read was extended by 250 bp and the coverage for each base was counted. Replicates of STAR ChIP-seq were pooled for the downstream analysis.
The ATAC-seq data were mapped to the zebrafish reference genome (danRer7) using Bowtie2 (version 2.2.2) (Langmead and Salzberg, 2012) with the parameters –t –q –N 1 –L 25. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. For downstream analysis, the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM). To minimize the batch and cell type variation, RPKM values across whole genome were further Z-score normalized. To visualize the CUT&RUN signals in the UCSC genome browser, each read was extended by 250 bp and the coverage for each base was counted.
Genome_build: danRer7
Supplementary_files_format_and_content: Matrix for scRNA-seq data, gene expression table for total RNA-seq data, Bigwig and narrowPeak for ChIP-seq and ATAC-seq data

organism: Danio rerio

source_name: embryo

growth_protocol: The wild-type AB strain was used in the experiments. The females after OMIS were fed with live adult brine shrimp thrice a day. All embryos were raised in Holtfreter’s solution at 28.5C and staged as described previously (Kimmel et al., 1995).

extract_protocol:
CUT&RUN was conducted based on previously published protocol (Xia et al., 2019) with modifications in cell permeation to adapt it for zebrafish embryos. Embryos were deyolked by tweezers manually and transferred into 1.5 mL conventional, non-low-binding tube (Axygen). Then tubes were flicked several times to disperse cells in embryos, and resuspended by 60 ul washing buffer (20 mM HEPES-KOH, pH = 7.5; 150 mM NaCl; 0.5 mM Spermidine and Roche complete protease inhibitor). 10 µl Concanavalin-coated magnetic beads (Polyscience, Cat 86057) for each sample were gently washed twice, resuspended by binding buffer (20 mM HEPES-KOH, pH = 7.5; 10 mM KCl; 1 mM CaCl2; 1 mM MnCl2), and added carefully to the cells.
The cells with beads were incubated at 23℃ for 30 min on Thermomixer (Eppendorf) at 400 rpm, then held at magnetic stand to exclude buffer, and resuspended by 75 µl antibody buffer (washing buffer supplied with 0.02% digitonin and 2 mM EDTA, freshly made) with H3K4me3 (validated homemade) (Zhang et al., 2016) antibody, or H3K27me3 antibody (Active Motif, Cat 61017), or H2AK119ub antibody (CST, Cat 8240s) diluted at ratio of 1:100. Then the samples were incubated at 4℃ on Thermomixer overnight at 400 rpm. On the second day, the samples were washed by digitonin-washing buffer several times on magnetic stand, and resuspended with 50 µl digitonin-washing buffer supplied with 700 ng/ml pA-MNase, which is kindly provided by Dr. Steven Henikoff, and incubated at 4℃ on Thermomixer for 3hrs at 400 rpm. After that, the cells were washed by digitonin-washing buffer on magnetic stand, and resuspended by 100 µl digitonin-washing buffer on ice for at least 2 min. Targeted region digestion was activated by adding 2 µl 100 mM CaCl2 for 30 min in ice, then stopped by 100 µl 2 X stop buffer (340 mM NaCl; 20 mM EDTA, pH = 8.0; 4 mM EGTA, pH = 8.0; 50 µg/ml RNase; 100 µg/ml glycogen; 0.02% digitonin suppled with spike-in DNA) and fully vortexed. To release fragments, the samples were incubated at 37℃ on Thermomixer at 400 rpm for 20 min. Then the supernatants were purified by phenol chloroform and ethanol purification, and subjected to Tru-seq library construction using NEBNext Ultra II DNA Library Prep kit (NEB, Cat E7645S) as standard protocols. The amplified DNA was size-selected using AMPure Beads for 200-800 bp DNA fragments. All libraries were sequenced by Illumina Hi-Seq 1500 or 2500 or XTen platform according to manufacturer’s instruction.

treatment_protocol: Briefly, on the first day of OMIS (Wu et al., 2018b), adult females at 5-12 month old were anesthetized in 550 µg/ml tricaine (Sigma, Cat A5040) in a petri dish. Then the fish was placed on a damp sponge with specific buffer (5.4 mM KCl, 136.8 mM NaCl, 4.2 mM NaHCO3, 0.44 mM KH2PO4, 0.25 mM Na2HPO4, and 0.5% (wt/vol) BSA). A cut was made on one side of belly to expose the ovary. The diluted MOs were microinjected into each oocyte. Rhodamine B (Sigma, Cat R8881) was co-injected with MOs as a dye. After injection, the wound on the belly was sewed with a surgical sewing needle carefully and quickly. Once the operation was done, the female was transferred into fish water supplemented with 32 µg/ml tricaine, 10 unit/ml penicillin and 10 µg/ml streptomycin (HyClone, Cat SV30010). Then the fish was transferred to fish water containing gradually reduced concentrations of tricaine. In the evening of the second day, the female was paired with a wild type male. In the morning of the third day, the pair started to chase and lay fertilized eggs naturally. The injected oocyte-derived embryos were identified by co-injected dye (rhodamine B) at very early developmental stages. The injection doses of standard control MO (cMO) were 5 ng per oocyte in the same assay. MOs were dissolved in RNase-free water, and heated to 65°C for 10 min before microinjection.

value: AB

tag: developmental stage

value: Shield

value: embryo

value: Oocyte microinjection with Rhodamine B and control MO at oogenesis III stage (GV)


title: MOLM13 [RNA-seq]

source_name: MOLM13 cell line

value: MOLM13 cell line


title: THP_1 [RNA-seq]

source_name: THP_1 cell line

value: THP_1 cell line


title: Human HepG2 ADCY9 knock down cells - si-1039-1


title: RAJI FBXO11 knock-out cell line [RAJI41]

description:
RAJI41
raw_counts.txt


title: K562_CTCF_RedChIP_rep1


title: K562_CTCF_RedChIP_input_rep1


title: Human HepG2 ADCY9 knock down cells - si-1039-4


title: Human HepG2 scrambled cells - Scr-1


title: Human HepG2 scrambled sample - Scr-5


title: hESC_EZH2_RedChIP_rep2


title: Ovarian_1

status: Public on Nov 12 2021

city: San Francisco

first: Hugo

last: Gonzalez

address: 513 Parnassus Avenue

department: Anatomy

institute: University of California San Francisco

data_processing:
After sequencing attemping 50,000 counts per cell captured by the 10X chip, Cell Ranger count pipeline (Version 3.0.2 from 10X Genomics) was used to map the FASTQ files to the human genome GRCh38, which generates a gene vs cell expression matrix (See Matrix.mtx.gz and Metrics_Summary.csv files).
The LogNormalized_Data was generated for each sample using the Seurat NormalizeData function. Briefly, counts for each cell are divided by the total counts for that cell and multiplied by the scale.factor 10000. This is then natural-log transformed using log1p
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts matrix
Supplementary_files_format_and_content: Features for downstream processing
Supplementary_files_format_and_content: Single Cell barcodes for downstream processing
Supplementary_files_format_and_content: Cell Ranger Quality Metrics per each sample
Supplementary_files_format_and_content: Normalized Expression per each sample
Supplementary_files_format_and_content: Annotations of the Cell types described in the study.

source_name: Human Brain Metastasis

extract_protocol: Single-cell libraries were generated via the Chromium Controller and the Single Cell Reagent Kit 3’ v2 (10x Genomics, Pleasanton, CA) according to the manufacturer’s instructions

tag: type of tumor

value: Metastatic Tumor, Brain Tumor

value: Ovarian Cancer Brain Metastasis


title: K562 [RNA-seq]

source_name: K562 cell line

value: K562 cell line


title: hESC_EZH2_RedChIP_input_rep1


title: Melan_3

value: Melanoma Brain Metastasis


title: Breast_1

value: Breast Cancer Brain Metastasis


title: Human HepG2 scrambled cells - Scr-4


title: PplusFeminus76hours1

status: Public on Oct 28 2021

city: Stanford

first: Yanniv

last: Dorone

address: 371 Jane Stanford Way

institute: Stanford University

data_processing:
Reads were mapped with HISAT2 to the Arabidopsis thaliana TAIR10 reference genome using the Galaxy (Version 2.1.0+galaxy5) web platform.
The resulting BAM files were then analyzed on R using the DESeq2 and TxDB.Athaliana.BioMart.plantsmart28 (Bioconductor) packages. Genes with padj<0.05 were considered differentially expressed.
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel

source_name: 7 day old shoots

extract_protocol:
RNeasy Plant Mini Kit (QIAGEN)
KAPA Biosystems RNA HyperPrep Kit

treatment_protocol: Arabidopsis wild-type plants (Col-0 accession) were grown on control (+Fe+P) for 7 days on 0.1X MS then transferred to three different medium: control (+Fe+P), iron deficiency (-Fe+P), and iron and phosphate deficiency conditions (-Fe-P). Shoots were collected 39 h, 52 h and 76 h after the transfer. For RNA-seq experiments, three biological replicates were used for each time point (39h, 52h and 76h) and each condition (+Fe+P, -Fe+P and -Fe-P) for a total of 27 samples.

tag: background ecotype

value: +P-Fe

tag: time

value: 76h after transfer

tag: tissue

value: shoots


title: Breast_1_Biological_Replicate


title: Melan_2


title: Melan_1