title: 542_20T

description: Strand orientation: forward

value: forward


title: HEK293, UninducedA76, replicate 4

status: Public on Feb 07 2025

type: SRA

city: Umea

first: Paulina

middle: H

last: Wanrooij

address: Kemihuset (K), Campus, Umeå Umeå universitet, 901 87 Umeå

country: Sweden

institute: Umea University

library_source: transcriptomic

data_processing:
Data files were assessed using FastQC, and read alignment was performed using STAR2.5.2b. On the WSL2 platform, featureCounts for Linux was utilized for quantification and generation of counts files.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Kidney

extract_protocol:
Total RNA was extracted from 16 frozen cell pellet samples using Qiagen RNeasy Plus kit standard RNA extraction protocol. Initial sample quality control was performed using Qubit and Fragment Analyzer.
RNA libraries were prepared by Azenta Life Sciences using Illumina’s PolyA selection method

tag: tissue

value: Kidney

tag: cell line

tag: cell type

value: Embryonic kidney

tag: treatment


title: 534_20T

city: Montréal

first: Claude

last: Perreault

state: Québec

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

description: Strand orientation: forward

data_processing:
Basecalls performed using Illumina RTA.
Samples demultiplexed using bcl2fastq 2.20.
Sequenced reads were trimmed for sequencing adapters and low quality extrimities
Expression values were computed using a pseudo-alignment to the reference transcriptome using Kallisto version 0.43.0
Assembly: GRCh38

molecule: polyA RNA

source_name: cutaneous melanoma

extract_protocol:
TriZol + RNeasy mini Kit (Qiagen)
cDNA libraries were prepared from total RNA using a PolyA selection and the Illumina TruSeq Stranded RNA Kit and were further amplified for sequencing.

value: cutaneous melanoma

tag: reference genome

value: Gencode 33

tag: strand orientation

tag: quantification

value: paired-end


title: 2883_18T

description: Strand orientation: forward


title: Sample 6_Rep2_H1993 CVT-11127 Treatment

city: New York

first: BiNGS

last: Core

address: 1470 Madison Ave

country: USA

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Adapter sequences trimmed with TrimGalore!(v0.6.5)
Gene level read counts are obtained by using Salmon (v1.2.1)
Counts table and DEG analysis completed using DeSeq2 (v1.28.1)
Assembly: hg38
Supplementary files format and content: csv, normalized counts

growth_protocol: H661, H358, H1993,H2228, H2122 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and 1% Pen-strep and 1% Glutmax  in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: LUAD cell lines were treated with CVT-11127 (10µM for 96 hours), equivalent concentration of DMSO was added to cotrol samples. Cells were maintained in RPMI with 10% fetal bovine serum (FBS) and 1% Pen-strep and 1% Glutmax  in humidified atmosphere with 5% CO2 at 37C

value: NSCLC, LUAD

tag: genotype

tag: time

value: Day 4


title: 258_20T

description: Strand orientation: forward


title: HEK293, InducedA76, replicate 3


title: HEK293, UninducedDMSO, replicate 4

value: DMSO


title: 30mo sample 1

city: Madison

first: Rozalyn

last: Anderson

state: WI

address: 2500 Overlook Terrace

institute: University of Wisconsin-Madison

description:
30mo-C12
edgeRglm_GENE_c30mo-c10mo.xlsx
edgeRglm_GENE_g30mo-g20mo.xlsx
rsem_GENE_TPM_102030Br_CtrlOnly.csv

data_processing:
Sequencing reads were trimmed to remove adaptors and low-quality bases
Trimmed reads were aligned to mm10 reference genome using STAR aligner
Differential gene expression analysis was conducted via EdgeR generalized linear model method
For lithium treated mouse brains, two batches were combined using Com-Bat seq.
Assembly: mm10
Supplementary files format and content: excel file from differential gene expression anaylsis conducted in EdgeR

organism: Mus musculus

source_name: brain

extract_protocol:
RNA was collected using Direct-zol RNA kit (Zymo Research).
RNA libraries were generated following the Illumina TruSeq RNA Sample preparation guide. mRNA libraries were generated using NEBNext Poly(A) mRNA Magnetic isolation module and NEBNext Ultara RNA library prep kit.

value: brain

tag: age


title: P291_23_10-PSA-F0_Log2 Signal

type: RNA

city: Gießen

first: Robert

last: Ringseis

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

country: Germany

institute: JLU Gießen

hyb_protocol: 3.8 µg of fragmented and labeled ss cDNA were hybridized to Applied Biosystems GeneChip Clariom S rat arrays for 16 h at 45°C and 60 rpm in an Applied Biosystems GeneChip hybridization oven 640.

scan_protocol: Hybridized arrays were washed and stained in an Applied Biosystems GeneChip Fluidics Station FS450, and the fluorescent signals were measured with an Applied Biosystems GeneChip Scanner 3000 7G System. Fluidics and scan functions were controlled by the Applied Biosystems GeneChip Command Console v4.3.3 software.

data_processing: Summarized probe set signals in log2 scale were calculated by using the GCCN-SST-RMA algorithm with the Applied Biosystems GeneChip Expression Console v1.4 Software. After exporting into Microsoft Excel, average signal values, comparison fold changes (FC) and significance P-values were calculated.

label: Biotin

organism: Gallus gallus

label_protocol: 200 ng of total RNA was used to generate double-stranded cDNA. 12 µg of subsequently synthesized cRNA were purified and reverse transcribed into single-stranded (ss) cDNA, whereat unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin.

growth_protocol: The five-week feeding trial with 72 male, 1-day-old broiler chickens (Cobb 500, Cobb-Vantress, Weidemar, Germany) was approved by the Animal Welfare Officer of the Justus Liebig University Giessen (approval no.: JLU 862_M). All experimental procedures described followed established guidelines for laboratory animals care and handling.

extract_protocol: Aliquots from the liver (20-30 mg) were used for total RNA extraction using TRIzol reagent (Invitrogen, Karlsruhe, Germany) according to the manufacturer´s protocol. Total RNA was analyzed for quantity and quality using an Infinite 200M microplate reader with a NanoQuant plate (both from Tecan, Mainz, Germany).

treatment_protocol: The broilers were randomly assigned to three different groups (4 broilers/cage, 6 cages/group), with a similar mean initial body weight across the groups. The broilers were housed in 2.1 m2 cages with nipple drinkers and feed automates and had free access to feed and water. The floor was covered with hemp-based litter (Hemparada, HempFlax Group B.V., Oude Pekela, Netherlands) which allowed scratching, pecking and dustbathing and was exchanged two times per week during the first two weeks and every two days during the last three weeks of the trial. In addition, broilers were provided with perches in elevated position for resting and sleeping. Light regime followed a schedule of 24 h:0 h, 23 h:1 h, 22 h:2 h, 21 h:3 h, 20 h:4 h, 19 h:5 h (light:dark) at days 1, 2, 3, 4, 5, 6, and 18 h:6 h from day 7 onward and the light intensity was constantly 40 Lux, as recommended by the breeder. The room temperature decreased from 28-29°C on day one, measured at pen height, to 23-24°C on day 35. Infrared lamps (Albert Kerbl GmbH, Buchbach, Germany) were used as additional heat sources during the first 6 days to adjust the temperature at the cage floor to 34°C. Mean relative humidity was 60.0 ± 1.9%. The groups were fed three different nutrient adequate diets containing either 0 (group PSA-F0), 25 (group PSA-F25) or 5% (group PSA-F50) g/kg diet of P. sapidus fruiting bodies in a three-phase feeding system (starter diet form day 1-10, grower diet from day 11-21, finisher diet from day 22-35). The composition of the diets met the broiler’s requirements of nutrients and energy according to the breeder’s recommendations (Cobb-Vantress, 2022). Diets were provided in crumbled form during the first three days, and in pellet form (2 mm diameter) from day 3 until the end of the trial. On days 1, 10, 21 and 35 body weight (individually) and feed intake (per cage) were determined. The feed:gain ratio was calculated from feed intake and body weight gains on cage basis.

value: Liver

value: 0 g/kg diet PSA fruiting bodies


title: Sample 5_Rep3_H1993 Control


title: 20mo sample 5

description:
20mo-C10
edgeRglm_GENE_c20mo-c10mo.xlsx
edgeRglm_GENE_g30mo-g20mo.xlsx
rsem_GENE_TPM_102030Br_CtrlOnly.csv


title: 1836_18T

description: Strand orientation: forward


title: 1772_19T

description: Strand orientation: forward


title: 20mo sample 4

description:
20mo-C09
edgeRglm_GENE_c20mo-c10mo.xlsx
edgeRglm_GENE_g30mo-g20mo.xlsx
rsem_GENE_TPM_102030Br_CtrlOnly.csv


title: HEK293, UninducedA76, replicate 3


title: P291_19_1-PSA-F0_Log2 Signal


title: Sample 5_Rep1_H1993 Control


title: Sample 4_Rep3_H358 CVT-11127 Treatment

value: KRASmut


title: Sample 5_Rep2_H1993 Control


title: HEK293, InducedDMSO, replicate 3

value: doxy+DMSO


title: 20mo sample 2

description:
20mo-C06
edgeRglm_GENE_c20mo-c10mo.xlsx
edgeRglm_GENE_g30mo-g20mo.xlsx
rsem_GENE_TPM_102030Br_CtrlOnly.csv


title: 1713_19T

description: Strand orientation: forward


title: Sample 4_Rep2_H358 CVT-11127 Treatment


title: 1758_19T

description: Strand orientation: forward


title: Sample 6_Rep1_H1993 CVT-11127 Treatment


title: HEK293, InducedA76, replicate 2


title: HEK293, UninducedDMSO, replicate 3


title: 30mo sample 2

description:
30mo-C15
edgeRglm_GENE_c30mo-c10mo.xlsx
edgeRglm_GENE_g30mo-g20mo.xlsx
rsem_GENE_TPM_102030Br_CtrlOnly.csv


title: 1367_16T

description: Strand orientation: forward


title: Sample 4_Rep1_H358 CVT-11127 Treatment


title: HEK293, InducedDMSO, replicate 2


title: 046005T2

description: Strand orientation: forward

source_name: lung adenocarcinoma

value: lung adenocarcinoma

value: Gencode 26


title: 045986T2

description: Strand orientation: forward

source_name: lung squamous cell carcinoma

value: lung squamous cell carcinoma


title: HEK293, UninducedA76, replicate 2


title: 10mo sample 4

description:
10mo-C08
edgeRglm_GENE_c20mo-c10mo.xlsx
edgeRglm_GENE_c30mo-c10mo.xlsx
rsem_GENE_TPM_102030Br_CtrlOnly.csv


title: Sample 3_Rep2_H358 Control


title: Sample 3_Rep3_H358 Control


title: HEK293, UninducedDMSO, replicate 2


title: 045961T2

description: Strand orientation: forward

value: forward


title: Sample 3_Rep1_H358 Control


title: 20mo sample 3

description:
20mo-C07
edgeRglm_GENE_c20mo-c10mo.xlsx
edgeRglm_GENE_g30mo-g20mo.xlsx
rsem_GENE_TPM_102030Br_CtrlOnly.csv


title: 10mo sample 2

description:
10mo-C06
edgeRglm_GENE_c20mo-c10mo.xlsx
edgeRglm_GENE_c30mo-c10mo.xlsx
rsem_GENE_TPM_102030Br_CtrlOnly.csv


title: 045903T2

description: Strand orientation: forward


title: 045722T2

description: Strand orientation: forward


title: 20mo sample 1

description:
20mo-C05
edgeRglm_GENE_c20mo-c10mo.xlsx
edgeRglm_GENE_g30mo-g20mo.xlsx
rsem_GENE_TPM_102030Br_CtrlOnly.csv


title: HEK293, InducedDMSO, replicate 1

value: Kidney


title: Sample 2_Rep3_H661 CVT-11127 Treatment

value: KRASWT


title: 10mo sample 5

description:
10mo-C09
edgeRglm_GENE_c20mo-c10mo.xlsx
edgeRglm_GENE_c30mo-c10mo.xlsx
rsem_GENE_TPM_102030Br_CtrlOnly.csv


title: HEK293, InducedA76, replicate 1

value: Embryonic kidney


title: 10mo sample 1

description:
10mo-C04
edgeRglm_GENE_c20mo-c10mo.xlsx
edgeRglm_GENE_c30mo-c10mo.xlsx
rsem_GENE_TPM_102030Br_CtrlOnly.csv


title: Sample 2_Rep2_H661 CVT-11127 Treatment


title: 042908T2

description: Strand orientation: forward


title: HEK293, UninducedDMSO, replicate 1


title: F_box_CRISPRcut_BC_ORF_SubA

city: Seattle

first: Jay

last: Shendure

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description:
SCF pilot barcode subassembly libraries
TableS1_BC_ORF_associations.csv

library_source: other

data_processing:
ORF-barcode subassembly. In order to associate ORFs to DNA barcodes, sequencing libraries were prepared from barcoded COMET libraries (see Subassembly of ORF-barcode pairs). Reads from tagmented COMET libraries were aligned to ORF sequences using bowtie2 v2.2.5 to determine which ORF was tagged. A custom bowtie2 index of ORF sequences was generated and aligned against. A summary output format of the data was then generated that included the read name, the degenerate barcode sequence, the bowtie2-determined tagged ORF and the mapping quality of the read, which was then used as input for further QC to determine the list of BC-associated ORFs. The initial list of barcodes and ORFs were filtered to exclude reads with a mapping quality score less than 31, barcodes that include any ‘N’ bases, and barcodes associated with common sequencing error modes (e.g., GGGGGGGGGGGGGGGGGGGGGGGGG). We then eliminated barcodes with fewer than 10 reads of supporting evidence, which guards against seemingly unique barcodes that actually include rarely occurring sequencing errors. Ambiguous barcodes were eliminated which mapped to more than one ORF, however, these were included if there was one ORF with more than 90% of the read evidence supporting one barcode. The remaining barcode-ORF pairs were then used to identify the ORF on a plasmid relying on the sequencing of just the barcode (Table S1).
Processing barcode-gRNA sequencing data. Amplicon sequencing reads of gDNA extracted from cells sorted by GFP:mCherry ratio contain two important pieces of information: the sequenced gRNA along with a barcode that was previously associated with a specific ORF. As a first step we convert the raw read data into a summary output format that includes ORF (determined with the previously generated barcode-ORF lookup table), the target identity of the sequenced gRNA, along with the raw sequencing information of the barcode and guide. Summary output files from libraries generated from different conditions and sorted bins are then combined into one file that is then used for statistical analysis.
Supplementary files format and content: TableS1_BC_ORF_associations.csv contains associations between barcodes and ORFs. The file contains associations for both the pilot SCF and short half-life TF screens, and associations from either screen can be subset from the file using the 'experiment' column.
Supplementary files format and content: pilot_count_table.csv contains read count data for the pilot SCF experiment. Read counts are provided for each barcode-target pair in each transfection replicate. Within individual transfection replicates, reads counts in each FACS bin are provided.
Supplementary files format and content: short_HL_TF_count_table.csv contains read count data for the short half-life transcription factor experiment. Read counts are provided for each barcode-target pair in each transfection replicate. Within individual transfection replicates, reads counts in each FACS bin are provided.
Library strategy: amplicon sequencing

molecule: other

organism: Escherichia coli

growth_protocol: K562 cells (CCL-243) were purchased from ATCC and maintained in RPMI 1640 medium (Gibco) supplied with 10% FBS (Hyclone) and penicillin/streptomycin (Gibco, 100 U/ mL).

extract_protocol:
Genomic DNA was extracted using the Qiagen Dneasy Blood and Tissue kit from sorted K562-rtTA-Cas9 cells that had been partitioned by FACS based on GFP:mCherry ratio.
Subassembly of ORF-barcode pairs: Plasmid libraries with gRNAs, barcodes, and ORFs were tagmented with N5 loaded Tn5 transposase (Diagenode). DNA fragments containing ORF-barcode information were enriched from the tagmented plasmid by two-step PCR. The first round of PCR utilized a primer that hybridizes upstream of the barcode region as well as an N5 specific primer that hybridizes to the tagmentation event. First round products were cleaned using Ampure beads and eluted in Qiagen EB. The second round completed the amplicon by adding sample indexes and Illumina sequencing adapters. PCR products were run on a pre-cast 6% TBE polyacrylamide gel (Thermo), and DNA fragments ranging in size from 400-1000 base pairs were excised from the gel and purified. The resulting library was quantified and sequenced on an Illumina instrument. Generation of gRNA-barcode Illumina amplicons: Genomic DNA was extracted from pellets of frozen cells using a DNEasy Blood and Tissue kit (Qiagen, 69504). Illumina amplicons containing gRNA and barcode information were amplified using two-step PCR. In the first round of PCR, genomic DNA from each bin was divided between eight 50 uL PCR reactions and amplified with primers that hybridize to the COMET construct upstream of the gRNA and downstream of the barcode. The eight PCRs were pooled, cleaned with 1X Ampure beads, and eluted in Qiagen EB. The eluted first round product was amplified with primers that added sample indexes and Illumina sequencing adapters. Final amplicons were again Ampure cleaned, quantified, and sequenced on an Illumina instrument.

value: lymphoblast

value: Cas9 and rtTA

tag: group

tag: perturbation

tag: sort day

tag: transfection replicate

tag: facs bin

tag: pcr replicate


title: S6: Sperm genomic DNA of abortion female spouse 3

type: genomic

city: Zhanjiang

first: Tianzhong

last: Ma

state: Guangdong

address: 57 People Avenue South

department: Reproductive Medicine Center

country: China

institute: Affiliated Hospital of Guangdong Medical University

description:
S6
Illumina Infinium® HumanMethylation450 BeadChip

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Infnium Methylation450 Array using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
The raw intensity data were loaded to a biocondutor package “minfi”. The raw data were normalized using the subset-quantile within array normalization (SWAN) method and probes with a detection p-value >= 0.01 in at least one sample were excluded from further analysis. Methylation values, referred to as β-values, were calculated as the ratio of the methylated signal intensity to the sum of the methylated and unmethylated signals after background subtraction. The β-values were reported as a DNA methylation score ranging from 0 (completely unmethylated) to 1 (fully methylated).
The total.txt contains Average Beta values

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Sperm of female spouse with recurrent spontaneous abortion

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

value: sperm

tag: subject status

value: abortion female spouse


title: Sample 2_Rep1_H661 CVT-11127 Treatment

value: NSCLC, LUAD

value: Day 4


title: 042544T2

description: Strand orientation: forward

tag: tissue

value: paired-end


title: kidney derived neutrophils, homozygous, Mm infected, rep6

city: Tampere

first: Sanna-Kaisa

middle: Emilia

last: Harjula

address: Arvo Ylpön katu 34

country: Finland

institute: University of Tampere

description: Library name: RNA35_H_MM_R

data_processing:
Reads were aligned to the reference genome GRz11 (ensembl_109_danio_rerio_grcz11_primary) with HISAT2.
Raw expression estimates (raw read counts) for genes (ensembl_109_danio_rerio_grcz11_primary) were counted using FeatureCounts.
Analysis of differentially expressed genes was performed with DESeq2
Assembly: GRz11
Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab-delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.

organism: Danio rerio

source_name: kidney

growth_protocol: Fish homozygous for pycardtpu5 mutation and WT controls (originally crossed to transgenic Tg(mpx:GFP)i114 (AB) to gain fluorescence in neutrophils) fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.

extract_protocol:
RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol.
Library construction was performed on the Illumina platform (paired-end sequencing, 150 bp read length) yielding > 20 million reads per sample.

treatment_protocol: Adult zebrafish were infected with 4-8 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.

value: kidney

value: neutrophils

value: homozygous for pycard (pycardtpu5 crossed to transgenic Tg(mpx:GFP)i114 (AB))

value: M. marinum infected


title: Sample 1_Rep3_H661 Control

tag: cell line

value: DMSO


title: kidney derived neutrophils, homozygous, Mm infected, rep5

description: Library name: RNA31_H_MM_R

tag: cell type


title: Sample 1_Rep2_H661 Control

tag: treatment


title: 042512T2

description: Strand orientation: forward

value: lung squamous cell carcinoma

tag: reference genome

value: Gencode 26


title: 045770T2

description: Strand orientation: forward

value: lung adenocarcinoma

tag: strand orientation

value: forward


title: S2: Sperm genomic DNA of spouse 2 in the control group

description:
S2
Illumina Infinium® HumanMethylation450 BeadChip

source_name: Sperm of female spouse of induced abortion

value: spouse in the control group


title: 10mo sample 3

description:
10mo-C07
edgeRglm_GENE_c20mo-c10mo.xlsx
edgeRglm_GENE_c30mo-c10mo.xlsx
rsem_GENE_TPM_102030Br_CtrlOnly.csv

value: brain


title: S1: Sperm genomic DNA of spouse 1 in the control group

description:
S1
Illumina Infinium® HumanMethylation450 BeadChip


title: S3: Sperm genomic DNA of spouse 3 in the control group

description:
S3
Illumina Infinium® HumanMethylation450 BeadChip


title: HEK293, UninducedA76, replicate 1

value: Kidney

value: Embryonic kidney


title: 045656T2

description: Strand orientation: forward

tag: quantification


title: 042464T2

description: Strand orientation: forward


title: P6: genomic DNA of abortive villus tissue from RM 3

description:
P6
Illumina Infinium® HumanMethylation450 BeadChip

source_name: Recurrent abortion female villus tissue

value: abortive villus tissue

value: RM


title: 042520T2

description: Strand orientation: forward


title: URI(+/D)Hep rep5

city: Madrid

first: Ruth

last: Álvarez-Díaz

address: C/ Melchor Fernández Almagro, 3

department: Molecular Oncology

country: Spain

institute: Spanish National Cancer Research Center (CNIO)

data_processing:
Raw images generated by the sequencer are submitted to analysis, per-cycle basecalling and quality score assignment with Illumina's Real Time Analysis integrated primary analysis software (RTA v2). Conversion of BCL (base calls) binary files to FASTQ format is subsequently performed with bcl2fastq2 (Illumina).
Fastq files were pre-processed to remove read polyA and sequencing adaptors, aligned to the mouse genome GRCmm39, and read counts were obtained with featureCounts
Assembly: GRCm39
Supplementary files format and content: Normalized counts were obtained using DESeq2

source_name: liver

extract_protocol:
Mice between 8- and 9-week-old were injected with the analgesic Buprex (1ug/mL) 20 min before surgeries, and then anesthetized by breathing isoflurane (2.5 % vol.). Two-thirds hepatectomy was aseptically performed as previously  described. Animals were sacrificed 48 hours after the surgery. Total RNA was extracted from frozen tissue or cells, using TriReagent.
RNA libraries were prepared using the "QuantSeq 3‘ mRNA-Seq V2 Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 191). Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. A UMI Second Strand Synthesis module was used, in which random primers featuring a 6 nt long Unique Molecular Identifier tag are used {to be addressed for bias correction at data analysis}. Directional cDNA libraries, stranded in the sense orientation,  were completed by PCR and sequenced in a single read format on an Illumina NovaSeq X instrument..

treatment_protocol: Mice were treated with tamoxifen for one week

value: liver

value: epithelilal

tag: genotype

value: URI(+/D)Hep


title: 715-18T

description: Strand orientation: forward

value: Gencode 33

value: paired-end


title: kidney derived neutrophils, homozygous, Mm infected, rep2

description: Library name: RNA15_H_MM_R

value: kidney

value: neutrophils

value: homozygous for pycard (pycardtpu5 crossed to transgenic Tg(mpx:GFP)i114 (AB))

value: M. marinum infected


title: S5: Sperm genomic DNA of abortion female spouse 2

description:
S5
Illumina Infinium® HumanMethylation450 BeadChip

value: sperm

value: abortion female spouse


title: URI(+/D)Hep rep3


title: short_half_life_TF_BC_ORF_SubA

description:
Short half-life TF barcode subassembly library
TableS1_BC_ORF_associations.csv

value: lymphoblast

value: Cas9 and rtTA


title: URI(+/D)Hep rep4


title: kidney derived neutrophils, homozygous, Mm infected, rep3

description: Library name: RNA16_H_MM_R


title: kidney derived neutrophils, homozygous, Mm infected, rep1

description: Library name: RNA14_H_MM_R


title: P5: genomic DNA of abortive villus tissue from RM 2

description:
P5
Illumina Infinium® HumanMethylation450 BeadChip


title: kidney derived neutrophils, homozygous, Mm infected, rep4

description: Library name: RNA17_H_MM_R


title: Sample 1_Rep1_H661 Control

value: NSCLC, LUAD

value: KRASWT

value: DMSO

tag: time

value: Day 4


title: kidney derived neutrophils, wt, Mm infected, rep6

description: Library name: RNA32_W_MM_R

value: wild type for pycard (pycardtpu5 crossed to transgenic Tg(mpx:GFP)i114 (AB))


title: 1682_16T

description: Strand orientation: forward

value: cutaneous melanoma

value: forward


title: URI(+/D)Hep rep2

value: liver

value: epithelial

value: URI(+/D)Hep


title: kidney derived neutrophils, wt, Mm infected, rep5

description: Library name: RNA29_W_MM_R

value: kidney

value: neutrophils


title: P4: genomic DNA of abortive villus tissue from RM 1

description:
P4
Illumina Infinium® HumanMethylation450 BeadChip

value: abortive villus tissue

value: RM


title: URI(+/D)Hep rep1


title: P3: genomic DNA of abortive villus tissue from control 3

description:
P3
Illumina Infinium® HumanMethylation450 BeadChip

source_name: Artificial abortion female villus tissue

value: control


title: kidney derived neutrophils, wt, Mm infected, rep3

description: Library name: RNA11_W_MM_R

value: M. marinum infected


title: 1496_16T

description: Strand orientation: forward

value: Gencode 33

value: paired-end


title: URI(+/+)Hep rep2

value: URI(+/+)Hep


title: 7324_1566_Vd

description: Strand orientation: reverse

value: lung squamous cell carcinoma

value: Gencode 26

value: reverse


title: kidney derived neutrophils, wt, Mm infected, rep1

description: Library name: RNA9_W_MM_R

value: wild type for pycard (pycardtpu5 crossed to transgenic Tg(mpx:GFP)i114 (AB))


title: 7901Vd_1100

description: Strand orientation: reverse

value: lung adenocarcinoma


title: 13058Vd_1770

description: Strand orientation: reverse


title: UC_2

status: Public on Feb 06 2025

city: Moscow

first: Alexander

last: Modestov

address: 8-2 Trubetskaya str.

country: Russia

institute: I.M. Sechenov First Moscow State Medical University

description: Library name: UC-2_S28_R1_001

data_processing:
RNA sequencing FASTQ files were processed with STAR aligner in ‘GeneCounts’ mode with the Ensembl human transcriptome annotation.
Assembly: hg38
Supplementary files format and content: comma-delimited file includes raw counts for each sample

source_name: tumor

extract_protocol:
Total RNA was extracted from FFPE samples with RNeasy FFPE Kit (Qiagen) following the manufacturer’s protocol. RNA concentration was measured fluorimetrically using Qubit 4 (Thermo Fisher Scientific). The RNA integrity was accessed by Tapestation 4150 (Agilent).
For depletion of ribosomal RNA and library preparation, the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche) was used. KAPA single-indexed adaptors (Roche) or KAPA unique dual indexed primers (Roche) were used for multiplexing samples in one sequencing run. Library concentrations and quality were measured with the Qubit 4 (Thermo Fisher Scientific) and Tapestation 4150 (Agilent).

value: tumor

tag: disease

value: Endometrial carcinoma


title: StS_1

description: Library name: StS_1_S24_R1_001

value: Soft tissue sarcoma


title: kidney derived neutrophils, wt, Mm infected, rep4

description: Library name: RNA28_W_MM_R

value: kidney


title: Fxr cko NEC pups_3

city: Tianjin

first: yuchao

last: Jing

address: No.22, Meteorological Tai Road, Tianjin

institute: Tianjin Medical University

description: Library name: sample8

data_processing:
RNA-Seq fastq files were first processed by fastp to remove adaptor and low-quality reads, then aligned to the reference genome using Hisat2 (v2.0.5). DEGs were identified by edgeR (v3.22.5). P values were adjusted using the Benjamini & Hochberg method. p<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression. Pathway analysis was performed using Metascape. For analysis of ferroptosis signatures, GSEA was performed by using the Broad Institute’s GSEA program.
Assembly: Hisat2
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Intestinal epithelium

extract_protocol:
RNA-Seq library preparation and sequencing were conducted by Novogene (Beijing, CN) on a NovaSeq 6000 machine for small intestine epithelium (IECs (EpCAM+CD45-) from Fxrfl/fl naïve, FxrΔIEC naïve, Fxrfl/fl NEC and FxrΔIEC NEC pups were sorted via BD FACS)
The end reading of 150bp pairing was generated. RNA-Seq fastq files were first processed by fastp to remove adaptor and low-quality reads, then aligned to the reference genome using Hisat2 (v2.0.5).

value: Intestinal epithelium

value: mouse intestinal epithelial cells

value: Fxr cko

value: NEC model


title: kidney derived neutrophils, wt, Mm infected, rep2

description: Library name: RNA10_W_MM_R

value: neutrophils

value: M. marinum infected


title: URI(+/+)Hep rep1

value: liver

value: epithelial


title: Fxr fl/fl  NEC pups_2

description: Library name: sample6

value: Fxr fl/fl


title: P2: genomic DNA of abortive villus tissue from control 2

description:
P2
Illumina Infinium® HumanMethylation450 BeadChip

value: abortive villus tissue

value: control


title: PC_21

description: Library name: PC_21_S2_R1_001

value: Pancreatic adenocarcinoma


title: URI(+/+)Hep rep3

value: URI(+/+)Hep


title: PC_14

description: Library name: PC_14_S1_R1_001

value: tumor


title: PC_32_2

description: Library name: PC-32-2_S15_ME_L001_R1_001


title: Fxr fl/fl  NEC pups_1

description: Library name: sample5


title: SkC_6

description: Library name: SkC_6_S67_R1_001

value: Skin carcinoma


title: Fxr cko naive pups_1

description: Library name: sample3

value: naïve


title: OT_1

description: Library name: OT-1_S7_ME_L001_R1_001

value: Borderline ovarian tumor


title: OC_33

description: Library name: OC33_S9_R1_001

value: Ovarian cancer


title: P1: genomic DNA of abortive villus tissue from control 1

description:
P1
Illumina Infinium® HumanMethylation450 BeadChip


title: Fxr fl/fl   naive pups_3

description: Library name: sample2

value: Intestinal epithelium

value: mouse intestinal epithelial cells


title: OC_14

description: Library name: OC14_S9_R1_001


title: OC_54

description: Library name: OC-54_S1_ME_L001_R1_001


title: PEox_3

description: Library name: sample6

source_name: ILC3s in small intestine lamina propria

extract_protocol:
RNA-Seq library preparation and sequencing were conducted by Novogene (Beijing, CN) on a NovaSeq 6000 machine for IECs (EpCAM+CD45-) from wild type pups were sorted via BD FACS) ( pretreated with vehicle or PEox)
The end reading of 150bp pairing was generated. RNA-Seq fastq files were first processed by fastp to remove adaptor and low-quality reads, then aligned to the reference genome using Hisat2 (v2.0.5).

value: ILC3s in small intestine lamina propria

value: Group 3 innate lymphoid cells (ILC3s)

value: wild type

value: Peox


title: PEox_2

description: Library name: sample5


title: PEox_1

description: Library name: sample4


title: Fxr fl/fl   naive pups_2

description: Library name: sample1


title: OC_48

description: Library name: OC-48_S8_ME_L001_R1_001


title: OC_50

description: Library name: OC-50_S4_ME_L001_R1_001


title: Fxr cko NEC pups_1

description: Library name: sample7

value: Fxr cko

value: NEC model


title: Vehicle_3

description: Library name: sample3

value: Vehicle


title: Vehicle_1

description: Library name: sample1


title: MN_SkC_6

description: Library name: MN-SkC-6_S4_ME_L001_R1_001

source_name: matched norm

value: matched norm


title: MN_PC_12

description: Library name: MN-PC-12_S7_ME_L001_R1_001

value: Pancreatic adenocarcinoma


title: Gq3, LPS

city: Changsha

first: Dai

last: Ruping

state: Hunan

address: Ren-Min Central Road

department: Anesthesiology

institute: The Second Xiangya Hospital of Central South University

description:
Library name: Samples6
Gq3_fpkm

data_processing:
RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads
Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).
The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).
Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.
Assembly: Genome reference: Mus musculus (mm10) Annotation source: Gencode vMXX or Ensembl release XX
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Lung

growth_protocol: N/A (No in vitro cell culture; only lung tissue samples were used.)

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according  to the manufacturer’s protocol.
RNA-seq libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, USA). mRNA was enriched using poly(A) selection, fragmented, and converted to cDNA, followed by ligation of sequencing adaptors and PCR amplification.

treatment_protocol: Mice were intranasally administered with LPS (20mg/kg) to induce acute lung injury

value: Lung


title: Gq1, LPS

description:
Library name: Samples4
Gq1_fpkm


title: mcherry3, LPS

description:
Library name: Samples3
mcherry3_fpkm


title: MN_OC_40

description: Library name: MN-OC-40_S13_ME_L001_R1_001


title: mcherry2, LPS

description:
Library name: Samples2
mcherry2_fpkm


title: S4: Sperm genomic DNA of abortion female spouse 1

description:
S4
Illumina Infinium® HumanMethylation450 BeadChip

value: sperm

value: abortion female spouse


title: OC_40

description: Library name: OC_40_S3_R1_001

value: tumor


title: MN_LS_6

description: Library name: MN-LS-6_S9_ME_L001_R1_001

value: Leiomyosarcoma


title: OC_42

description: Library name: OC-42_S4_ME_L001_R1_001

value: Ovarian cancer


title: MN_CC_92

description: Library name: MN-CC-92_S8_ME_L001_R1_001

value: Colorectal cancer


title: MN_GC_41

description: Library name: MN-GC-41_S3_ME_L001_R1_001

value: Stomach cancer


title: Vehicle_2

description: Library name: sample2

value: ILC3s in small intestine lamina propria


title: mcherry1, LPS

description:
Library name: Samples1
mcherry1_fpkm


title: NC_5

description: Library name: NC-5_S1_ME_L001_R1_001

value: Carcinoma of unknown primary


title: Col TCV 1

city: Gif-sur-Yvette

first: Thomas

last: Blein

address: Avenue des Sciences

country: France

institute: CNRS

description: Matrix column: Col_TCV_1

data_processing:
The sequencing adapters were removed using cutadapt (v2.10) and sequence matching Arabidopsis ribosomal or transfer RNA were discarded using bowtie (v1.3.1).
The reads of length 21nt, 22nt and 24nt were then mapped on TAIR10 genome with the help of ShortStack (v3.8.5) without mismatch (--mismatches 0), keeping all primary multi-mapping (--bowtie_m all) and correcting for multi-mapped reads according to the uniquely mapped reads (--mmap u).
For each gene annotation in Araport11 (coding genes, non-coding RNA and miRNA precursor), the accumulation of 21/22nt was counted with ShortStack.
The number of sequence corresponding to each mature miRNA of Arabidopsis in miRBase (v22) was used to measure miRNA abundance.
Assembly: Arabidopsis Araport11
Supplementary files format and content: tab-delimited text files include raw 21/22nt siRNA count values for each gene from Araport11 in each Sample
Supplementary files format and content: tab-delimited text files include raw miRNA count values for each Sample
Supplementary files format and content: 21nt coverage files as bigwig
Supplementary files format and content: 22nt coverage files as bigwig

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Arabidopsis seeds were sown in vitro on a nutritive medium (1.3% S-medium Duchefa, 1% Phytoblend agar) and vernalized at 4°C for at least 2 days before being transferred to soil in culture chambers. Plants were grown at 23°C, 70% humidity, 120 μE.m−2 of and lighting 8 h light/16 h dark (short-days) photoperiod during 20 days.

extract_protocol:
Total RNA was isolated in a NaCl/SDS buffer followed by phenol extraction as described in Gy, I. et al. 2007 and treated with DNAse according to manufacturer’s instructions
Small RNA libraries were constructed from 1µg of total RNA treated with DnaseI using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina® kit (New England Biolabs) according to manufacturer’s instructions.

treatment_protocol: For virus infection, 20-day-old plants grown under short-day conditions were infected with TCV by mechanical inoculation.

value: leaf

value: wild type

value: TCV


title: MN_CC_82

description: Library name: MN-CC-82_S13_ME_L001_R1_001


title: MN_PC_14_1

description: Library name: MN-PC-14-1_S5_ME_L001_R1_001


title: female 4-week-old C57BL/6J mouse epiphyses digestion

city: Baltimore

first: Satoru

last: Otsuru

state: MD

address: 670 W Baltimore Street

institute: UMB Department of Orthopaedics, Otsuru Lab

description: Library name: 3402

library_source: transcriptomic single cell

data_processing:
Data were processed using the 10× Genomics workflow. Cell Ranger (10× Genomics) was used for demultiplexing, barcode assignment, and unique molecular identifier (UMI) quantification. Downstream analysis was performed using Seurat v5.1. Cells with >7,500 and <1000 expressed genes and >5% mitochondrial transcripts were excluded. Data were normalized using the SCTransform normalization method before principal component analysis and UMAP. Pseudotime analysis was performed using the Monocle 3 package in R.
Assembly: Mouse mm10
Supplementary files format and content: h5
Supplementary files format and content: 10X count matrix

source_name: Hindlimb epiphyses

extract_protocol:
Chondrocytes were isolated from the growth plate according to a previously described protocol with some modifications. Briefly, after careful removal of soft tissues including the perichondrium, the epiphyses in the distal femur and proximal tibia were dislodged from the metaphyseal end at the osteochondral junction just below the growth plate. The growth plates attached to the epiphyses were then digested in HBSS (Ca-Mg-) with 2 units of Liberase TM (#5401119001, Sigma) at 37°C for 3 cycles of 30-minute incubations with agitation. We divided the digestion period into three cycles and washed the released cells with HBSS in each cycle to minimize the potential transcriptomic alterations due to prolonged digestion. Released cells were mechanically disassociated into a single-cell suspension by gently passing through an 18-gauge needle on a 10 mL syringe 5-10 times, followed by filtering through a 70-µm cell strainer. Hematopoietic cells (CD45+, #103105, BioLegend) and red blood cells (Ter119+, #116207, BioLegend) were excluded by magnetic beads (BLD-480071, BioLegend) using the MACS manual separator (Miltenyi Biotec). Cell concentration (1,840,000 cells/ml) and viability (96%) were quantified and considered suitable for downstream analysis (cell viability > 70%).
After encapsulation into emulsion droplets in the Chromium Controller (10× Genomics), libraries were constructed using 3’ GEM Library Prep (10× Genomics). cDNA libraries were profiled on a NovaSeq6000 sequencer using 100-cycle paired-end reads, targeting 10,000 cells per sample and 50,000 reads per cell.

value: Hindlimb epiphyses

value: wildtype


title: MN_CC_85

description: Library name: MN-CC-85_S6_ME_L001_R1_001

value: matched norm


title: Gq2, LPS

description:
Library name: Samples5
Gq2_fpkm


title: Col Mock 3

description: Matrix column: Col_Mock_3

value: Mock


title: PC_12

description: Library name: PC-12_S1_R1_001

value: Pancreatic adenocarcinoma


title: M_22

description: Library name: M-22_S3_ME_L001_R1_001

value: Melanoma


title: MN_CC_115

description: Library name: MN-CC-115_S5_ME_L001_R1_001


title: M_14

description: Library name: M-14_S23_R1_001


title: Col TCV 3

description: Matrix column: Col_TCV_3


title: Col Mock 2

description: Matrix column: Col_Mock_2


title: NoSelect_KO6

city: Philadelphia

middle: G

last: Brooks

address: 3400 Civic Center Blvd

department: ITMAT

institute: University of Pennsylvania

description: Library name: NoSelect_KO6

data_processing:
PCR duplicates were removed using umi-tools v1.1.1. Reads were quantified with Salmon v1.4.0  (with options "-l A --softclip --softclipOverhangs --biasSpeedSamp 10 -p 6 --gcBias --posBias --seqBias --numBootstraps 50") using the GRCm38 genome and Ensembl v75 annotation.
Assembly: GRCm38, ensembl v75
Supplementary files format and content: salmons.gene.counts.txt provides gene-level read counts for all samples. Gene IDs are given in the first column. The file is in tab-separated values format.

source_name: Liver

growth_protocol: Adult C57b/6 mice and Bmal1 knock-outs 8-18 weeks in age were bred in-house.

extract_protocol:
The mice were euthanized through carbon dioxide induced asphyxiation lung samples were dissected and snap-frozen in liquid nitrogen. RNA was extracted from the tissue using TRIzol (ThermoFisher Scientific, catalog no. 15596018) and RNeasy Mini Kit (Qiagen, catalog no. 74104), according to manufacturers’ protocols.
Except where noted, we constructed all libraries according to the manufacturer’s protocols and used 11 cycles of PCR during the final library amplification step. To allow us to assess duplication rates with UMI sequences, we used the xGen UDI-UMI adapters (IDT, catalog no. 10005903) for all libraries, diluting the initial 15 μM stock of adapters to 1.5 μM in NGS adapter buffer (10 mM Tris pH 8.0, 0.1 mM EDTA, 100 mM NaCl). We used the TruSeq Stranded mRNA library preparation kit (Illumina, catalog no. 20020594) and the TruSeq Stranded Total RNA Human/Mouse/Rat library preparation kit (Illumina, catalog no. 20020596) to prepare the PolyA and rRNA pull-down libraries, respectively. For the rRNA digestion libraries, we used the Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit (Illumina, catalog no. 20040525). This kit uses a different strategy than the TruSeq kits for ligating indexed adapters to cDNA fragments that is not compatible with the xGen adapters. In order to use the same adapters, and their included UMIs, across all libraries, we modified the protocol for the Illumina Stranded Total RNA Prep Ligation as follows: 1) During the ‘Ligate Adapters’ step, replace the RNA Index Anchors with the diluted xGen adapters, and 2) during the ‘Amplify Library’ step, replace the Index Adapters with the PCR Primer Cocktail (PPC) from the TruSeq Stranded Total RNA kit. We performed all other steps according to the manufacturer’s protocol. All PolyA and ribo-depleted libraries used 200 ng of input RNA. For the ‘No Select’ libraries, we used 15 ng of total RNA as input into the TruSeq Stranded Total RNA library preparation protocol, skipping the ‘Deplete rRNA’ step and starting with the ‘Fragment and Denature RNA’ step (see supplementary methods for detailed protocol). All remaining steps in the library preparation used reagents from the TruSeq Stranded Total RNA library preparation kit and followed that protocol. Since the majority of reads from the No Select library come from rRNA reads, we prepared and sequenced three No Select libraries from each sample/condition in order to get a sufficiently diverse sampling of non rRNA molecules.

value: Liver

value: KO

tag: Sex

value: female

tag: ribosomal depletion

value: No selection


title: M_21

description: Library name: M_21_S1_L003_R1_001

value: tumor


title: Col TCV 2

description: Matrix column: Col_TCV_2


title: Col Mock 1

description: Matrix column: Col_Mock_1


title: LS_6

description: Library name: LS_6_S4_R1_001

value: Leiomyosarcoma


title: LS_1

description: Library name: LS_1_S1_R1_001


title: GC_41

description: Library name: GC-41_S4_ME_L001_R1_001

value: Stomach cancer


title: chr11chr17 TCV 3

description: Matrix column: chr11-chr17_TCV_3

value: chr11 chr17 double mutant


title: GC_39

description: Library name: GC-39_S6_ME_L001_R1_001

value: Stomach adenocarcinoma


title: NoSelect_WT5

description: Library name: NoSelect_WT5

source_name: lung

value: lung

value: WT


title: chr11chr17 TCV 2

description: Matrix column: chr11-chr17_TCV_2

value: leaf

value: TCV


title: CC_96

description: Library name: CC-96_S1_ME_L001_R1_001

value: Colorectal cancer


title: chr11chr17 TCV 1

description: Matrix column: chr11-chr17_TCV_1


title: CC_94

description: Library name: CC-94_S1_ME_L001_R1_001


title: NoSelect_KO4

description: Library name: NoSelect_KO4


title: CC_93

description: Library name: CC-93_S10_ME_L001_R1_001


title: chr11chr17 Mock 3

description: Matrix column: chr11-chr17_Mock_3

value: Mock


title: NoSelect_KO5

description: Library name: NoSelect_KO5


title: NoSelect_WT6

description: Library name: NoSelect_WT6


title: CC_5

description: Library name: CC-5_S20_L008_R1_001


title: NoSelect_WT3

description: Library name: NoSelect_WT3


title: CC_127_2

description: Library name: CC-127-2_S9_ME_L001_R1_001


title: chr11chr17 Mock 1

description: Matrix column: chr11-chr17_Mock_1


title: CC_46

description: Library name: CC-46_S24_R1_001


title: CC_107

description: Library name: CC-107_S15_ME_L001_R1_001


title: CC_83

description: Library name: CC_83_S25_R1_001


title: NoSelect_KO3

description: Library name: NoSelect_KO3


title: chr11chr17 Mock 2

description: Matrix column: chr11-chr17_Mock_2


title: PolyA_KO6

description: Library name: PolyA_KO6

value: PolyA selection


title: CC_82

description: Library name: CC_82_S3_R1_001


title: CC_18

description: Library name: CC_18_S9_R1_001


title: NoSelect_WT4

description: Library name: NoSelect_WT4


title: 81_SFMC_TCR, CD45RO+ CD8+ PD-1+ TIGIT+ CD127-

city: Toronto

first: Michael

last: Tang

address: 60 Leonard Ave. 5KD-408

institute: University Health Network

description:
Library name: 81 PD-1+TIGIT+_TCR
10x Genomics

data_processing:
Raw scRNA-seq data were preprocessed using the Cell Ranger Single Cell Software Suite (v.5.0.1) provided by 10X Genomics for demultiplexing cellular barcodes, read alignment and generation of the gene-cell matrix under the GRCh38 human reference genome.
Assembly: GRCh38 human reference genome
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Synovial Fluid

extract_protocol:
CD45RO+ CD8+ T cells were FACS sorted. Single cells were encapsulated in Gel-beads in emulsion (GEMs) using 5' gene expression library construction (10X Genomics).
V(D)J amplification from cDNA aand V(D)J library construction were performed with Chromium Next GEM Single Cell 5' Reagent Kits v2 (10x Genomics) following manufacturer's protocols. Both 5' gene expression and V(D)J enriched libraries were quantified and evaluated via bioanalyzer high sensitivity chip (Agilent) prior to sequencing.

treatment_protocol: FACS-sorted for CD45RO+ CD3+ CD8+ cells

value: Synovial Fluid

value: Primary cells

value: Synovial Fluid Mononuclear cells

value: FACS-sorted


title: CC_115

description: Library name: CC_115_S26_R1_001


title: PolyA_WT6

description: Library name: PolyA_WT6

value: female


title: BlC_1

description: Library name: BlC_1_S5_R1_001

value: tumor

value: Urothelial carcinoma


title: PolyA_KO5

description: Library name: PolyA_KO5

value: KO


title: 81_SFMC_GEX, CD45RO+ CD8+ PD-1+ TIGIT+ CD127-

description:
Library name: 81 PD-1+TIGIT+_GEX
10x Genomics


title: BC_60

description: Library name: BC60_S9_R1_001

value: Breast cancer


title: PolyA_WT5

description: Library name: PolyA_WT5


title: AdC_5

description: Library name: AdC_5_S3_R1_001

value: Adrenocortical carcinoma


title: 76_SFMC_GEX, CD45RO+ CD8+ PD-1+ TIGIT+ CD127-

description:
Library name: 76 PD-1+ TIGIT+_GEX
10x Genomics


title: BC_66

description: Library name: BC-66_S21_R1_001


title: PolyA_KO4

description: Library name: PolyA_KO4

value: lung


title: BC_70

description: Library name: BC-70_S4_R1_001


title: CC_99

description: Library name: CC-99_S10_ME_L001_R1_001


title: Intestinal_Organoids_6h_IFNg_iMEK_rep2

city: Kyoto

first: Takuya

last: Yamamoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: CiRA

country: Japan

institute: Kyoto University

data_processing:
Illumina RTA version 4.12.2 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
The sequenced reads were mapped to the mm10 mouse reference genome using STAR (version 2.7.11a), with the GENCODE M23 annotation gtf file after trimming adaptor sequences and low-quality bases by cutadapt-4.6.
The raw count matrix was created using HTSeq (version 2.0.5) with GENCODE M23 annotation gtf file.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RawCounts values for each Sample

source_name: derived from small intestine

growth_protocol: The proximal half of the small intestines of young mice (2-4 months) were dissected, washed with cold PBS (Mg-/Ca-) and opened. Villi were removed by scraping with glass slides. The tissues were cut into 3-5mm fragments and washed 5-6 times in cold PBS (Mg-/Ca-) with gentle shaking by hand. The pieces were then incubated for 30 min at 4°C in PBS (Mg-/Ca-) containing 5mM EDTA. Crypts were then mechanically isolated by vigorous shaking, and filtered through a 70-um mesh to remove remaining villus and tissue fragments. Isolated crypts were counted and embedded in Matrigel (Corning) at 10 crypts per µL. Twenty-five microlitres drops of Matrigel with crypts were plated on a 48-well plate (Iwaki) and cultured in advanced DMEM/F12 (Thermo Fisher Scientific) medium containing 1X GlutaMax (Thermo Fisher Scientific), 10 mM HEPES (Thermo Fisher Scientific), 100 U/mL penicillin/streptomycin (Thermo Fisher Scientific), 1X N2 supplement (Thermo Fisher Scientific), 1X B27 supplement (Thermo Fisher Scientific), 50 ng ml/mL mouse recombinant EGF (R&D Systems), 100 ng ml/mL mouse recombinant Noggin (PeproTech), 500 ng ml/mL human recombinant R-spondin-1 (R&D Systems), and 1 µM N-acetyl-l-cysteine (Sigma‒Aldrich). Then, 10 µM Y27632 (WAKO) was added for the first two days. The medium was changed every other day.

extract_protocol:
RNA was isolated with and RNeasy micro kit (Qiagen).
The RNAseq libraries were generated using the Illumina Stranded mRNA Prep, Ligation Kit (Illumina), according to the manufacturer’s instructions.

treatment_protocol: On the fourth day after plating, intestinal organoids were treated with 1.5 ng/mL mouse recombinant IFN-g (PeproTech) and/or 3 µM iMEK (PD0325901, WAKO) for 1 hour, 6 hours and 24 hours.

value: derived from small intestine

value: Intestinal organoids

value: Intestinal epithelial cells

value: WT

tag: strain


title: Intestinal_Organoids_24h_IFNg_rep2


title: Intestinal_Organoids_6h_iMEK_rep2


title: PolyA_WT3

description: Library name: PolyA_WT3


title: PolyA_WT4

description: Library name: PolyA_WT4


title: 73-4_SFMC_TCR, CD45RO+ CD8+ PD-1+ TIGIT+ CD127-

description:
Library name: 73-4 PD-1+TIGIT+_TCR
10x Genomics


title: Intestinal_Organoids_6h_IFNg_rep2


title: HC1660_PBMC_TCR, CD45RO+ CD8+

description:
Library name: HC1660_TCR
10x Genomics

source_name: Peripheral Blood

value: Peripheral Blood

value: Peripheral Blood Mononuclear cells


title: Intestinal_Organoids_24h_IFNg_iMEK_rep2


title: Intestinal_Organoids_24h_Control_rep2


title: HC1788_PBMC_GEX, CD45RO+ CD8+

description:
Library name: HC1788_GEX
10x Genomics


title: Intestinal_Organoids_1h_IFNg_iMEK_rep2


title: PolyA_KO2

description: Library name: PolyA_KO2

value: PolyA selection


title: Intestinal_Organoids_1h_IFNg_rep2


title: 73-4_SFMC_GEX, CD45RO+ CD8+ PD-1+ TIGIT+ CD127-

description:
Library name: 73-4 PD-1+TIGIT+_GEX
10x Genomics

value: Synovial Fluid

value: Primary cells


title: PolyA_WT2

description: Library name: PolyA_WT2


title: HC1660_PBMC_GEX, CD45RO+ CD8+

description:
Library name: HC1660_GEX
10x Genomics

value: FACS-sorted


title: HC1788_PBMC_TCR, CD45RO+ CD8+

description:
Library name: HC1788_TCR
10x Genomics


title: Intestinal_Organoids_6h_Control_rep2


title: Intestinal_Organoids_24h_iMEK_rep2


title: Intestinal_Organoids_1h_Control_rep2


title: Intestinal_Organoids_1h_iMEK_rep2


title: Intestinal_Organoids_0h_rep2


title: PolyA_KO1

description: Library name: PolyA_KO1

value: female


title: PolyA_KO3

description: Library name: PolyA_KO3


title: 76_SFMC_TCR, CD45RO+ CD8+ PD-1+ TIGIT+ CD127-

description:
Library name: 76 PD-1+ TIGIT+_TCR
10x Genomics

value: Synovial Fluid Mononuclear cells


title: HC546_PBMC_TCR, CD45RO+ CD8+

description:
Library name: HC546_TCR
10x Genomics


title: Intestinal_Organoids_24h_IFNg_iMEK_rep1


title: Intestinal_Organoids_24h_iMEK_rep1


title: HC546_PBMC_GEX, CD45RO+ CD8+

description:
Library name: HC546_GEX
10x Genomics


title: RiboZero_KO6

description: Library name: RiboZero_KO6

value: rRNA pull-down


title: Intestinal_Organoids_24h_IFNg_rep1


title: Fxr cko naive pups_2

description: Library name: sample4

value: Intestinal epithelium

value: mouse intestinal epithelial cells

value: Fxr cko

value: naïve


title: Intestinal_Organoids_6h_IFNg_iMEK_rep1

value: derived from small intestine


title: RiboZero_WT6

description: Library name: RiboZero_WT6

value: lung


title: HC1564_PBMC_GEX, CD45RO+ CD8+

description:
Library name: HC1564_GEX
10x Genomics


title: Intestinal_Organoids_24h_Control_rep1

value: Intestinal organoids

value: Intestinal epithelial cells


title: Intestinal_Organoids_6h_Control_rep1

value: WT


title: Intestinal_Organoids_1h_iMEK_rep1


title: Intestinal_Organoids_6h_IFNg_rep1


title: RiboZero_WT5

description: Library name: RiboZero_WT5


title: HC1564_PBMC_TCR, CD45RO+ CD8+

description:
Library name: HC1564_TCR
10x Genomics

value: Peripheral Blood

value: Peripheral Blood Mononuclear cells


title: PB81_PBMC_TCR, CD45RO+ CD8+

description:
Library name: PB81_TCR
10x Genomics


title: RiboZero_KO5

description: Library name: RiboZero_KO5

value: KO


title: RiboZero_KO4

description: Library name: RiboZero_KO4


title: PB81_PBMC_GEX, CD45RO+ CD8+

description:
Library name: PB81_GEX
10x Genomics

value: Primary cells


title: PB74_PBMC_TCR, CD45RO+ CD8+

description:
Library name: PB74_TCR
10x Genomics

value: FACS-sorted


title: Intestinal_Organoids_1h_Control_rep1


title: Intestinal_Organoids_0h_rep1


title: RiboZero_WT4

description: Library name: RiboZero_WT4

value: female


title: R108_rhizo_72hr_rep4

city: Cologne

first: Tak

last: Lee

address: Carl-von-Linne weg 10

institute: Max Planck Institute for Plant Breeding Research

data_processing:
The quality of the fastq files were validated with fastqc
Sequence reads were trimmed for adapter and repetitive sequences with Cutadept
The resulting reads from the raw fastq data were quality controlled and and mapped to the M. truncatula reference genome version 4.0 with STAR 2.7.3a
The raw count values were calculated with featureCounts in R package Rsubread
Assembly: Mt4.0v1
Supplementary files format and content: tab separated files with raw count values

organism: Medicago truncatula

source_name: 2-3mm segment of root

growth_protocol: Seeds were scarified, surface sterilized with 10 % (v/v) bleach solution, stratified for 3 days  at 4 °C and germinated on water agar plates. Plants were grown in sterile conditions in controlled  environment rooms at 22 °C (80 % humidity, 16 h light/8 h dark, 300 μmol m2 s-1 light intensity)  on filter paper-lined agar media in sealed plates unless otherwise specified. For rhizobial spot  inoculation seedlings were grown for 2 days on buffered nodulation medium (BNM) (Ehrhardt et  al., 1992) supplemented with 1 μM aminoethoxyvinylglycine (AVG; Sigma-Aldrich Company  Ltd, Darmstadt, Germany) at 22 °C (16 hours light/8 hours dark, 300 μmol m-2 s-1 light intensity).

extract_protocol:
Total RNA was isolated with the RNeasy PlantMini Kit (Qiagen) following the manufacturer’s instructions.
The library was constructed with Illumina TruSeq® Stranded mRNA HT kit

treatment_protocol: Sinorhizobium meliloti strain 2011 (Lerouge et al., 1990) was grown in minimal medium  supplemented with 3 μM luteolin (Sigma-Aldrich Company Ltd, Darmstadt, Germany) and diluted  to a final concentration of 0.02 OD 600 nm using Fahraeus medium (Boisson-Dernier et al., 2001).  The mock treatment consisted of Fahraeus medium with luteolin diluted to an equivalent  concentration as the inoculum. Approximately 1 μL of S. meliloti suspension or mock treatment  was inoculated onto the susceptibility zone (where the root hairs first appear) and marked by  puncturing the filter paper alongside the site of inoculation. After 24 and 72 hours

value: 2-3mm segment of root

value: wild type ecotype R108

value: rhizobia S. meliloti 2011


title: PolyA_WT1

description: Library name: PolyA_WT1

value: PolyA selection


title: PB74_PBMC_GEX, CD45RO+ CD8+

description:
Library name: PB74_GEX
10x Genomics


title: R108_rhizo_72hr_rep3


title: Intestinal_Organoids_6h_iMEK_rep1


title: R108_rhizo_72hr_rep2


title: RiboZero_KO3

description: Library name: RiboZero_KO3

value: rRNA pull-down


title: R108_rhizo_72hr_rep1


title: Intestinal_Organoids_1h_IFNg_iMEK_rep1


title: PB76_PBMC_TCR, CD45RO+ CD8+

description:
Library name: PB76_TCR
10x Genomics


title: R108_mock_72hr_rep2

value: mock


title: RiboZero_KO2

description: Library name: RiboZero_KO2


title: R108_mock_72hr_rep1


title: R108_mock_72hr_rep4


title: Intestinal_Organoids_1h_IFNg_rep1

value: derived from small intestine


title: noot1noot2_rhizo_72hr_rep3

value: noot1noot2 mutant in R108 background


title: RiboZero_WT2

description: Library name: RiboZero_WT2

value: lung


title: R108_mock_72hr_rep3


title: RiboZero_WT3

description: Library name: RiboZero_WT3


title: PB76_PBMC_GEX, CD45RO+ CD8+

description:
Library name: PB76_GEX
10x Genomics


title: PB73-4_PBMC_GEX, CD45RO+ CD8+

description:
Library name: PB73-4_GEX
10x Genomics


title: noot1noot2_rhizo_72hr_rep2


title: PB73-4_PBMC_TCR, CD45RO+ CD8+

description:
Library name: PB73-4_TCR
10x Genomics


title: RiboZero_KO1

description: Library name: RiboZero_KO1


title: noot1noot2_rhizo_72hr_rep1


title: SF81_SFMC_TCR, CD45RO+, CD8+

description:
Library name: SF81_TCR
10x Genomics

value: Synovial Fluid

value: Synovial Fluid Mononuclear cells


title: noot1noot2_rhizo_24hr_rep4


title: RiboZero_WT1

description: Library name: RiboZero_WT1

value: WT


title: noot1noot2_rhizo_24hr_rep3


title: SF81_SFMC_GEX, CD45RO+, CD8+

description:
Library name: SF81_GEX
10x Genomics


title: noot1noot2_rhizo_24hr_rep2


title: noot1noot2_rhizo_24hr_rep1


title: NOOT1NOOT2_OE_rep3

source_name: regenerated root structure

value: regenerated root structure

value: wild type ecotype Jemalong A17 cultivar Jester transformed with pLjUBI:NOOT1NOOT2


title: SF74_SFMC_TCR, CD45RO+, CD8+

description:
Library name: SF74_TCR
10x Genomics

value: Primary cells


title: Liver_NoSelect_Slow_Medium_B2_rep2

description: Library name: Liver_NoSelect_Slow_Medium_B2_rep2

data_processing:
Ribosomal content was removed from all samples computationally (see https://github.com/itmat/normalization). PCR duplicates were removed using umi-tools v1.1.1. Reads were quantified with Salmon v1.9.0 (options: "-l ISF --seqBias --gcBias --posBias --dumpEq") using the GRCm38 genome and Ensembl v102 annotation. Quantifications were aggregated using R v4.4.0 and tximeta v1.22.1.
Assembly: GRCm38, ensembl v102
Supplementary files format and content: Processed file contains gene-level read count estimates of all samples. The format is a tab-separated spreadsheet. The first column gives gene identifiers.

growth_protocol: A wild-type, twelve-week-old male C57BL/6J mouse was bred in-house at the animal facility of the University of Pennsylvania.

extract_protocol:
The mouse  was euthanized through carbon dioxide induced asphyxiation and liver and heart  samples were dissected and snap-frozen in liquid nitrogen. RNA was extracted from the tissue using TRIzol (ThermoFisher Scientific, catalog no. 15596018) and RNeasy Mini Kit (Qiagen, catalog no. 74104), according to manufacturers’ protocols.
Except where noted, we constructed all libraries according to the manufacturer’s protocols and used 13 cycles of PCR during the final library amplification step. To allow us to assess duplication rates with UMI sequences, we used the xGen UDI-UMI adapters (IDT, catalog no. 10005903) for all libraries, diluting the initial 15 μM stock of adapters to 3 μM in NGS adapter buffer (10 mM Tris pH 8.0, 0.1 mM EDTA, 100 mM NaCl).  We used the TruSeq Stranded mRNA library preparation kit (Illumina, catalog no. 20020594) and the TruSeq Stranded Total RNA Human/Mouse/Rat library preparation kit (Illumina, catalog no. 20020596) to prepare the PolyA and rRNA pull-down libraries, respectively. For the rRNA digestion libraries, we used the Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit (Illumina, catalog no. 20040525). This kit uses a different strategy than the TruSeq kits for ligating indexed adapters to cDNA fragments that is not compatible with the xGen adapters. In order to use the same adapters, and their included UMIs, across all libraries, we modified the protocol for the Illumina Stranded Total RNA Prep Ligation as follows: 1) During the ‘Ligate Adapters’ step, replace the RNA Index Anchors with the diluted xGen adapters, and 2) during the ‘Amplify Library’ step, replace the Index Adapters with the PCR Primer Cocktail (PPC) from the TruSeq Stranded Total RNA kit. We performed all other steps according to the manufacturer’s protocol. All PolyA and ribo-depleted libraries used 200 ng of input RNA.  For the ‘No Select’ libraries, we used 20 ng of total RNA as input into the TruSeq Stranded Total RNA library preparation protocol, skipping the ‘Deplete rRNA’ step and starting with the ‘Fragment and Denature RNA’ step (see supplementary methods for detailed protocol). All remaining steps in the library preparation used reagents from the TruSeq Stranded Total RNA library preparation kit and followed that protocol. Since the majority of reads from the No Select library come from rRNA reads, we prepared and sequenced three No Select libraries from each sample/condition in order to get a sufficiently diverse sampling of non rRNA molecules.  For the experiments where we varied RNA fragmentation, we used the following times for the 94°C incubation during the fragment RNA step: 2 minutes (short), 8 minutes (medium), or 12 minutes (long). Similarly, for experiments where we varied PCR ramp rates, we used the following Thermocycler ramp rate settings during the library amplification step: 3°C/s (fast), 1.5°C/s (medium), or 0.5°C/s (slow).

value: Liver

value: No selection

tag: fragment length

value: Medium

tag: pcr ramp_rate

value: Slow


title: Liver_NoSelect_Slow_Medium_B2_rep3

description: Library name: Liver_NoSelect_Slow_Medium_B2_rep3

value: female


title: SF74_SFMC_GEX, CD45RO+, CD8+

description:
Library name: SF74_GEX
10x Genomics

value: FACS-sorted


title: NOOT1NOOT2_OE_rep2


title: NOOT1NOOT2_OE_rep1


title: noot1noot2_mock_72hr_rep1

value: 2-3mm segment of root


title: SF76_SFMC_TCR, CD45RO+, CD8+

description:
Library name: SF76_TCR
10x Genomics


title: Liver_NuRibo_Fast_Short_B2

description: Library name: Liver_NuRibo_Fast_Short_B2

value: rRNA digestion

value: Short

value: Fast


title: Liver_NuRibo_Medium_Short_B2

description: Library name: Liver_NuRibo_Medium_Short_B2


title: noot1noot2_mock_72hr_rep2

value: noot1noot2 mutant in R108 background

value: mock


title: SF76_SFMC_GEX, CD45RO+, CD8+

description:
Library name: SF76_GEX
10x Genomics

value: Synovial Fluid

value: Synovial Fluid Mononuclear cells


title: Liver_NoSelect_Slow_Medium_B2_rep1

description: Library name: Liver_NoSelect_Slow_Medium_B2_rep1


title: noot1noot2_mock_24hr_rep2


title: noot1noot2_mock_24hr_rep3


title: SF73-4_SFMC_TCR, CD45RO+, CD8+

description:
Library name: SF73-4_TCR
10x Genomics


title: noot1noot2_mock_24hr_rep4


title: Liver_NuRibo_Slow_Short_B2

description: Library name: Liver_NuRibo_Slow_Short_B2


title: noot1noot2_mock_24hr_rep1


title: MN_OC_54

description: Library name: MN-OC-54_S2_ME_L001_R1_001

value: matched norm

value: Ovarian cancer


title: lsh1_rhizo_72hr_rep3

value: lsh1 mutant in R108 background

value: rhizobia S. meliloti 2011


title: Liver_NuRibo_Fast_Medium_B2

description: Library name: Liver_NuRibo_Fast_Medium_B2

value: Liver


title: lsh1_rhizo_72hr_rep2


title: Human BM cells from WT mice, male and female, UBA1wt, scRNAseq

city: Segrate

first: Roberta

last: Alfieri

state: MI

address: Via Fratelli Cervi 93

department: ITB

country: Italy

institute: CNR

description: Library name: WT_mice

data_processing:
Preliminary analysis using the CellRanger using default parameters.
Filtering, Normalization, Scaling using the R package Seurat.
Identification of clusters using the Louvain algorithm privded by the R package Seurat.
Identification of differentially expressed genes using the Seurat function FindAllMarkers with default parameters.
Assembly: GRCh38, GRCm38
Supplementary files format and content: matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz

source_name: Bone marrow

extract_protocol:
Cell suspensions were diluted in PBS with 0.04% BSA to a final concentration of 1 × 106 cells/mL. Vitality was assessed for each individual sample. Approximately 20,000 cells were loaded onto a single-cell chip for gel bead-in-emulsion (GEM) generation using the 10x Genomics Chromium Controller (10× Genomics).
3′mRNA-seq gene expression libraries were constructed using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 (10x Genomics) according to the manufacturer’s guidelines. All reactions were performed in a C1000 Touch Thermal Cycler (Bio-Rad Laboratories). Twelve cycles were used for cDNA amplification, while the number of total cycles for the sample index PCR was calculated based on the cDNA concentration. Amplified cDNA and final libraries were evaluated using a Tape Station 4200 (Agilent Technologies) with a high sensitivity chip. scRNA-seq libraries were sequenced on an Illumina NovaSeq6000 with the standard sequencing protocol of R1 28; I1 10; I2 10; R2 90 nt read length.

value: Bone marrow

value: human CD34+/-


title: Liver_NuRibo_Medium_Medium_B2

description: Library name: Liver_NuRibo_Medium_Medium_B2

value: female

value: Medium


title: lsh1_rhizo_72hr_rep1

value: 2-3mm segment of root


title: Human BM cells from VEXAS mice, male and female, UBA1 mut, scRNAseq

description: Library name: Vexas_mice


title: lsh1_rhizo_24hr_rep3


title: lsh1_rhizo_24hr_rep2


title: Liver_NuRibo_Slow_Medium_B2

description: Library name: Liver_NuRibo_Slow_Medium_B2

value: rRNA digestion

value: Slow


title: lsh1_rhizo_24hr_rep1


title: Liver_NuRibo_Fast_Long_B2

description: Library name: Liver_NuRibo_Fast_Long_B2

value: Long

value: Fast


title: lsh1_mock_72hr_rep1

value: mock


title: TDPhigh-8, snATAC

city: Atlanta

first: Hsiao-Lin

middle: V.

last: Wang

state: GA

address: 615 Michael Street,, Whitehead Biomedical Research Building, Room 355,

department: School of Medicine, Department of Human Genetics

institute: Emory University

description:
Library name: sample 52
10x Genomics Chromium Single Cell Multiome

library_source: genomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x Genomics Cell Ranger ARC (cellranger-arc-2.0.0)
Assembly: hg38
Supplementary files format and content: Tab-separated values files, matrix files, alignment files, and ATAC-seq fragment files

source_name: dorsolateral prefrontal cortex

extract_protocol:
Tissue sections were frozen and stored at -80°C. 20 mg frozen tissues were thawed in 1 mL cold homogenization buffer (260 mM sucrose, 30 mM KCl, 10 mM NaCl2, 20 mM Tricine-KOH pH 7.8, 1 mM DTT, 0.5 mM Spermidine, 0.2 mM Spermine, 0.3% NP40, cOmplete Protease inhibitor (Roche), and Ribolock) and homogenized in a pre-chilled Dounce. Cell lysates were passed through a 70 µm Flowmi cell strainer before separation using a discontinuous iodixanol gradient and centrifuge at 1480 g at 4°C for 20 min in a swinging bucket centrifuge with the brake off. The nuclei band located at the interface between 30% and 40% iodixanol was collected and washed in RSB-T wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20)
Libraries were generated using the 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression kit following the manufacturer’s instructions, with the following modifications. Per sample, 16,100 nuclei were resuspended in 1x diluted nuclei buffer (10x Genomics) with 2% BSA (Sigma) with a capture target of 10,000 nuclei. ATAC libraries were sequenced to target of 25,000 read-pairs per nucleus and RNA libraries were sequenced to 20,000 read-pairs per nucleus on an Illumina NovaSeq 6000 instrument at the Florida State University Translational Science Laboratory. The matched RNA and ATAC libraries were processed using the 10x Genomics Cell Ranger ARC (cellranger-arc-2.0.0) pipeline with default parameters and aligned to the hg38 human genome assembly (refdata-cellranger-arc-GRCh38-2020-A-2.0.0).

value: dorsolateral prefrontal cortex

value: cortical cells

value: C9orf72 HRE

tag: batch


title: Liver_NuRibo_Slow_Long_B2

description: Library name: Liver_NuRibo_Slow_Long_B2


title: TDPhigh-7, snATAC

description:
Library name: sample 51
10x Genomics Chromium Single Cell Multiome


title: Liver_NuRibo_Medium_Long_B2

description: Library name: Liver_NuRibo_Medium_Long_B2


title: TDPhigh-6, snATAC

description:
Library name: sample 50
10x Genomics Chromium Single Cell Multiome


title: lsh1_mock_24hr_rep1


title: lsh1lsh2_rhizo_72hr_rep4

value: lsh1lsh2 mutant in R108 background


title: SF73-4_SFMC_GEX, CD45RO+, CD8+

description:
Library name: SF73-4_GEX
10x Genomics

value: Synovial Fluid

value: Primary cells

value: Synovial Fluid Mononuclear cells

value: FACS-sorted


title: TDPhigh-5, snATAC

description:
Library name: sample 49
10x Genomics Chromium Single Cell Multiome


title: Liver_OldRibo_Fast_Short_B2

description: Library name: Liver_OldRibo_Fast_Short_B2

value: Liver

value: rRNA pull-down

value: Short


title: TDPhigh-4, snATAC

description:
Library name: sample 48
10x Genomics Chromium Single Cell Multiome


title: lsh1lsh2_rhizo_72hr_rep2

value: 2-3mm segment of root

value: rhizobia S. meliloti 2011


title: Liver_OldRibo_Medium_Short_B2

description: Library name: Liver_OldRibo_Medium_Short_B2

value: female

value: Medium


title: TDPhigh-3, snATAC

description:
Library name: sample 47
10x Genomics Chromium Single Cell Multiome


title: lsh1lsh2_rhizo_72hr_rep1


title: Liver_OldRibo_Slow_Short_B2

description: Library name: Liver_OldRibo_Slow_Short_B2

value: Slow


title: TDPhigh-2, snATAC

description:
Library name: sample 46
10x Genomics Chromium Single Cell Multiome


title: lsh1_mock_72hr_rep3

value: lsh1 mutant in R108 background

value: mock


title: lsh1_mock_72hr_rep4


title: lsh1lsh2_rhizo_24hr_rep3


title: lsh1_mock_24hr_rep3


title: Liver_OldRibo_Fast_Medium_B2

description: Library name: Liver_OldRibo_Fast_Medium_B2

value: Fast


title: TDPhigh-1, snATAC

description:
Library name: sample 45
10x Genomics Chromium Single Cell Multiome

value: dorsolateral prefrontal cortex

value: cortical cells

value: C9orf72 HRE


title: lsh1_mock_24hr_rep2


title: LSH1LSH2_OE_rep3

value: regenerated root structure

value: wild type ecotype Jemalong A17 cultivar Jester transformed with pLjUBI:LSH1LSH2


title: LSH1LSH2_OE_rep2


title: Liver_OldRibo_Medium_Medium_B2

description: Library name: Liver_OldRibo_Medium_Medium_B2


title: TDPmed-5, snATAC

description:
Library name: sample 44
10x Genomics Chromium Single Cell Multiome


title: LSH1LSH2_OE_rep1


title: lsh1lsh2_rhizo_72hr_rep3

value: lsh1lsh2 mutant in R108 background


title: noot1noot2_mock_72hr_rep3

value: noot1noot2 mutant in R108 background


title: Liver_OldRibo_Slow_Medium_B2

description: Library name: Liver_OldRibo_Slow_Medium_B2

value: Liver

value: rRNA pull-down


title: lsh1lsh2_mock_72hr_rep3

value: 2-3mm segment of root


title: lsh1lsh2_mock_72hr_rep4


title: TDPmed-4, snATAC

description:
Library name: sample 43
10x Genomics Chromium Single Cell Multiome


title: lsh1lsh2_mock_72hr_rep1


title: lsh1lsh2_mock_72hr_rep2


title: Liver_OldRibo_Medium_Long_B2

description: Library name: Liver_OldRibo_Medium_Long_B2

value: Long


title: lsh1lsh2_rhizo_24hr_rep2

value: rhizobia S. meliloti 2011


title: TDPmed-2, snATAC

description:
Library name: sample 41
10x Genomics Chromium Single Cell Multiome


title: lsh1lsh2_mock_24hr_rep4


title: Liver_OldRibo_Slow_Long_B2

description: Library name: Liver_OldRibo_Slow_Long_B2

value: female


title: lsh1lsh2_rhizo_24hr_rep4


title: lsh1lsh2_mock_24hr_rep2


title: MN_OC_48

description: Library name: MN-OC-48_S12_ME_L001_R1_001

value: matched norm

value: Ovarian cancer


title: lsh1lsh2_rhizo_24hr_rep1


title: lsh1lsh2_mock_24hr_rep1

value: mock


title: TDPmed-3, snATAC

description:
Library name: sample 42
10x Genomics Chromium Single Cell Multiome


title: lsh1lsh2_mock_24hr_rep3


title: Liver_NoSelect_Slow_Medium_B1_rep3

description: Library name: Liver_NoSelect_Slow_Medium_B1_rep3

value: No selection

value: Medium

value: Slow


title: TDPneg-6, snATAC

description:
Library name: sample 39
10x Genomics Chromium Single Cell Multiome

value: dorsolateral prefrontal cortex

value: cortical cells

value: C9orf72 HRE


title: TDPmed-1, snATAC

description:
Library name: sample 40
10x Genomics Chromium Single Cell Multiome


title: Liver_OldRibo_Fast_Long_B2

description: Library name: Liver_OldRibo_Fast_Long_B2

value: Fast


title: TDPneg-5, snATAC

description:
Library name: sample 38
10x Genomics Chromium Single Cell Multiome


title: Liver_NoSelect_Slow_Medium_B1_rep2

description: Library name: Liver_NoSelect_Slow_Medium_B1_rep2


title: H1975-TRE-dCa9-KRAB-TRIDENT gRNA2 rep2

city: Boston

first: Jonathan

middle: David

state: MA

address: 3 Blackfan Circle, Rm. 424

institute: BIDMC

description: Library name: KREG10 KD 2 B

data_processing:
Raw sequencing reads were aligned to a reference transcriptome generated from the Ensembl v104 human transcriptome with salmon v1.4.0 using options “--seqBias --useVBOpt --gcBias --posBias --numBootstraps 30 --validateMappings”.
Assembly: hg38
Supplementary files format and content: .sf files from salmon v1.4.0. The columns represent the following: Name: the name of the target transcript provided in the input transcript database (FASTA file). Length: the length of the target transcript in nucleotides. EffectiveLength: the computed effective length of the target transcript. TPM: the estimate of the relative abundance of this transcript in units of Transcripts Per Million (TPM). NumReads: the estimate of the number of reads mapping to each transcript that was quantified.

growth_protocol: H1975-TRE-dCas9-KRAB cells with relevant gRNAs were cultutes in 1X RPMI with 10% Tet-Free FBS (Takara Bio, 1% Pen/Strep, 1mg/ml G418 and 1ug/ml puromycin. Cells were grown in humidified chamber at 37 °C and 5% CO2.

extract_protocol:
Total RNA was extracted using the mirVana Total RNA Isolation kit (Thermo Fisher) as per manufacturers protocol and RNA quality was assessed using TapeStation. RNA with RIN > 9.0 was used for RNAseq library preparation and 1ug of RNA was used.
Libraries were prepared with 1μg of RNA using the KAPA RNA HyperPrep Kit with RiboErase as per manufacturers protocol. Library quality was assessed using TapeStation and quantified by qPCR.

treatment_protocol: Cells wee treated with 4ug/ml of doxycycline to induce expression of dCas9-KRAB

value: non-small cell lung cancer cell lines

value: TRE-dCas9-KRAB-TRIDENT gRNA2

value: doxycycline


title: H1975-TRE-dCa9-KRAB-TRIDENT gRNA1 rep3

description: Library name: KREG10 KD 1 C

value: TRE-dCas9-KRAB-TRIDENT gRNA1


title: H1975-TRE-dCa9-KRAB-TRIDENT gRNA2 rep3

description: Library name: KREG10 KD 2 C


title: H1975-TRE-dCa9-KRAB-TRIDENT gRNA2 rep1

description: Library name: KREG10 KD 2 A


title: TDPneg-4, snATAC

description:
Library name: sample 37
10x Genomics Chromium Single Cell Multiome


title: Liver_NoSelect_Slow_Medium_B1_rep1

description: Library name: Liver_NoSelect_Slow_Medium_B1_rep1

value: Liver


title: TDPneg-3, snATAC

description:
Library name: sample 36
10x Genomics Chromium Single Cell Multiome


title: H1975-TRE-dCa9-KRAB-NTgRNA control rep3

description: Library name: Control C

value: TRE-dCas9-KRAB-NT control


title: Liver_PolyA_Fast_Short_B1

description: Library name: Liver_PolyA_Fast_Short_B1

value: female

value: PolyA selection

value: Short


title: Liver_PolyA_Medium_Short_B1

description: Library name: Liver_PolyA_Medium_Short_B1


title: H1975-TRE-dCa9-KRAB-NTgRNA control rep2

description: Library name: Control B


title: TDPneg-2, snATAC

description:
Library name: sample 35
10x Genomics Chromium Single Cell Multiome


title: Heart_NoSelect_Slow_Medium_B1

description: Library name: Heart_NoSelect_Slow_Medium_B1

source_name: Heart

value: Heart


title: Multiome, TNBC organoid cells, MS177, ATAC

city: Chapel Hill

first: Elizabeth

last: Brunk

state: NC

address: 250 Bell Tower Dr.  4352 Genome Sciences Bldg.

department: Pharmacology, Lineberger Comprehensive Cancer Center, UNC School of Medicine

institute: University of North Carolina at Chapel Hill

description: Library name: TNBC_organoid_MS177_ATAC

data_processing:
Raw FASTQ data was aligned to GRCh38 using Cell Ranger. We kept cells with less than 20% mitochondrial transcript proportions, nucleosome signal less than 2,  TSS.enrichment more than 1, ATAC read counts in the range of 1000-70,000, and RNA read counts in the range of 1000-25,000.
Assembly: GRCh38
Supplementary files format and content: RDS object :Organoid_TNBC_JQ1_MS177_24hr_3_conditions_with_gene_activity_with_cluster_identities_with_doublets_classification_01082025.rds

source_name: Tumor organoid model

extract_protocol:
Cells in single-cell suspension were prepared following the 10X Chromium Single Cell Multiome ATAC + Gene Expression platform protocol.
Library preparation were performed according to manufacturer’s protocols.

treatment_protocol: The TNBC organoid was treated by DMSO or JQ1 or MS177 for 24 hour.

value: Tumor organoid model

value: Organoid model

value: Cancer cell


title: Multiome, TNBC organoid cells, JQ1, GEX

description: Library name: TNBC_organoid_JQ1_RNA


title: Multiome, TNBC organoid cells, control, ATAC

description: Library name: TNBC_organoid_control_ATAC

value: Control


title: H1975-TRE-dCa9-KRAB-NTgRNA control rep1

description: Library name: Control A


title: Multiome, TNBC organoid cells, MS177, GEX

description: Library name: TNBC_organoid_MS177_RNA


title: TDPneg-1, snATAC

description:
Library name: sample 34
10x Genomics Chromium Single Cell Multiome

value: dorsolateral prefrontal cortex

value: cortical cells


title: Multiome, TNBC organoid cells, JQ1, ATAC

description: Library name: TNBC_organoid_JQ1_ATAC


title: Liver_PolyA_Fast_Medium_B1

description: Library name: Liver_PolyA_Fast_Medium_B1

value: Medium

value: Fast


title: Multiome, TNBC organoid cells, control, GEX

description: Library name: TNBC_organoid_control_RNA


title: H1975-TRE-dCa9-KRAB-TRIDENT gRNA1 rep2

description: Library name: KREG10 KD 1 B

value: non-small cell lung cancer cell lines


title: Control-7, snATAC

description:
Library name: sample 33
10x Genomics Chromium Single Cell Multiome

value: WT


title: Liver_PolyA_Medium_Medium_B1

description: Library name: Liver_PolyA_Medium_Medium_B1


title: Control-6, snATAC

description:
Library name: sample 32
10x Genomics Chromium Single Cell Multiome


title: Inhibitor combination experiment

city: Nijmegen

first: Melde

last: Witmond

address: Heyendaalseweg 135

country: Netherlands

institute: Radboud University

description:
Antibody-derived oligonucleotide
DS113_plateA

data_processing:
*library strategy: ID-seq
bcl2fastq conversion v2.16.0.10
Pseudo-alignment of reads to antibody-specific barcodes and well-specific barcodes with kallisto and BUStools
Data normalisation by geometric mean scaling factor
Assembly: Pseudo-alignment to antibody-specific barcodes
Supplementary files format and content: Processed data: Matrix table with raw and normalized counts for every (phospho-)protein for every sample, including detailed target protein information and sample treatment information.
Supplementary files format and content: ID-seq barcode info: Index files used for matching reads to the antibody- and well-specific barcodes.

molecule: protein

source_name: B-cells

growth_protocol: Cells were cultured in RPMI 1640 medium supplemented with 10% (v/v) fetal bovine serum (FBS) and 1% (v/v) penicillin/streptomycin (P/S) at a density of 0.20-2.0*106 cells/mL in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
The immunodetection by sequencing (ID-seq) of fixed cells was based on the work of Van Buggenum et al. (2018)20 with some modifications to optimise the procedure for B-cell lines. Briefly, PFA-fixed cells in 96-well plates (0.25*106 cells/well) were centrifuged for 5 min at 1500 rcf and permeabilised for 10 min in NF water with 100 mM Tris-HCl, 150 mM NaCl and 0.1% Triton X-100 at RT. Samples were then blocked for 30 min at RT with blocking buffer (DPBS with 3% BSA, 20 µg/mL single-stranded salmon sperm DNA, 0.1% Triton X-100, 1/50 FcR blocking reagent). After centrifugation, cells were resuspended in 30 µL staining solution, consisting of 0.15 µg/mL of each DNA-labelled antibody in blocking buffer (see Suppl. Table S1 for all antibody information), and incubated overnight at 4°C. Cells were washed 6x with 3% BSA in DPBS, consisting of 4 wash steps with immediate centrifugation and 2 wash steps with 15 min incubation at RT before centrifugation. At the last wash step, samples were transferred to a new 96-well plate, resuspended in 50 µL release buffer, consisting of 30 mM dithiothreitol (DTT) in 200 mM NaHCO3 (pH 8-9) and incubated for at least 1.5 hours to release the antibody barcodes (Ab barcodes) from the antibodies. Cells were then centrifuged for 5 min at 1500 rcf and the supernatant with the released Ab barcodes was collected.
To prepare ID-seq libraries, well-specific barcodes for each plate were attached to the released Ab barcodes by mixing 9 µL released Ab barcodes with 0.5 µM final concentration well barcode (all complete barcode and primer sequences are listed in Suppl. Table S3, see Suppl. Table S4 for well-specific barcodes) and incubated for 30 min at 25°C. To elongate the annealed well barcodes and Ab barcodes, a polymerase reaction was performed with Klenow Fragment (3´→ 5´ exo-). 1.5 mM dNTP, 0.15 units/µL Klenow Fragment and 7.5 mM MgCl2 (final concentrations) was added per well and incubated for 10 min at 21°C, followed by 60 min at 37°C and a final 10 min at 21°C in a T100 Thermal Cycler (BioRad). All samples were pooled, purified with the Zymo DNA Clean & Concentrator-5 purification kit according to the manufacturer’s protocol and eluted in NF water. The concentration of ID-seq libraries was measured after each purification step with the Qubit dsDNA High Sensitivity Assay kit according to the manufacturer’s protocol. Then, an amplification PCR was performed. One reaction contained approximately 5 ng input DNA, 1x Q5 Reaction Buffer, 200 µM dNTP, 0.5 µM forward primer, 0.5 µM reverse primer, 0.02 units/µL Q5 High-Fidelity DNA polymerase, and NF water (50 µL total volume). The PCR program on a T100 Thermal Cycler (BioRad) consisted of 3 min at 98°C followed by 10 cycles of 15 sec at 98°C, 20 sec at 68°C, and 60 sec at 72°C, and finished with 60 sec at 72°C. The PCR product was purified with the Zymo purification kit and eluted in NF water. An index PCR was performed to attach Illumina sequencing adapters. One reaction contained approximately 4 ng input DNA, 1x KAPA HiFi HotStart Ready mix, 0.3 µM Nextera forward primer (Suppl. Table S3), 0.3 µM unique indexing reverse primer (containing a Nextflex 8bp index, see Suppl. Table S5), and NF water (25 µL total volume). The PCR program on a T100 Thermal Cycler (BioRad) consisted of 45 sec at 98°C followed by 5 cycles of 20 sec at 98°C, 30 sec at 64°C, and 20 sec at 72°C, and finished with 60 sec at 72°C. Finally, the PCR product was purified with the Zymo purification kit and eluted in NF water. ID-seq library sizes and quality were checked on a 2100 BioAnalyzer (Agilent) with the Agilent High Sensitivity DNA kit according to the manufacturer’s protocol. Paired-end sequencing of the ID-seq libraries was performed on an NextSeq500 sequencer (Illumina) with a target sequencing depth of approximately 1500 reads per antibody per sample.

treatment_protocol: Before experiments, cells underwent a medium change to serum-poor medium (RPMI 1640 medium with 2% FBS and 1% P/S) and were allowed to rest for 60 min at 37°C (at 3.3*106 cells/mL). Inhibitors of SYK (R406, referred to as iSYK), BTK (ibrutinib, referred to as iBTK), and NFκB (QNZ, referred to as iNFκB) were dissolved in DMSO. 0.5*10^6 cells per well were distributed in 96-well plates, inhibitors were added at 0, 0.1, 1, 10, 100 µM final concentrations (keeping the DMSO content at 1%), and incubated for 60 min at 37°C with 5% CO2. For combination treatments, the respective combinations of inhibitors were prepared in separate tubes first and then distributed in 96-well plates, keeping the final DMSO content at 1%. Both 0 µM with DMSO and 0 µM with PBS were taken along as controls. Then, the stimulus was added, either PBS or 15 µg/mL F(ab')₂ Fragment Goat Anti-Human IgA + IgG + IgM (H+L) (anti-Ig) + 15 mM hydrogen peroxide (H2O2) final concentrations, and incubated for 20 min at 37°C with 5% CO2. Sample fixation with 4% paraformaldehyde (PFA) was performed for 15 min at room temperature (RT) and was stopped via centrifugation for 5 min at 1500 rcf and resupination in phosphate buffered saline (PBS). Samples were split into two aliquots (0.25*106 cells each) and transferred to 96-well plates to facilitate measurements with both phospho flow cytometry and immunodetection by sequencing (ID-seq).

value: B-cells

value: Inhibitor combination experiment


title: Liver_PolyA_Slow_Short_B1

description: Library name: Liver_PolyA_Slow_Short_B1

value: Liver

value: Slow


title: H1975-TRE-dCa9-KRAB-TRIDENT gRNA1 rep1

description: Library name: KREG10 KD 1 A

value: TRE-dCas9-KRAB-TRIDENT gRNA1

value: doxycycline


title: Inhibitor dose experiment, active signaling

description:
Antibody-derived oligonucleotide
DS108_data_processed.csv
DS018_plateB

value: Inhibitor dose experiment


title: Control-5, snATAC

description:
Library name: sample 31
10x Genomics Chromium Single Cell Multiome


title: Control-4, snATAC

description:
Library name: sample 30
10x Genomics Chromium Single Cell Multiome


title: Inhibitor dose experiment, basal signaling

description:
Antibody-derived oligonucleotide
DS108_data_processed.csv
DS108_plateA


title: RAID_veh1-12_gp13-24

city: Utrecht

first: Frank

last: Riemers

address: Uppsalalaan 8

institute: Utrecht University

description:
Mixed-sample-RAID
SORT-seq

data_processing:
Paired end reads obtained by automated CEL-seq2 were aligned to the transcriptome using bwa with default parameters.
The mapped reads were counted using STAR. Reads mapping to multiple loci were discarded.
Read counts were processed and analyzed using the Seurat package
Assembly: hg38
Supplementary files format and content: Tab-separated counts per plate

source_name: RPE

extract_protocol:
Cells were collected by trypsinization, washed with PBS after which the RAID cells were fixed with 0.5mM dithiobis(succinimidyl propionate)(DSP) in Sodium Phosphate buffered Saine (pH 8.4) for 45 minutes at room temperature at a concentration of 1 million cells per 2.5ml. Next, DSP was neutralized by incubating the cells with quench buffer (100mM Tris, pH 7.5, 150mM NaCl) for 10 minutes and cell clumps were removed usmg a 70µm cell strainer. Cells were icubated for 30 minutes with BP buffer (PFBB:PBS, 1:1, supplemented with 0.1% Triton•X-100 and 2 U/mL RNAsin plus) to permeabilize the cells, after which samples were incubated overnight with antibodies in BP buffer. Samples were filtered using a 40 um cell strainer and incubated with DAPI (0.2 ug/mL) prior to loading of samples on the flow cytometer. Fresh cells were directly loaded on the flow cytometry. For both fresh and fixed cells, Geminin1-110-expressing cells were selected and sorted into the captuture plates on a BD Influx cell sorter. The reducing agent already present in the capture plates was sufficient to decrosslink the RAID fixed cells prior to single cell RNA sequencing.
Single Cell Discoveries, where single-cell RNA sequencing was performed according to the SORT-seq protocol. Cells were heat-lysed at 65° C followed by cDNA synthesis. After second-strand cDNA synthesis, all the barcoded material from one plate was pooled into one library and amplified using in vitro transcription (IVT). Following amplification, library preparation was done following the CEL-Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers (Illumina). The DNA library was paired-end sequenced on an Illumina Nextseq™ 500, high output, with a 1x75 bp Illumina kit. CELSeq 2, CB: 8bp, UMI: 6bp R1 starts with a 6bp UMI  followed by a 8bp cell barcode. R2 ends with a 6bp random primer.

treatment_protocol: 2 conditions were employed in this experiment: RPE_veh received no doxycycline and no gemcitabine/prexasertib, RPE_gp received no doxycycline and 4 nM gemcitabine/10 nM Prexasertib for 16 hours. For each condition, cells were either freshly sorted (fresh) or sorted after reversible fixing and intracellular staining (RAID).

value: RPE

value: TetOn HRAS G12V

value: RAID / veh


title: Liver_PolyA_Fast_Long_B1

description: Library name: Liver_PolyA_Fast_Long_B1

value: female

value: PolyA selection

value: Long


title: RPE_dox_gp replicate3

description: SORT-seq

extract_protocol:
Cells were collected by trypsinization, washed with PBS after which cells were fixed with 0.5mM dithiobis(succinimidyl propionate)(DSP) in Sodium Phosphate buffered Saine (pH 8.4) for 45 minutes at room temperature at a concentration of 1 million cells per 2.5ml. Next, DSP was neutralized by incubating the cells with quench buffer (100mM Tris, pH 7.5, 150mM NaCl) for 10 minutes and cell clumps were removed usmg a 70µm cell strainer. Cells were icubated for 30 minutes with BP buffer (PFBB:PBS, 1:1, supplemented with 0.1% Triton•X-100 and 2 U/mL RNAsin plus) to permeabilize the cells, after which samples were incubated overnight with antibodies in BP buffer. Samples were filtered using a 40 um cell strainer and incubated with DAPI (0.2 ug/mL) prior to loading of samples on the flow cytometer.  Cells were sorter into the captuture plates on a BD Influx cell sorter.
Single Cell Discoveries, where single-cell RNA sequencing was performed according to the SORT-seq protocol. Cells were heat-lysed at 65° C followed by cDNA synthesis. After second-strand cDNA synthesis, all the barcoded material from one plate was pooled into one library and amplified using in vitro transcription (IVT). Following amplification, library preparation was done following the CEL-Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers (Illumina). The DNA library was paired-end sequenced on an Illumina Nextseq™ 500, high output, with a 1x75 bp Illumina kit

treatment_protocol: 4 conditions were employed in this experiment: RPE_veh_control received no doxycycline and no gemcitabine/prexasertib, RPE_dox_control received 0.2 ug/mL doxycycline for 24 hours and no gemictabine/perxasertib, RPE_veh_gp received no doxycycline and 4 nM gemcitabine/10 nM Prexasertib for 16 hours, and RPE_dox_gp received 0.2 ug/mL doxycycline for 24 hours followed by 4 nM gemcitabine/10 nM prexasertib for 16 hours. REP_veh_control and RPE_dox_control were sorted into one 384 well plate each, while RPE_veh_gp and RPE_dox_gp were sorted into 3 384-well plates each.


title: Liver_PolyA_Medium_Long_B1

description: Library name: Liver_PolyA_Medium_Long_B1

value: Medium


title: RPE_dox_gp replicate2

description: SORT-seq


title: RPE_dox_gp replicate1

description: SORT-seq


title: Control-3, snATAC

description:
Library name: sample 29
10x Genomics Chromium Single Cell Multiome

value: dorsolateral prefrontal cortex

value: cortical cells


title: Control-2, snATAC

description:
Library name: sample 28
10x Genomics Chromium Single Cell Multiome

value: WT


title: RPE_control_gp replicate3

description: SORT-seq


title: RPE_control_gp replicate1

description: SORT-seq


title: Liver_PolyA_Slow_Long_B1

description: Library name: Liver_PolyA_Slow_Long_B1


title: RPE_control_gp replicate2

description: SORT-seq