title: Jurkat cells, sgRELA, Day 7, biol rep 2, library rep 2

city: Shinjuku-ku

first: Kazuyoshi

last: Ishigaki

state: Tokyo

address: 9N3 Center for Integrated Medical Research, 35 Shinanomachi

department: Department of Microbiology and Immunology

institute: Keio University

description:
Library name: sample35
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0017A1_02

data_processing:
Paired-end sequence reads were trimmed to remove Nextera/Tn5 adapter sequences (CTGTCTCTTATA) using cutadapt (v1.18) with a minimum length cutoff of 20 bp.
Trimmed reads were aligned to the human reference genome GRCh38 with GENCODE v47 annotation using STAR (v2.7.9a).
Gene-level read counts were quantified using RNA-SeQC 2 (v2.4.2) with the GENCODE v47 GTF.
Assembly: GRCh38 (GENCODE v47)
Supplementary files format and content: A tab-delimited gene-level count matrix in which rows correspond to genes (GENCODE v47 gene IDs) and columns correspond to samples; values represent raw read counts. Gene IDs are GENCODE v47 Ensembl gene IDs with version suffixes removed.

source_name: Jurkat-dCas9-VP64 (CRISPRa stable line)

growth_protocol: Jurkat cells stably expressing dCas9-VP64 were maintained in RPMI medium supplemented with 10% fetal bovine serum and sodium pyruvate at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
For each sample, total RNA was extracted from 3x10^5 cells using the MagMAX mirVana Total RNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions.
RamDA-seq libraries were prepared from 100 pg of total RNA per sample according to the published RamDA-seq protocol. The resulting cDNA libraries were indexed, pooled, and sequenced on an Illumina platform to generate paired-end reads.

treatment_protocol: Jurkat-dCas9-VP64 cells were transduced with pXPR-based lentiviral guide RNA expression vectors encoding either a single guide RNA targeting RELA (sgRELA) or a control guide RNA (sgControl) for CRISPRa-mediated gene activation. After transduction, cells were selected with puromycin for 3 days to enrich for sgRNA-transduced cells. Transductions were performed in triplicate for each condition. Cells were harvested at five, six, and seven days post-transduction.

value: Jurkat-dCas9-VP64 (CRISPRa stable line)

value: T lymphocyte

value: dCas9-VP64 (CRISPRa); mCherry+

tag: sgrna

value: RELA

tag: time

value: Day 7

tag: biological replicate

tag: technical replicate


title: Jurkat cells, sgRELA, Day 7, biol rep 3, library rep 2

status: Public on Jun 29 2026

type: SRA

country: Japan

description:
Library name: sample36
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0018A1_02

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype


title: TGFB1 2

city: Cambridge

first: Simon

last: Koplev

address: Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Puddicombe Way

department: Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

description: Library name: Sample:38

data_processing:
Resulting .fastq raw files were quality checked using FASTQC v. 0.11.9 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and MULTIQC v. 1.14. (https://github.com/MultiQC/MultiQC), before quantification using KALLISTO (https://github.com/pachterlab/kallisto) v. 0.48.0 with default settings. Processing of raw files was run in a Python virtual (v. 3.10.8) environment using CGATcore v. 12.2.0 pipeline framework (https://doi.org/10.12688/f1000research.18674.2).
Assembly: hg38
Supplementary files format and content: matrix of kallisto unnormalised counts for all samples (.csv)

source_name: intestine

growth_protocol: The Ccd-18Co colon fibroblast cell line was obtained from ATCC (#CRL-1459) up to passage 20. Ccd-18Co were maintained and expanded and maintained in full growth medium (MEM-alpha Sigma #12571063), Penicillin-Streptomycin (Thermo # 15140148) and 20% FBS (Thermo #A5209501). For experiments, fibroblast cultures were seeded at 25,000 cells in 200ul full growth medium in 48-well format tissue culture plates, unless stated otherwise.

extract_protocol:
RNA was isolated using the Qiagen RNeasey Mini kit (Qiagen #74104) or Zymo Quick-RNA 96 kits (ZymoResearch #R-1052) with the optional on-column DNA digestion step. Isolates from cell cultures were prepared by direct lysis in RNA lysis buffer, followed by RNA isolation with the Zymo RNA extraction kits including on-column DNase treatment. Isolated RNA was stored at –80C until further processing or shipped to service providers.
Libraries were prepared according to manufacturer's instructions, using NEBNext Ultra II RNA Library Prep Kit for Illumnia. Resulting libraries were sequenced on an Illumina NovaSeq6000.

treatment_protocol: Ccd-18Co were seeded at 25,000 cells in 200ul of full growth medium in 48-well format tissue culture plates. After attachment, cells were stimulated with cytokines in serum-free medium (10ng/ml for each cytokine, except IL-1B 0.1ng/ml). Cellular extracts were prepared immediately after stimulation period.

tag: tissue

value: intestine

value: fibroblast


title: clone59_3

city: Klosterneuburg

first: Florian

middle: M

last: Pauler

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria (IST Austria)

description:
Library name: 366685
SMART-Seq v3

library_source: transcriptomic single cell

data_processing:
Alignment was performed using STAR (v.2.7.9a) on GRCm39 and Gencode vM27 with STAR parameters: --outFilterMultimapNmax 1, --outSAMstrandField intronMotif, --outFilterIntronMotifs RemoveNoncanonical, --outFilterScoreMinOverLread 0.22, --outFilterMatchNminOverLread 0.22. Note that we only used the R2 reads from paired end sequencing for this analysis. Reads in exonic and intronic regions (Gencode vM27) were counted using the aligned bam files produced by STAR and summarizeOverlaps (GenomicAlignments v1.40.0, R v4.4.0) with singleEnd=TRUE, mode = "IntersectionNotEmpty", ignore.strand = T, inter.feature = T parameters.
Assembly: GRCm39
Supplementary files format and content: Matrix in csv format with columns corresponding to cells and rows to genes. One file for exonic and one file for intronic reads is given.

organism: Mus musculus

source_name: cerebral organoid

growth_protocol: mESCs were plated at high density so that colonies covered approximately half of the well area after 2 days of incubation. Medium was changed 1-2 hours prior to dissociation with StemPro Accutase (Thermo Fisher Scientific) or CTS TrypLE (Thermo Fisher Scientific) for 5 min at 37°C. Cells were counted with an automated cell counter, and were only used if >90% of cells were alive based on Trypan blue staining (Thermo Fisher Scientific). mESCs were centrifuged for 5 min at 200 x g, resuspended in Solution 1, and plated at a density of 3500 cells/microwell in a 24w-Aggrewell plate (Stem Cell Technologies). Solution 1 contained G-MEM (Thermo Fisher Scientific), 10% knockout serum replacement (Thermo Fisher Scientific), 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 2 mM GlutaMAX, 50 U/ml Penicillin/Streptomycin and WNT inhibitor (3 µM, IWR1, Sigma). No SMAD inhibitors were used as they were not required to direct cortical differentiation in mouse. Embryoid bodies were generated by day (D) 1, which were then transferred to 10 cm dishes with fresh Solution 1 and 2% growth factor-reduced Matrigel (Corning). On D5, organoids were gently pipetted to remove Matrigel and Solution 2 was added, containing DMEM/F12 (Thermo Fisher Scientific), 1% N2 supplement (Thermo Fisher Scientific), 0.1 mM non-essential amino acids, 2 mM GlutaMAX, 50 U/ml Penicillin/Streptomycin, 1% chemically defined lipid concentrate (Thermo Fisher Scientific), and heparin (1 mg/ml; Sigma). On D7, organoids were transferred to 6-well plates and placed on an orbital shaker at low speed (50 r.p.m.) to prevent organoid fusion. From D9, organoids were grown in medium containing a 50:50 mix of DMEM/F12 and Neurobasal (Thermo Fisher Scientific), 0.5% N2, 1% B27 (Thermo Fisher Scientific), 0.5 mM non-essential amino acids, 2 mM GlutaMAX, 50 U/ml pen/strep, 1% chemically defined lipid concentrate, and 50 mM 2-mercaptoethanol. Throughout the protocol medium was replaced as necessary every 2-3 days, and orbital shaker speed was increased after D9 (80 r.p.m.). Fused organoids and/or organoids that failed to grow were discarded throughout the procedure. Standard cell culture conditions (37°C with 5% CO2) were applied throughout all procedures.

extract_protocol:
Organoids with MADM clones induced at D13 were collected at D20 for MADM-CloneSeq. The sample collection steps for MADM-CloneSeq were adapted from previously published protocols (PMID: 38968076). Organoids were kept in cell culture membrane (Millicell) in oxygenated (95% O2, 5% CO2) artificial cerebrospinal fluid (ACSF) containing (in mM): 118 NaCl, 2.5 KCl, 1.25 NaH2PO4, 1.5 MgSO4, 1 CaCl2, 10 Glucose, 3 Myo-inositol, 30 Sucrose, 30 NaHCO3 prepared   with ultra-distilled water; pH=7.4, at 35C, until sample collection. All work surface and equipment were cleaned using RNase away solution (Thermo Fisher Scientific) prior to experiments. Single organoids were transferred to a LNscope 240XY miscroscope (Luigs & Neumann) and superfused with ACSF at a rate of 0.5 ml/min at room temperature. Individual clones were visualized under a 20x objective and by using ImageJ software. To observe red or green fluorescence, light was emitted from a LED light source (CoolLED, Andover, UK). Glass pipettes (B150-86-10, Sutter Instrument, Novato, CA) previously autoclaved, were pulled using a P-1000 pipette puller (Sutter Instrument) to generate pipettes with an opening of around 3-5ym. Before use, each pipette was filled with 3.5yl of pipette solution which consisted of RNase inhibitor (Takara, 1.95%) in RNase-free PBS (Invitrogen) filtered through a 0.22mm filter. Red or green fluorescent neurons were approached with the pipette under positive pressure to avoid tissue contamination of the pipette tip. When contact with cell membrane was made, tight seal formation was achieved under IR/DIC visualization. The complete aspiration of the cell body was immediately performed by applying a gentle and steady suction while monitoring under fluorescence and typically takes 5-10 s. The negative pressure was removed immediately once the target cell was collected and the pipette was carefully withdrawn from the acute slice to avoid contamination. The content of each pipette was directly transferred into individual PCR tubes and kept at -80C until cDNA library preparation.
cDNA libraries for individual MADM-CloneSeq cells were were prepared using Smart-seq3 protocol (PMID 32518404) in 3 batches (96well plates).

treatment_protocol: Stock solutions of 4-hydroxytamoxifen (4-OHT, Sigma) were generated by dilution in 100% ethanol to a concentration 1000-fold greater (20-80 µM) than the working solution. A concentration of 60 nM 4-OHT was used for D13. If 4-OHT treatment occurred on a day without medium change, medium was removed from wells containing organoids to be treated and placed in a tube, 4-OHT was added, and medium was added back to wells. After 24 h, medium was completely replaced and organoids were washed 1x with PBS.

value: cerebral organoid

tag: plate

tag: cloneid

tag: color

value: G

tag: clone type

value: N

tag: clone size


title: Jurkat cells, sgRELA, Day 7, biol rep 1, library rep 2

description:
Library name: sample34
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0016A1_02


title: IFNG 4

description: Library name: Sample:36


title: IFNG 3

description: Library name: Sample:35


title: clone59_2

description:
Library name: 366684
SMART-Seq v3


title: clone59_1

description:
Library name: 366683
SMART-Seq v3


title: Jurkat cells, sgControl, Day 7, biol rep 3, library rep 2

description:
Library name: sample33
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0015A1_02

value: non-targeting


title: Jurkat cells, sgControl, Day 7, biol rep 2, library rep 2

description:
Library name: sample32
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0014A1_02


title: IFNA 4

description: Library name: Sample:32


title: IFNA 3

description: Library name: Sample:31


title: Jurkat cells, sgControl, Day 7, biol rep 1, library rep 2

description:
Library name: sample31
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0013A1_02


title: clone58_3

description:
Library name: 366681
SMART-Seq v3


title: IFNA 1

description: Library name: Sample:29


title: IL22 4

description: Library name: Sample:28


title: clone58_2

description:
Library name: 366680
SMART-Seq v3


title: Jurkat cells, sgRELA, Day 6, biol rep 2, library rep 2

description:
Library name: sample29
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0011A1_02

value: Day 6


title: IL22 3

description: Library name: Sample:27


title: IL22 2

description: Library name: Sample:26


title: clone58_1

description:
Library name: 366679
SMART-Seq v3

value: R


title: IL22 1

description: Library name: Sample:25


title: Jurkat cells, sgRELA, Day 6, biol rep 1, library rep 2

description:
Library name: sample28
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0010A1_02


title: IL17A 4

description: Library name: Sample:24


title: IL17A 3

description: Library name: Sample:23


title: Jurkat cells, sgControl, Day 6, biol rep 3, library rep 2

description:
Library name: sample27
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0009A1_02


title: IL17A 2

description: Library name: Sample:22


title: IL17A 1

description: Library name: Sample:21


title: Jurkat cells, sgControl, Day 6, biol rep 2, library rep 2

description:
Library name: sample26
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0008A1_02


title: IL13 4

description: Library name: Sample:20


title: clone57_3

description:
Library name: 366676
SMART-Seq v3


title: IL13 3

description: Library name: Sample:19


title: IL13 2

description: Library name: Sample:18


title: clone57_2

description:
Library name: 366675
SMART-Seq v3


title: Jurkat cells, sgRELA, Day 5, biol rep 3, library rep 2

description:
Library name: sample24
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0006A1_02

value: Day 5


title: IL6 4

description: Library name: Sample:16


title: IL6 3

description: Library name: Sample:15


title: Jurkat cells, sgRELA, Day 5, biol rep 2, library rep 2

description:
Library name: sample23
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0005A1_02


title: IL6 1

description: Library name: Sample:13


title: Jurkat cells, sgRELA, Day 5, biol rep 1, library rep 2

description:
Library name: sample22
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0004A1_02


title: IL1B 4

description: Library name: Sample:12


title: clone56_1

description:
Library name: 366672
SMART-Seq v3

value: SN


title: IL1B 3

description: Library name: Sample:11


title: Jurkat cells, sgControl, Day 5, biol rep 3, library rep 2

description:
Library name: sample21
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0003A1_02


title: IL1B 2

description: Library name: Sample:10


title: clone55_3

description:
Library name: 366671
SMART-Seq v3


title: IL1B 1

description: Library name: Sample:9


title: Jurkat cells, sgControl, Day 5, biol rep 2, library rep 2

description:
Library name: sample20
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0002A1_02


title: Jurkat cells, sgControl, Day 5, biol rep 1, library rep 2

description:
Library name: sample19
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0001A1_02


title: unstimulated 3.

description: Library name: Sample:3


title: unstimulated 2.

description: Library name: Sample:2


title: clone55_1

description:
Library name: 366669
SMART-Seq v3


title: unstimulated 1.

description: Library name: Sample:1


title: Jurkat cells, sgRELA, Day 7, biol rep 3, library rep 1

description:
Library name: sample18
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0018A1_01


title: stimulated_DMSO 6

description: Library name: Sample 18

library_source: genomic

data_processing:
Paired-end ATAC-seq data were processed with the ENCODE ATAC-seq pipeline v2.2.3 (https://github.com/ENCODE-DCC/atac-seq-pipeline), including adaptor trimming, alignment to hg38, with cross-correlation analysis enabled, and peak calling with MACS2. Based on the csaw_workflow (https://github.com/reskejak/ATAC-seq), consensus peak sets were assembled across condition with GRanges from narrowPeak files filtered for 300k peaks and p<0.01. Peaks were then counted using csaw v1.32.0 with maximum fragment length of 1,000 excluding peaks overlapping with blacklist_hg38_unified, resulting in 334,857 consensus peaks across 18 samples and 3 conditions. Peaks were further filtered for low abundance at log2CPM > -3. Normalization factors for background correction at 10k bp bins were computed with the trimmed mean method. Adjacent peaks were then merged within 500bp up to a maximum of 5kb consecutive peaks. The resulting peaks were annotated with ChIPseeker v1.34.1 according to the TxDb.Hsapiens.UCSC.hg38.knownGene genome database.
Assembly: TxDb.Hsapiens.UCSC.hg38.knownGene
Supplementary files format and content: Paired-end ATAC-seq data were processed with the ENCODE ATAC-seq pipeline v2.2.3 (https://github.com/ENCODE-DCC/atac-seq-pipeline), including adaptor trimming, alignment to hg38, with cross-correlation analysis enabled, and peak calling with MACS2.

molecule: genomic DNA

extract_protocol:
For chromatin accessibility profiling of bulk cell populations (Ccd18-Co intestinal fibroblasts), the Omni-ATAC protocol was followed for nuclei isolation and library preparation was followed. Briefly, fibroblasts were collected by trypsin-based detachment and pelleted by centrifugation. After confirming viability of > 95% (Trypan blue hemacytometer), nuclei were isolated by incubating cells for 3 minutes on ice in nuclei isolation buffer containing 0.1% NP-40, 0.1% Tween20 and 0.01% Digitonin. Following washes, nuclei were transposed (Illumina Nextera Tn5 transposase contained in #FC-121-1030) for 30minutes at 37C with 1000rpm mixing.
Transposed DNA fragments were isolated using Qiagen MinElute PCR Purification Kit (#28004) and pre-amplified for 5 cycles using NEBNext High Fidelity 2x PCR Master Mix (#M0541) and Illumina Nextera primers (#FC-121-1030). At this stage, the additionally required amplification cycles were determined by SYBR green (Invitrogen #S7563) based quantitative PCR. After amplification for additional cycles (between 3-6), amplified DNA was cleaned up using Qiagen MinElute kit and quantified using KAPA absolute quantification kit (Roche #07960166001). Resulting libraries were quality-controlled on an Agilent TapeStation 4200 using High Sensitivity DNA Screen Tape analysis D1000 (Agilent #5067-5584). Libraries were then pooled and size selected using Ampure XP beads (Beckman # A63880), before re-quantification by TapeStation and adjustment to 2.8 pM and sequencing on an Illumina NextSeq500.

treatment_protocol: Ccd-18Co were seeded at 25,000 cells in 200ul of full growth medium in 48-well format tissue culture plates. After attachment, cells were subjected to three pulses (1 pulse: 72h of cytokines in serum-free medium followed by 96h of recovery in full growth medium) of cytokine cocktail (TNF, OSM and IL-17A at 10ng/ml each; IL-1B at 0.1 ng/ml) stimulations. After a resting period of 1 week, Ccd-18Co were subjected to DMSO or 250nM Belinostat, each diluted 1:5000 in serum-free medium for a total of 5 days. After the 5 days, cells were returned to full growth medium. Cell extracts for ATACseq were prepared 2 weeks after the final epigenetic modulator treatment.


title: stimulated_DMSO 5

description: Library name: Sample 17


title: clone54_2

description:
Library name: 366668
SMART-Seq v3


title: Jurkat cells, sgRELA, Day 7, biol rep 2, library rep 1

description:
Library name: sample17
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0017A1_01


title: clone54_1

description:
Library name: 366667
SMART-Seq v3


title: stimulated_DMSO 3

description: Library name: Sample 15


title: Jurkat cells, sgRELA, Day 7, biol rep 1, library rep 1

description:
Library name: sample16
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0016A1_01


title: clone55_2

description:
Library name: 366670
SMART-Seq v3


title: clone53_2

description:
Library name: 366666
SMART-Seq v3


title: stimulated_DMSO 1

description: Library name: Sample 13


title: Jurkat cells, sgControl, Day 7, biol rep 3, library rep 1

description:
Library name: sample15
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0015A1_01


title: stimulated_Belinostat 6

description: Library name: Sample 12


title: clone53_1

description:
Library name: 366665
SMART-Seq v3


title: stimulated_Belinostat 5

description: Library name: Sample 11


title: TNF 4

description: Library name: Sample:44


title: stimulated_DMSO 4

description: Library name: Sample 16


title: Jurkat cells, sgControl, Day 7, biol rep 2, library rep 1

description:
Library name: sample14
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0014A1_01


title: stimulated_Belinostat 4

description: Library name: Sample 10


title: TGFB1 1

description: Library name: Sample:37


title: clone52_3

description:
Library name: 366664
SMART-Seq v3


title: stimulated_Belinostat 3

description: Library name: Sample 9


title: IFNG 2

description: Library name: Sample:34


title: clone58_4

description:
Library name: 366682
SMART-Seq v3


title: IFNG 1

description: Library name: Sample:33


title: Jurkat cells, sgControl, Day 7, biol rep 1, library rep 1

description:
Library name: sample13
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0013A1_01


title: IFNA 2

description: Library name: Sample:30


title: stimulated_DMSO 2

description: Library name: Sample 14


title: stimulated_Belinostat 2

description: Library name: Sample 8


title: clone52_2

description:
Library name: 366663
SMART-Seq v3


title: Jurkat cells, sgRELA, Day 6, biol rep 3, library rep 2

description:
Library name: sample30
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0012A1_02


title: stimulated_Belinostat 1

description: Library name: Sample 7


title: Jurkat cells, sgRELA, Day 6, biol rep 3, library rep 1

description:
Library name: sample12
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0012A1_01


title: clone52_1

description:
Library name: 366662
SMART-Seq v3


title: unstimulated 5

description: Library name: Sample 5


title: unstimulated 6

description: Library name: Sample 6


title: clone57_5

description:
Library name: 366678
SMART-Seq v3


title: Jurkat cells, sgRELA, Day 6, biol rep 2, library rep 1

description:
Library name: sample11
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0011A1_01


title: unstimulated 4

description: Library name: Sample 4


title: clone57_4

description:
Library name: 366677
SMART-Seq v3


title: clone51_2

description:
Library name: 366661
SMART-Seq v3


title: unstimulated 3

description: Library name: Sample 3


title: clone51_1

description:
Library name: 366660
SMART-Seq v3


title: unstimulated 1

description: Library name: Sample 1


title: unstimulated 2

description: Library name: Sample 2


title: Jurkat cells, sgRELA, Day 6, biol rep 1, library rep 1

description:
Library name: sample10
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0010A1_01


title: Jurkat cells, sgControl, Day 6, biol rep 1, library rep 2

description:
Library name: sample25
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0007A1_02


title: Jurkat cells, sgControl, Day 6, biol rep 3, library rep 1

description:
Library name: sample9
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0009A1_01


title: clone50_4

description:
Library name: 366659
SMART-Seq v3


title: ∆SARS2+SARS2-1xFLAG, no dox, 9 days, rep3

city: Ann Arbor

first: Christina

last: Del Greco

state: MI

address: 1241 Catherine Street

country: USA

institute: University of Michigan

description: Library name: 8962-CDG-18

data_processing:
AGC used BCL Convert Conversion Software v4.0 (Illumina) was used to generate de-multiplexed Fastq files
AGC trimmed reads using Cutadapt v2.3
Reads were aligned to reference genome GRch38 using HISAT2 and samtools to generate .bam files
Counts were obtained using subread featureCounts using grch38 annotations
Differential expression values were calculated using DESeq2
Assembly: GRch38
Supplementary files format and content: tab-delimited text file includes counts for each sample obtained using featureCounts
Supplementary files format and content: excel files containing differential expression fold changes, significance values, and counts for experimental vs control samples

growth_protocol: cells were cultured in IMDM media under standard cell culture conditions

extract_protocol:
RNA was harvested using Trizol/chloroform and the Rneasy Mini Kit (Qiagen)
Libraries were constructed by the University of Michigan Advanced Genomics Core (AGC) using 151-bp paired-end sequencing library preparation as described in the manufacturer's protocol (Illumina NovaSeq)

treatment_protocol: cells were grown with continuous 15ng/mL doxycycline until doxycycline removal for experimental conditions

tag: treatment

value: No dox


title: ∆SARS2+SARS2-1xFLAG, no dox, 9 days, rep2

description: Library name: 8962-CDG-17


title: Jurkat cells, sgControl, Day 6, biol rep 2, library rep 1

description:
Library name: sample8
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0008A1_01


title: ∆SARS2+SARS2-1xFLAG, no dox, 9 days, rep1

description: Library name: 8962-CDG-16


title: IL13 1

description: Library name: Sample:17


title: Jurkat cells, sgControl, Day 6, biol rep 1, library rep 1

description:
Library name: sample7
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0007A1_01


title: ∆SARS2+SARS2-1xFLAG, no dox, 6 days, rep3

description: Library name: 8962-CDG-15


title: clone50_3

description:
Library name: 366658
SMART-Seq v3


title: ∆SARS2+SARS2-1xFLAG, no dox, 6 days, rep2

description: Library name: 8962-CDG-14


title: Jurkat cells, sgRELA, Day 5, biol rep 3, library rep 1

description:
Library name: sample6
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0006A1_01


title: ∆SARS2+SARS2-1xFLAG, no dox, 6 days, rep1

description: Library name: 8962-CDG-13


title: clone50_2

description:
Library name: 366657
SMART-Seq v3


title: IL6 2

description: Library name: Sample:14


title: ∆SARS2+SARS2-1xFLAG, no dox, 3 days, rep3

description: Library name: 8962-CDG-12


title: clone57_1

description:
Library name: 366674
SMART-Seq v3


title: clone50_1

description:
Library name: 366656
SMART-Seq v3


title: ∆SARS2+SARS2-1xFLAG, no dox, 3 days, rep2

description: Library name: 8962-CDG-11


title: clone49_5

description:
Library name: 366655
SMART-Seq v3


title: ∆SARS2+SARS2-1xFLAG, no dox, 3 days, rep1

description: Library name: 8962-CDG-10


title: Jurkat cells, sgRELA, Day 5, biol rep 1, library rep 1

description:
Library name: sample4
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0004A1_01


title: ∆SARS2+SARS2-1xFLAG, plus dox, rep2

description: Library name: 8962-CDG-8

value: Plus dox


title: ∆SARS2+SARS2-1xFLAG, plus dox, rep1

description: Library name: 8962-CDG-7


title: Hap1, plus dox, rep2

description: Library name: 8962-CDG-5

value: Unmodified parental


title: Jurkat cells, sgControl, Day 5, biol rep 3, library rep 1

description:
Library name: sample3
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0003A1_01

value: Jurkat-dCas9-VP64 (CRISPRa stable line)

value: T lymphocyte


title: Jurkat cells, sgControl, Day 5, biol rep 2, library rep 1

description:
Library name: sample2
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0002A1_01

value: dCas9-VP64 (CRISPRa); mCherry+


title: clone49_3

description:
Library name: 366653
SMART-Seq v3


title: Hap1, plus dox, rep1

description: Library name: 8962-CDG-4


title: clone49_2

description:
Library name: 366652
SMART-Seq v3


title: Jurkat cells, sgControl, Day 5, biol rep 1, library rep 1

description:
Library name: sample1
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0001A1_01


title: clone49_1

description:
Library name: 366651
SMART-Seq v3


title: Hap1, no dox, rep1

description: Library name: 8962-CDG-1


title: hiPSC-derived microglia, tri-culture, rep4

city: STANFORD

first: Takeshi

last: Uenaka

state: California

address: 265 Campus Drive G3145, SIM1 Bldg - 3rd floor

institute: Stanford University

description: Library name: Tri_4

data_processing:
Processed data files were generated from raw RNA-seq reads as follows. Reads were processed from FASTQ files and aligned to the human reference genome GRCh38 using HISAT2 version 2.1.0 with the following key parameters: default parameters. Gene annotation from Ensembl release 115 GTF was used for quantification.
Gene-level abundance was quantified using featureCounts version 2.12.3. Counting was performed in paired-end mode with unstranded settings. Reads were quantified using an exon-based approach, and exon-level counts were summarized to gene-level counts using gene_id from the annotation file.
The file `RNA_Triculture_Monoculture_Rawdata.csv` contains the resulting gene-level raw count matrix. The file `RNA_Triculture_Monoculture_TPMnormalization.csv` contains the corresponding TPM-normalized expression matrix. TPM values were calculated from FPKM values, using the formula: TPM_i = (FPKM_i / sum(FPKM_j)) * 10^6 (where FPKM_i is the FPKM of gene i and sum(FPKM_j) is the sum of all FPKM values in the sample), with gene lengths defined as the sum of non-overlapping exon lengths for each specific gene.
No additional filtering was applied to the processed matrices prior to deposition.
Assembly: GRCh38 (human), using the primary assembly reference sequence: Homo_sapiens.GRCh38.dna.primary_assembly.fa
Supplementary files format and content: File name: RNA_Triculture_Monoculture_Rawdata.csv, Format: CSV, Content: Gene-level raw count matrix. Rows represent Ensembl gene IDs. Columns represent 8 bulk RNA-seq samples (Mono_1–Mono_4 and Tri_1–Tri_4). Values represent raw read counts per gene per sample.
Supplementary files format and content: File name: RNA_Triculture_Monoculture_TPMnormalization.csv Format: CSV Content: Gene-level TPM-normalized expression matrix. Rows represent Ensembl gene IDs. Columns represent 8 bulk RNA-seq samples (Mono_1–Mono_4 and Tri_1–Tri_4). Values represent TPM-normalized expression values per gene per sample.

source_name: iPSC-derived microglia

extract_protocol:
GFP-labeled microglia from mono-culture and tri-culture conditions were isolated by FACS directly into tubes containing TRIzol LS and stored at −80°C until RNA extraction. Four independent batches of samples were processed in parallel, and RNA was extracted using the RNeasy MinElute Cleanup Kit (Qiagen) according to the manufacturer’s protocol.
Total RNA samples were submitted to Novogene, where RNA-seq libraries were prepared.

treatment_protocol: Microglial mono-cultures were supplemented with IL-34 and M-CSF at final concentrations of 100 ng/mL and 10 ng/mL, respectively, three times per week. Tri-cultures were maintained without exogenous cytokines, with medium changes performed three times per week. Cultures were harvested two weeks after microglial plating.

value: iPSC-derived microglia

value: Human Embryonic Stem Cells

tag: batch


title: GSC20 vector control rep B

city: Los Angeles

first: Aram

last: Modrek

state: Ca

address: 1441 EastLake Ave

institute: USC

description: Library name: control_B

data_processing:
For data processing, adapters along with low-quality bases were trimmed using Trimmomatic. The resulting reads were aligned to the human reference genome (hg38) with STAR, and additional alignments were performed against other species and common contaminants for quality control. Normalized genome browser tracks were generated to visualize coverage, and the 5′/3′ bias was assessed with Picard. Gene-level counts were then summarized to create a genes-by-samples matrix, and differential gene expression analysis was conducted using standard DESeq2 (version 1.46.0) procedures.
Assembly: GRCh38/hg38
Supplementary files format and content: CSV file with gene names as rows and sample names as columns (fpkm.csv)

source_name: Brain tumor

growth_protocol: Cells were grown in serum-free stem cell media in non-adherant plates.

extract_protocol:
RNA extracted using Qiagen AllPrep DNA/RNA kit following manufacturer’s instructions.
TruSeq Stranded Total RNA Gold protocol with RiboZero rRNA depletion (Illumina).

treatment_protocol: Treated with 10 ng/uL doxycycline for 3 hours to induce CRISPR-Cas9 guide RNA expression.

value: Brain tumor

value: human glioblastmoma (patient derived)

value: control


title: GSC20 vector control rep A

description: Library name: control_A


title: GSC20 mtg483 2wk rep B

description: Library name: c483_2wk_B

value: mtgRNA


title: clone48_4

description:
Library name: 366650
SMART-Seq v3

value: cerebral organoid

value: G


title: clone48_3

description:
Library name: 366649
SMART-Seq v3


title: hiPSC-derived microglia, tri-culture, rep3

description: Library name: Tri_3


title: GSC20 mtg483 2wk rep A

description: Library name: c483_2wk_A


title: GSC20 mtg483 3hr rep B

description: Library name: c483_3hr_B


title: hiPSC-derived microglia, tri-culture, rep2

description: Library name: Tri_2


title: clone48_2

description:
Library name: 366648
SMART-Seq v3


title: hiPSC-derived microglia, tri-culture, rep1

description: Library name: Tri_1


title: GSC20 mtg142 2wk rep B

description: Library name: c142_2wk_B


title: hiPSC-derived microglia, mono-culture, rep4

description: Library name: Mono_4


title: GSC20 mtg142 2wk rep A

description: Library name: c142_2wk_A


title: clone48_1

description:
Library name: 366647
SMART-Seq v3

value: R


title: GSC20 mtg142 3hr rep B

description: Library name: c142_3hr_B


title: clone47_4

description:
Library name: 366646
SMART-Seq v3


title: hiPSC-derived microglia, mono-culture, rep3

description: Library name: Mono_3


title: LS8817, day3, Palbo, rep2, RNA

city: New York

first: Viviana

middle: I.

last: Risca

state: NY

address: 1230 York Ave, Box 176

department: Laboratory of Genome Architecture and Dynamics

institute: The Rockefeller University

description:
Library name: Biorep2_Palbo_day3
kallisto quantification of transcripts for Biorep2_Palbo_day3

data_processing:
For RNA samples sent to Novogene for sequencing, reads containing adapters, N > 10% (N represents the base cannot be determined) and low quality (Qscore<= 5) base were filtered out.  For RNA samples sent to Plasmidsaurus for sequencing, quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3.
Pseudoalignment and quantification of transcripts were performed with kallisto for LS8817 cells. Alignment and quantification of transcripts were performed with STAR v2.7.10a for MCF7 cells.
for LS8817 cells, kallisto counts were imported into R using tximport v1.14.2, and counts matrix normalized by sequencing depth was generated using was DESeq2 v1.26.0  for MCF7 cells, STAR counts were imported into R and counts matrix normalized by sequencing depth was generated using was DESeq2 v1.26.0
Assembly: hg38
Supplementary files format and content: files ending in kallisto_abundance.tsv is the abundance estimates of transcripts by kallisto
Supplementary files format and content: Files ending in ReadsPerGene.out.tab is the abundance counts of transcripts by STAR.
Supplementary files format and content: MCF7_RNA_counts_Cycling.vs.FulvPalbo.clean.txt is the counts of transcripts by STAR for all samples from the 21 day 100 nM palbociclib + 10 nM fulvestrant timecourse experiment

source_name: soft tissue sarcoma

growth_protocol: LS8817 Cells were cultured in DMEM high glucose no glutamine (11960044, Gibco™), supplemented with 9% FBS (10082147, Gibco™), 1% of 100x GlutaMAX™ Supplement (35050061, Gibco™) and 1% of 10,000U/mL penicillin/streptomycin (15140122, Gibco™) and maintained at 37°C and 5% CO2.  Human MCF-7 cells (RRID:CVCL_0031) were cultured in in 75 cm2 flasks DMEM/F-12 (#Cat 10565018, Thermo Fisher Scientific) supplemented with GlutaMAX, 10% Fetal Bovine Serum (Cat# F4135, Sigma-Aldrich) and 1% Penicillin-Streptomycin at 37 °C and 5% CO2.

extract_protocol:
RNA extraction was done using the Quick-RNA Microprep Kit (Zymo Research, cat# R1050).
Total RNA from at least 2 biological replicates per condition was sent to Novogene for stranded library preparation and sequencing. cDNA libraries were made with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB cat# E7765). For MCF7 samples treated with  MCF7 cells were treated with 100 nM doxorubicin, 1 uM palbociclib or 100 nM palbociclib + 10 nM fulvestrant, samples were sent to PlasmidSaurus for forward-stranded library preparation. Plasmidsaurus'  RNA-seq service sequences polyadenylated (poly-A) eukaryotic transcripts using a 3′ end-counting approach to provide gene-level counts only, where a short stretch of RNA (~90nt) located within the last 300-400nt of the transcript is sequenced.

treatment_protocol: Cells were passaged at a 1:3 ratio one day before drug treatment and treated with drugs at the specified concentrations, with media changes every 2–3 days until harvest.

value: soft tissue sarcoma

value: liposarcoma

value: TetON FLAG-MDM2

value: day3 palbociclib (1 uM)


title: clone47_3

description:
Library name: 366645
SMART-Seq v3

value: SN


title: LS8817, day3, Doxo, rep2, RNA

description:
Library name: Biorep2_Doxo_day3
kallisto quantification of transcripts for Biorep2_Doxo_day3

value: day3 doxorubicin (100nM)


title: hiPSC-derived microglia, mono-culture, rep2

description: Library name: Mono_2


title: hiPSC-derived microglia, mono-culture, rep1

description: Library name: Mono_1


title: clone47_1

description:
Library name: 366643
SMART-Seq v3


title: LS8817, day28, Palbo, rep1, RNA

description:
Library name: Biorep1_Palbo_day28
kallisto quantification of transcripts for Biorep1_Palbo_day28

value: day28 palbociclib (1 uM)


title: ∆SARS2+SARS2-1xFLAG Hap1 Cells + H448L SARS2+int14-myc grown without dox - rep3

description:
Library name: H448L_SARS2_Rep3
Processed data column name: 4LJFHN_12

data_processing:
Data was processed by Plasmidsaurus using their pipeline to obtain gene counts, differential expression, and other analyses provided upon receipt of data
Assembly: GRCh38_114
Supplementary files format and content: tab-seprated value (tsv) files containing counts for each gene

molecule: polyA RNA

extract_protocol:
Cell lysates (lysed with Zymo DNA/RNA Shield)  were submitted to Plasmidsaurus, which completed RNA extraction
Cell lysates (lysed with Zymo DNA/RNA Shield) were submitted to Plasmidsaurus, which completed library construction using poly-A mRNA capture, second strand synthesis and tagmentation to generate double-stranded cDNA, and Illumina library amplification


title: clone46_4

description:
Library name: 366642
SMART-Seq v3


title: LS8817, day21, Palbo, rep1, RNA

description:
Library name: Biorep1_Palbo_day21
kallisto quantification of transcripts for Biorep1_Palbo_day21

value: day21 palbociclib (1 uM)


title: LS8817, day21, Doxo, rep2, RNA

description:
Library name: Biorep2_Doxo_day21
kallisto quantification of transcripts for Biorep2_Doxo_day21

value: day21 doxorubicin (100nM)


title: clone46_3

description:
Library name: 366641
SMART-Seq v3


title: LS8817, day21, Doxo, rep1, RNA

description:
Library name: Biorep1_Doxo_day21
kallisto quantification of transcripts for Biorep1_Doxo_day21


title: ∆SARS2+SARS2-1xFLAG Hap1 Cells + H448L SARS2+int14-myc grown without dox - rep1

description:
Library name: H448L_SARS2_Rep1
Processed data column name: 4LJFHN_10


title: clone46_2

description:
Library name: 366640
SMART-Seq v3


title: LS8817, day14, Palbo, rep1, RNA

description:
Library name: Biorep1_Palbo_day14
kallisto quantification of transcripts for Biorep1_Palbo_day14

value: day14 palbociclib (1 uM)


title: LS8817, day14, Doxo, rep2, RNA

description:
Library name: Biorep3_Doxo_day14
kallisto quantification of transcripts for Biorep3_Doxo_day14

value: day14 doxorubicin (100nM)


title: clone46_1

description:
Library name: 366639
SMART-Seq v3


title: LS8817, day14, Doxo, rep1, RNA

description:
Library name: Biorep1_Doxo_day14
kallisto quantification of transcripts for Biorep1_Doxo_day14


title: ∆SARS2+SARS2-1xFLAG Hap1 Cells + R227Q SARS2+int14-myc grown without dox - rep2

description:
Library name: R227Q_SARS2_Rep2
Processed data column name: 4LJFHN_5


title: LS8817, day14, Palbo, rep2, RNA

description:
Library name: Biorep3_Palbo_day14
kallisto quantification of transcripts for Biorep3_Palbo_day14


title: LS8817, day10, Palbo, rep1, RNA

description:
Library name: Biorep3_Palbo_day10
kallisto quantification of transcripts for Biorep3_Palbo_day10

value: day10 palbociclib (1 uM)


title: clone45_13

description:
Library name: 366638
SMART-Seq v3

value: N


title: ∆SARS2+SARS2-1xFLAG Hap1 Cells + R227Q SARS2+int14-myc grown without dox - rep3

description:
Library name: R227Q_SARS2_Rep3
Processed data column name: 4LJFHN_6


title: LS8817, day10, Doxo, rep1, RNA

description:
Library name: Biorep3_Doxo_day10
kallisto quantification of transcripts for Biorep3_Doxo_day10

value: day10 doxorubicin (100nM)


title: ∆SARS2+SARS2-1xFLAG Hap1 Cells + R227Q SARS2+int14-myc grown without dox - rep1

description:
Library name: R227Q_SARS2_Rep1
Processed data column name: SDKYMR_3


title: LS8817, Cycling, rep3, RNA

description:
Library name: Biorep3_Cycling_day0
kallisto quantification of transcripts for Biorep3_Cycling_day0


title: LS8817, Cycling, rep2, RNA

description:
Library name: Biorep2_Cycling_day0
kallisto quantification of transcripts for Biorep2_Cycling_day0


title: Jurkat cells, sgRELA, Day 5, biol rep 2, library rep 1

description:
Library name: sample5
column name in raw_counts_all_samples.txt: N002_HT002_G01_J0001_01B_0005A1_01

value: Jurkat-dCas9-VP64 (CRISPRa stable line)

value: T lymphocyte

value: dCas9-VP64 (CRISPRa); mCherry+

value: RELA

value: Day 5


title: clone45_12

description:
Library name: 366637
SMART-Seq v3

value: cerebral organoid

value: G


title: ∆SARS2+SARS2-1xFLAG, plus dox, rep3

description: Library name: 8962-CDG-9

value: Plus dox


title: ∆SARS2+SARS2-1xFLAG Hap1 Cells + WT SARS2+int14-myc grown without dox - rep3

description:
Library name: WT_SARS2_Rep3
Processed data column name: 4LJFHN_3

value: wild-type


title: Hap1, plus dox, rep3

description: Library name: 8962-CDG-6

value: Unmodified parental


title: clone49_4

description:
Library name: 366654
SMART-Seq v3


title: Hap1, no dox, rep3

description: Library name: 8962-CDG-3

value: No dox


title: LS8817, Cycling, rep1, RNA

description:
Library name: Biorep1_Cycling_day0
kallisto quantification of transcripts for Biorep1_Cycling_day0

value: soft tissue sarcoma

value: liposarcoma

value: TetON FLAG-MDM2


title: clone45_11

description:
Library name: 366636
SMART-Seq v3


title: ∆SARS2+SARS2-1xFLAG Hap1 Cells + WT SARS2+int14-myc grown without dox - rep2

description:
Library name: WT_SARS2_Rep2
Processed data column name: SDKYMR_2


title: Hap1, no dox, rep2

description: Library name: 8962-CDG-2


title: PiZZ5

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description:
Library name: FAN-24-0009
Transcriptome profile of organoids PiZ , biological rep5

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a The expression levels of genes were determined with HTseq-counts 0.9.1
Assembly: Hg38
Supplementary files format and content: normalised_counts_withAnnotation-6.tsv

source_name: Intestine

growth_protocol: To generate hSIOs from iPSCs, we first directed iPSCs to differentiate into definitive endoderm (DE) using Activin A for 3 days. The DE cells were then exposed to FGF4 for 4 days to induce mid- and hind-gut spheroid formation. These spheroids were subsequently embedded in matrigel and cultured with R-Spondin1, Noggin, and EGF to facilitate their maturation into hSIOs (McCracken et al 2011).

extract_protocol:
For gene expression analyses, total RNA was extracted according to the manufacturer's instructions (RNeasy Mini Kit). Total RNA was quantified using the Qubit 4.0 fluorimetric Assay (Thermo Fisher Scientific). RNA extracted was precisely quantified and mixed at 10ng/µL.
NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostic srl)

treatment_protocol: hSIOs were collected for RNA extraction at the end of the differentiation protocol.

value: Intestine

value: human small intestinal organoids (hSIOs)

value: PiZZ


title: PiZZ4

description:
Library name: FAN-24-0008
Transcriptome profile of organoids PiZ , biological rep4


title: PiZZ3

description:
Library name: FAN-24-0007
Transcriptome profile of organoids PiZ , biological rep3


title: clone45_10

description:
Library name: 366635
SMART-Seq v3

value: N


title: ∆SARS2+SARS2-1xFLAG Hap1 Cells + WT SARS2+int14-myc grown without dox - rep1

description:
Library name: WT_SARS2_Rep1
Processed data column name: SDKYMR_1


title: PiZZ2

description:
Library name: FAN-24-0006
Transcriptome profile of organoids PiZ , biological rep2


title: clone45_9

description:
Library name: 366634
SMART-Seq v3


title: PiZZ1

description:
Library name: FAN-24-0005
Transcriptome profile of organoids PiZ , biological rep1


title: PiMM4

description:
Library name: FAN-24-0004
Transcriptome profile of organoids control, biological rep4

value: PiMM


title: T04.

city: Dalian

first: Dachuan

last: Shen

address: No. 10, Xuefu Street, Dalian Economic and Technological Development Zone

country: China

institute: Dalian University

description: Library name: sdc_30gy2

data_processing:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Messenger RNA was purified from total RNA using poly-T oligo-attached  magnetic beads. After fragmentation, the first strand cDNA was  synthesized using random hexamer primers followed by the second  strand cDNA synthesis. The library was ready after end repair, A-tailing,  adapter ligation, size selection, amplification, and purification.
Messenger RNA was purified from total RNA using poly-T oligo-attached  magnetic beads. After fragmentation, the first strand cDNA was  synthesized using random hexamer primers. Then the second strand  cDNA was synthesized using dUTP, instead of dTTP. The directional  library was ready after end repair, A-tailing, adapter ligation, size  selection, USER enzyme digestion, amplification, and purification.
The clustering of the index-coded samples was performed on a cBot  Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS  (Illumia) according to the manufacturer’s instructions. After cluster  generation, the library preparations were sequenced on an Illumina  Novaseq platform and 150 bp paired-end reads were generated.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: cell line

extract_protocol:
RNA was harvested using Trizol reagent. 0.2 ug of total RNA was used for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cell line

value: Human lung squamous cell carcinoma cell


title: clone45_8

description:
Library name: 366633
SMART-Seq v3


title: GSC20 mtg483 3hr rep A

description: Library name: c483_3hr_A

value: Brain tumor

value: human glioblastmoma (patient derived)

value: mtgRNA


title: PiMM3

description:
Library name: FAN-24-0003
Transcriptome profile of organoids control, biological rep3


title: T03.

description: Library name: sdc_30gy1


title: PiMM2

description:
Library name: FAN-24-0002
Transcriptome profile of organoids control, biological rep2


title: PiMM1

description:
Library name: FAN-24-0001
Transcriptome profile of organoids control, biological rep1


title: clone45_7

description:
Library name: 366632
SMART-Seq v3

value: cerebral organoid

value: G


title: T02.

description: Library name: sdc_0gy2


title: GSC20 mtg142 3hr rep A

description: Library name: c142_3hr_A


title: non-targeting, rep6, group B

city: La Jolla

first: Brian

last: Yee

state: CA

address: 9500 Gilman Dr

department: Health

institute: UCSD

description: Library name: NT-BG293LV06-74B

data_processing:
Quality of reads were assessed using fastqc.
Reads were trimmed.
Reads were aligned to hg38 reference and quantified with salmon.
Assembly: hg38
Supplementary files format and content: quant.sf files contain transcript quantifications

growth_protocol: HEK293XT cells were seeded onto 12-well plates at a density of 0.1x106 cells per well in 1mL of DMEM + 10% FBS and grown overnight.

extract_protocol:
RNA extraction was completed using the Maxwell RSC simplyRNA tissue kit .
RNA-seq libraries were prepared using the TruSeq Stranded mRNA library preparation kit and the IDT for Illumina TruSeq RNA UD Index set for samples having greater than 50% knockdown of the RBP.

treatment_protocol: The media was replaced the following day using fresh media containing 8ug/mL polybrene (Hexadimethrine bromide) and 100ul of lentivirus specific to RBP open reading frames. The lentiviral medium was removed after 24h and replaced with fresh media containing 4ug/mL Puromycin and incubated in a standard tissue culture incubator for 48h.

value: human embryonic kidney

value: control


title: clone45_6

description:
Library name: 366631
SMART-Seq v3


title: non-targeting, rep5, group B

description: Library name: NT-BG293LV06-73B


title: T01.

description: Library name: sdc_0gy1


title: non-targeting, rep6, group A

description: Library name: NT-BG293LV06-74


title: LS8817, day3, Doxo, rep1, RNA

description:
Library name: Biorep1_Doxo_day3
kallisto quantification of transcripts for Biorep1_Doxo_day3

value: soft tissue sarcoma

value: day3 doxorubicin (100nM)


title: clone47_2

description:
Library name: 366644
SMART-Seq v3

value: R

value: SN


title: LS8817, day3, Palbo, rep1, RNA

description:
Library name: Biorep1_Palbo_day3
kallisto quantification of transcripts for Biorep1_Palbo_day3

value: liposarcoma

value: TetON FLAG-MDM2

value: day3 palbociclib (1 uM)


title: clone45_5

description:
Library name: 366630
SMART-Seq v3

value: N


title: non-targeting, rep5, group A

description: Library name: NT-BG293LV06-73


title: T06

description: Library name: si2_2

data_processing:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

value: cell line


title: LS8817, day28, Palbo, rep2, RNA

description:
Library name: Biorep2_Palbo_day28
kallisto quantification of transcripts for Biorep2_Palbo_day28

value: day28 palbociclib (1 uM)


title: non-targeting, rep4, group B

description: Library name: NT-BG293LV06-38B


title: T05

description: Library name: si2_1

value: Human lung squamous cell carcinoma cell


title: non-targeting, rep4, group A

description: Library name: NT-BG293LV06-38


title: clone45_4

description:
Library name: 366629
SMART-Seq v3


title: non-targeting, rep3, group B

description: Library name: NT-BG293LV06-37B


title: clone45_3

description:
Library name: 366628
SMART-Seq v3


title: non-targeting, rep3, group A

description: Library name: NT-BG293LV06-37


title: T04

description: Library name: si1_2


title: non-targeting, rep1, group B

description: Library name: NT-BG293LV06-1B


title: T03

description: Library name: si1_1


title: non-targeting, rep2, group B

description: Library name: NT-BG293LV06-2B


title: clone45_2

description:
Library name: 366627
SMART-Seq v3


title: non-targeting, rep2, group A

description: Library name: NT-BG293LV06-2


title: non-targeting, rep1, group A

description: Library name: NT-BG293LV06-1


title: clone45_1

description:
Library name: 366626
SMART-Seq v3


title: T02

description: Library name: NC_2


title: ZMAT3 knockdown, rep2, group B

description: Library name: ZMAT3-BG293LV06-80B

value: knockdown


title: ZMAT3 knockdown, rep1, group B

description: Library name: ZMAT3-BG293LV06-79B


title: clone44_4

description:
Library name: 366625
SMART-Seq v3


title: T01

description: Library name: NC_1


title: ∆SARS2+SARS2-1xFLAG Hap1 Cells + H448L SARS2+int14-myc grown without dox - rep2

description:
Library name: H448L_SARS2_Rep2
Processed data column name: 4LJFHN_11


title: cloneNA_3

description:
Library name: 366624
SMART-Seq v3


title: ZC3HAV1 knockdown, rep1, group A

description: Library name: ZC3HAV1-BG293LV06-35


title: ZC3HAV1 knockdown, rep2, group A

description: Library name: ZC3HAV1-BG293LV06-36


title: scramble_nucleo_Rep3

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

institute: University of Turin

description: Subcellular RNA-seq of nuclear polyA+ RNA in control mouse keratinocytes infected with sh-scramble (ctrl), replicate 3

data_processing:
Following quality controls, sequencing reads were  aligned to the mouse reference genome (mm10/GRCm38.p6) using STAR v2.7.1a with options: --outFilterMultimapNmax 10 --outFilterMultimapScoreRange 1 –outFilterMismatchNmax 999 –outFilterMismatchNoverLmax 0.04. Gene expression levels were quantified with featureCounts v1.6.1 (options: -t exon -g gene_name) using the GENCODE Release M23 annotation. Multi-mapped reads were excluded from quantification.
Assembly: mm10/GRCm38.p6
Supplementary files format and content: Tab-delimited text file of raw read counts per gene/samples.

source_name: Keratinocytes

growth_protocol: Mouse keratinocytes were grownin low-calcium Dulbecco’s modified Eagle medium supplemented with 10% FBS, 100 U ml−1 penicillin–streptomycin, HCE cocktail consisting of hydrocortisone 0.5 μg ml−1, insulin 5 μg ml−1 (Thermo Fisher), cholera enterotoxin 10−10 M (Sigma-Aldrich) and EGF 10 ng ml−1 (PeproTech) and cultured at 37 °C in a humidifiedatmosphere, with 8% CO2.

extract_protocol:
For nucleus/cytoplasm fractionation freshly harvested 5 x 10^6 mouse keratinocytes (expressing shRNAs for Cbx3 or a scramble shRNA) were lysed in a hypotonic buffer containing RNAse inhibitors on ice for 20min (10mM HEPES pH7.9, 60mM KCl, 1mM DTT, 1mM EDTA, 0.075% NP40) followed by subsequent centrifugation (16,000 × g, for 5 min at 4 °C). The supernatant was retained as cytoplasmic fraction. The nuclei pellet was washed in a washing buffer (10mM HEPES pH7.9, 60mM KCl, 1mM DTT, 1mM EDTA), centrifuged (16,000 × g for 15 min at 4 °C) and then resuspended in a hypertonic nuclear buffer (20mM Tris pH 8.0, 1.5mM MgCl2, 420mM NaCl, 0.2mM  EDTA, 25% Glycerol and 1:100 Protease-inhibitor Mix M). Pellet was dispersed with a pipette and passed through a 27 G needle 5 times. After 10 min-incubation on ice, nuclei were centrifuged (16,000 × g for 15 min at 4 °C) to collect supernatant as nuclear fraction. RNA was extracted from cytoplasmatic and nuclear fraction, using the RNeasy Mini Kit (Qiagen).
For library preparation, the quantity and quality of the starting RNA were checked by Qubit and Bioanalyzer (Agilent). 1 μg of total RNA was subjected to poly(A) selection, and libraries were prepared using the Illumina stranded mRNA following the manufacturer’s instructions. Libraries were sequenced on Illumina NextSeq 1000 System.

value: Keratinocytes

tag: replicate

tag: condition

tag: compartment

value: nucleo

tag: shRNA

value: sh-Scramble

tag: shRNA type


title: scramble_nucleo_Rep4

description: Subcellular RNA-seq of nuclear polyA+ RNA in control mouse keratinocytes infected with sh-scramble (ctrl), replicate 4


title: YWHAG knockdown, rep2, group B

description: Library name: YWHAG-BG293LV06-76B

value: human embryonic kidney


title: YWHAG knockdown, rep1, group B

description: Library name: YWHAG-BG293LV06-75B


title: clone44_3

description:
Library name: 366623
SMART-Seq v3

value: cerebral organoid

value: G


title: YTHDF1 knockdown, rep2, group B

description: Library name: YTHDF1-BG293LV06-64B


title: clone44_2

description:
Library name: 366622
SMART-Seq v3


title: scramble_nucleo_Rep2

description: Subcellular RNA-seq of nuclear polyA+ RNA in control mouse keratinocytes infected with sh-scramble (ctrl), replicate 2


title: YTHDF1 knockdown, rep1, group B

description: Library name: YTHDF1-BG293LV06-63B


title: WDR6 knockdown, rep2, group B

description: Library name: WDR6-BG293LV06-90B


title: clone44_1

description:
Library name: 366621
SMART-Seq v3


title: scramble_nucleo_Rep1

description: Subcellular RNA-seq of nuclear polyA+ RNA in control mouse keratinocytes infected with sh-scramble (ctrl), replicate 1


title: TRNAU1AP knockdown, rep2, group B

description: Library name: TRNAU1AP-BG293LV06-32B


title: WDR6 knockdown, rep1, group B

description: Library name: WDR6-BG293LV06-89B


title: cloneNA_2

description:
Library name: 366620
SMART-Seq v3


title: scramble_cyto_Rep4

description: Subcellular RNA-seq of cytoplasmic polyA+ RNA in control mouse keratinocytes infected with sh-scramble (ctrl), replicate 4

value: cyto


title: scramble_cyto_Rep3

description: Subcellular RNA-seq of cytoplasmic polyA+ RNA in control mouse keratinocytes infected with sh-scramble (ctrl), replicate 3


title: TRNAU1AP knockdown, rep1, group B

description: Library name: TRNAU1AP-BG293LV06-31B


title: TPD52L2 knockdown, rep1, group B

description: Library name: TPD52L2-BG293LV06-83B


title: clone43_2

description:
Library name: 366619
SMART-Seq v3


title: TPD52L2 knockdown, rep2, group B

description: Library name: TPD52L2-BG293LV06-84B


title: STAU2 knockdown, rep2, group B

description: Library name: STAU2-BG293LV06-82B


title: scramble_cyto_Rep2

description: Subcellular RNA-seq of cytoplasmic polyA+ RNA in control mouse keratinocytes infected with sh-scramble (ctrl), replicate 2


title: clone43_1

description:
Library name: 366618
SMART-Seq v3


title: STAU2 knockdown, rep1, group B

description: Library name: STAU2-BG293LV06-81B


title: SRP68 knockdown, rep2, group A

description: Library name: SRP68-BG293LV06-54


title: scramble_cyto_Rep1

description: Subcellular RNA-seq of cytoplasmic polyA+ RNA in control mouse keratinocytes infected with sh-scramble (ctrl), replicate 1


title: SRP68 knockdown, rep1, group A

description: Library name: SRP68-BG293LV06-53


title: SMNDC1 knockdown, rep2, group B

description: Library name: SMNDC1-BG293LV06-92B


title: Cbx3_sh33_UT_3_run2

description: Deep polyA+ RNA-seq of Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #2), replicate 3, run 2

data_processing:
Following quality controls, sequencing reads were  aligned to the mouse reference genome (mm10/GRCm38.p6) using STAR v2.7.1a with options: --outFilterMultimapNmax 10 --outFilterMultimapScoreRange 1 –outFilterMismatchNmax 999 –outFilterMismatchNoverLmax 0.04. Gene expression levels were quantified with featureCounts v1.6.1 (options: -t exon -g gene_name) using the GENCODE Release M23 annotation. Multi-mapped reads were excluded from quantification.
Assembly: mm10/GRCm38.p6
Supplementary files format and content: None

extract_protocol:
RNA was extracted from 5 x 10^6 mouse keratinocytes (expressing shRNAs for Cbx3 or a scramble shRNA), using the RNeasy Mini Kit (Qiagen).
For library preparation, the quantity and quality of the starting RNA were checked by Qubit and Bioanalyzer (Agilent). 1 μg of total RNA was subjected to poly(A) selection, and libraries were prepared using the TruSeq RNA Sample Prep Kit (Illumina) following the manufacturer’s instructions. Libraries were sequenced on Illumina NextSeq 1000 System.

tag: run

value: Cbx3 KD

tag: shRNA id


title: clone42_1

description:
Library name: 366616
SMART-Seq v3

value: R


title: SCAF8 knockdown, rep2, group A

description: Library name: SCAF8-BG293LV06-52

tag: cell line

tag: cell type


title: SMNDC1 knockdown, rep1, group B

description: Library name: SMNDC1-BG293LV06-91B


title: SCAF8 knockdown, rep1, group A

description: Library name: SCAF8-BG293LV06-51


title: clone41_6

description:
Library name: 366615
SMART-Seq v3

tag: tissue

tag: genotype


title: clone42_2

description:
Library name: 366617
SMART-Seq v3

tag: plate

tag: cloneid


title: Cbx3_sh33_UT_3_run1

description: Deep polyA+ RNA-seq of Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #2), replicate 3, run 1


title: sh-white-H3K36me2-Input-rep1

city: Shanghai

first: Yu

last: Liang

address: Yueyang Road 320

department: SIBCB

institute: CEMCS, CAS

data_processing:
Adapters were trimmed via cutadapt (v 4.1) with parameters -e 0.1 -O 3 -m 55 --quality-cutoff 25, then using bowtie2 with default parameters aligned reads to dm6 and TE sequences.  Functions “view” and “sort” of samtools (v 1.9) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further deduplicated by picard (v2.18.7) and converted to bed files by the bedtools (v2.25.0) bamToBed command. BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig.
Assembly: dm6; Drosophila TE consensus sequence
Supplementary files format and content: bigwig

organism: Drosophila melanogaster

source_name: Pupa 4d hindgut

extract_protocol:
Tissues were dissected in ice-cold PBS and fixed in 1.8% PFA. Samples were sonicated and protein-DNA complexes were immunoprecipitated. DNA was purified by using Phenol/Chloroform and precipitated by using ethanol.
Libraries for ChIP-Seq were prepared by using TruePrep DNA Library Prep Kit V2 for Illumina® (Vazyme, CAT#: TD502/TD503). The libraries were purified by RNAClean XP beads and sent to Novogene for quality control and sequencing.

value: Pupa 4d hindgut

tag: chip antibody

value: sh-white


title: day1survived_9

city: Tokyo

first: Riho

last: Saito

address: 7-3-1 Hongo Bunkyo-ku

department: Graduate School of Pharmaceutical Sciences

institute: University of Tokyo

description: Library name: Sample9

data_processing:
Sequences were mapped to the mouse reference genome (mm10) with the use of STAR (v 2.7.10a). Raw read counts of each gene was calculated using featureCounts (v2.0.1).
Assembly: mm10
Supplementary files format and content: csv file includes raw read counts for each sample

source_name: Blood

extract_protocol:
Approximately 150 µl of blood was collected from the tail artery into a tube containing 100 µl of 50 mM EDTA-2K in PBS. The red blood cells were lysed with ACK lysing buffer (Thermo, A1049201). Cells were incubated at 4°C for 15 min firstly with anti-CXCR2 antibody (1:50, clone SA044G4, BioLegend, 149304) and subsequently with anti-PE microbeads (1:100, Miltenyi Biotec, 130-048-801). Subsequently, cells were subjected to Magnetic Activated Cell Sorting (MACS) (Miltenyi Biotec) and magnetically retained cells were eluted from the MS column and collected by centrifugation for 5 min at 400 x g/4°C. Total RNA was isolated from isolated with the use of RNAiso Plus reagent (Takara).
RNA libraries were prepared using SMART-Seq Stranded Kit (Takara) following manufacturer’s protocols.
Sequencing was carried out on an Illumina NextSeq 2000 platform with paired-end 36 bp reads or on a DNBSEQ-G400RS platform with 100 bp single-end reads. For DNBSEQ-G400RS sequencing, adaptor sequences were converted into the DNBSEQ format using the MGIEasy Universal Library Conversion Kit (App-A) (MGI).

treatment_protocol: 8 weeks old C57B6J WT male mice received intranasal vesicular stomatitis virus infection with 1.0 x 10^7 PFU in 50μl PBS under 5% isoflurane anesthesia. Their survival and body weight were monitored for 14 days. Mice lost more than 30% of body weight at the time of the infection or survived over 14 days after the infection was euthanized for humane endpoint.

value: Blood

value: CXCR2+ cells

value: C57B6J WT

value: VSV (New Jersey) intranasal infection

tag: group

value: Survival group


title: Control scalp scRNA-seq – CON266

first: Juan

last: Ruano

address: 1230 York ave

institute: Rockefeller University

description:
Library name: CON266
Control scalp skin biopsy

data_processing:
Raw sequencing reads were demultiplexed, aligned and quantified using Cell Ranger (10x Genomics).
Reads were aligned to the human reference genome (GRCh38).
Filtered feature-barcode matrices were generated for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: Processed data consist of Cell Ranger filtered feature-barcode matrices (matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz) and quality control summary files.

source_name: scalp skin

extract_protocol:
Scalp skin biopsies were enzymatically and mechanically dissociated to generate single-cell suspensions according to standard protocols.
Single-cell RNA-seq libraries were generated using the 10x Genomics Chromium Single Cell 3′ Library Prep Kit following the manufacturer’s instructions.

value: scalp skin

value: single cell


title: day1survived_8

description: Library name: Sample8

tag: treatment


title: RPS19BP1 knockdown, rep2, group B

description: Library name: RPS19BP1-BG293LV06-88B

value: knockdown


title: RPS19BP1 knockdown, rep1, group B

description: Library name: RPS19BP1-BG293LV06-87B


title: Cbx3_sh33_UT_2_run2

description: Deep polyA+ RNA-seq of Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #2), replicate 2, run 2

value: Keratinocytes


title: clone41_5

description:
Library name: 366614
SMART-Seq v3

tag: color

tag: clone type

value: N

tag: clone size


title: RNPS1 knockdown, rep2, group A

description: Library name: RNPS1-BG293LV06-9

value: human embryonic kidney


title: clone41_4

description:
Library name: 366613
SMART-Seq v3

value: cerebral organoid

value: G


title: Cbx3_sh33_UT_2_run1

description: Deep polyA+ RNA-seq of Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #2), replicate 2, run 1

tag: replicate

tag: condition

value: Cbx3 KD


title: RNPS1 knockdown, rep1, group A

description: Library name: RNPS1-BG293LV06-10


title: Cbx3_sh33_UT_1_run2

description: Deep polyA+ RNA-seq of Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #2), replicate 1, run 2

tag: shRNA

tag: shRNA type


title: RBM5 knockdown, rep1, group A

description: Library name: RBM5-BG293LV06-49


title: RBM4 knockdown, rep2, group A

description: Library name: RBM4-BG293LV06-48


title: clone41_3

description:
Library name: 366612
SMART-Seq v3


title: RBM5 knockdown, rep2, group A

description: Library name: RBM5-BG293LV06-50


title: RBM4 knockdown, rep1, group A

description: Library name: RBM4-BG293LV06-47


title: clone41_2

description:
Library name: 366611
SMART-Seq v3


title: Cbx3_sh12_UT_3_run2

description: Deep polyA+ RNA-seq of Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #1), replicate 3, run 2

tag: run

tag: shRNA id


title: Cbx3_sh33_UT_1_run1

description: Deep polyA+ RNA-seq of Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #2), replicate 1, run 1

tag: cell type


title: RBM42 knockdown, rep1, group B

description: Library name: RBM42-BG293LV06-85B

tag: cell line


title: clone41_1

description:
Library name: 366610
SMART-Seq v3

tag: tissue

tag: genotype


title: RBM22 knockdown, rep2, group A

description: Library name: RBM22-BG293LV06-12


title: clone40_5

description:
Library name: 366609
SMART-Seq v3

tag: plate

tag: cloneid

value: SN


title: Cbx3_sh12_UT_3_run1

description: Deep polyA+ RNA-seq of Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #1), replicate 3, run 1


title: RBM42 knockdown, rep2, group B

description: Library name: RBM42-BG293LV06-86B


title: RBM14 knockdown, rep2, group A

description: Library name: RBM14-BG293LV06-30


title: RBM22 knockdown, rep1, group A

description: Library name: RBM22-BG293LV06-11


title: Cbx3_sh12_UT_2_run2

description: Deep polyA+ RNA-seq of Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #1), replicate 2, run 2


title: clone40_4

description:
Library name: 366608
SMART-Seq v3


title: RBM14 knockdown, rep1, group A

description: Library name: RBM14-BG293LV06-29


title: Cbx3_sh12_UT_2_run1

description: Deep polyA+ RNA-seq of Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #1), replicate 2, run 1


title: clone40_3

description:
Library name: 366607
SMART-Seq v3

value: R


title: RBM11 knockdown, rep2, group A

description: Library name: RBM11-BG293LV06-46


title: RBM11 knockdown, rep1, group A

description: Library name: RBM11-BG293LV06-45


title: RBM10 knockdown, rep2, group A

description: Library name: RBM10-BG293LV06-20


title: clone40_2

description:
Library name: 366606
SMART-Seq v3


title: PRPF4 knockdown, rep2, group B

description: Library name: PRPF4-BG293LV06-70B


title: Cbx3_sh12_UT_1_run1

description: Deep polyA+ RNA-seq of Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #1), replicate 1, run 1


title: PRPF4 knockdown, rep1, group B

description: Library name: PRPF4-BG293LV06-69B


title: RBM10 knockdown, rep1, group A

description: Library name: RBM10-BG293LV06-19


title: Cbx3_sh12_UT_1_run2

description: Deep polyA+ RNA-seq of Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #1), replicate 1, run 2


title: PPP1CA knockdown, rep2, group A

description: Library name: PPP1CA-BG293LV06-58


title: clone39_10

description:
Library name: 366604
SMART-Seq v3


title: Cbx3_scramble_UT_3_run2

description: Deep polyA+ RNA-seq of control mouse keratinocytes infected with sh-scramble (ctrl), replicate 3, run 2

value: Control

value: sh-Scramble


title: PPP1CA knockdown, rep1, group A

description: Library name: PPP1CA-BG293LV06-57


title: PPIA knockdown, rep2, group A

description: Library name: PPIA-BG293LV06-44


title: clone39_9

description:
Library name: 366603
SMART-Seq v3


title: PPIA knockdown, rep1, group A

description: Library name: PPIA-BG293LV06-43


title: Anakinra, KC-CM, a

first: Jared

middle: S

last: Simmons

institute: University of California, San Diego

description: Library name: ana_dial_a

data_processing:
Cell Ranger (10X Genomics) with default parameters was used to perform sample demultiplexing, barcode processing, alignment to the mm10 reference genome, and gene counting
Assembly: mm10
Supplementary files format and content: _barcodes.tsv.gz barcodes in tab-separated values files for each sample (scRNA-seq)
Supplementary files format and content: _features.tsv.gz gene symbols in tab-separated values files for each sample (scRNA-seq)
Supplementary files format and content: _matrix.mtx.gz counts matrices in matrix files for each sample (scRNA-seq)
Supplementary files format and content: bulk_filtered_counts.txt filtered count matrix by gene symbol (rows) and sample (columns) (RNA-seq)

source_name: human preadipocyte

extract_protocol:
Single-cell suspensions generated from mouse skin
10X Genomics Chromium GEM-X Single Cell 3'

value: human preadipocyte

value: wild type

tag: treatment 1

value: 24h PBS

tag: treatment 2

value: 4h KC-CM


title: PBS, KC-CM, b

description: Library name: pbs_dial_b

value: 24h Anakinra

value: 4h PBS


title: Cbx3_scramble_UT_3_run1

description: Deep polyA+ RNA-seq of control mouse keratinocytes infected with sh-scramble (ctrl), replicate 3, run 1


title: PBS, KC-CM, c

description: Library name: pbs_dial_c


title: PCBP3 knockdown, rep2, group A

description: Library name: PCBP3-BG293LV06-42

tag: treatment

value: knockdown


title: PCBP3 knockdown, rep1, group A

description: Library name: PCBP3-BG293LV06-41


title: clone39_8

description:
Library name: 366602
SMART-Seq v3

data_processing:
Alignment was performed using STAR (v.2.7.9a) on GRCm39 and Gencode vM27 with STAR parameters: --outFilterMultimapNmax 1, --outSAMstrandField intronMotif, --outFilterIntronMotifs RemoveNoncanonical, --outFilterScoreMinOverLread 0.22, --outFilterMatchNminOverLread 0.22. Note that we only used the R2 reads from paired end sequencing for this analysis. Reads in exonic and intronic regions (Gencode vM27) were counted using the aligned bam files produced by STAR and summarizeOverlaps (GenomicAlignments v1.40.0, R v4.4.0) with singleEnd=TRUE, mode = "IntersectionNotEmpty", ignore.strand = T, inter.feature = T parameters.
Assembly: GRCm39
Supplementary files format and content: Matrix in csv format with columns corresponding to cells and rows to genes. One file for exonic and one file for intronic reads is given.

tag: color

tag: clone type


title: Cbx3_scramble_UT_2_run2

description: Deep polyA+ RNA-seq of control mouse keratinocytes infected with sh-scramble (ctrl), replicate 2, run 2

value: Keratinocytes

tag: replicate


title: clone39_7

description:
Library name: 366601
SMART-Seq v3

value: N

tag: clone size


title: PCBP1 knockdown, rep2, group B

description: Library name: PCBP1-BG293LV06-68B

value: human embryonic kidney


title: Cbx3_scramble_UT_2_run1

description: Deep polyA+ RNA-seq of control mouse keratinocytes infected with sh-scramble (ctrl), replicate 2, run 1

tag: condition

tag: shRNA


title: clone40_1

description:
Library name: 366605
SMART-Seq v3

value: cerebral organoid


title: PCBP1 knockdown, rep1, group B

description: Library name: PCBP1-BG293LV06-67B


title: PARN knockdown, rep2, group A

description: Library name: PARN-BG293LV06-28


title: clone39_6

description:
Library name: 366600
SMART-Seq v3


title: Cbx3_scramble_UT_1_run2

description: Deep polyA+ RNA-seq of control mouse keratinocytes infected with sh-scramble (ctrl), replicate 1, run 2

tag: run

tag: shRNA type


title: clone39_5

description:
Library name: 366599
SMART-Seq v3


title: input_2

description: Input DNA of Cbx3 IP replicate 2

data_processing:
Following quality controls (performed with FastQC v0.11.2), paired-end sequencing reads were aligned to the mouse reference genome (mm10/GRCm38) using Bowtie v2.3.5.1 [Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).]. Duplicated alignments (identified by Picard MarkDuplicates, https://broadinstitute.github.io/picard) and low-quality alignments/multi-mapping reads were excluded using SAMtools v1.6 [Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009)]. Immunoprecipitation and corresponding control (Input DNA) datasets were treated identically. Peak calling was performed for each IP against its matched Input DNA using MACS v2.1.4 [Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).] (command: callpeak -g mm --nomodel -f BAMPE -q 0.05). Input-normalized ChIP-seq fold-enrichment signal tracks were obtained using MACS v2.1.4 [Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).] (command: callpeak -g mm --nomodel -f BAMPE -q 0.05 --SPMR -B and bdgcmp -m FE).  For Cbx3 ChIP-seq, braod peak calling was performed using epic2 [Endre Bakken Stovner, Pål Sætrom, epic2 efficiently finds diffuse domains in ChIP-seq data, Bioinformatics, Volume 35, Issue 21, November 2019] (command: --genome mm10 --false-discovery-rate-cutoff 0.05 --guess-bampe).
Assembly: GRCm38/mm10
Supplementary files format and content: BigWig files of input-normalized signal tracks.
Supplementary files format and content: NarrowPeak files of called peaks.

extract_protocol:
ChIP was performed on mouse keratinocytes cross-linked in 1% formaldehyde  for 15 minutes at RT. After blocking the cross-link with 0.125 M glycine for 5 minutes and washing with PBS containing protease  inhibitors, the pellets were resuspended in Lysis buffer (5mM HEPES pH7.9, 85mM KCl, 0.5 NP-40) incubated on ice for 10 min and centrifuged 200 × g for 5 min at 4°C. Chromatin was sonicated to achieve fragment lengths of approximately 0.2-0.5 kb and then subjected to Immunoprecipitation using H3K27ac, Cbx3, Suv420h2 and Ehmt2 antibodies and Protein G Dynabeads in immunoprecipitation buffer (56.25mM HEPES pH7.9, 157.2mM NaCl, 1mM EDTA, 1.125% Triton X-100, 0.1% Na-deoxycholate). After washes with LiCl Wash buffer (100 mM Tris pH 8.0, 100 mM Tris pH 8.0, 1% NP-40, 1% Na-deoxycholate) and with TE Buffer (10 mM Tris, 1 mM EDTA) the material was resuspend in Elution buffer (1 % SDS, 0.1 M NahCo3 Sodium hydrogen carbonate ) to be reverse crosslinked overnight at 65 °C O/N, treated with proteinase K and RNase A and purified by kit QiaQuick PCR Purification Kit.
Starting from 10 ng of ChIP eluted sample, the library was produced for the genome wide analysis following the NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina® (E 6240L NEB) manufacturer’s instructions. Libraries were sequenced on Illumina NextSeq 500 and 1000 platforms.

treatment_protocol: H3K27ac ChIP-seq were performed in Cbx3, Suv420h2 and Ehmt2 knockdown (KD) and control (scramble shRNA) mouse keratinocytes. Cbx3 ChIP-seq was performed on wild type mouse keratynocites.

tag: cell type

tag: chip antibody

value: Input

value: no treatment


title: MBNL2 knockdown, rep2, group A

description: Library name: MBNL2-BG293LV06-14

tag: cell line


title: clone39_3

description:
Library name: 366597
SMART-Seq v3

extract_protocol:
Organoids with MADM clones induced at D13 were collected at D20 for MADM-CloneSeq. The sample collection steps for MADM-CloneSeq were adapted from previously published protocols (PMID: 38968076). Organoids were kept in cell culture membrane (Millicell) in oxygenated (95% O2, 5% CO2) artificial cerebrospinal fluid (ACSF) containing (in mM): 118 NaCl, 2.5 KCl, 1.25 NaH2PO4, 1.5 MgSO4, 1 CaCl2, 10 Glucose, 3 Myo-inositol, 30 Sucrose, 30 NaHCO3 prepared   with ultra-distilled water; pH=7.4, at 35C, until sample collection. All work surface and equipment were cleaned using RNase away solution (Thermo Fisher Scientific) prior to experiments. Single organoids were transferred to a LNscope 240XY miscroscope (Luigs & Neumann) and superfused with ACSF at a rate of 0.5 ml/min at room temperature. Individual clones were visualized under a 20x objective and by using ImageJ software. To observe red or green fluorescence, light was emitted from a LED light source (CoolLED, Andover, UK). Glass pipettes (B150-86-10, Sutter Instrument, Novato, CA) previously autoclaved, were pulled using a P-1000 pipette puller (Sutter Instrument) to generate pipettes with an opening of around 3-5ym. Before use, each pipette was filled with 3.5yl of pipette solution which consisted of RNase inhibitor (Takara, 1.95%) in RNase-free PBS (Invitrogen) filtered through a 0.22mm filter. Red or green fluorescent neurons were approached with the pipette under positive pressure to avoid tissue contamination of the pipette tip. When contact with cell membrane was made, tight seal formation was achieved under IR/DIC visualization. The complete aspiration of the cell body was immediately performed by applying a gentle and steady suction while monitoring under fluorescence and typically takes 5-10 s. The negative pressure was removed immediately once the target cell was collected and the pipette was carefully withdrawn from the acute slice to avoid contamination. The content of each pipette was directly transferred into individual PCR tubes and kept at -80C until cDNA library preparation.
cDNA libraries for individual MADM-CloneSeq cells were were prepared using Smart-seq3 protocol (PMID 32518404) in 3 batches (96well plates).

tag: tissue

tag: genotype


title: clone39_4

description:
Library name: 366598
SMART-Seq v3

tag: plate

tag: cloneid


title: input_1

description: Input DNA of Cbx3 IP replicate 1


title: MBNL1 knockdown, rep1, group A

description: Library name: MBNL1-BG293LV06-17


title: MBNL1 knockdown, rep2, group A

description: Library name: MBNL1-BG293LV06-18


title: clone39_2

description:
Library name: 366596
SMART-Seq v3


title: LSM1 knockdown, rep1, group A

description: Library name: LSM1-BG293LV06-61


title: Cbx3_1

description: Cbx3 IP replicate 1


title: clone39_1

description:
Library name: 366595
SMART-Seq v3


title: LSM10 knockdown, rep2, group B

description: Library name: LSM10-BG293LV06-66B


title: Cbx3_2

description: Cbx3 IP replicate 2


title: LSM10 knockdown, rep1, group B

description: Library name: LSM10-BG293LV06-65B


title: clone38_2

description:
Library name: 366594
SMART-Seq v3

value: SN


title: LGALS3 knockdown, rep1, group A

description: Library name: LGALS3-BG293LV06-25


title: ChIPseq_Suv420h2_sh34_Rep2_input

description: Input DNA in sh-Suv420h2 (KD sh #2) replicate 2


title: HNRNH2 knockdown, rep2, group B

description: Library name: HNRNPH2-BG293LV06-72B


title: clone38_1

description:
Library name: 366593
SMART-Seq v3

value: R


title: HNRNPF knockdown, rep2, group A

description: Library name: HNRNPF-BG293LV06-56


title: clone37_3

description:
Library name: 366592
SMART-Seq v3

value: G


title: ChIPseq_Suv420h2_sh34_Rep1_input

description: Input DNA in sh-Suv420h2 (KD sh #2) replicate 1


title: ChIPseq_Suv420h2_sh34_Rep2_ac

description: H3K27ac IP in sh-Suv420h2 (KD sh #2) replicate 2


title: ChIPseq_Suv420h2_sh34_Rep1_ac

description: H3K27ac IP in sh-Suv420h2 (KD sh #2) replicate 1


title: clone37_2

description:
Library name: 366591
SMART-Seq v3


title: Posterior hindlimb, wild-type-hZRS404G>A, H3K27me3, rep2

city: Irvine

first: Evgeny

last: Kvon

address: 836 Health Sciences Road

institute: University of California, Irvine

description: Library name: Sample6

data_processing:
Paired-end reads were aligned to the mm10 reference genome using Bowtie2 with the following parameters: -end-to-end --very-sensitive --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 70.
Samtools, version 1.15.1 was used to generate, sort and index bam files, from which bigwig files were generated using deeptools, version 3.5.1.
Assembly: Wild-type samples = mm10 reference genome Wild-type + reporter samples = A custom mm10 genome (mm10 reference and an extra chromosome for the hZRS transgene reporter). Knock-in + reporter samples = A custom mm10 genome (mm10 with variant mouse ZRS allele replacing the wild type ZRS at chromosome 5 and an extra chrosome for the hZRS transgene reporter)
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: Posterior hindlimb

extract_protocol:
Hindlimb cells were dissected, dissociated, sorted, and then immobilized onto ConA-magnetic beads. Following the CUT&Tag-direct protocol (version 4), bead-bound cells were incubated with primary and secondary antibodies then Tn5 for transposition. DNA libraries were then barcoded and indexed before being sequenced.
cDNA library construction was performed by Novogene and pair-end sequenced to an average depth of 25M reads per sample.

value: Posterior hindlimb

tag: strain background

value: FVB

value: wild-type

tag: batch


title: GRB2 knockdown, rep2, group A

description: Library name: GRB2-BG293LV06-8

tag: treatment


title: ChIPseq_Suv420h2_sh24_Rep2_input

description: Input DNA in sh-Suv420h2 (KD sh #1) replicate 2


title: ChIPseq_Suv420h2_sh24_Rep2_ac

description: H3K27ac IP in sh-Suv420h2 (KD sh #1) replicate 2


title: clone36_3

description:
Library name: 366589
SMART-Seq v3

tag: color

tag: clone type


title: EIF4B knockdown, rep2, group A

description: Library name: EIF4B-BG293LV06-16


title: clone36_2

description:
Library name: 366588
SMART-Seq v3

tag: clone size


title: Central hindlimb, wild-type-hZRS404G>A, H3K27me3, rep1

description: Library name: Sample3

source_name: Central hindlimb

value: Central hindlimb


title: EIF4B knockdown, rep1, group A

description: Library name: EIF4B-BG293LV06-15


title: ChIPseq_Suv420h2_sh24_Rep1_input

description: Input DNA in sh-Suv420h2 (KD sh #1) replicate 1

tag: replicate

tag: condition


title: Anterior hindlimb, wild-type-hZRS404G>A, H3K27me3, rep2

description: Library name: Sample2

source_name: Anterior hindlimb

value: Anterior hindlimb


title: clone36_1

description:
Library name: 366587
SMART-Seq v3


title: ChIPseq_Suv420h2_sh24_Rep1_ac

description: H3K27ac IP in sh-Suv420h2 (KD sh #1) replicate 1

tag: shRNA


title: Anterior hindlimb, wild-type-hZRS404G>A, H3K27me3, rep1

description: Library name: Sample1


title: ChIPseq_Scramble_Rep2_input

description: Input DNA in sh-scramble-2 (Ehmt2, Suv420h2 ctrl) replicate 2

tag: shRNA type


title: Stingfl/fl Cdh5-Cre- mouse liver, biological replicate 3

city: Xi'an

first: Lin

last: Wang

state: Shaanxi

address: West Changle Road 169

institute: Xijing Hospital, Air Force Medical University

description:
Library name: NC-119
Bulk RNA-seq of mouse liver tissue.

data_processing:
Raw reads were quality-controlled using fastp (v0.23.2) and aligned to the mm10 reference genome using HISAT2 (v2.2.1).
Gene expression was quantified as read counts and normalized TPM values using RSEM (v1.3.3).
Differential expression analysis was performed using DESeq2 (v1.38.3).
Assembly: mm10 (GRCm38)
Supplementary files format and content: Tab-delimited text files containing gene expression values (read counts and TPM) for all samples.

source_name: liver

growth_protocol: Mice were maintained under specific pathogen-free conditions. Stingfl/fl Cdh5-Cre+ and Stingfl/fl Cdh5-Cre- mice were generated and maintained on a normal chow diet until 8 weeks of age.

extract_protocol:
Total RNA was extracted from liver tissues using standard RNA extraction protocols.
Strand-specific RNA-seq libraries were constructed using the standard protocol for Illumina sequencing. mRNA was enriched using Oligo(dT) magnetic beads to capture polyA-tailed transcripts, fragmented, and reverse-transcribed into cDNA. After end repair, A-tailing, and adapter ligation, ~200 bp cDNA fragments were selected using AMPure XP beads, PCR-amplified, and sequenced.

treatment_protocol: Mice were fed a choline-deficient, L-amino acid-defined, high-fat diet (CDAHFD) for 10 weeks to induce MASH.

value: liver

tag: cell type

value: liver sinusoidal endothelial cells

value: Stingfl/fl Cdh5-Cre- (littermate control)

value: CDAHFD for 10 weeks


title: clone35_4

description:
Library name: 366585
SMART-Seq v3

value: N


title: ChIPseq_Scramble_Rep2_ac

description: H3K27ac IP in sh-scramble-2 (Ehmt2, Suv420h2 ctrl) replicate 2

value: Keratinocytes

tag: chip antibody


title: clone35_3

description:
Library name: 366584
SMART-Seq v3

value: cerebral organoid


title: CPSF6 knockdown, rep1, group A

description: Library name: CPSF6-BG293LV06-5

tag: cell line

value: human embryonic kidney

value: knockdown


title: ChIPseq_Scramble_Rep1_input

description: Input DNA in sh-scramble-2 (Ehmt2, Suv420h2 ctrl) replicate 1

value: Input


title: Stingfl/fl Cdh5-Cre- mouse liver, biological replicate 1

description:
Library name: NC-58
Bulk RNA-seq of mouse liver tissue.

tag: tissue


title: clone35_2

description:
Library name: 366583
SMART-Seq v3

tag: genotype

value: R


title: ChIPseq_Scramble_Rep1_ac

description: H3K27ac IP in sh-scramble-2 (Ehmt2, Suv420h2 ctrl) replicate 1


title: CNOT2 knockdown, rep2, group A

description: Library name: CNOT2-BG293LV06-22


title: Stingfl/fl Cdh5-Cre+ mouse liver, biological replicate 3

description:
Library name: KO-93
Bulk RNA-seq of mouse liver tissue.

value: Stingfl/fl Cdh5-Cre+ (endothelial-specific Sting knockout)


title: LSM1 knockdown, rep2, group A

description: Library name: LSM1-BG293LV06-62


title: CNOT2 knockdown, rep1, group A

description: Library name: CNOT2-BG293LV06-21


title: ChIPseq_Ehmt2_sh2_Rep2_input

description: Input DNA in sh-Ehmt2 (KD sh #2) replicate 2


title: Stingfl/fl Cdh5-Cre+ mouse liver, biological replicate 2

description:
Library name: KO-75
Bulk RNA-seq of mouse liver tissue.


title: clone34_5

description:
Library name: 366581
SMART-Seq v3

tag: plate


title: Posterior hindlimb, wild-type-hZRS404G>A, H3K27me3, rep1

description: Library name: Sample5

value: Posterior hindlimb


title: AKNAK knockdown, rep2, group B

description: Library name: AHNAK-BG293LV06-78B


title: ChIPseq_Ehmt2_sh2_Rep2_ac

description: H3K27ac IP in sh-Ehmt2 (KD sh #2) replicate 2


title: GRB2 knockdown, rep1, group A

description: Library name: GRB2-BG293LV06-7


title: Stingfl/fl Cdh5-Cre+ mouse liver, biological replicate 1

description:
Library name: KO-57
Bulk RNA-seq of mouse liver tissue.


title: clone34_4

description:
Library name: 366580
SMART-Seq v3

tag: cloneid


title: ChIPseq_Ehmt2_sh2_Rep1_input

description: Input DNA in sh-Ehmt2 (KD sh #2) replicate 1


title: AKNAK knockdown, rep1, group B

description: Library name: AHNAK-BG293LV06-77B


title: clone34_3

description:
Library name: 366579
SMART-Seq v3


title: mononuclear cells, quadriceps, 9 hours post BaCl2-induced acute muscle injury

first: Gregory

middle: Robert

last: Smith

address: 1 Gustave L. Levy Pl

department: Neurology

institute: Mount Sinai Hospital

description: Library name: Q9H

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: quadriceps

extract_protocol:
Cryo-preserved cells were used directely for library construction for scRNA-seq. Cells were thawed, washed, and resuspended at 1,000 cells/ul for processing 10x scRNAseq v3.1 protocol.
10X Genomics Single Cell 3' Reagent Kits V3.1, following the User Guidelines. Briefly, GEM RNAseq was performed as described (10x Genomics, Pleasanton, CA), following the Single Cell 3’ Reagents Kits V3 User Guides. Cells were filtered, counted on a Nexcelome instrument, and the final concentration was set at 1,000 cells/μl for cells. The amount of cells or nuclei loaded on the chip was determined based on the 10X Genomics protocol. The 10X chip (Chromium Single Cell 3’ v3 chip kit B PN-2000060) was loaded to target 5,000 cells final. Reverse-transcription was performed in the emulsion and cDNA was amplified before library construction following the Chromium protocols v3. Each library was tagged with a different index for multiplexing (Chromium i7 Multiplex kit PN-12062). Quality control and quantification of the amplified cDNA were assessed on a Bioanalyzer (High-Sensitivity DNA Bioanalyzer kit). Sequencing was carried out at the New York Genome Center on Illumina Novaseq using  98+26 paired-end reads.

value: quadriceps

value: muscle mononuclear cells

value: multiple cell types

value: WT

value: Mice receives intramuscular injection of BaCl2 (100 ul, 1.2% (w/v)) at quadriceps. 9 hours after injection, injured quadriceps were collected for analysis.


title: RNPS1, HEK293T, IP, replicate 2 eCLIP

description: Library name: RNPS1-HEK293T-2 IP

data_processing:
eCLIP data was analyzed using Skipper (Boyle et al., 2023) with default parameters and sample-matched adapter sequences.
Assembly: hg38
Supplementary files format and content: Tab-delimited file containing reproducible enriched RBP binding regions identified using Skipper.

growth_protocol: HEK293T cells were cultured in 10cm cell culture dishes for each RBP

extract_protocol:
Cells were lysed and and sonicated in eCLIP lysis buffer, and RNA was fragmented using RNase I and complexes were immunoprecipitated with RBP specific or V5-antibody.
eCLIP library construction was performed in accordance with Yeo laboratory standard operating procedures (Blue et al., 2022)


title: ChIPseq_Ehmt2_sh2_Rep1_ac

description: H3K27ac IP in sh-Ehmt2 (KD sh #2) replicate 1


title: mononuclear cells, quadriceps, 2 hours post BaCl2-induced acute muscle injury

description: Library name: Q2H

value: Mice receives intramuscular injection of BaCl2 (100 ul, 1.2% (w/v)) at quadriceps. 2 hours after injection, injured quadriceps were collected for analysis.


title: clone34_2

description:
Library name: 366578
SMART-Seq v3


title: RNPS1, HEK293T, IP, replicate 1 eCLIP

description: Library name: RNPS1-HEK293T-1 IP


title: ChIPseq_Ehmt2_sh1_Rep2_input

description: Input DNA in sh-Ehmt2 (KD sh #1) replicate 2


title: LT24_Tci

city: Marseille

first: Laura

last: BRAUD

address: 27 boulevard Leï Roure

country: France

institute: Institut Paoli Calmettes (IPC)

description: Library name: Sample 15

data_processing:
reads mapped to reference genome using Subread-align (v1.6.4)
reads filtered using samtools view -F4 (v1.9)
raw read counts at gene levels using featureCounts (v1.6.4)
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw counts for each sample

source_name: Liver

extract_protocol:
Total RNA was harvested using RNeasy extraction kit (Qiagen 74104)
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase treatment. After adenylation of the 3’ ends of DNA fragments, Adaptor with hairpin loop structure was ligated to prepare for hybridization. In order to select cDNA fragments in the reange of 370-420 bp, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, using the Universal and Index (X) primers. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Liver

value: Primary cells

value: Bulk of cells

value: Standard Diet (SD)


title: clone34_1

first: Florian

last: Pauler

institute: Institute of Science and Technology Austria (IST Austria)

description:
Library name: 366577
SMART-Seq v3

source_name: cerebral organoid

value: cerebral organoid

value: G

value: N


title: RNPS1, HEK293T, input, replicate 2 eCLIP

description: Library name: RNPS1-HEK293T-2 IN

value: human embryonic kidney


title: ChIPseq_Ehmt2_sh1_Rep2_ac

description: H3K27ac IP in sh-Ehmt2 (KD sh #1) replicate 2

value: Keratinocytes


title: RNPS1, HEK293T, input, replicate 1 eCLIP

description: Library name: RNPS1-HEK293T-1 IN