title: LS8817, day21, Palbo, rep2, RNA

description:
Library name: Biorep2_Palbo_day21
kallisto quantification of transcripts for Biorep2_Palbo_day21

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

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.

value: soft tissue sarcoma

value: liposarcoma

value: TetON FLAG-MDM2

value: day21 palbociclib (1 uM)


title: L984T_CI

status: Public on Jun 29 2026

type: SRA

city: Marseille

first: Laura

last: BRAUD

address: 27 boulevard Leï Roure

country: France

institute: Institut Paoli Calmettes (IPC)

description: Library name: Sample 12

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

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.

tag: tissue

value: Liver

tag: cell line

value: Primary cells

tag: cell type

value: Bulk of cells

tag: genotype

tag: treatment

value: Standard Diet (SD)


title: clone33_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: 366576
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.

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: SN

tag: clone size


title: LT20_3_Tci

description: Library name: Sample 14


title: ChIPseq_Ehmt2_sh1_Rep1_input

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

country: Italy

institute: University of Turin

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

library_source: genomic

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.

molecule: genomic DNA

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:
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.

value: Keratinocytes

tag: chip antibody

value: Input

tag: replicate

tag: condition

tag: shRNA

tag: shRNA type


title: NUDT21(CPSF5) knockdown, rep2, group A

city: La Jolla

first: Brian

last: Yee

state: CA

address: 9500 Gilman Dr

department: Health

country: USA

institute: UCSD

description: Library name: NUDT21-BG293LV06-4

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

molecule: polyA RNA

organism: Homo sapiens

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: knockdown


title: PARN knockdown, rep1, group A

description: Library name: PARN-BG293LV06-27


title: cloneNA_1

description:
Library name: 366574
SMART-Seq v3


title: Cbx3_scramble_UT_1_run1

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

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: Control

tag: shRNA id

value: sh-Scramble


title: MBNL2 knockdown, rep1, group A

description: Library name: MBNL2-BG293LV06-13


title: NUDT21(CPSF5) knockdown, rep1, group A

description: Library name: NUDT21-BG293LV06-3


title: LT20_1_Tci

description: Library name: Sample 13

tag: tissue


title: clone33_2

description:
Library name: 366575
SMART-Seq v3

value: R


title: RBM22, HEK293T, IP, replicate 2 eCLIP

description: Library name: RBM22-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)

tag: cell line


title: RBM22, HEK293T, IP, replicate 1 eCLIP

description: Library name: RBM22-HEK293T-1 IP

tag: cell type


title: seCLIP_IP_M_Rep2

description: Cbx3 seCLIP (IP), medium band (M), replicate 2

data_processing:
Raw sequencing reads were processed using a bioinformatics workflow based on: Blue, S.M., Yee, B.A., Pratt, G.A. et al. Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq. Nat Protoc 17, 1223–1265 (2022). https://doi.org/10.1038/s41596-022-00680-z.
Assembly: mm10/GRCm38.p6
Supplementary files format and content: BigWig files of signal tracks, normalized by sequencing depth (read counts per million). BED files containg genomic coordinates of reproducible RNA binding sites (peaks).
Library strategy: seCLIP

molecule: nuclear RNA

extract_protocol:
Mouse keratynocites replicates were crosslinked at 254-nm UV with 400 mJoules/cm 2 using the CL-3000 UV crosslinker, harvested on ice cold PBS and pelleted by centrifugation. Cell pellets were flash frozen in liquid nitrogen and stored at -80 degrees until ready to perform the experiment. Cells were then subjeted to cytoplasm/nuclear fractionation. Immunoprecipitation for CBX3 was performed on nuclear fraction. Subsequent protocol was followed following Blue et al., 2022 using the ECLIPSEBIO RBP-eCLIP kit.
Libraries generated using the seCLIP-seq method were sequenced using SE50 conditions on the Illumina NextSeq1000.

tag: antibody

tag: type

value: IP

tag: band

value: M


title: ChIPseq_Ehmt2_sh1_Rep1_ac

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


title: LGALS3 knockdown, rep2, group A

description: Library name: LGALS3-BG293LV06-26

tag: treatment


title: L981T_CI

description: Library name: Sample 11

tag: genotype


title: seCLIP_IP_M_Rep1

description: Cbx3 seCLIP (IP), medium band (M), replicate 1


title: RBM22, HEK293T, input, replicate 2 eCLIP

description: Library name: RBM22-HEK293T-2 IN


title: clone33_1

description:
Library name: 366573
SMART-Seq v3

tag: plate

tag: cloneid

tag: color

tag: clone type


title: T_992

description: Library name: Sample 10


title: RBM22, HEK293T, input, replicate 1 eCLIP

description: Library name: RBM22-HEK293T-1 IN


title: seCLIP_IP_L_Rep2

description: Cbx3 seCLIP (IP), lower band (L), replicate 2

tag: replicate

value: L

tag: condition


title: clone32_3

description:
Library name: 366572
SMART-Seq v3

tag: clone size


title: p_941_T

description: Library name: Sample 9

value: Liver


title: clone32_2

description:
Library name: 366571
SMART-Seq v3


title: seCLIP_IP_L_Rep1

description: Cbx3 seCLIP (IP), lower band (L), replicate 1


title: RBM10, HEK293T, IP, replicate 2 eCLIP

description: Library name: RBM10-HEK293T-2 IP


title: p_663_T

description: Library name: Sample 8

value: Primary cells


title: clone32_1

description:
Library name: 366570
SMART-Seq v3


title: RBM10, HEK293T, IP, replicate 1 eCLIP

description: Library name: RBM10-HEK293T-1 IP


title: seCLIP_IP_H_Rep2

description: Cbx3 seCLIP (IP), higher band (H), replicate 2

value: H


title: p_662_T

description: Library name: Sample 7

value: Bulk of cells

value: Standard Diet (SD)


title: clone31_3

description:
Library name: 366569
SMART-Seq v3

value: cerebral organoid

value: G


title: seCLIP_IP_H_Rep1

description: Cbx3 seCLIP (IP), higher band (H), replicate 1

value: Keratinocytes


title: RBM10, HEK293T, input, replicate 2 eCLIP

description: Library name: RBM10-HEK293T-2 IN


title: clone31_2

description:
Library name: 366568
SMART-Seq v3

value: SN


title: RBM10, HEK293T, input, replicate 1 eCLIP

description: Library name: RBM10-HEK293T-1 IN

value: human embryonic kidney


title: seCLIP_INPUT_M_Rep2

description: Size-matched input (SMI) RNA (Control), medium band (M), replicate 2

value: Size-matched input (SMI) RNA

value: INPUT


title: L981_CI

description: Library name: Sample 5


title: clone31_1

description:
Library name: 366567
SMART-Seq v3


title: MBNL2, HEK293T, IP, replicate 2 eCLIP

description: Library name: MBNL2-HEK293T-2 IP


title: seCLIP_INPUT_M_Rep1

description: Size-matched input (SMI) RNA (Control), medium band (M), replicate 1


title: NT_992

description: Library name: Sample 4


title: clone30_5

description:
Library name: 366566
SMART-Seq v3


title: p_941

description: Library name: Sample 3


title: MBNL2, HEK293T, input, replicate 2 eCLIP

description: Library name: MBNL2-HEK293T-2 IN


title: seCLIP_INPUT_L_Rep1

description: Size-matched input (SMI) RNA (Control), lower band (L), replicate 1


title: seCLIP_INPUT_H_Rep2

description: Size-matched input (SMI) RNA (Control), higher band (H), replicate 2


title: p_961

description: Library name: Sample 1


title: clone30_3

description:
Library name: 366564
SMART-Seq v3


title: clone30_2

description:
Library name: 366563
SMART-Seq v3


title: MBNL2, HEK293T, input, replicate 1 eCLIP

description: Library name: MBNL2-HEK293T-1 IN


title: LGALS3, HEK293T, IP, replicate 2 eCLIP

description: Library name: LGALS3-HEK293T-2 IP


title: seCLIP_INPUT_H_Rep1

description: Size-matched input (SMI) RNA (Control), higher band (H), replicate 1


title: sh33_protr_rep3

description: Subcellular RNA-seq of cell protrusions polyA+ RNA in Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #2), 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.

extract_protocol:
Cell protrusions were isolated from mouse keratinocytes (expressing shRNAs for Cbx3, or a scramble shRNA) as described before (Mardakheh M. et al., 2020) with some modiﬁcations to also fractionate the cytoplasm and the nucleus. 2 million cells were seeded on the top of 5 mg/ml collagen-I coated 24.5 mm polycarbonate transwell ﬁlters with 3 μm pore size (Greiner Bio-one) in complete DMEM. Cells were allowed to adhere without the addition of media to the bottom chamber of the transwells. Subsequently, the media on the top of the transwell ﬁlter was replaced by FBS and epidermal growth factor free DMEM, and protrusions were induced by addition of complete DMEM to the bottom chamber. Transwells were then washed with cold PBS, and protrusions were collected by shaving the bottom of the ﬁlter using a glass coverslip dipped in lysis buffer containing RNAse inhibitor (50mM Tris 1M HCl pH7.5, 100mM NaCl, 1% NP40, 0.1%SDS, 0.5%DOC). The cell-body fraction was subsequently purified by direct addition of the hypotonic cytoplasmatic buffer containing RNAse inhibitors on ice for 20min (10mM HEPES pH7.9, 60mM KCl, 1mM DTT, 1mM EDTA, 0.075% NP40) to the top of the ﬁlter, 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 protrusion, cytoplasm and nucleus fractions 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 stranded mRNA Sample Prep Kit (Illumina) following the manufacturer’s instructions. Libraries were sequenced on Illumina NextSeq 1000 System.

tag: compartment

value: protrusions

tag: shRNA

tag: shRNA type


title: LGALS3, HEK293T, IP, replicate 1 eCLIP

description: Library name: LGALS3-HEK293T-1 IP

tag: cell line


title: clone29_3

description:
Library name: 366561
SMART-Seq v3

tag: tissue


title: LGALS3, HEK293T, input, replicate 2 eCLIP

description: Library name: LGALS3-HEK293T-2 IN

tag: cell type


title: sh33_protr_rep2

description: Subcellular RNA-seq of cell protrusions polyA+ RNA in Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #2), replicate 2


title: sh33_protr_rep1

description: Subcellular RNA-seq of cell protrusions polyA+ RNA in Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #2), replicate 1


title: LGALS3, HEK293T, input, replicate 1 eCLIP

description: Library name: LGALS3-HEK293T-1 IN


title: clone29_1

description:
Library name: 366559
SMART-Seq v3

value: R


title: sh33_nucl_rep3

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

value: nucleo


title: Pdgfra-Il1r1, Vehicle

first: Jared

middle: S

last: Simmons

institute: University of California, San Diego

description: Library name: pos_vehic

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: skin

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

value: skin

tag: treatment 1

value: 14h vehicle


title: clone28_7

description:
Library name: 366558
SMART-Seq v3

value: N


title: GRB2, HEK293T, IP, replicate 1 eCLIP

description: Library name: GRB2-HEK293T-1 IP


title: sh33_nucl_rep2

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


title: Il1r1-fl Control, Vehicle

description: Library name: neg_vehic

value: Il1r1-fl/fl control


title: clone28_6

description:
Library name: 366557
SMART-Seq v3


title: GRB2, HEK293T, input, replicate 2 eCLIP

description: Library name: GRB2-HEK293T-2 IN


title: sh33_nucl_rep1

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


title: LLC-GFP tumor-bearing lungs, PDGFRa+ fibroblasts (enriched)

city: New York

first: Nicholas

last: Arpaia

address: 701 W 168TH ST HHSC 906

institute: Columbia University Irving Medical Center

description: Library name: NO002

data_processing:
cellranger-6.1.2
Samples were then demultiplexed for HTOs
Single Cell 3' v3
Assembly: mm10-2020-A
Supplementary files format and content: h5 files

source_name: tumor-bearing lungs

extract_protocol:
10X Genomics Chromium Platform
10X Genomics Chromium Platform with demultiplexing for HTOs

treatment_protocol: C57B6/JN mice (n=3) were intravenously injected with 1.5e5 LLC-GFP cells. After 17 days, lungs of mice were harvested. Tumor tissue and normal-adjacent lung tissue were seperated utilizing microdissection techniques and each tissue was labeled using seperate hashtag oligos (HTOs; (n=6)). Usting magnetic bead negative enrichment and single cell sorting techniques (FACS), we isolated live GFP-CD45- CD31-, EPCAM-, CD146- PDGFRa+ cells

value: tumor-bearing lungs

value: PDGFRa+ fibroblasts

value: C57BL/6 mice, female


title: clone28_5

description:
Library name: 366556
SMART-Seq v3

value: cerebral organoid


title: GRB2, HEK293T, input, replicate 1 eCLIP

description: Library name: GRB2-HEK293T-1 IN


title: L984_CI

description: Library name: Sample 6

value: Liver

value: Primary cells

value: Bulk of cells

value: Standard Diet (SD)


title: sh33_cyto_rep3

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

value: Keratinocytes

value: cytoplasm


title: seCLIP_INPUT_L_Rep2

description: Size-matched input (SMI) RNA (Control), lower band (L), replicate 2

tag: antibody

value: Size-matched input (SMI) RNA

tag: type

value: INPUT

tag: band

value: L


title: MBNL2, HEK293T, IP, replicate 1 eCLIP

description: Library name: MBNL2-HEK293T-1 IP

value: human embryonic kidney


title: LLC-GFP tumor-bearing lungs, all cells

description: Library name: NO001

treatment_protocol: C57B6/JN mice (n=3) were intravenously injected with 1.5e5 LLC-GFP cells. After 17 days, lungs of mice were harvested. Tumor tissue and normal-adjacent lung tissue were seperated utilizing microdissection techniques and each tissue was labeled using seperate hashtag oligos (HTOs; (n=6)). Cells were then sequenced with the 10X Illumina platform

value: All cells

tag: genotype


title: clone28_4

description:
Library name: 366555
SMART-Seq v3

tag: plate

tag: cloneid

value: G

value: N


title: clone30_4

description:
Library name: 366565
SMART-Seq v3

tag: color

tag: clone type

value: SN


title: EIF4B, HEK293T, IP, replicate 2 eCLIP

description: Library name: EIF4B-HEK293T-2 IP


title: p_663

description: Library name: Sample 2

tag: treatment


title: LLC-GFP tumor- bearing murine lung lobe, rep2

description:
Library name: AG-F-6091
Fresh frozen lungs for spatial transcriptomics

data_processing:
spaceranger-1.3.1
Spatial 3' v1
Assembly: mm10-2020-A
Supplementary files format and content: h5, png, json, csv, jpg
Library strategy: Spatial Transcriptomics

source_name: Lung

extract_protocol:
Tumor-bearing lungs were flash frozen and sectioned (8um thickness) onto 10X Visium slide
Spatial Transcriptome sequencing libraries were prepared with 10XGenomics Visiium Spatial Gene Expression Slides and Reagents kit according to manufactureres construction

value: Lung

value: Lung tissue


title: clone28_3

description:
Library name: 366554
SMART-Seq v3

value: cerebral organoid

tag: clone size


title: sh33_cyto_rep2

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

tag: replicate

tag: condition

tag: compartment


title: clone56_2

description:
Library name: 366673
SMART-Seq v3


title: clone30_1

description:
Library name: 366562
SMART-Seq v3

value: R


title: sh33_cyto_rep1

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

tag: shRNA

tag: shRNA type


title: PBS_gex

city: St Louis

first: Junedh

last: Amrute

state: MO

address: 660 S Euclid Ave

institute: Washington University School of Medicine

description: Library name: PBS_gex

data_processing:
Can be found in Methods Mineura et al, 2026
Assembly: GRCm39
Supplementary files format and content: .rds

source_name: mouse lung

extract_protocol:
Lung tissue digestion and single cell suspension preparation were performed as previously described (doi:10.1016/j.ajt.2025.08.021). Two lungs were pooled from each group at day 14 post-transplant. Samples were submitted to the Washington University Genome Technology Access Center for single nuclear genome-scale metabolic model and library construction.
Library preparation was conducted with Chromium GEM-X Single Cell 3' Reagent Kits v4 (10x Genomics). Libraries were sequenced on NovaSeq 6000.

tag: tissue

value: mouse lung


title: EIF4B, HEK293T, IP, replicate 1 eCLIP

description: Library name: EIF4B-HEK293T-1 IP

tag: cell line

tag: cell type


title: LLC-GFP tumor- bearing murine lung lobe, rep1

description:
Library name: AG-F-6090
Fresh frozen lungs for spatial transcriptomics


title: clone28_2

description:
Library name: 366553
SMART-Seq v3


title: NP_gex

description: Library name: NP_gex


title: EIF4B, HEK293T, input, replicate 2 eCLIP

description: Library name: EIF4B-HEK293T-2 IN


title: Liver metastases from ZDHHC17-silenced (shZdhhc17) 4T1 cells

city: Leuven

first: Juan

last: Fernández-García

address: Campus Gasthuisberg, O&N4, Herestraat 49, box 912

department: VIB-KU Leuven Center for Cancer Biology

country: Belgium

institute: VIB/KU Leuven

description:
Library name: shZDHHC17
BD Rhapsody

data_processing:
Libraries were first subject to shallow sequencing on an Illumina NextSeq2000 (P3 flow cell, 51-8-0-90) and, after quality check, were sequenced deeper on an Illumina NovaSeq6000 (S2 flow cell, 51-8-0-90), all at the VIB Nucleomics Core (www.nucleomics.be).
The BD Rhapsody Sequence Analysis Pipeline (BD Biosciences; version 2.0) was used to map the FASTQ files generated upon sequencing to the GRCm38 (mm10-2020-A) mouse reference genome. The resulting single-cell gene expression data were analysed within the R/Bioconductor framework (www.r-project.org and www.bioconductor.org).
Raw unique molecular identifier (UMI) count matrices for both samples (shSCR and shZdhhc17) were first imported using Seurat (v4.1.0) (www.satijalab.org/seurat), and immediately subject to ambient RNA correction on a per-sample basis, using a customized version of the SoupX (v1.6.2) R pipeline (https://github.com/constantAmateur/SoupX). Specifically, two modifications were applied to the standard SoupX pipeline. First, the automatically determined (global) ambient contamination fractions for each of the samples were multiplicatively increased by a factor of 5, to account for the fact that, as reported in the literature, the automatic determination method tends to underestimate ambient contamination levels for single-cell RNA-sequencing data. Second, rather than assuming a fixed contamination fraction for all cells, the latter was adapted for each cell based on its specific library size (total UMI counts), to achieve a uniform distribution of subtracted counts across all cells in each sample, in keeping with the nature of the ambient RNA contamination problem.
Ambient-corrected count matrices for the two samples were then merged together and converted for further processing with Monocle3-alpha (v2.99.3) (www.github.com/cole-trapnell-lab/monocle-release/tree/monocle3_alpha). Low-quality cells were filtered out based on standard quality-control metrics, with thresholds chosen based on evaluating quality-control histograms for the merged dataset. In particular, cells were filtered based on their mitochondrial RNA content (allowing for a maximum of 15%), library size (removing cells with total UMI counts below 500), and number of detected genes (removing cells expressing fewer than 250 genes). Genes not expressed in any of the cells remaining after quality-control filtering were ignored in all subsequent analyses. Size-factor and variance-stabilizing normalization (based on fitting to a negative binomial distribution) were then applied to the filtered dataset, and highly variable genes (HVGs) were identified based on their departure from the average normalized dispersion versus expression trend observed among all genes. After excluding mitochondrial, ribosomal protein, and cell cycle-associated genes, the top 1,000 HVGs with size-factor normalized expression levels above 0.02 were selected. Principal component analysis (PCA) was then performed on the size factor-normalized and variance-stabilized count matrix restricted to these genes only, followed by 2D uniform manifold approximation and projection (UMAP) dimensional reduction based on the resulting top 50 principal components (with correlation distance metric, number of neighbors = 15, and minimum distance = 0.1). After that, cells were clustered in the UMAP plane by applying Monocle3-alpha’s implementation of the Louvain graph-based algorithm at high resolution (resolution = 0.001, with kNN = 9), in order to attain a fine-grained cluster structure (138 clusters).
The resulting fine-grained clusters were then manually annotated to specific cell types, based on evaluating the expression profiles of several cell type-specific markers across the different fine-grained clusters. These cell-type annotations were further refined based on a second (analogous) step of dimensional reduction and clustering, applied separately to each of the preliminarily annotated cell-types. This in turn allowed us to more easily identify and filter out ambiguous clusters, most notably those originating from heterogeneous cell multiplets, characterized by simultaneously presenting markers associated to two or more cell types. Our multiplet identification was confirmed based on the distribution of doublet scores estimated across the different cells in each separate sample using the R package scDblFinder (v1.8.0) (https://bioconductor.org/packages/release/bioc/html/scDblFinder.html).
Specifically for the case of neutrophils, the latter were identified upon the first (global) clustering step based on expression of the markers S100a8, S100a9, Ly6g, and Retnlg, with ~ 9% of the cells initially annotated as neutrophils being re-annotated as potential multiplets (and thus excluded from all subsequent analyses) upon neutrophil-specific clustering refinement. Formal sub-clustering was then performed on the remaining neutrophils by applying unsupervised clustering in the PCA space, based again on Monocle3-alpha’s implementation of the Louvain algorithm, but now with default resolution/kNN parameters. The latter resulted in the identification of 9 different neutrophil clusters or subsets.
Marker genes for each of these subsets were inferred within the Seurat framework, using the function FindMarkers (with default parameters other than not imposing a fold-change threshold for output gene filtering) to compare each of the 9 subsets to the combination of all other subsets. In brief, the output of FindMarkers for each subset "s" was first filtered to include only genes enriched in that subset relative to the combination of all other subsets (log2FC > 0). A specificity score for that subset was then calculated for each of the remaining genes as SPEC = Xs × (1 – Xrest/2), where Xs and Xrest represent the fraction of cells expressing that gene within subset "s" and all other subsets, respectively. Genes were then ranked within each subset based on a combined marker score, defined as the product MS = log2FC ×  SPEC for each gene, with the top ranked genes for each subset being considered as potential markers. To ensure uniqueness among the markers assigned to different subsets, the list of potential markers for each subset was further filtered to include only genes presenting a higher marker score MS in that subset relative to all other subsets. The top 20 (unique) markers for each subset remaining after this filtering step were used to annotate the different neutrophil subsets to specific phenotypes. Subsets showing a substantial overlap (> 50%) between their top 100 potential markers (before imposing the marker-uniqueness constraint) were in turn annotated to the same phenotype (e.g. Early-Stage, NETosis, Migration).
Assembly: mm10 (GRCm38 mm10-2020-A)
Supplementary files format and content: The raw-count output of the BD Rhapsody Sequence Analysis Pipeline is provided in the form of MatrixMarket sparse matrices with gene|cell ID|counts triplets (matrix.mtx.gz), together with the corresponding gene (features.tsv.gz) and cell ID (barcodes.tsv.gz) index files, within a separate tar archive for each sample (Counts_SID.tar, where SID = shSCR or shZDHHC17 is the sample identifier). In addition, analogous supplementary files are provided containing a merged gene|cell ID|counts sparse matrix for the combination of both samples (Counts_FINAL.tar), after performing ambient RNA correction, filtering out cells based on quality-control metrics (mitochondrial RNA content, library size, and number of detected genes), and removing genes not expressed in any of the cells remaining after quality-control filtering. The latter are accompanied by text-based tables (GeneMetaData_FINAL.txt, CellMetaData_FINAL.txt) with all relevant gene/cell meta data needed to reproduce the results of the final analysis, including quality-control metrics, cell-type annotations, fine-grained cluster assignments, and UMAP coordinates. Finally, analogous text-based tables (GeneMetaData_NEUTROPHILS.txt, CellMetaData_NEUTROPHILS.txt) are also provided with the relevant gene/cell meta data corresponding to the neutrophil sub-clustering analysis, together with an additional text-based table with relevant metrics for the top 20 (unique) marker genes used to annotate each of the 9 neutrophil clusters identified by our neutrophil sub-clustering analysis (MarkerGenes_NEUTROPHILS.txt). A description of the full contents of all the above text-based tables is provided in a separate text file (FileContentsDescription.txt).

source_name: Liver metastases

growth_protocol:
4T1 murine triple-negative (ER-/PR-/HER2-) breast-cancer cells were purchased from the American Type Culture Collection (ATCC), and were grown in Roswell Park Memorial Institute (RPMI) 1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin (50 units/mL) and 1% streptomycin (50 µg/mL), in a temperature-controlled humidified incubator at 37°C, with 5% CO₂ and 95% relative humidity. Cells were routinely tested negative for Mycoplasma infection using the MycoAlert Detection Kit (Lonza).
ZDHHC17-silenced 4T1 cells (shZdhhc17) were generated using the short hairpin RNA (shRNA)-expressing lentiviral TRC1 pLKO.1-shRNA vector with a puromycin selection. As negative control, a non-targeting scrambled shRNA (shSCR) sequence was used. For this, lentivirus was produced by transfecting HEK293T cells with psPAX2, PMD2.6 and lentiviral vectors using Lipofectamine 2000. After an overnight transduction, medium was refreshed for 24h and cells were selected with puromycin (2µg/ml) for 72h. shRNA-based silencing was confirmed by RT-qPCR.

extract_protocol:
Following mice euthanasia, livers were perfused through the left ventricle for full body perfusion, extracted, and briefly washed in blood bank saline. Liver metastases from mice injected with 4T1 shSCR (n = 3) and 4T1 shZdhhc17 (n = 3) were then dissected under the microscope, and subsequently incubated at 37 °C for 45 min with a solution of 0.3 mg/ml liberase (Roche) and 1 µg/ml DNase1 in 2 ml of DMEM/F12 supplemented with 5% fetal bovine serum. The dissociated metastases were quenched with FACS buffer (3% fetal bovine serum in PBS supplemented with 2 mM EDTA), filtered through a 70-µm cell strainer, and centrifuged for 5 min at 300g. The cell pellets were then washed, centrifuged for 5 min at 300g, incubated with ACK lysis buffer (Merck) and strained with a 40 µm cell strainer. Single-cell suspensions were then counted, and the same number of cells were pooled together from the 3 independent liver-metastases dissociations performed per group (shSCR or shZdhhc17). The cells were then resuspended in cell culture medium and loaded on a BD Rhapsody cartridge with a targeted capture of 15,000 cells per group.
Reverse transcription, cDNA amplification, and library construction were performed following the manufacturer’s instructions (23-24117(02)).

treatment_protocol: ZDHHC17-silenced (shZdhhc17) or control (shSCR) 4T1 cells were injected intrasplenically into 6-8 week-old female BALB/c mice (250,000 cells/injection), with spleens being surgically removed 2 minutes after cancer-cell injection.  After 14 days, mice were euthanized with an intraperitoneal injection of 10 µl/g containing ketamine (100 mg/kg) and xylazine (10 mg/kg).

tag: strain

value: BALB/c

tag: age

value: 6-8 weeks-old

tag: Sex

value: Female

value: Liver metastases

tag: injected cell_line

tag: injected cell_type

value: Triple-negative breast cancer

tag: injected cell-line_genotype

value: ZDHHC17-silenced (shZdhhc17)

tag: days post_injection


title: sh33_cb_rep3

description: Subcellular RNA-seq of cell body polyA+ RNA in Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #2), replicate 3

value: Keratinocytes

value: cell body


title: sh33_cb_rep2

description: Subcellular RNA-seq of cell body polyA+ RNA in Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #2), replicate 2


title: EIF4B, HEK293T, input, replicate 1 eCLIP

description: Library name: EIF4B-HEK293T-1 IN

value: human embryonic kidney


title: clone28_1

description:
Library name: 366552
SMART-Seq v3

tag: genotype

tag: plate

tag: cloneid

tag: color

tag: clone type


title: Pdgfra-Il1r1, S aureus

description: Library name: pos_staph

value: skin

tag: treatment 1

value: 14h S aureus


title: Liver metastases from control (shSCR) 4T1 cells

description:
Library name: shSCR
BD Rhapsody

value: Control (shSCR)


title: clone27_2

description:
Library name: 366551
SMART-Seq v3

value: G

value: SN

tag: clone size


title: clone29_2

description:
Library name: 366560
SMART-Seq v3

tag: tissue

value: cerebral organoid


title: sh33_cb_rep1

description: Subcellular RNA-seq of cell body polyA+ RNA in Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #2), replicate 1

tag: replicate

tag: condition

tag: compartment

tag: shRNA

tag: shRNA type


title: CPSF6, HEK293T, IP, replicate 2 eCLIP

description: Library name: CPSF6-HEK293T-2 IP

tag: cell line

tag: cell type


title: Liver metastases from ZDHHC17-silenced (shZdhhc17) 4T1 cells, replicate 3

description:
Library name: 4T1.shZDHHC17.R3
4T1.shZDHHC17.R3

data_processing:
Purified dual-indexed sequence-libraries of each sample were equimolarly pooled and sequenced on an Illumina NovaSeq 6000 (v1.5 kit, single read 100 (100-10-10-0)) at the VIB Nucleomics Core (www.nucleomics.be).
Following demultiplexing, reads for each sample originating from different sequencing lanes were concatenated, and the resulting merged reads were subject to optical-duplicate removal and adapter trimming using the BBMap suite (v38.98; https://sourceforge.net/projects/bbmap) modules clumpify (parameters: dupedist=12000 dedupe=t optical=t) and BBDuk (parameters: ktrim=r k=20 mink=10 hdist=1 minlength=50), respectively. Trimmed-read quality control was then performed using FastQC (v0.11.8; https://www.bioinformatics.babraham.ac.uk/projects/fastqc). High-quality reads were then mapped to the mm39 reference mouse genome (GRCm39, Gencode build vM30) using STAR (v2.6.1; https://github.com/alexdobin/STAR), and further quantified using HTSeq’s (v0.9.1; https://htseq.readthedocs.io) htseq-count module (parameters: --stranded='reverse' --mode=union --nonunique=none). All the above steps were carried out using the VSC (Flemish Supercomputer Center) infrastructure, funded by the Research Foundation - Flanders (FWO) and the Flemish Government.
Gene counts for all 6 samples collected under the 2 conditions of interest (shSCR and shZdhhc17) were first filtered to keep only genes expressed in at least 2 out of 3 samples for at least one of the two conditions.  Differential expression analysis was then performed within the DESeq2 (v1.34.0; https://bioconductor.org/packages/release/bioc/html/DESeq2.html) framework on the remaining (24167) genes, in order to determine differentially expressed genes between shZdhhc17 and shSCR metastases.
DESeq2-derived log fold-changes (log2FC) and P-values for all genes in the shZdhhc17 versus shSCR contrast were further combined to derive a ranking metric of the form RM = -log10(P-value) × log2FC. Pre-ranked gene-set enrichment analysis (GSEA; https://www.gsea-msigdb.org/gsea) was then performed based on this ranking metric, using the R package fgsea (v1.20.0; https://github.com/ctlab/fgsea; fgsea-multilevel implementation with 10000 initial permutations and no lower bound for P-value estimation), and considering a collection of 3065 mouse gene sets. The latter comprised all HALLMARK and CURATED (C2) gene sets in the Broad Institute Molecular Signatures Database (MSigDB; https://www.gsea-msigdb.org/gsea/msigdb) except for those in category C2:CGP, all of them obtained using the R package msigdbr (v7.4.1; https://igordot.github.io/msigdbr), plus all KEGG (https://www.genome.jp/kegg) metabolism gene sets, obtained by querying KEGG's REST API (https://www.kegg.jp/kegg/rest). Only gene sets containing between 3 and 1500 genes (out of those with available differential expression analysis results) were considered for GSEA. Gene sets with either positive/negative (enriched/depleted in shZdhhc17 versus shSCR metastases, respectively) normalized enrichment scores (NES) were ranked based on their absolute NES.
Assembly: mm39 (GRCm39, Gencode build vM30)
Supplementary files format and content: The raw-count matrix for all 6 samples included in the study is provided as a tab-separated text file (rawCounts.txt), after filtering out genes with no expression in at least 2 out of 3 samples for at least one of the two conditions considered in the study. The first two columns of this file contain respectively gene stable IDs and symbols. For genes without defined symbols, stable IDs are used in their place. Genes with different stable IDs but annotated to identical symbols are designated by appending .X to the latter, where X = 2...N, with N being the total number of times the same symbol is annotated to different stable IDs. Text-based tab-separated tables are also provided with the results of DESeq2-based differential expression analysis (DESeq2results.txt) and GSEA (GSEAresults.txt). The latter are accompanied by a text file (DESeq2GSEAColumnDescription.txt) describing the contents of the various columns in each of the two files, and a gmt file with the gene-set collection used for GSEA (GeneSets_mmHC2KEGGmet.gmt).

growth_protocol:
4T1 murine triple-negative (ER-/PR-/HER2-) breast-cancer cells were purchased from the American Type Culture Collection (ATCC), and were grown in Roswell Park Memorial Institute (RPMI) 1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin (50 units/mL) and 1% streptomycin (50 µg/mL), in a temperature-controlled humidified incubator at 37°C, with 5% CO₂ and 95% relative humidity. Cells were routinely tested negative for Mycoplasma infection using the MycoAlert Detection Kit (Lonza).
ZDHHC17-silenced 4T1 cells (shZdhhc17) were generated using the short hairpin RNA (shRNA)-expressing lentiviral TRC1 pLKO.1-shRNA vector with a puromycin selection. As negative control, a scrambled shRNA (shSCR) sequence was used. For this, lentivirus was produced by transfecting HEK293T cells with psPAX2, PMD2.6 and lentiviral vectors using Lipofectamine 2000. After an overnight transduction, medium was refreshed for 24h and cells were selected with puromycin (2µg/ml) for 72h. shRNA-based silencing was confirmed by RT-qPCR.

extract_protocol:
Following mice euthanasia, livers were extracted, and liver metastases from mice injected with 4T1 shSCR (n = 3) and 4T1 shZdhhc17 (n = 3) were dissected under the microscope. RNA was then isolated from the dissected metastases using Trizol reagent (Thermo Scientific). RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-8000 (Nanodrop Technologies) and RNA integrity and concentration were assessed using the Bionalyzer RNA Nano kit (Agilent).
Per sample, 500 ng of total RNA were used as input for RNA-sequencing library preparation. Using the Illumina Stranded mRNA Sample Prep Kit (protocol version: # 1000000124518 v02 (April 2021)), poly-A containing mRNA molecules were purified from the total RNA input using poly-dT oligo-attached magnetic beads. The purified mRNA was then fragmented, converted into first strand cDNA in a reverse transcription reaction using random primers and Actinomycin D, and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using dUTP to achieve strand specificity. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which pre-index anchors were ligated preparing the fragments for dual indexing. Anchor-ligated fragments were then purified using magnetic beads. Finally, enrichment PCR was carried out to enrich those DNA fragments that have anchor-ligated DNA fragments and to add indexes and primer sequences for cluster generation.

treatment_protocol: ZDHHC17-silenced (shZdhhc17) or control (shSCR) 4T1 cells were injected hydrodynamically in the tail vein of 6-8 week-old female BALB/c mice (500,000 cells/injection). After 10 days, mice were euthanized with an intraperitoneal injection of Dolethal (50µl of 60 mg/mL).

tag: strain

tag: age

tag: Sex

tag: injected cell_line

tag: injected cell_type

tag: injected cell-line_genotype


title: CPSF6, HEK293T, IP, replicate 1 eCLIP

description: Library name: CPSF6-HEK293T-1 IP


title: clone27_1

description:
Library name: 366550
SMART-Seq v3

tag: genotype

tag: plate

tag: cloneid

tag: color

tag: clone type


title: sh12_protr_rep2

description: Subcellular RNA-seq of cell protrusions polyA+ RNA in Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #1), replicate 2

tag: replicate

tag: condition

value: protrusions


title: Il1r1-fl/fl Control, S aureus

description: Library name: neg_staph

tag: tissue

value: Il1r1-fl/fl control

tag: treatment 1


title: Liver metastases from ZDHHC17-silenced (shZdhhc17) 4T1 cells, replicate 2

description:
Library name: 4T1.shZDHHC17.R2
4T1.shZDHHC17.R2

value: BALB/c

tag: days post_injection


title: sh12_protr_rep3

description: Subcellular RNA-seq of cell protrusions polyA+ RNA in Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #1), replicate 3

tag: cell type

tag: compartment

tag: shRNA

tag: shRNA type


title: CPSF6, HEK293T, input, replicate 2 eCLIP

description: Library name: CPSF6-HEK293T-2 IN

tag: cell line


title: clone26_3

description:
Library name: 366548
SMART-Seq v3

value: N

tag: clone size


title: clone26_4

description:
Library name: 366549
SMART-Seq v3


title: Liver metastases from ZDHHC17-silenced (shZdhhc17) 4T1 cells, replicate 1

description:
Library name: 4T1.shZDHHC17.R1
4T1.shZDHHC17.R1

tag: strain

tag: age

value: 6-8 weeks-old

tag: Sex

value: Female

tag: injected cell_line

tag: injected cell_type

tag: injected cell-line_genotype


title: clone37_1

description:
Library name: 366590
SMART-Seq v3

tag: genotype

tag: plate

tag: cloneid

tag: color

value: R

tag: clone type


title: CPSF6, HEK293T, input, replicate 1 eCLIP

description: Library name: CPSF6-HEK293T-1 IN

tag: cell type


title: sh12_protr_rep1

description: Subcellular RNA-seq of cell protrusions polyA+ RNA in Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #1), replicate 1

tag: replicate

tag: condition

tag: compartment


title: Liver metastases from control (shSCR) 4T1 cells, replicate 3

description:
Library name: 4T1.shSCR.R3
4T1.shSCR.R3

tag: tissue

value: Liver metastases

value: Triple-negative breast cancer

tag: days post_injection


title: unstimulated 4.

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:4

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.

value: intestine

tag: cell line

value: fibroblast


title: clone26_2

description:
Library name: 366547
SMART-Seq v3

tag: clone size


title: sh12_nucl_rep3

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

value: Keratinocytes

value: nucleo

tag: shRNA

tag: shRNA type


title: CPSF5, HEK293T, IP, replicate 2 eCLIP

description: Library name: CPSF5-HEK293T-2 IP

value: human embryonic kidney


title: sh12_nucl_rep2

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


title: Liver metastases from control (shSCR) 4T1 cells, replicate 2

description:
Library name: 4T1.shSCR.R2
4T1.shSCR.R2

tag: strain

tag: age

tag: Sex

tag: injected cell_line

tag: injected cell_type

value: Control (shSCR)


title: clone26_1

description:
Library name: 366546
SMART-Seq v3

tag: genotype

tag: plate

tag: cloneid

tag: color


title: CPSF5, HEK293T, IP, replicate 1 eCLIP

description: Library name: CPSF5-HEK293T-1 IP

tag: cell type


title: Liver metastases from control (shSCR) 4T1 cells, replicate 1

description:
Library name: 4T1.shSCR.R1
4T1.shSCR.R1

tag: injected cell-line_genotype


title: CPSF5, HEK293T, input, replicate 2 eCLIP

description: Library name: CPSF5-HEK293T-2 IN


title: clone25_3

description:
Library name: 366545
SMART-Seq v3

tag: tissue

value: G

tag: clone type


title: sh12_cyto_rep3

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

tag: replicate

tag: condition

tag: compartment

value: cytoplasm


title: clone25_2

description:
Library name: 366544
SMART-Seq v3

value: cerebral organoid

tag: clone size


title: CPSF5, HEK293T, input, replicate 1 eCLIP

description: Library name: CPSF5-HEK293T-1 IN

tag: cell line


title: PiZ_4

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

institute: Tigem

description:
Library name: 202307050939_NP-9_S53_L002_R1_001
Transcriptome profile of liver from PiZ mouse, biological rep3

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: mm10
Supplementary files format and content: Piz_2_RLog_NormalizedCounts.txt

source_name: Intestine

growth_protocol: Intestine was collected from 6-week-old WT and PiZ mice

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)

value: Intestine

value: PiZ


title: clone25_1

description:
Library name: 366543
SMART-Seq v3

value: N


title: sh12_cyto_rep2

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

tag: shRNA

tag: shRNA type


title: SMNDC1 non-target 2 biol rep 2

city: Irvine

first: Yoseop

last: Yoon

address: 1002 Health Sciences Rd

institute: University of California Irvine

description: Library name: YY97

data_processing:
PAS-seq data analysis was conducted as described by (Wang et al., 2021).
Assembly: hg38
Supplementary files format and content: bigwig

growth_protocol: All HEK293T cell lines were cultured in DMEM (Dulbecco's Modified Eagle Medium, high glucose, pyruvate) (Gibco, 11995065) supplemented with 10% FBS (fetal bovine serum) (Sigma, F0926-100ML).

extract_protocol:
TRIZOL
2µg of total RNA was used for PAS-seq library preparation, adhering to the protocol detailed in our methodological paper (Yoon et al., 2021).

treatment_protocol: Protein knockdown samples were generated using short targeting RNA (shRNA) plasmids from the MISSION lentiviral collection (Sigma-Aldrich). HEK293XT cells were seeded onto 12-well plates at a density of 0.1x106 cells per well in 1mL of DMEM (LifeTech, 11995065) + 10% FBS and grown overnight. The media was replaced the following day using fresh media containing 8ug/mL polybrene (Hexadimethrine bromide - Sigma Aldrich cat# H9268) 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 cell

tag: treatment

value: siRNA

tag: batch

value: C


title: sh12_cyto_rep1

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


title: PiZ_3

description:
Library name: 202307050939_NP-8_S52_L002_R1_001
Transcriptome profile of liver from PiZ mouse, biological rep2

tag: genotype


title: SMNDC1 non-target 2 biol rep 1

description: Library name: YY96


title: clone24_5

description:
Library name: 366542
SMART-Seq v3

tag: plate


title: PiZ_2

description:
Library name: 202307050939_NP-7_S51_L002_R1_001
Transcriptome profile of liver from PiZ mouse, biological rep1


title: clone24_4

description:
Library name: 366541
SMART-Seq v3

tag: cloneid

value: R


title: sh12_cb_rep3

description: Subcellular RNA-seq of cell body polyA+ RNA in Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #1), replicate 3

value: cell body


title: clone24_3

description:
Library name: 366540
SMART-Seq v3

tag: color


title: WDR6 non-target 2 biol rep 1

description: Library name: YY94

tag: cell type


title: sh12_cb_rep2

description: Subcellular RNA-seq of cell body polyA+ RNA in Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #1), replicate 2


title: sh12_cb_rep1

description: Subcellular RNA-seq of cell body polyA+ RNA in Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #1), replicate 1


title: clone24_2

description:
Library name: 366539
SMART-Seq v3


title: Anopheles gambiae infected with early-selected Vavraia culicis lineage 5 biological replicate 3

city: Vancouver

first: Luis

middle: M.

last: Silva

state: British Columbia

address: 2212 Main Mall

department: Department of Zoology

country: Canada

institute: The University of British Columbia

description:
Library name: E53
Pool of 10 adult female Anopheles gambiae infected with early-selected Vavraia culicis lineage 5, biological replicate 3; column name in processed expression matrix: E53

data_processing:
Demultiplexing was performed with bcl2fastq2 v2.20.
Adapters and low-quality bases were removed with Cutadapt, reads shorter than 40 nt were discarded, and reads mapping to rRNA were removed with fastq_screen. Filtered reads were aligned to a concatenated Anopheles gambiae and Vavraia culicis reference using STAR. Gene-level counts were obtained with htseq-count.
Assembly: Anopheles gambiae assembly GCA_943734735.2 and Vavraia culicis floridensis assembly GCA_000192795.1
Supplementary files format and content: File_S9_data1.txt: tab-delimited processed host gene expression matrix for all 48 samples, with gene identifiers, sample expression values and gene annotation columns.

organism: Anopheles gambiae

source_name: whole adult female mosquito

growth_protocol: Anopheles gambiae Kisumu larvae were reared under standard insectary conditions at 26 ± 1 °C, 70 ± 5% relative humidity and a 12 h light:12 h dark cycle. Freshly hatched larvae were reared at 50 larvae in 80 ml distilled water and fed daily with fish food. Adult females were maintained with constant access to 6% sucrose solution.

extract_protocol:
Total RNA was extracted from independent pools of 10 adult females using the Qiagen RNeasy Universal Plus kit. Adults were homogenized in QIAzol reagent with stainless steel beads, genomic DNA was removed according to the manufacturer protocol, and RNA was eluted in nuclease-free water.
RNA quality was assessed on an Agilent Fragment Analyzer. Libraries were prepared from 250 ng total RNA per sample using the Illumina Stranded mRNA Prep kit with unique dual indices and sequenced as 150 bp single-end reads on an Illumina NovaSeq 6000 platform.

treatment_protocol: On day 2 of larval development, mosquitoes were exposed to 10,000 Vavraia culicis spores per larva from the relevant parasite lineage. Treatments were uninfected controls, an unselected reference parasite lineage, five early-selected parasite lineages and five late-selected parasite lineages. Adult females were sampled on day 10 of adulthood, when infections were chronic and sporulating.

value: whole adult female mosquito

value: Kisumu


title: scramble_protr_rep3

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

value: Keratinocytes

value: protrusions

value: sh-Scramble


title: WT_1

description:
Library name: 202307050939_NP-1_S45_L002_R1_001
Transcriptome profile of liver from control mouse, biological rep1

value: WT


title: clone24_1

description:
Library name: 366538
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.

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).


title: RPS19BP1 non-target 2 biol rep 1

description: Library name: YY92


title: clone23_3

description:
Library name: 366537
SMART-Seq v3

value: G

value: SN


title: E11-5-Cramp1-WT-liver_rep2

city: Shanghai

first: Yu

last: Liang

address: Yueyang Road 320

department: SIBCB

country: China

institute: CEMCS, CAS

description: E11.5-Cramp1-WT-liver_vs_E11.5-Cramp1-KO-liver.transposon.abundance_rep1andrep2.csv

data_processing:
The expression of genes and transposons was analyzed and quantified by piPipes.
Assembly: dm6 and Drosophila TE consensus sequence for fruitfly; mm10 and repBase sequence for mouse.
Supplementary files format and content: csv

source_name: E11.5d Liver

extract_protocol:
Total RNA was extracted by using TRIzol Reagent (Invitrogen, CAT#: 15596018) and precipitated by isopropanol. 10µg of total RNA was treated with DNase and then purified by RNA Clean & Concentrator-5 (Zymo research, CAT#: R1016).
One µg of purified RNA was used for RNA-Seq library preparation by utilizing TruSeq Stranded Total RNA Library Prep kit (Illumina, CAT#: 20020596).

value: E11.5d Liver

value: Cramp1 heterozygote


title: RBM42 non-target 2 biol rep 1

description: Library name: YY90


title: scramble_protr_rep1

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


title: clone23_1

description:
Library name: 366535
SMART-Seq v3

value: cerebral organoid


title: E11-5-Cramp1-KO-liver_rep2

value: Cramp1 mutant


title: scramble_nucl_rep3

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

value: nucleo


title: non-target 3 biol rep 5

description: Library name: YY89

value: human embryonic kidney cell

value: siRNA


title: E11-5-Cramp1-WT-liver_rep1


title: non-target 3 biol rep 4

description: Library name: YY88

value: C


title: scramble_nucl_rep2

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


title: E11-5-Cramp1-KO-liver_rep1


title: non-target 3 biol rep 3

description: Library name: YY87


title: clone22_1

description:
Library name: 366533
SMART-Seq v3

value: R


title: scramble_nucl_rep1

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


title: E13-5-Cramp1-WT-liver_rep2

description: E13_5-Cramp1-WT-liver_vs_E13_5-Cramp1-KO-liver.transposon.abundance_rep1andrep2.csv

source_name: E13.5d Liver

value: E13.5d Liver


title: clone21_7

description:
Library name: 366532
SMART-Seq v3

value: N


title: non-target 3 biol rep 2

description: Library name: YY86


title: scramble_cyto_rep3

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

value: Keratinocytes

value: cytoplasm


title: E13-5-Cramp1-KO-liver_rep2


title: clone21_6

description:
Library name: 366531
SMART-Seq v3


title: non-target 3 biol rep 1

description: Library name: YY85


title: STAU2 biol rep 2

description: Library name: YY84

value: B


title: E13-5-Cramp1-WT-liver_rep1


title: clone21_5

description:
Library name: 366530
SMART-Seq v3


title: scramble_cyto_rep1

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

value: sh-Scramble


title: clone21_4

description:
Library name: 366529
SMART-Seq v3

value: G


title: STAU2 biol rep 1

description: Library name: YY83


title: scramble_cb_rep3

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

value: cell body


title: RBM42 non-target 2 biol rep 2

description: Library name: YY91


title: Cramp1_WT_scRNAseq

description: 10x Genomics

data_processing:
Sequenced reads were aligned to mouse reference genome mm10 by using CellRanger (v7.1.0) and scTE (v1.0). Outputs were imported into R (v 4.2.2) for downstream analysis using Seurat (v 4.4.0).
Assembly: mm10
Supplementary files format and content: h5ad

extract_protocol:
Livers were minced on ice and dissociated into single-cell suspensions. Dissociated cells were washed with 1×DPBS containing 2% FBS. Cells were stained with AO/Pl, and viability was assessed using a Countstar Fluorescence Cell Analyzer (Aber Instruments).
Single cell RNA-seq library preparation and sequencing were performed by Benagen.


title: scramble_cb_rep2

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


title: ZMAT3 biol rep 2

description: Library name: YY82


title: Cramp1_KO_scRNAseq

description: 10x Genomics


title: clone21_2

description:
Library name: 366527
SMART-Seq v3


title: scramble_cb_rep1

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


title: ZMAT3 biol rep 1

description: Library name: YY81


title: clone21_1

description:
Library name: 366526
SMART-Seq v3


title: Preterm infant saliva miRNA - H11 (Control)

type: RNA

city: Almaty

first: Iskander

last: Isgandarov

address: Timiryazev 45

country: Kazakhstan

institute: Institute of plant biology and biotechnology

hyb_protocol: Labeled samples hybridized to Affymetrix GeneChip miRNA 4.1 Array using GeneTitan Multi-Channel (MC) instrument, 96-well plate format, per Affymetrix miRNA Assay protocol.

scan_protocol: Arrays scanned using Affymetrix GeneTitan MC instrument.

data_processing: Raw CEL files imported in R using oligo package (v1.74.0). RMA normalization applied (background=FALSE). All 36,353 probe set intensity values (RMA log2 scale) provided in Matrix table. Probe set names correspond to Affymetrix miRNA-4_1-st-v1 annotation (20160922). For differential expression: human miRNA probes (n=2,578) filtered by mean log2 intensity >5; limma (v3.66.0) with empirical Bayes, Benjamini-Hochberg FDR correction.

label: biotin

source_name: Saliva

label_protocol: RNA (100 ng) labeled with Affymetrix FlashTag Biotin HSR RNA Labeling Kit per manufacturer protocol. Poly(A) tailing performed at 37°C for 15 min; ligation with 5X FlashTag Biotin HSR Ligation Mix and T4 DNA Ligase at 25°C for 30 min.

growth_protocol: N/A - clinical study; preterm newborns managed per standard NICU protocols.

extract_protocol: Saliva was collected from each preterm infant at days 10-14 of life, one hour prior to feeding, by sterile syringe aspiration. Samples were placed in RNAprotect Cell Reagent and transported to the laboratory within 2 hours on ice. After pre-clearing, 100 µl saliva served as input for RNA extraction. Total RNA including the miRNA fraction was isolated using the MagMAX mirVana Total RNA Isolation Kit (Thermo Fisher Scientific) on a KingFisher Flex automated platform, per manufacturer instructions.

treatment_protocol: N/A - no experimental treatment applied.

tag: disease status

value: Control

tag: gestational age (weeks)

tag: birth weight (g)

tag: age at sampling (days of life)

tag: rds

value: grade 1

tag: surfactant administration

value: no

tag: mechanical ventilation from birth

tag: ivh

value: grade 3


title: sh33_nucleo_Rep4

description: Subcellular RNA-seq of nuclear polyA+ RNA in Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #2), replicate 4

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.

tag: replicate

tag: condition

tag: compartment

value: nucleo

tag: shRNA


title: AHNAK biol rep 2

description: Library name: YY80

tag: cell line

value: human embryonic kidney cell

tag: treatment

tag: batch


title: Preterm infant saliva miRNA - H10 (Control)

value: grade 2

value: yes


title: clone20_2

description:
Library name: 366525
SMART-Seq v3

tag: tissue

value: cerebral organoid

tag: genotype

tag: plate

tag: cloneid

tag: color

tag: clone type

value: SN

tag: clone size


title: sh33_nucleo_Rep3

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

tag: cell type

tag: shRNA type


title: AHNAK biol rep 1

description: Library name: YY79

value: siRNA


title: E13-5-Cramp1-KO-liver_rep1

value: E13.5d Liver

value: Cramp1 mutant


title: clone20_1

description:
Library name: 366524
SMART-Seq v3

value: R


title: sh33_nucleo_Rep2

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

value: Keratinocytes


title: Preterm infant saliva miRNA - H09 (Control)

tag: disease status

tag: gestational age (weeks)

tag: birth weight (g)

tag: age at sampling (days of life)

tag: rds

tag: surfactant administration

tag: mechanical ventilation from birth

tag: ivh

value: absent


title: YWHAG biol rep 2

description: Library name: YY78

tag: cell line

tag: treatment

tag: batch

value: B


title: clone19_2

description:
Library name: 366523
SMART-Seq v3

tag: tissue

tag: genotype

tag: plate

tag: cloneid


title: sh33_nucleo_Rep1

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

tag: cell type

tag: replicate

tag: condition

tag: compartment

tag: shRNA


title: YWHAG biol rep 1

description: Library name: YY77


title: Preterm infant saliva miRNA - H05 (Control)

tag: disease status

value: Control

tag: gestational age (weeks)

tag: birth weight (g)

tag: age at sampling (days of life)


title: clone21_3

description:
Library name: 366528
SMART-Seq v3

tag: color

tag: clone type

value: N

tag: clone size


title: Preterm infant saliva miRNA - H04 (Control)

tag: rds

value: grade 1

tag: surfactant administration

value: no

tag: mechanical ventilation from birth

tag: ivh


title: sh33_cyto_Rep4

description: Subcellular RNA-seq of cytoplasmic polyA+ RNA in Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #2), replicate 4

value: cyto

tag: shRNA type


title: HNRNPH2 biol rep 2

description: Library name: YY76

tag: cell line

tag: cell type

value: human embryonic kidney cell

tag: treatment

tag: batch


title: clone19_1

description:
Library name: 366522
SMART-Seq v3

tag: tissue

tag: genotype

tag: plate

tag: cloneid

value: G


title: HNRNPH2 biol rep 1

description: Library name: YY75


title: clone18_3

description:
Library name: 366521
SMART-Seq v3


title: Preterm infant saliva miRNA - H03 (Control)

tag: disease status

tag: gestational age (weeks)

tag: birth weight (g)

tag: age at sampling (days of life)

value: grade 2

value: yes


title: sh33_cyto_Rep3

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

tag: replicate

tag: condition

tag: compartment

tag: shRNA


title: clone18_2

description:
Library name: 366520
SMART-Seq v3

value: cerebral organoid

tag: color

tag: clone type

value: SN

tag: clone size


title: sh12_nucl_rep1

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

tag: cell type

value: nucleo

tag: shRNA type


title: PiZ_5

description:
Library name: 202307050939_NP-10_S54_L002_R1_001
Transcriptome profile of liver from PiZ mouse, biological rep4

tag: tissue

value: Intestine

value: PiZ


title: sh33_cyto_Rep2

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

value: Keratinocytes


title: Preterm infant saliva miRNA - H02 (Control)

tag: rds

tag: surfactant administration

tag: mechanical ventilation from birth

tag: ivh

value: grade 3


title: PRPF4 biol rep 2

description: Library name: YY74

tag: cell line

tag: treatment

value: siRNA

tag: batch

value: B


title: clone18_1

description:
Library name: 366519
SMART-Seq v3

tag: genotype

tag: plate

tag: cloneid


title: PRPF4 biol rep 1

description: Library name: YY73


title: Preterm infant saliva miRNA - H01 (Control)

tag: disease status

value: Control

tag: gestational age (weeks)

tag: birth weight (g)

tag: age at sampling (days of life)

value: absent


title: sh33_cyto_Rep1

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

tag: cell type

tag: replicate

tag: condition

tag: compartment

tag: shRNA


title: WDR6 non-target 2 biol rep 2

description: Library name: YY95

value: C


title: clone17_9

description:
Library name: 366518
SMART-Seq v3

tag: tissue

tag: color

tag: clone type

value: N

tag: clone size


title: WT_5

description:
Library name: 202307050939_NP-5_S49_L002_R1_001
Transcriptome profile of liver from control mouse, biological rep4

value: WT


title: sh12_nucleo_Rep4

description: Subcellular RNA-seq of nuclear polyA+ RNA in Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #1), replicate 4

tag: shRNA type


title: PCBP1 biol rep 2

description: Library name: YY72

tag: cell line

value: human embryonic kidney cell

tag: treatment

tag: batch


title: Preterm infant saliva miRNA - G12 (BPD)

tag: disease status

value: BPD

tag: rds

tag: surfactant administration

tag: mechanical ventilation from birth

tag: ivh

value: grade 1


title: ROI 120, Patient 22, Primary tumor bed, NMPR

city: Beijing

first: Rongzhen

last: Li

state: 北京Beijing

address: Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing 100730, China

institute: Peking Union Medical College

description: Library name: ROI 120

data_processing:
The raw FASTQ files were run through GeoMx NGS pipelines to acquire digital count conversions and initial data files for further analysis.
The initial data were further processed using quality control (QC) and normalization. RNA data were normalized using Total Count normalization with a scaling factor set at 10,210.
Assembly: mm10
Supplementary files format and content: csv file include normalized count data

source_name: Non-small cell lung cancer, Primary tumor bed

extract_protocol:
Formalin-fixed and paraffin-embedded (FFPE) tissues were used to construct tissue microarrays (TMAs). Cores (2.0 mm in diameter) were punched from each FFPE block and arrayed across two recipient TMA blocks. Five-μm-thick TMA sections were deparaffinized and rehydrated, and regions of interest (ROIs) were selected based on immunofluorescence morphology markers.
RNA extraction was performed using the NanoString GeoMx Digital Spatial Profiler according to the manufacturer’s protocol. Briefly, TMA sections were processed and regions of interest (ROIs) were selected based on immunofluorescence morphology markers. Each ROI was sequentially decoupled from the oligonucleotides using ultraviolet (UV) light. UV-cleavable oligos coupled with individual genes were cleaved and collected from all ROIs using a digital mirror device-guided UV illumination. The resultant oligos were amplified by polymerase chain reaction (PCR) amplified (Bio-Rad Laboratories, Hercules, CA, USA) using GeoMx Seq Code primers for downstream library construction.

treatment_protocol: Interventions included pembrolizumab at a fixed dose of 200 mg combined with carboplatin (area under the curve 5) or cisplatin 75mg/m2, pemetrexed at 500 mg/m2 for nonsquamous cell carcinoma, and paclitaxel at 175 mg/m2 or nab-paclitaxel at 260 mg/m2 for squamous cell carcinoma. Surgery was performed after at least two cycles of neoadjuvant therapy. All patients received adjuvant pembrolizumab for up to one year after surgery. To ensure that all patients received four cycles of perioperative chemotherapy, adjuvant chemotherapy was given to patients who had not received adequate neoadjuvant therapy. The surgical approaches were chosen by the surgeon.


title: WT_4

description:
Library name: 202307050939_NP-4_S48_L002_R1_001
Transcriptome profile of liver from control mouse, biological rep3

tag: genotype


title: clone17_8

description:
Library name: 366517
SMART-Seq v3

value: cerebral organoid

tag: plate

tag: cloneid

value: G


title: WT_3

description:
Library name: 202307050939_NP-3_S47_L002_R1_001
Transcriptome profile of liver from control mouse, biological rep2


title: sh12_nucleo_Rep3

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

tag: cell type

tag: replicate

tag: condition

tag: compartment

value: nucleo

tag: shRNA


title: RPS19BP1 non-target 2 biol rep 2

description: Library name: YY93


title: PCBP1 biol rep 1

description: Library name: YY71


title: Preterm infant saliva miRNA - G11 (Control)

tag: gestational age (weeks)

tag: birth weight (g)

tag: age at sampling (days of life)

value: grade 2

value: yes


title: clone17_7

description:
Library name: 366516
SMART-Seq v3

tag: tissue

tag: color

tag: clone type

tag: clone size


title: sh12_nucleo_Rep2

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

value: Keratinocytes

tag: shRNA type


title: Preterm infant saliva miRNA - G09 (Control)

tag: disease status

tag: rds

value: grade 3

tag: surfactant administration

tag: mechanical ventilation from birth

tag: ivh


title: LSM10 biol rep 2

description: Library name: YY70

tag: cell line

tag: cell type

tag: treatment

value: siRNA

tag: batch


title: clone17_6

description:
Library name: 366515
SMART-Seq v3

tag: genotype

tag: plate

tag: cloneid


title: scramble_protr_rep2

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

extract_protocol:
Cell protrusions were isolated from mouse keratinocytes (expressing shRNAs for Cbx3, or a scramble shRNA) as described before (Mardakheh M. et al., 2020) with some modiﬁcations to also fractionate the cytoplasm and the nucleus. 2 million cells were seeded on the top of 5 mg/ml collagen-I coated 24.5 mm polycarbonate transwell ﬁlters with 3 μm pore size (Greiner Bio-one) in complete DMEM. Cells were allowed to adhere without the addition of media to the bottom chamber of the transwells. Subsequently, the media on the top of the transwell ﬁlter was replaced by FBS and epidermal growth factor free DMEM, and protrusions were induced by addition of complete DMEM to the bottom chamber. Transwells were then washed with cold PBS, and protrusions were collected by shaving the bottom of the ﬁlter using a glass coverslip dipped in lysis buffer containing RNAse inhibitor (50mM Tris 1M HCl pH7.5, 100mM NaCl, 1% NP40, 0.1%SDS, 0.5%DOC). The cell-body fraction was subsequently purified by direct addition of the hypotonic cytoplasmatic buffer containing RNAse inhibitors on ice for 20min (10mM HEPES pH7.9, 60mM KCl, 1mM DTT, 1mM EDTA, 0.075% NP40) to the top of the ﬁlter, 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 protrusion, cytoplasm and nucleus fractions 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 stranded mRNA Sample Prep Kit (Illumina) following the manufacturer’s instructions. Libraries were sequenced on Illumina NextSeq 1000 System.

tag: replicate

tag: condition

tag: compartment

value: protrusions

tag: shRNA

value: sh-Scramble


title: sh12_nucleo_Rep1

tag: shRNA type


title: LSM10 biol rep 1

description: Library name: YY69

value: B


title: Preterm infant saliva miRNA - G08 (BPD)

tag: disease status

tag: gestational age (weeks)

tag: birth weight (g)

tag: age at sampling (days of life)

value: absent


title: clone23_2

description:
Library name: 366536
SMART-Seq v3

tag: tissue

tag: color

value: R

tag: clone type

value: SN

tag: clone size


title: sh12_cyto_Rep4

description: Subcellular RNA-seq of cytoplasmic polyA+ RNA in Cbx3-silenced mouse keratinocytes infected with sh-Cbx3 (KD sh #1), replicate 4

tag: cell type

value: cyto


title: clone17_5

description:
Library name: 366514
SMART-Seq v3

tag: genotype

value: N


title: YTHDF1 biol rep 2

description: Library name: YY68

tag: cell line

value: human embryonic kidney cell

tag: treatment

tag: batch


title: Preterm infant saliva miRNA - G07 (BPD)

value: BPD

tag: rds

tag: surfactant administration

tag: mechanical ventilation from birth

tag: ivh

value: grade 1


title: clone17_4

description:
Library name: 366513
SMART-Seq v3

value: cerebral organoid

tag: plate

tag: cloneid

value: G


title: YTHDF1 biol rep 1

description: Library name: YY67


title: Preterm infant saliva miRNA - G06 (BPD)

tag: disease status

tag: gestational age (weeks)

tag: birth weight (g)

value: grade 2

value: yes


title: sh12_cyto_Rep3

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

value: Keratinocytes

tag: replicate

tag: condition

tag: compartment

tag: shRNA

tag: shRNA type


title: LSM1 biol rep 2

description: Library name: YY66

tag: cell line

tag: cell type

value: siRNA


title: sh12_cyto_Rep2

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


title: clone17_3

description:
Library name: 366512
SMART-Seq v3

tag: tissue

tag: genotype

tag: color

tag: clone type

tag: clone size


title: clone17_2

description:
Library name: 366511
SMART-Seq v3

tag: plate


title: Preterm infant saliva miRNA - G05 (BPD)

tag: age at sampling (days of life)

tag: rds

value: grade 3

tag: surfactant administration

tag: mechanical ventilation from birth

tag: ivh


title: clone22_2

description:
Library name: 366534
SMART-Seq v3

tag: cloneid


title: LSM1 biol rep 1

description: Library name: YY65

tag: treatment

tag: batch


title: Preterm infant saliva miRNA - G03 (BPD)

tag: disease status

tag: gestational age (weeks)

tag: birth weight (g)


title: sh12_cyto_Rep1

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

tag: cell type

tag: replicate

tag: condition

tag: compartment

tag: shRNA

tag: shRNA type


title: clone17_1

description:
Library name: 366510
SMART-Seq v3

tag: tissue

tag: genotype

tag: plate

tag: color

tag: clone type

tag: clone size


title: DZIP3 biol rep 2

description: Library name: YY64

tag: cell line

tag: treatment


title: M_A_5

city: Tel aviv

first: Nitay

last: Zuk-Bar

address: Chaim Levanon St 55

country: Israel

institute: Tel aviv university

description: Library name: M_A_5

data_processing:
The E14 RNA-seq data were preprocessed using the Seq2Science pipeline (van der Sande et al. 2023) with the default settings. Briefly, we aligned the reads to the mm10 mouse reference genome using STAR (Dobin et al. 2013).
Gene counting was done using HTSeq (Anders et al. 2015), and transcripts per million (TPM) normalization was done using Salmon (Patro et al. 2017).
Assembly: mouse mm10
Supplementary files format and content: tab-separated text files include raw reads count for each samples
Library strategy: spatial transcriptomics

source_name: Axons

extract_protocol:
Geo-seq (Chen et al. 2017). E12 and E14 mouse embryonic heads were fresh frozen embedded in OCT and cryosectioned at a thickness of 12 μm.
Geo-seq (Chen et al. 2017). Total RNA pellets were dissolved in a lysis solution (4M GuSCN), followed by reverse transcription using SuperScript II reverse transcriptase (Invitrogen), and whole transcription amplification with KAPA HiFi HotStart ReadyMix (2×; KAPA Biosystems). cDNA library was constructed using the Nextera XT Library Prep Kit (Illumina).

value: Axons

value: Mutant

tag: batch


title: clone16_19

description:
Library name: 366509
SMART-Seq v3

tag: cloneid


title: DZIP3 biol rep 1

description: Library name: YY63

value: B


title: clone16_18

description:
Library name: 366508
SMART-Seq v3


title: M_V_5

description: Library name: M_V_5

source_name: Ventral

value: Ventral