title: SAMMY-seq,MEFwtLamAtrunc,rep3,S4

city: Milan

first: Chiara

last: Lanzuolo

address: Via Francesco Sforza 35

country: Italy

institute: CNR and Istituto Nazionale Genetica Molecolare

description: Library name: MEFwt_R3_LamATrunc_S4_D11.fastq.gz

data_processing:
alignment step with BWA70 (v0.7.17-r1188) setting -n 2 -k 2,
alignment duplicates were marked and removed with Picard (v2.23.9),
filtered all the reads with mapping quality lower than 1 with Samtools
Assembly: mm10
Supplementary files format and content: bigwig and bedfiles

organism: Mus musculus

source_name: mouse embryonic fibroblast (MEF)

growth_protocol: WT MEFs were grown at 37 °C in a humidified incubator with 5% CO2 in high glucose DMEM (Sigma-Aldrich, D5671) supplemented with 10% FCS (v/v), 2 mM L-glutamine (Sigma-Aldrich, G7513) and 1% penicillin-streptomycin (Sigma-Aldrich, P078)

extract_protocol:
The 4f-SAMMY-seq  fractionation was performed on 250.000 MEFs. Cells were washed twice in cold PBS and resuspended in 600 μL of cold cytoskeleton-Triton buffer (CSK-Triton buffer: 10 mM PIPES pH 6.8, 100 mM NaCl, 1 mM EGTA, 300 mM Sucrose, 3 mM MgCl2, 1mM PMSF, Protease Inhibitor Cocktail Roche 04693116001, 1 mM DTT, 0.5% Triton X-100). After 10 minutes on a rotator at 4°C, samples were centrifugated for 3 minutes at 900g at 4°C and the cytoskeletal structure were collected as S1 fraction. Pellets were then washed for 10 minutes on the rotator at 4°C with an additional volume of the CSK-Triton buffer, resuspended in 100 μL of cytoskeleton buffer (CSK buffer: 10 mM PIPES pH 6.8, 100 mM NaCl, 1 mM EGTA, 300 mM Sucrose, 3 mM MgCl2, 1mM PMSF, 1X Protease Inhibitor Cocktail Roche 04693116001) and incubated with 6 U of DNase I (Invitrogen, AM2222) for 60 min at 37°C. To stop digestion, ammonium sulphate was added in the CSK buffer to a final concentration of 250 mM. After 5 min on ice, samples were pelleted at 900g for 3 min at 4°C and the supernatant, containing digested chromatin fragments, was collected as S2 fraction. The pellet was then washed with 200 μL of CSK buffer and pelleted at 3000g for 3 min at 4°C. Afterwards, the pellet was resuspended in 100 μL of CSK-NaCl buffer (10 mM PIPES pH 6.8, 2 M NaCl, 1 mM EGTA, 300 mM Sucrose, 3 mM MgCl2, 1mM PMSF, 1X Protease Inhibitor Cocktail Roche 04693116001), incubated 10 min on a rotator at 4°C, centrifuged at 3000g 3 min at 4°C and the supernatant was conserved as S3 fraction. Finally, after two washes in 200 μL of CSK-NaCl buffer, pellets were solubilized in in 8M urea for 10 minutes at RT and the final suspension was labelled as S4
The libraries for SAMMY-seq were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, BE7645L) and the NEBNext Multiplex Oligos for Illumina (NEB, BE6440S).

treatment_protocol: WT MEFs were transfected with plasmids encoding full-length (LA 1-646) or truncated Lamin A (LA 1-429), both tagged with eGFP, using Lipofectamine 3000 reagent (Thermo Fisher Scientific, L3000001), according to the manufacturer’s protocol. After 24 hours of transfection, eGFP-positive cells were sorted, reseeded, and incubated for an additional 24 hours before being collected for 4f-SAMMY-seq analysis.

value: mouse embryonic fibroblast (MEF)

value: Transfection with a plasmid encoding truncated Lamin A (LA 1-429), which lacks the C-terminal tail


title: SAMMY-seq,MEFwtLamAtrunc,rep3,S2S

status: Public on May 28 2025

type: SRA

description: Library name: MEFwt_R3_LamATrunc_S2S_A11.fastq.gz

library_source: genomic

molecule: genomic DNA

tag: cell type

tag: treatment


title: SG16374548_253949448093_2_2_0974-006-900_hr24

type: RNA

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

country: USA

institute: WRAIR

hyb_protocol: cRNA was hybridized to a human genome microarray (Agilent Technologies) following manufacturer's instructions

scan_protocol: Scanned on a Agilent Technologies Scanner G2600D Images were quantified using Agilent Feature Extraction Software

data_processing:
Agilent Feature Extraction Software (v 10.7) was used for background subtraction and GeneSpring v.10.1 (Agilent Technologies, Inc., CA) software was used to conduct the preliminary data filtration and statistical analysis.
processed_data: Logratio (test/reference)

molecule: total RNA

organism: Homo sapiens

source_name: Whole Blood

label_protocol: Total RNA (200-2000ng) was used as starting material, which was amplified using the Quick Amp Two-Color Kit (Agilent Technologies).The labelled cDNA was purified using an RNeasy Mini Kit (Qiagen, Hilden, Germany), and eluted, labelled cRNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific Inc, Waltham, MA, USA).

growth_protocol: growth protocol is not applicable

extract_protocol: Total RNA was isolated using the PAXgene Blood RNA kit (Qiagen, Valencia, CA) following manufacturer directions

treatment_protocol: treatment protocol is not applicable

tag: age

tag: gender

value: Male

value: Alive

tag: timepoint

source_name: Agilent's Universal Human Reference RNA

tag: reference

value: Agilent's Universal Human Reference RNA


title: SAMMY-seq,MEFwtLamA,rep3,S4

description: Library name: MEFwt_R3_LamA_S4_H9.fastq.gz

value: Transfection with plasmid encoding full-length Laminn A (LA 1-646)


title: +Rapa, Tachyzoite, biol rep 4

city: Wuhan

first: bolin

last: Fan

state: hubei

address: hubei

country: China

institute: Huazhong Agricultural University

description:
TranRaPa_4
Transcription of Dicre-iGRA1 strains treated with plus Rapamycin drug

library_source: transcriptomic

data_processing:
Clean reads were mapped to the T. gondii GT1 genome (ToxoDB) using Hisat2 software
Transcript levels were calculated using the transcript per million (TPM) method, and differentially expressed genes were identified using DESeq2 v1.24.0 with a p-value < 0.01 and a minimum fold change of 2.
Assembly: T. gondii reference genome (TGGT1)
Supplementary files format and content: raw counts for each sample

organism: Toxoplasma gondii

source_name: Tachyzoite culture

growth_protocol: To obtain tachyzoite samples, parasites were cultured in human foreskin fibroblasts (HFF), in Dulbecco’s Modified Eagle Medium (DMEM) (Sigma-Aldrich, USA), supplemented with 2% heat-inactivated fetal bovine serum (FBS) (Gibco, USA), 1% penicillin-streptomycin, and 5 mM L-glutamine. In order to obtain samples of bradyzoites, parasites were cultured in RPMI 1640 medium (pH = 8.2) containing 1% fetal bovine serum, along with ambient CO2.

extract_protocol:
Intracellular parasites were harvested, released by needle passage, and purified by filtration through membranes with 3 μm pore size to remove host cell debris. Total RNA was extracted from purified parasites using transZol Up reagent (TransGen Biotech, China) following the manufacturer’s instructions. The RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent, USA).
Libraries for RNA sequencing were prepared using the TruSeq RNA Sample Prep Kit (Illumina, USA) and sequenced on a DNBSEQ-T7 sequencer (MGI Tech Co., Ltd, China) with the PE150 model.

treatment_protocol: To obtain tachyzoite samples, RH-Dicre-iGRA1  was grown under normal culture conditions, and  was required to be treated with plus or minus Rapamycin drug, to obtain tachyzoite samples.

value: Tachyzoite culture

tag: genotype

value: plus Rapamycin drug


title: SAMMY-seq,MEFwtLamA,rep3,S3

description: Library name: MEFwt_R3_LamA_S3_G9.fastq.gz


title: SAMMY-seq,MEFwtLamAtrunc,rep3,S2L

description: Library name: MEFwt_R3_LamATrunc_S2L_B11.fastq.gz


title: SG16374548_253949448109_2_2_0974-015-900_hr132


title: SG16374548_253949448306_2_1_0974-014-900_hr120


title: SG16374548_253949448110_1_3_0974-003-900_hr4


title: SG16374548_253949447272_1_1_0974-004-900_hr8


title: SG16374548_253949448112_1_2_0974-002-900_hr2


title: SG16374548_253949447599_2_3_0974-005-900_hr12


title: SAMMY-seq,MEFwtLamA,rep3,S2S

description: Library name: MEFwt_R3_LamA_S2S_E9.fastq.gz


title: SG16374548_253949448304_2_2_0974-001-900_hr0


title: SAMMY-seq,MEFwtLamA,rep3,S2L

description: Library name: MEFwt_R3_LamA_S2L_F9.fastq.gz


title: SG16374548_253949448308_1_3_0972-018-900_hr168

value: Deceased


title: SAMMY-seq,MEFwtLamAtrunc,rep2,S4

description: Library name: MEFwt_R2_LamATrunc_S4_D8.fastq.gz


title: SG16374548_253949448102_2_4_0974-008-900_hr48


title: SG16374548_253949448102_1_3_0972-017-900_hr156


title: SAMMY-seq,MEFwtLamAtrunc,rep2,S3

description: Library name: MEFwt_R2_LamATrunc_S3_C8.fastq.gz


title: SAMMY-seq,MEFwtLamAtrunc,rep3,S3

description: Library name: MEFwt_R3_LamATrunc_S3_C11.fastq.gz


title: SAMMY-seq,MEFwtLamAtrunc,rep2,S2S

description: Library name: MEFwt_R2_LamATrunc_S2S_A8.fastq.gz


title: SG16374548_253949448093_1_1_0972-015-900_hr132


title: SAMMY-seq,MEFwtLamAtrunc,rep2,S2L

description: Library name: MEFwt_R2_LamATrunc_S2L_B8.fastq.gz


title: SG16374548_253949447592_2_4_0972-014-900_hr120


title: SG16374548_253949447551_2_3_0972-012-900_hr108


title: SAMMY-seq,MEFwtLamAtrunc,rep1,S4

description: Library name: MEFwt_R1_LamATrunc_S4_E3.fastq.gz


title: SG16374548_253949448305_2_1_0972-011-900_hr96


title: SAMMY-seq,MEFwtLamA,rep1,S4

description: Library name: MEFwt_R1_LamA_S4_F4.fastq.gz


title: SG16374548_253949447552_1_2_0972-008-900_hr48


title: SG16374548_253949448098_1_1_0972-008-900_hr60


title: SAMMY-seq,MEFwtLamAtrunc,rep1,S2L

description: Library name: MEFwt_R1_LamATrunc_S2L_H4.fastq.gz


title: SAMMY-seq,MEFwtLamAtrunc,rep1,S2S

description: Library name: MEFwt_R1_LamATrunc_S2S_G4.fastq.gz


title: SAMMY-seq,MEFwtLamA,rep1,S3

description: Library name: MEFwt_R1_LamA_S3_C4.fastq.gz


title: SAMMY-seq,MEFwtLamA,rep1,S2L

description: Library name: MEFwt_R1_LamA_S2L_B4.fastq.gz


title: SAMMY-seq,MEFwtLamA,rep1,S2S

description: Library name: MEFwt_R1_LamA_S2S_A4.fastq.gz


title: SG16374548_253949448111_2_3_0972-006-900_hr24


title: SAMMY-seq,MEFwtLamAtrunc,rep0,S4

description: Library name: MEFwt_LamATrunc_S4_F3_S48.fastq.gz


title: SG16374548_253949448096_2_3_0972-016-900_hr144


title: SG16374548_253949447594_2_2_0972-005-900_hr12


title: SAMMY-seq,MEFwtLamAtrunc,rep0,S3

description: Library name: MEFwt_LamATrunc_S3_H11_S51.fastq.gz


title: SG16374548_253949447593_2_3_0972-004-900_hr8


title: SAMMY-seq,MEFwtLamAtrunc,rep0,S2L

description: Library name: MEFwt_LamATrunc_S2L_H12_S47.fastq.gz


title: SAMMY-seq,MEFwtLamAtrunc,rep1,S3

description: Library name: MEFwt_R1_LamATrunc_S3_B1.fastq.gz


title: SG16374548_253949448332_2_4_0972-002-900_hr2


title: SAMMY-seq,MEFwtLamA,rep0,S4

description: Library name: MEFwt_LamA_S4_G12_S46.fastq.gz


title: SAMMY-seq,MEFwtLamAtrunc,rep0,S2S

description: Library name: MEFwt_LamATrunc_S2S_G11_S50.fastq.gz


title: SAMMY-seq,MEFwtLamA,rep0,S2S

description: Library name: MEFwt_LamA_S2S_E11_S48.fastq.gz


title: SG16374548_253949448109_2_4_0972-003-900_hr4


title: SG16374548_253949447554_2_2_0968-018-900_hr168


title: SG16374548_253949448309_1_4_0972-011-900_hr84


title: SG16374548_253949448328_2_1_0972-001-900_hr0


title: SG16374548_253949448304_2_1_0972-009-900_hr72


title: SAMMY-seq,MEFwtLamA,rep0,S2L

description: Library name: MEFwt_LamA_S2L_F12_S45.fastq.gz


title: ChIP,MEFwtlamin,rep1,Input

description: Library name: MEF_wt_lamin_INPUT.fastq.gz

data_processing:
alignment step with BWA70 (v0.7.17-r1188) setting -n 2 -k 2,
alignment duplicates were marked and removed with Picard (v2.23.9),
filtered all the reads with mapping quality lower than 1 with Samtools
Assembly: mm10
Supplementary files format and content: bigwidg and bediles

growth_protocol: WT MEFs were grown at 37 °C in a humidified incubator with 5% CO2 in high glucose DMEM (Sigma-Aldrich, D5671) supplemented with 10% FCS (v/v), 2 mM L-glutamine (Sigma-Aldrich, G7513) and 1% penicillin-streptomycin (Sigma-Aldrich, P0781).

extract_protocol:
WT MEFs were grown to 90% confluence in DMEM (Gibco, 10566-016) supplemented with 10% (v/v) FBS (Gibco,10270106) and then fixed 10 min at RT with 1% formaldehyde (Sigma-Aldrich, F8775), adding 1:10 of formaldehyde solution (50 mM HEPES-KOH pH 7.5, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, and 11% formaldehyde) on cultured cells. Formaldehyde was then quenched with addition of Glycine (Carlo Erba, 453807) to a final concentration of 125 mM for 5 min at RT, followed by two washes with cold 1xPBS.  Cross-linked cells were rapidly collected in a falcon tube by scraping on ice and centrifuged at 2000 g at 4 °C.  Pellets of 3x106 cells were stored at -80 °C until sonication. Each 3x106 cell pellet was resuspended in 600 μl of cold Lysis Buffer: 50 mM HEPES-KOH, pH 7.5, 10 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100. After 10 min on a rotator at 4 °C, samples were centrifuged for 5 min at 1350g at 4 °C and resuspended in 130 μl of sonication buffer: 10 mM Tris-HCl pH 8.0, 2 mM EDTA, 1x Protease Inhibitor Cocktail (Roche, 04693116001), 1 mM PMSF (Sigma-Aldrich, 93482) and 0,1% SDS. Cells were subjected to lysis on ice for 1 h and homogenised by pipetting every 15 min. Total extracted chromatin was sonicated in a Covaris M220 focused-ultrasonicator using snap cap microTUBEs (Covaris, 520045) (water bath set to 7 °C, peak power 75.0, duty factor 10.0, cycles/burst 250, duration 420 s). Fragmentation of chromatin to an average size of 150-500bp was checked on Agilent 2100 Bioanalyzer using High Sensitivity DNA Kit (Agilent, 5067-4626). Samples were dilute to a final concentration 0.1% SDS by adding 1 volume of equilibration buffer: 10 mM Tris-HCl pH 8.0, 233 mM NaCl, 1.66% Triton X-100, 0.166% Deoxycholic acid sodium salt (DOC), 1 mM EDTA, 1x Protease Inhibitor Cocktail (Roche, 04693116001), 1 mM PMSF (Sigma-Aldrich, 93482and 0,1% SDS (for Lamin A/C). Samples were then centrifuged at 14000 g for 10 min at 4 °C to pellet insoluble material. Supernatants were quantified using Nanodrop 1000 spectrophotometer and 150 ug of chromatin was used for Lamin A/C immunoprecipitation in a final volume of 300 μl of IP buffer: 10 mM Tris-HCl pH8, 140 mM NaCl, 1.66% Triton X-100, 0.166% DOC, 0.1% SDS, 1 mM EDTA, 1x Protease Inhibitor Cocktail (Roche, 04693116001); 1 mM PMSF (Sigma-Aldrich, 93482). 3% of total chromatin was preserved at 4 °C as input normalization-control for each experimental condition. The remaining chromatin was incubated overnight on a rotator at 4 °C with 15 μl of Lamin A/C (Abcam. ab26300) antibodies. 20 μl of Protein G beads (Life Technology, 1004D) for each IP were washed twice in 0.1% BSA/IP buffer and incubated on rotator overnight at 4 °C. On the next day, protein G beads were added to each sample and incubated on rotator for 2 hours at 4 °C. Beads/IP complexes were then washed 10 min on rotator at 4 °C twice with IP buffer, twice with high-salt IP buffer: 10 mM Tris-HCl pH 8, 500 mM NaCl, 1.66% Triton X-100, 0.166% DOC, 0.1% SDS, 1 mM EDTA, 1x Protease Inhibitor Cocktail (Roche, 04693116001); 1 mM PMSF (Sigma-Aldrich, 93482); twice with RIPA-LiCl buffer: (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 250 mM LiCl, 0.5% DOC, 0.5% NP-40, 1x Protease Inhibitor Cocktail (Roche, 04693116001); 1 mM PMSF (Sigma-Aldrich, 93482); twice with 10 mM Tris-HCl pH 8.0. Crosslinking was reversed by incubating the beads and input at 65 °C overnight with 100 μl of Elution buffer: 10 mM Tris-HCl pH 8, 0,5 mM EDTA, 300 mM, and 0.4% SDS. The next day, all samples were diluted with 100 μl of 1x TE buffer, treated with 2.5 U of RNAse cocktail (Ambion, AM2286) at 37 °C for 120 min, followed by addition of 100 ug of Proteinase K (Invitrogen, AM2548) at 55 °C for 120 min. DNA was then isolated using phenol/chloroform (Sigma-Aldrich, 77617) extraction, followed by a back extraction of phenol/chloroform with additional volume of 1x TE buffer. DNA was precipitated in 2 volumes of cold ethanol, 0.3 M sodium acetate and 20 ug glycogen (Ambion AM9510) for overnight at -20 °C. Pellets were suspended in 31 μl of nuclease-free water and quantified using Qubit 2.0 fluorometer with Qubit dsDNA HS Assay Kits (Invitrogen, Q32854).
The libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, BE7645L) and NEBNext Multiplex Oligos for Illumina (NEB, BE6440S). Libraries were then qualitatively and quantitatively checked and run on the TapeStation System


title: SG16374548_253949448110_2_2_0968-017-900_hr156


title: SG16374548_253949447553_1_2_0972-007-900_hr36


title: ChIP,MEFwtlamin,rep1,LaminAC_IP

description: Library name: MEF_wt_ChIP_lamin_AC_IP.fastq.gz


title: SG16374548_253949447553_2_2_0968-012-900_hr108


title: SG16374548_253949447556_2_1_0968-012-900_hr96


title: SG16374548_253949448100_2_4_0968-015-900_hr132


title: SAMMY,MEFwt,rep2,S4

data_processing:
alignment step with BWA70 (v0.7.17-r1188) setting -n 2 -k 2,
alignment duplicates were marked and removed with Picard (v2.23.9),
filtered all the reads with mapping quality lower than 1 with Samtools
Assembly: mm10
Supplementary files format and content: files with name_RPKM.bw are processed as follow. For each alignment a coverage analysis has been performed using Deeptools 72 (v3.5.0) bamCoverage function.The reads were extended up to 250 bp and RPKM normalization method has been used. The mm10 size was considered of 2652783500 bp
Supplementary files format and content: bed files with name_cmpartments.bed are computed as described. chromatin compartmentalizaton  are computed from the name_RPKM.bw step. The compartments are computed as described in the 4f-SAMMY-seq paper (cit?) , by firstly obtain the Euclidean distance of each genomic bin using the dist function method="euclidean", then following the calder procedure to segment the chromatin in subcompartments. However, for this dataset, we have limited compartments calling to a broader level, resulting in only two categories: A compartments and B compartments. The chromatin consensus state of wild-type compartments is constructed by labelling each genomic bin (50kb) according to the most recurring call across samples. We assigned compartment shifts based on whether each 50kb genomic bin received a concordant or discordant compartment classification between wild-type consensus and each mutant consensus.
Supplementary files format and content: the enrichment ratios with name samples_S2SvsS3_mle.bw for each sample using the SAMMY fractions, we used the spp  package (v1.16.0). The reads were additionally filtered with 'remove.local.tag.anomalies', and the differential enrichment was computed using 'get.smoothed.enrichment.mle' function setting 'tag.shift = 0' and 'background.density.scaling = TRUE'. The resulting computed signal correspondsofthe log2 ratio between the two sequenced fractions per each sample. The enrichment ratios between fractions are used for subsequent analyses. To maximise comparability and obtain ChIP-seq IP over INPUT genomic profiles, we computed the ratios using again spp with the same parameters for SAMMY-seq enrichment ratios.
Supplementary files format and content: transcripts tpm and tx2gene files are generated using the pipeline of nf-core/rnaseq version (https://zenodo.org/records/3503887, v3.8)
Library strategy: SAMMY-seq

source_name: mouse_embryonic_fibroblast (MEF)

extract_protocol:
Total RNA was extracted from one million cells for each condition in triplicate using TRI-Reagent (Sigma, T9424) following the recommended guidelines. The 4f-SAMMY-seq  fractionation was performed on 500.000 MEFs. Cells were washed twice in cold PBS and resuspended in 600 μL of cold cytoskeleton-Triton buffer (CSK-Triton buffer: 10 mM PIPES pH 6.8, 100 mM NaCl, 1 mM EGTA, 300 mM Sucrose, 3 mM MgCl2, 1mM PMSF, Protease Inhibitor Cocktail Roche 04693116001, 1 mM DTT, 0.5% Triton X-100). After 10 minutes on a rotator at 4°C, samples were centrifugated for 3 minutes at 900g at 4°C and the cytoskeletal structure were collected as S1 fraction. Pellets were then washed for 10 minutes on the rotator at 4°C with an additional volume of the CSK-Triton buffer, resuspended in 100 μL of cytoskeleton buffer (CSK buffer: 10 mM PIPES pH 6.8, 100 mM NaCl, 1 mM EGTA, 300 mM Sucrose, 3 mM MgCl2, 1mM PMSF, 1X Protease Inhibitor Cocktail Roche 04693116001) and incubated with 12 U of DNase I (Invitrogen, AM2222) for 60 min at 37°C. To stop digestion, ammonium sulphate was added in the CSK buffer to a final concentration of 250 mM. After 5 min on ice, samples were pelleted at 900g for 3 min at 4°C and the supernatant, containing digested chromatin fragments, was collected as S2 fraction. The pellet was then washed with 200 μL of CSK buffer and pelleted at 3000g for 3 min at 4°C. Afterwards, the pellet was resuspended in 100 μL of CSK-NaCl buffer (10 mM PIPES pH 6.8, 2 M NaCl, 1 mM EGTA, 300 mM Sucrose, 3 mM MgCl2, 1mM PMSF, 1X Protease Inhibitor Cocktail Roche 04693116001), incubated 10 min on a rotator at 4°C, centrifuged at 3000g 3 min at 4°C and the supernatant was conserved as S3 fraction. Finally, after two washes in 200 μL of CSK-NaCl buffer, pellets were solubilized in in 8M urea for 10 minutes at RT and the final suspension was labelled as S4.  For ChIP-seq experiments, the immortalized MEFs were grown to 90% confluence and then fixed in DMEM (Gibco, 10566-016) supplemented with 10% (v/v) FBS (Gibco,10270106), using 1:10 formaldehyde solution (50mM Hepes-KOH pH7.5, 100mM NaCl, 1mM EDTA, 0.5mM EGTA and 11% formaldehyde) for 10 minutes at RT. Formaldehyde was then quenched with addition of Glycine to a final concentration of 125 mM for 5 minutes at RT, followed by two washes with cold 20% FBS/PBS.  Cross-linked cells were rapidly collected in a falcon tube by scraping on ice and washed twice for 15 minutes at 2000g at 4°C.  Pellets of 3 million cells were transfer to a 1.5mL microcentrifuge tube and stored at -80°C until sonication. Cell pellets were resuspended in 600 μL of cold Lysis Buffer 1 (50 mM Hepes-KOH, pH 7.5, 10 mM NaCl, 1 mM  EDTA, 10% glycerol, 0.5% NP-40 and 0.25% Triton X-100). After 10 minutes on a rotating wheel at 4°C, samples were centrifugated for 5 minutes at 1350g at 4°C and resuspended in 130 ul of sonication buffer (10 mM TrisHCl pH 8.0, 2 mM EDTA, 0.25% SDS, 1mM PMSF and 1X Protease Inhibitors Cocktail). Cell pellets were subjected to lysis on ice for 1h pipetting every 15 min. Total extracted chromatin was sonicated in a Covaris M220 focused-ultrasonicator using snap cap microTUBEs (Covaris, 520045) (water bath 7°C, peak power 75.0, duty factor 10.0, cycles/burst 250, duration 420 seconds). Fragmentation of chromatin to an average size of 150-500bp was checked on Agilent 2100 Bioanalyzer. Equilibration buffer (10mM Tris pH8, 233mM NaCl, 1.66% Triton X-100, 0.166% DOC, 1mM EDTA, 1mM PMSF, 1X Protease Inhibitors Cocktail) was added to every sample to bring solution to IP buffer composition (10 mM TrisHCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% DOC, 1% Triton X-100 1mM PMSF, 1X protease inhibitors). Samples were then spun at 14000g for 10 minutes at 4°C to pellet insoluble material. Supernatants were quantified using Nanodrop 1000 spectrophotometer in order to use 80 μg of chromatin per histone modifications-IP. Each sample was bring to 300 ul using IP buffer and 3% of total chromatin was preserved at 4°C as input normalization-control for each experimental condition. Remaining chromatin was incubated with H3K9me3 (Ab, 8898), H3K27ac (Ab, 4729) and H3K4me3 (07-473) per each IP-sample and incubated overnight on a rotating wheel at 4°C. Protein G beads (Life Technology, 1004D) were washed twice in 0.1% BSA/IP buffer, resuspended in the same buffer and incubated on rotating wheel overnight at 4°C. On the next day, 20ul of protein G beads were added to each sample and incubated on the rotating wheel at 4°C for 2 hours. Beads were then washed 10 min on wheel at 4°C twice with IP buffer, twice with high-salt IP buffer (500 mM NaCl instead of 140 mM), twice with RIPA-LiCL buffer (10 mM TrisHCl pH 8.0, 1 mM EDTA, 250 mM LiCl, 0.5% DOC, 0.5% NP-40, 1X PMSF, 1X protease inhibitors) and once with 10 mM TrisHCl pH 8.0. Crosslinking was reversed by incubating the beads at 65°C overnight woth 100  ul of Elution buffer (10 mM TrisHCl pH 8.0, 5 mM EDTA, 300mM, 0.4% SDS). Input chromatin was also decrosslinked in elution buffer overnight at 65°C. On the next day, all samples were diluted with one volume of TE 10:1, treated with 5 ul of RNase cocktail (Ambion, AM2286) at 37°C for 2 hours and then with 5 ul of 20mg/mL Proteinase K (Thermo Scientific, EO0491) at 55°C for 2 hours. Finally, the DNA was isolated through phenol-chloroform extraction and precipitated. Pellets were suspended in 31ul of nuclease-free water and quantified using Qubit 2.0 fluorometer with Qubit dsDNA HS Assay Kits (Invitrogen, Q32854).
The libraries for SAMMY-seq and ChIP-seq sample were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, BE7645L) and NEBNext Multiplex Oligos for Illumina (NEB, BE6440S). For each RNA sample, 10 ng of total RNA was used to construct strand specific RNAseq library with SMARTer Stranded Total RNA-Seq Kit  (Takara, 634487).

value: mouse_embryonic_fibroblast (MEF)

value: WT MEF


title: SG16374548_253949448329_2_1_0968-010-900_hr72


title: SAMMY,MEFwt,rep2,S3


title: SAMMY,MEFwt,rep2,S2S


title: SG16374548_253949448327_1_1_0968-009-900_hr60


title: SAMMY,MEFwt,rep2,S2L


title: SG16374548_253949448328_1_2_0968-008-900_hr48


title: SAMMY-seq,MEFwtLamA,rep0,S3

description: Library name: MEFwt_LamA_S3_F11_S49.fastq.gz


title: SG16374548_253949447596_2_2_0968-007-900_hr36


title: SAMMY,MEFwt,rep3,S3


title: SG16374548_253949446591_2_2_0968-006-900_hr24


title: SG16374548_253949448102_2_1_0968-005-900_hr12


title: SAMMY,MEFwt,rep3,S2S


title: SAMMY,MEFBDKO,rep3,S4

value: LBDKO MEF


title: SG16374548_253949447555_2_2_0968-003-900_hr4


title: SAMMY,MEFBDKO,rep3,S3


title: SG16374548_253949448103_2_3_0968-004-900_hr8


title: SG16374548_253949448095_2_4_0967-009-900_hr60


title: SAMMY,MEFACKO,rep3,S4

value: LmnaKO MEF


title: SG16374548_253949447598_2_1_0968-002-900_hr2


title: SAMMY,MEFACKO,rep3,S3


title: SG16374548_253949448101_1_3_0968-011-900_hr84


title: SG16374548_253949447554_1_2_0967-010-900_hr72


title: SG16374548_253949448104_2_4_0967-007-900_hr36


title: SAMMY,MEFwt,rep3,S4


title: SAMMY,MEFACKO,rep3,S2S


title: SAMMY,MEFBDKO,rep3,S2L


title: SG16374548_253949447597_1_2_0967-004-900_hr8


title: SAMMY,MEFwt,rep3,S2L


title: SG16374548_253949447553_1_1_0967-001-900_hr0


title: SAMMY,MEFACKO,rep2,S4


title: SG16374548_253949448101_2_3_0966-020-900Day21


title: SAMMY,MEFBDKO,rep2,S4


title: SG16374548_253949447596_1_1_0967-003-900_hr4


title: SG16374548_253949447595_2_4_0967-002-900_hr2


title: SAMMY,MEFBDKO,rep2,S2S


title: SAMMY,MEFBDKO,rep3,S2S


title: SAMMY,MEFACKO,rep2,S3


title: SG16374548_253949448094_1_2_0966-017-900_hr156


title: SG16374548_253949447271_2_2_0968-001-900_hr0


title: SG16374548_253949448328_2_2_0967-006-900_hr24


title: SG16374548_253949448099_2_1_0966-016-900_hr144


title: SAMMY,MEFwt,rep1,S4


title: SAMMY,MEFACKO,rep2,S2L


title: SAMMY,MEFBDKO,rep2,S2L


title: SG16374548_253949446591_1_4_0966-013-900_hr108


title: SG16374548_253949448331_1_1_0966-015-900_hr132


title: SAMMY,MEFwt,rep1,S2S


title: SG16374548_253949447270_2_1_0966-014-900_hr120


title: SAMMY,MEFACKO,rep2,S2S


title: SG16374548_253949448096_2_2_0966-018-900_hr168


title: SG16374548_253949448308_1_1_0966-019-900_Day14


title: SAMMY,MEFACKO,rep3,S2L


title: SAMMY,MEFwt,rep1,S2L


title: SAMMY,MEFwt,rep1,S3


title: SG16374548_253949448307_2_4_0966-011-900_hr84


title: SAMMY,MEFBDKO,rep2,S3


title: SG16374548_253949448306_1_2_0966-010-900_hr72


title: SG16374548_253949448110_1_4_0966-009-900_hr60


title: SAMMY,MEFBDKO,rep1,S4


title: SG16374548_253949448309_2_2_0966-008-900_hr48


title: SAMMY,MEFBDKO,rep1,S2S


title: SG16374548_253949448104_1_3_0966-012-900_hr96


title: SG16374548_253949448329_2_2_0966-007-900_hr36


title: SAMMY,MEFACKO,rep1,S4


title: SAMMY,MEFBDKO,rep1,S2L


title: CBX2 antibody, DMSO treated SU-DIPGXIII-H3K27M, rep2

city: Edinburgh

first: Gerry

last: Brien

address: Western General Hospital  Crewe Road South

department: Institute of Genetics and Cancer

country: United Kingdom

institute: University  of Edinburgh

description:
Library name: DMSO-CBX2-Rep2
10% mouse cells was used as spike-in chromatin.
DMSO_CBX2.merged.sorted.av.bw

data_processing:
RNA-seq analysis involved: Paired-end reads from sequencing were aligned to the GRCh38 genome build (GCA_000001405.15 assembly) using the HISAT2 aligner (https://doi.org/10.1038/s41587-019-0201-4). Read extraction was performed with the featureCounts program (doi:10.1093/bioinformatics/btt656) using the corresponding GTF reference annotation and keeping only primary alignments. Read counts table and sample metadata were imported into R, and Differentially expressed genes were determined using DESeq2 (doi:10.1186/s13059-014-0550-8).
CUT&RUN-Rx analysis involved:  adding the 'mm10_' prefix to chromosome names, creating a human/mouse hybrid genome by combining hg38 with mm10, aligning reads with Bowtie2 (v 2.3.5.1), filtering, and converting to BAM format using SAMtools (v 1.10).  Normalization was performed using the spike-in reads, and RRPM-normalized bigwig files were generated with deepTools' bamCoverage ( v 3.3.0). Peaks were called using macs2 (v 2.2.7.1) with paramaters broad --broad-cutoff 0.05, converted to bed format, and processed to generate consensus peak sets using MSPC (-r Bio -w 1e-4 -s 1e-8 -c 2) (v 5.4.0) and bedtools. Finally, peaks were annotated with HOMER
Assembly: hg38
Supplementary files format and content: bigwig files contain average CUT&RUN signal for biological replicates.
Supplementary files format and content: csv files contain the output from DESeq, i.e. differentially expressed genes in sgRNA-KO conditions compared to DIPGXIII sgLUC cells, and the gene abundance data quantified using htseq-count.
Library strategy: CUT&Run

source_name: Brain

growth_protocol: All cell lines were grown as monolayers on CellBIND plates (Fisher Scientific) with DMEM/F12 (1:1) supplemented with Penicillin-Streptomycin (100U/mL; Gibco), Bovine albumin fraction V solution (7.5%; Gibco), MEM Non-essential amino acids solution (100X; Gibco), beta-mercaptoethanol (50mM; Gibco), N2 and B27 (Life Technologies), Laminin (R&D Systems; 2μg/mL), epidermal growth factor and fibroblast growth factor 2 (Peprotech; 10 ng/mL) as previously described (Conti et al. 2005).

extract_protocol:
For CUT&RUN-Rx, cells were harvested using Accutase (STEMCELL Technologies) and counted. Following counting mouse NSCs were spiked-in to human DIPGXIII cell suspensions (1:10 cell number ratio). Cells were fixed in culture media containing 0.1% formaldehyde at room temperature for 1 min. Formaldehyde was quenched with glycine at 0.125 M, followed by a 5-min incubation at room temperature. Fixed cells were washed with PBS. Fixed cells were incubated on ice for 10 min in nuclear extraction buffer (20mM HEPES pH 7.5, 10mM KCL, 0.1% Triton X-100, 20% Glycerol,1X protease inhibitor cocktail and 0.5mM spermidine). Extracted nuclei were collected by centrifugation (4ºC, 600g) and resuspended in cold nuclei extraction buffer (100µL per sample). CUT&RUN was performed following Epicypher CUT&RUN Protocol v1.5.1. CUT&RUN DNA was purified using the Monarch PCR & DNA Cleanup Kit (New England Biolabs) in accordance with the manufacturer’s instructions.  For RNA-seq, RNA was extracted from harvested cells (n=2 replicates) using Quick-RNA microprep kit (Zymocat#R1051).
CUT&RUN-Rx library preparation was performed using the NEBNext Ultra II DNA Library Kit for Illumina (E7645) according to the manufacturer’s protocol. For RNA-seq, poly(A) mRNA enrichment and library preparation were performed by Genewiz.

treatment_protocol: For CUT&RUN, SU-DIPGXIII cells were treated with 2µM Tazemetostat or DMSO for 6 days where indicated (with TAZ or DMSO in the file and sample names). Otherwise, SU-DIPGXIII-H3K27M (Parental) and SU-DIPGXIII-H3K27M-KO cells were untreated for CUT&RUN (indicated by P or KO in the file and sample names). For RNA-seq, SU-DIPGXIII-H3K27M cells constitutively express Cas9 and an sgRNA targeting the indicated gene.

tag: tissue

value: Brain

tag: cell line

value: SU-DIPGXIII

value: Patient-derived Diffuse Midline Glioma cells

value: DMSO


title: SG16374548_253949448330_2_3_0966-006-900_hr24


title: SAMMY,MEFACKO,rep1,S2L


title: SAMMY,MEFACKO,rep1,S3


title: SAMMY,MEFBDKO,rep1,S3


title: ChIP,MEFwt,rep2,Input

data_processing:
alignment step with BWA70 (v0.7.17-r1188) setting -n 2 -k 2,
alignment duplicates were marked and removed with Picard (v2.23.9),
filtered all the reads with mapping quality lower than 1 with Samtools
Assembly: mm10
Supplementary files format and content: files with name_RPKM.bw are processed as follow. For each alignment a coverage analysis has been performed using Deeptools 72 (v3.5.0) bamCoverage function.The reads were extended up to 250 bp and RPKM normalization method has been used. The mm10 size was considered of 2652783500 bp
Supplementary files format and content: bed files with name_cmpartments.bed are computed as described. chromatin compartmentalizaton  are computed from the name_RPKM.bw step. The compartments are computed as described in the 4f-SAMMY-seq paper (cit?) , by firstly obtain the Euclidean distance of each genomic bin using the dist function method="euclidean", then following the calder procedure to segment the chromatin in subcompartments. However, for this dataset, we have limited compartments calling to a broader level, resulting in only two categories: A compartments and B compartments. The chromatin consensus state of wild-type compartments is constructed by labelling each genomic bin (50kb) according to the most recurring call across samples. We assigned compartment shifts based on whether each 50kb genomic bin received a concordant or discordant compartment classification between wild-type consensus and each mutant consensus.
Supplementary files format and content: the enrichment ratios with name samples_S2SvsS3_mle.bw for each sample using the SAMMY fractions, we used the spp  package (v1.16.0). The reads were additionally filtered with 'remove.local.tag.anomalies', and the differential enrichment was computed using 'get.smoothed.enrichment.mle' function setting 'tag.shift = 0' and 'background.density.scaling = TRUE'. The resulting computed signal correspondsofthe log2 ratio between the two sequenced fractions per each sample. The enrichment ratios between fractions are used for subsequent analyses. To maximise comparability and obtain ChIP-seq IP over INPUT genomic profiles, we computed the ratios using again spp with the same parameters for SAMMY-seq enrichment ratios.
Supplementary files format and content: transcripts tpm and tx2gene files are generated using the pipeline of nf-core/rnaseq version (https://zenodo.org/records/3503887, v3.8)

tag: chip antibody


title: SG16374548_253949448109_2_1_0966-005-900_hr12


title: SG16374548_253949448103_1_4_0966-004-900_hr8


title: SAMMY,MEFACKO,rep1,S2S


title: SG16374548_253949448106_1_4_0966-003-900_hr4


title: SG16374548_253949448304_2_3_0962-020-900_Day21


title: SG16374548_253949448098_2_2_0966-002-900_hr2


title: ChIP,MEFwt,rep2,H3K9me3

value: (Abcam, ab8898)


title: ChIP,MEFwt,rep1,H3K4me3

value: (Sigma-Aldrich, 07-473)


title: SG16374548_253949448112_2_2_0962-018-900_hr168

value: Male


title: SG16374548_253949448105_1_4_0962-019-900Day14

value: Alive


title: SG16374548_253949448309_2_4_0966-001-900_hr0

value: Agilent's Universal Human Reference RNA


title: ChIP,MEFwt,rep1,H3K27ac

value: (Abcam, ab4729)


title: SG16374548_253949448101_2_1_0962-016-900_hr144


title: ChIP,MEFBDKO,rep2,Input


title: SG16374548_253949448100_1_4_0962-014-900_hr120


title: SG16374548_253949448106_2_2_0962-015-900_hr132


title: ChIP,MEFBDKO,rep2,H3K9me3


title: ChIP,MEFACKO,rep2,Input


title: SG16374548_253949448099_1_3_0962-013-900_hr108


title: ChIP,MEFACKO,rep2,H3K9me3


title: ChIP,MEFBDKO,rep1,Input


title: SG16374548_253949447270_2_2_0962-012-900_hr96


title: ChIP,MEFACKO,rep1,Input


title: SG16374548_253949447272_2_1_0962-010-900_hr72


title: SG16374548_253949448098_1_2_0962-011-900_hr84


title: ChIP,MEFwt,rep1,Input


title: ChIP,MEFwt,rep1,H3K9me3


title: ChIP,MEFACKO,rep1,H3K9me3


title: SG16374548_253949448329_1_4_0962-009-900_hr60


title: RNA,MEFwt,rep4

data_processing:
nf-core/rnaseq version (https://zenodo.org/records/3503887, v3.8) with options --aligner star_salmon --gtf gencode.vM25.basic.annotation.HAVANA.protein_coding.gtf.gz --skip_bbsplit --remove_ribo_rna --save_non_ribo_reads --skip_biotype_qc --gencode
Assembly: mm10
Supplementary files format and content: transcripts tpm and tx2gene files are generated using the pipeline of nf-core/rnaseq version (https://zenodo.org/records/3503887, v3.8)


title: SG16374548_253949448328_1_3_0962-007-900_hr36


title: RNA,MEFwt,rep3


title: SG16374548_253949447554_1_3_0962-006-900_hr24


title: SG16374548_253949448327_1_2_0962-005-900_hr12


title: RNA,MEFwt,rep2


title: RNA,MEFLMNACKO,rep3


title: RNA,MEFLMNBDKO,rep2


title: SG16374548_253949447601_1_1_0962-003-900_hr4


title: RNA,MEFLMNBDKO,rep3


title: ChIP,MEFBDKO,rep1,H3K9me3


title: RNA,MEFLMNACKO,rep2


title: SG16374548_253949447555_1_4_0962-004-900_hr8


title: SG16374548_253949447552_1_3_0962-002-900_hr2


title: RNA,MEFLMNBDKO,rep1


title: RNA,MEFLMNACKO,rep1


title: SG16374548_253949448097_1_3_0961-007-900_hr36

value: Female


title: SG16374548_253949447271_1_2_0962-001-900_hr0


title: SG16374548_253949447601_1_3_0961-005-900_hr12


title: SG16374548_253949448098_1_4_0961-006-900_hr24


title: Young,Lymphoma,ATACseq,rep3

city: Tampa

first: Rebecca

last: Hesterberg

address: 12902 Magnolia Dr.

institute: Moffitt Cancer Center

description: ActiveMotif

data_processing:
Read adapters were detected using BBMerge (v37.02) and subsequently removed with cutadapt (v1.8.1).
Processed raw reads were then aligned to mouse genome mm10 using BOWTIE2 (v2.4.1).
Peak Calling was performed performed to identify regions of open chromatin  using MACS2 (v 2.1.1.20160309).
Only peaks significantly enriched than background with q <0.01 were considered confident and subjected for downstream analysis.
Peaks were annotated by ChIPseeker (v1.32.1) [5] with gene model TxDb.Mmusculus.UCSC.mm10.knownGene (v 3.10.0).
Consensus peak identifiers were obtained by GenomicRanges (v1.48.0).
Peaks were then normalized and differential analysis between experimental groups were evaluated using DEseq2 (v1.36.0).
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: narrowpeak

source_name: spleen

extract_protocol:
To assay accessible chromatin, nuclei were isolated from 75,000 isolated CD4+ T cells and ATAC-seq libraries were prepared using the ActiveMotif ATAC-seq Kit following the manufacturer’s protocol (ActiveMotif, Carlsbad, CA).
Following tagmentation and PCR amplification, the libraries were assessed for the expected size distribution on the Agilent TapeStation 4200 (Agilent Technologies) and quantified using the Kapa Library Quantification Kit (Roche). The final libraries were normalized, denatured, and sequenced on the Illumina NextSeq 2000 sequencer using a P1-100 flow cell to generate approximately 35-40M million 60-base read-pairs per sample (Illumina, Inc.).

value: spleen

value: T & NK cells

value: lymphoma transplant


title: SG16374548_253949448330_2_1_0961-004-900_hr8


title: Young,Ctrl,ATACseq,rep3

description: ActiveMotif

value: non-tumor-bearing control


title: Young,Lymphoma,ATACseqr,rep1

description: ActiveMotif


title: SG16374548_253949447553_1_3_0962-008-900_hr48


title: SG16374548_253949448099_2_4_0961-003-900_hr4


title: SG16374548_253949448096_1_3_0961-001-900_hr0


title: SG16374548_253949448306_2_4_0960-020-900_Day21


title: Young,Ctrl,ATACseq,rep2

description: ActiveMotif


title: Young,Ctrl,ATACseq,rep1

description: ActiveMotif


title: SG16374548_253949448093_2_1_0961-002-900_hr2


title: Aged,Lymphoma,ATACseq,rep2

description: ActiveMotif


title: Aged,Lymphoma,ATACseq,rep3

description: ActiveMotif


title: SG16374548_253949448308_1_2_0960-019-900_Day14


title: SG16374548_253949448108_2_2_0960-017-900_hr156


title: SG16374548_253949448307_2_1_0960-018-900_hr168


title: Aged,Lymphoma,ATACseq,rep1

description: ActiveMotif


title: Aged,Ctrl,ATACseq,rep3

description: ActiveMotif


title: Aged,Ctrl,ATACseq,rep1

description: ActiveMotif


title: SG16374548_253949448106_1_1_0960-016-900_hr144


title: SG16374548_253949448105_2_2_0960-015-900_hr132


title: SK-UT-1 RNA-seq

city: Tokyo

first: Kohei

last: Kumegawa

address: 3-8-31 Ariake, Koto-ku

country: Japan

institute: Japanese Foundation for Cancer Research

description: Library name: 20220816R-SK-UT-1-DMSO_S7

data_processing:
Sequence reads were trimmed to extract adaptor sequences using Skewer (v0.2.2) and mapped to the hg38 genome using spliced transcript alignment to a reference (v.2.7.8a). Mapped reads were counted using feature counts (v.2.0.10).
Assembly: hg38
Supplementary files format and content: count matrix

extract_protocol:
Total RNA was extracted using the abovementioned method and used for library preparation using the SMARTer Stranded Total RNA Sample Prep Kit (TaKaRa Bio, Tokyo, Japan).
The library was prepared using an RNA Sample Prep Kit (TaKaRa Bio, Shiga, Japan).


title: SK-LMS-1 RNA-seq

description: Library name: 20220816R-SK-LMS-1-DMSO_S5


title: SG16374548_253949448104_2_2_0960-014-900_hr120


title: Young,Lymphoma,ATACseq,rep2

description: ActiveMotif


title: SG16374548_253949448102_1_1_0960-012-900_hr96


title: SK-UT1 γH2AX Combination

description: Library name: 20230222C-2303-8-U-Combi_S4

data_processing:
Raw reads were aligned to hg38 using bowtie2 (v.2.4.2). Multialigned reads and PCR copies were eliminated using Picard (v.2.25.3; http://broadinstitute.github.io/picard/). Bedtools (v2.30.0) was used to filter reads that overlapped with the blacklist of the Encyclopedia of DNA Elements (ENCODE). MACS2 (v 2.2.7.1) was used to call peaks with the parameter ‘‘--keep-dup auto -q 0.1.’’
Assembly: hg38
Supplementary files format and content: narrowPeak

extract_protocol:
After culturing, 5 × 106 uLMS cells were collected using 0.25% trypsin-EDTA (FUJIFILM Wako Pure Chemical Corporation). The cell pellets were cross-linked with 1% formaldehyde solution (FUJIFILM Wako Pure Chemical Corporation) for 10 min at 37°C and treated with 0.125 M glycine (FUJIFILM Wako Pure Chemical Corporation) for 5 min at 25°C. After lysing the cells in lysis buffer (see Additional file 1: Table S3), DNA fragmentation was performed by sonication with a Covaris S220 (Covaris, Woburn, MA, USA) for 200 cycles for 10 min.
The fragmented DNA underwent ChIP and was incubated overnight at 4 °C with Dynabeads Protein G (Thermo Fisher Scientific) with 2.5 µg of anti-gamma H2A.X (phospho S139) antibody (Abcam, Cat. #ab2893, Lot: GR3446449-2). Next, we washed the beads with low-salt, high-salt, and LiCl immune complex wash buffers (see Additional file 1: Table S3) at 4°C for 5 min, followed by washing with TE buffer (see Additional file 1: Table S3) for 5 min at 25°C. The fragments were extracted using an elution buffer (see Additional file 1: Table S3). Libraries were prepared using a ThruPLEX DNA-Seq Kit (TaKaRa Bio).

value: 1 µM OTS186935 + 0.5 µM doxorubicin


title: SG16374548_253949448103_1_1_0960-013-900_hr108


title: SG16374548_253949448099_1_2_0960-011-900_hr84


title: SK-UT1 γH2AX DOX

description: Library name: 20230222C-2303-7-U-DOX_S3

value: 0.5 µM doxorubicin


title: SG16374548_253949448094_2_2_0960-010-900_hr72


title: SK-UT1 γH2AX OTS

description: Library name: 20230222C-2303-6-U-OTS_S2


title: SG16374548_253949448330_1_4_0960-009-900_hr60


title: SG16374548_253949448327_2_4_0960-008-900_hr48


title: Diversity Outbred mESCs, S/LIF + 2i,B3B_8_WA

city: New York

first: Yingqian

middle: Ada

last: Zhan

state: New York

address: 430 East 67th Street

department: EPIGENETICS RESEARCH CENTER

institute: MSKCC

data_processing:
Bismark pipeline was adopted to map DNA methylation sequencing reads and determine cytosine methylation states.
Trim Galore v0.6.4 was used to remove raw reads with low-quality (less than 20) and adapter sequences.
The trimmed sequence reads were C(G) to T(A) converted and mapped to similarly converted reference mouse genome (mm10) using default Bowtie 2 settings within Bismark.
Duplicated reads were discarded. The remaining alignments were then used for cytosine methylation calling by Bismark methylation extractor. And the CpG sites with read coverage less than 10 were removed from the downstream analyses.
Then the count matrix was mapped to the targeted regions by using the function getCoverage() with the regions from a R package bsseq (v1.26.0).
Assembly: mm10
Supplementary files format and content: text files containing beta values for all samples at CpG and target regions with CpG coverage greater than 10

source_name: embryonic stem cells

extract_protocol:
Genomic DNA extraction from Cell Pellet
NEBNext® EM-seq™ Kit for Twist Targeted Methylation Sequencing, 96 Samples (Twist Bioscience, 101976)
EM-seq

value: embryonic stem cells

value: Serum/LIF +2i culture


title: SG16374548_253949447601_2_3_0960-006-900_hr24


title: Diversity Outbred mESCs, S/LIF + 2i,B3B_31_WA


title: Diversity Outbred mESCs, S/LIF + 2i,B3B_26_WA


title: Diversity Outbred mESCs, S/LIF + 2i,B3A_7_WA


title: SG16374548_253949447598_1_4_0960-004-900_hr8


title: Aged,Ctrl,ATACseq,rep2

description: ActiveMotif


title: Diversity Outbred mESCs, S/LIF + 2i,B3A_44_WA


title: Diversity Outbred mESCs, S/LIF + 2i,B3A_36_WA


title: SG16374548_253949447596_1_4_0960-002-900_hr2


title: SG16374548_253949447597_1_4_0960-003-900_hr4


title: Diversity Outbred mESCs, S/LIF + 2i,B3A_21_WA


title: SG16374548_253949447594_2_3_0960-001-900_hr0


title: Diversity Outbred mESCs, S/LIF + 2i,B2_9_WA


title: SG16374548_253949448107_1_4_0956-018-900_hr168


title: SG16374548_253949448306_1_4_0956-017-900_hr156


title: Diversity Outbred mESCs, S/LIF + 2i,B2_11_WA


title: SG16374548_253949448106_1_3_0956-014-900_hr120


title: SG16374548_253949448305_1_3_0956-016-900_hr144


title: Diversity Outbred mESCs, S/LIF + 2i,B2_8_WA


title: Diversity Outbred mESCs, S/LIF + 2i,B2_5_WA


title: SK-UT1 γH2AX Ctrl

description: Library name: 20230222C-2303-5-U-NC_S1

value: 0.1% DMSO


title: SG16374548_253949447600_2_3_0956-015-900_hr132


title: Diversity Outbred mESCs, S/LIF + 2i,B1_D4_WA


title: SG16374548_253949448105_1_2_0956-013-900_hr108


title: SG16374548_253949447593_2_1_0956-011-900_hr84


title: Diversity Outbred mESCs, S/LIF + 2i,B1_C17_WA


title: SG16374548_253949447556_1_2_0956-009-900_hr60


title: Diversity Outbred mESCs, S/LIF + 2i,B1_C16_WA


title: SG16374548_253949447599_2_2_0960-005-900_hr12


title: Diversity Outbred mESCs, S/LIF + 2i,B1_B5_WA


title: SG16374548_253949447555_1_1_0956-008-900_hr48


title: SG16374548_253949447599_2_4_0956-012-900_hr96


title: Diversity Outbred mESCs, S/LIF + 2i,B1_B33_WA


title: SG16374548_253949447592_1_3_0956-010-900_hr72


title: SG16374548_253949448104_1_1_0956-007-900_hr36


title: Diversity Outbred mESCs, S/LIF + 2i,B3B_8


title: SG16374548_253949448097_1_2_0956-004-900_hr8


title: Diversity Outbred mESCs, S/LIF + 2i,B3B_39


title: Diversity Outbred mESCs, S/LIF + 2i,B3B_41


title: Diversity Outbred mESCs, S/LIF + 2i,B3B_44


title: Diversity Outbred mESCs, S/LIF + 2i,B3B_7


title: Diversity Outbred mESCs, S/LIF + 2i,B3B_36


title: Diversity Outbred mESCs, S/LIF + 2i,B3B_31


title: Diversity Outbred mESCs, S/LIF + 2i,B3B_35


title: SG16374548_253949446602_1_3_0956-006-900_hr24


title: Diversity Outbred mESCs, S/LIF + 2i,B3B_40


title: SG16374548_253949447551_1_3_0956-005-900_hr12


title: Diversity Outbred mESCs, S/LIF + 2i,B3B_38


title: SG16374548_253949448112_2_1_0953-008-900_hr48


title: SG16374548_253949447270_1_3_0956-003-900_hr4


title: SG16374548_253949448096_1_1_0956-002-900_hr2


title: Diversity Outbred mESCs, S/LIF + 2i,B3B_27


title: Diversity Outbred mESCs, S/LIF + 2i,B3B_25


title: SG16374548_253949446591_1_2_0956-001-900_hr0


title: SG16374548_253949448107_1_2_0953-006-900_hr24


title: SG16374548_253949448110_2_3_0953-010-900_hr72


title: Diversity Outbred mESCs, S/LIF + 2i,B3B_18


title: Diversity Outbred mESCs, S/LIF + 2i,B3B_20


title: Diversity Outbred mESCs, S/LIF + 2i,B3B_17


title: Diversity Outbred mESCs, S/LIF + 2i,B3B_26


title: SG16374548_253949448108_2_4_0953-007-900_hr36


title: SG16374548_253949448331_1_2_0953-005-900_hr12


title: SG16374548_253949447553_2_3_0951-017-900_hr156


title: Diversity Outbred mESCs, S/LIF + 2i,B3B_23


title: SG16374548_253949448094_1_1_0951-016-900_hr144


title: SG16374548_253949447272_2_2_0951-015-900_hr132


title: Diversity Outbred mESCs, S/LIF + 2i,B3A_7


title: SG16374548_253949448330_1_2_0953-004-900_hr8


title: SG16374548_253949448329_1_2_0951-014-900_hr120


title: Diversity Outbred mESCs, S/LIF + 2i,B3B_19


title: SG16374548_253949447597_2_4_0953-002-900_hr2


title: Diversity Outbred mESCs, S/LIF + 2i,B3A_35


title: SG16374548_253949447594_2_4_0953-001-900_hr0


title: Diversity Outbred mESCs, S/LIF + 2i,B3A_36


title: SG16374548_253949448095_1_2_0951-018-900_hr168


title: SG16374548_253949447592_1_4_0951-007-900_hr36


title: Diversity Outbred mESCs, S/LIF + 2i,B3B_15


title: Diversity Outbred mESCs, S/LIF + 2i,B3A_9


title: Diversity Outbred mESCs, S/LIF + 2i,B3A_44


title: Diversity Outbred mESCs, S/LIF + 2i,B3A_3


title: Diversity Outbred mESCs, S/LIF + 2i,B3A_29


title: SG16374548_253949448332_1_1_0951-012-900_hr96


title: SG16374548_253949448306_2_3_0951-011-900_hr84


title: Diversity Outbred mESCs, S/LIF + 2i,B3A_37


title: Diversity Outbred mESCs, S/LIF + 2i,B3A_21


title: SG16374548_253949447593_1_2_0951-009-900_hr60


title: SG16374548_253949447554_2_4_0951-003-900_hr4


title: SG16374548_253949448307_2_3_0951-008-900_hr48


title: Diversity Outbred mESCs, S/LIF + 2i,B3A_16


title: Diversity Outbred mESCs, S/LIF + 2i,B3A_33


title: Diversity Outbred mESCs, S/LIF + 2i,B3A_15


title: SG16374548_253949448094_2_4_0950-004-900_hr8


title: SG16374548_253949447556_1_3_0951-007-900_hr24


title: Diversity Outbred mESCs, S/LIF + 2i,B3A_14


title: SG16374548_253949447553_2_4_0950-003-900_hr4


title: SG16374548_253949446603_2_1_0951-013-900_hr108


title: SG16374548_253949447555_1_2_0951-005-900_hr12


title: SG16374548_253949448304_1_3_0951-004-900_hr8


title: Diversity Outbred mESCs, S/LIF + 2i,B3A_26


title: Diversity Outbred mESCs, S/LIF + 2i,B3A_23


title: SG16374548_253949448111_1_4_0951-001-900_hr0


title: Diversity Outbred mESCs, S/LIF + 2i,B3A_10


title: Diversity Outbred mESCs, S/LIF + 2i,B3A_34


title: SG16374548_253949448106_2_1_0950-006-900_hr24


title: Diversity Outbred mESCs, S/LIF + 2i,B3A_30


title: Diversity Outbred mESCs, S/LIF + 2i,B2_9


title: Diversity Outbred mESCs, S/LIF + 2i,B2_8


title: SG16374548_253949448101_1_1_0942-018-900_hr168

value: Deceased


title: SG16374548_253949448309_1_3_0950-005-900_hr12


title: Diversity Outbred mESCs, S/LIF + 2i,B3A_11


title: SG16374548_253949448309_2_3_0942-017-900_hr156


title: Diversity Outbred mESCs, S/LIF + 2i,B2_7


title: SG16374548_253949447272_1_3_0942-019-900Day14


title: SG16374548_253949447551_2_1_0942-016-900_hr144


title: Diversity Outbred mESCs, S/LIF + 2i,B3A_20


title: SG16374548_253949446603_2_2_0942-015-900_hr132


title: Diversity Outbred mESCs, S/LIF + 2i,B2_5


title: Diversity Outbred mESCs, S/LIF + 2i,B2_3


title: SG16374548_253949447271_1_1_0942-013-900_hr108


title: Diversity Outbred mESCs, S/LIF + 2i,B2_31


title: SG16374548_253949447554_2_3_0942-012-900_hr96


title: Diversity Outbred mESCs, S/LIF + 2i,B2_2A


title: SG16374548_253949447556_1_4_0942-011-900_hr84


title: SG16374548_253949446603_2_4_0950-002-900_hr2


title: SG16374548_253949447593_1_1_0942-010-900_hr72


title: Diversity Outbred mESCs, S/LIF + 2i,B2_28


title: Diversity Outbred mESCs, S/LIF + 2i,B2_2


title: SG16374548_253949447551_2_4_0950-001-900_hr0


title: Diversity Outbred mESCs, S/LIF + 2i,B2_24


title: SG16374548_253949448332_2_1_0942-008-900_hr48


title: Diversity Outbred mESCs, S/LIF + 2i,B2_27


title: SG16374548_253949448093_1_2_0942-007-900_hr36


title: Diversity Outbred mESCs, S/LIF + 2i,B2_22


title: SG16374548_253949448097_2_4_0942-006-900_hr24


title: SG16374548_253949448100_2_3_0942-005-900_hr12


title: Diversity Outbred mESCs, S/LIF + 2i,B2_18


title: SG16374548_253949448111_2_1_0942-003-900_hr4


title: Diversity Outbred mESCs, S/LIF + 2i,B2_12


title: Diversity Outbred mESCs, S/LIF + 2i,B2_1


title: Diversity Outbred mESCs, S/LIF + 2i,B2_11


title: Diversity Outbred mESCs, S/LIF + 2i,B2_32


title: SG16374548_253949448107_1_3_0940-019-900Day14


title: SG16374548_253949448304_1_4_0942-002-900_hr2


title: Diversity Outbred mESCs, S/LIF + 2i,B1_D4


title: SG16374548_253949448111_1_3_0940-020-900Day21


title: Diversity Outbred mESCs, S/LIF + 2i,B1_C17


title: SG16374548_253949448305_1_4_0942-001-900_hr0


title: SG16374548_253949448105_2_4_0940-018-900_hr168


title: Diversity Outbred mESCs, S/LIF + 2i,B1_C16


title: Diversity Outbred mESCs, S/LIF + 2i,B1_C13


title: Diversity Outbred mESCs, S/LIF + 2i,B1_B5


title: SG16374548_253949448328_1_1_0942-009-900_hr60


title: SG16374548_253949448104_2_3_0940-017-900_hr156


title: Diversity Outbred mESCs, S/LIF + 2i,B1_B45


title: SG16374548_253949448099_2_3_0940-014-900_hr120


title: SG16374548_253949448332_1_3_0940-012-900_hr96


title: Diversity Outbred mESCs, S/LIF + 2i,B1_B43


title: Diversity Outbred mESCs, S/LIF + 2i,B1_B44


title: Diversity Outbred mESCs, S/LIF + 2i,B1_B41


title: SG16374548_253949447601_2_4_0940-010-900_hr72


title: SG16374548_253949448107_2_1_0942-004-900_hr8


title: Diversity Outbred mESCs, S/LIF + 2i,B2_17


title: Diversity Outbred mESCs, S/LIF + 2i,B1_B40


title: Diversity Outbred mESCs, S/LIF + 2i,B1_B39


title: SG16374548_253949448328_2_4_0940-011-900_hr84


title: SG16374548_253949447598_2_3_0940-008-900_hr48


title: SG16374548_253949447597_1_1_0940-007-900_hr36


title: Diversity Outbred mESCs, S/LIF + 2i,B1_B37


title: Diversity Outbred mESCs, S/LIF + 2i,B1_B33


title: SG16374548_253949447596_2_1_0940-006-900_hr24


title: Diversity Outbred mESCs, S/LIF + 2i,B1_B29


title: SG16374548_253949447593_2_2_0940-005-900_hr12


title: SG16374548_253949447554_2_1_0940-004-900_hr8


title: SG16374548_253949447553_2_1_0940-003-900_hr4


title: Diversity Outbred mESCs, S/LIF + 2i,B1_B22


title: SG16374548_253949447552_2_4_0940-002-900_hr2


title: Diversity Outbred mESCs, S/LIF + 2i,B1_B25


title: Diversity Outbred mESCs, S/LIF + 2i,B1_B19


title: SG16374548_253949448103_1_2_0940-016-900_hr144


title: SG16374548_253949448095_2_1_0940-013-900_hr108


title: SG16374548_253949447271_1_4_0940-001-900_hr0


title: Diversity Outbred mESCs, S/LIF + 2i,B1_B18


title: Diversity Outbred mESCs, S/LIF + 2i,B1_B15


title: US22502722_253949423827_2_3 - 0936-009

description: US22502722_253949423827_2_3 - 0936-009


title: Diversity Outbred mESCs, S/LIF + 2i,B1_B14


title: SG16374548_253949448304_1_2_0929-013-900_hr108


title: Diversity Outbred mESCs, S/LIF + 2i,B1_A9


title: SG16374548_253949447600_2_1_0940-009-900_hr60


title: US22502722_253949423827_2_4 - 0936-010

description: US22502722_253949423827_2_4 - 0936-010


title: Diversity Outbred mESCs, S/LIF + 2i,B1_B37N


title: Diversity Outbred mESCs, S/LIF + 2i,B1_A23


title: SG16374548_253949448112_1_3_0929-012-900_hr96


title: Diversity Outbred mESCs, S/LIF + 2i,B1_B27


title: SG16374548_253949448110_2_4_0929-010-900_hr84


title: Diversity Outbred mESCs, S/LIF + 2i,B1_A22


title: SG16374548_253949448109_1_2_0929-010-900_hr72


title: SG16374548_253949448100_1_3_0929-007-900_hr36


title: SG16374548_253949448097_2_1_0929-008-900_hr48


title: CD34_stem_cell_3

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

institute: University of Padova

description:
circRNA_expression_per_sample_CD34.csv
circRNA_lin_expr_CD34.csv

data_processing:
CircRNAs were identified and quantified from RNA-seq data by CirComPara v0.6.3 using 9 backsplice detection method combinations.
Methods included in CircComPara v.0.6.3: reads were  co-linearly mapped to reference genome with HISAT2 and processed with Cufflinks; co-linearly unmapped reads were analyzed with CIRI, CIRCexplorer and findcirc to detect circRNAs.
CircRNA annotation and all analyses were based on the Ensembl GRCh38 human genome and annotation v93.
Assembly: hg38
Supplementary files format and content: “circRNA_expression_per_sample_*.csv” files report circRNA backsplice genomic coordinates, the overlapping gene(s) and the read count (as defined by CirComPara) for each sample, as a comma-separated table with circRNA IDs as rows and samples as columns.
Supplementary files format and content: “circRNA_lin_expr_*.csv” files report the read count of the linear gene expression at the backsplice junction for each sample, as a comma-separated table with circRNA IDs as rows and samples as columns.

source_name: cord blood

growth_protocol: The RS4;11 cell line was cultured in RPMI medium at 10% of FBS and 1% of streptamicyin and glutamine. For PDX, BCP-ALL blasts were isolated from the spleen of mice transplanted with patient derived cells by i.v. injection.

extract_protocol:
RNA was exctracted with Trizol
Truseq Total RNA with Ribo Zero for MLL-AF4 rearranged samples. Treatment with Ribonuclease R, Lucigen RNR07250 for CD34+ samples.

treatment_protocol: No treatment

value: cord blood

value: hematopoietic stem cells

tag: type of_leukemia

value: healthy donor

value: CD34+ cells


title: CD34_stem_cell_2


title: CD34_stem_cell_1


title: SG16374548_253949448331_2_4_0929-004-900_hr12

value: Male

value: Alive

value: Agilent's Universal Human Reference RNA


title: MLL-AF4_rearranged_cell_line

description: circRNA_expression_per_sample_RS4-11.csv

source_name: bone marrow

value: bone marrow

value: hematopoietic cells

value: BCP-ALL

tag: translocation


title: SG16374548_253949448102_1_2_0929-004-900_hr24


title: US22502722_253949423802_2_4 - 0932-001

description: US22502722_253949423802_2_4 - 0932-001

value: Female


title: SG16374548_253949448093_1_4_0929-004-900_hr8


title: SG16374548_253949448309_1_2_0929-003-900_hr4


title: SG16374548_253949448328_1_4_0929-002-900_hr2


title: MLL-AF4_rearranged_patient_4

description:
circRNA_expression_per_sample_MLLre.csv
circRNA_lin_expr_MLLre.csv

value: bone marrow cells

value: BM cells isolated at diagnosis


title: SG16374548_253949448305_2_2_0929-001-900_hr0


title: Diversity Outbred mESCs, S/LIF + 2i,B1_A5

value: embryonic stem cells


title: MLL-AF4_rearranged_patient_3


title: MLL-AF4_rearranged_PDX_1

value: BCP-ALL cells isolated from patient-derived xenograft


title: SG16374548_253949447598_2_4_0928-012-900_hr108


title: MLL-AF4_rearranged_patient_2


title: SG16374548_253949447597_2_3_0928-012-900_hr96


title: SG16374548_253949448108_2_3_0928-011-900_hr84


title: iMacs and MoMs - HTO

city: Glasgow

first: Paschalina

last: Chrysostomidou

address: University Avenue

institute: University of Glasgow

description: Library name: Human_macrophages_HTO

library_source: other

data_processing:
Reads were mapped to the human genome (GRCh38-3.0.0) using 10X CellRanger (version 7.0.0). Analysis was carried out using the Seurat package (version 5.2.1) in RStudio (version 4.4.2), as previously described (Stuart et al., 2019). Samples were deconvoluted by the addition of HTO information using cellhashR (v 1.0.3).
Assembly: Human GRCh38
Supplementary files format and content: Tab-separated values and matrix files, RStudio files
Library strategy: CITE-seq

molecule: protein

source_name: iPSCs/Blood

growth_protocol: Sensory neurons were differentiated from iPSCs and maintained in N2/B27 Plus medium (Neurobasal Plus medium, 2% B27 Plus supplement, 1% N2 supplement, 1% Glutamax) supplemented with 25ng/ml BDNF, GDNF, NT3 and NGF, and Matrigel. iMacs were generated from iPSCs and maintained in flasks in X-VIVO15 media supplemented with 100ng/ml M-CSF, 25ng/ml IL3, 1% Glutamax, 0.055mM β-mercaptoethanol and 1% antibiotic-antimycotic (anti-anti). MoMs were maintained in RPMI 160 medium containing 10% foetal calf serum, 1% anti-anti and 50ng/ml M-CSF. For co-cultures, cells were cultured in Neurobasal Plus medium, 2% B27 Plus supplement, 1% N2 supplement, 1% Glutamax supplemented with 25ng/ml BDNF, GDNF, NT3 and NGF, and 10ng/ml M-CSF. All cells were kept at 37C, 5% CO2.

extract_protocol:
Cells from all conditions were generated, collected, processed and sequenced in parallel. On the day of isolation, cultures were enzymatically dissociated with 30 minutes of Accutase (ThermoFisher) followed by brief mechanical dissociation with a fire polished pipette. Single cell suspensions were transferred to phosphate buffered saline (PBS) containing 1:1000 eBioscience™ Fixable Viability Dye eFluor™ 780 (ThermoFisher) and incubated on ice for 20 minutes. Samples were maintained in dark conditions from this point onwards. Samples were centrifuged and washed in fluorescence-activated cell sorting (FACS) buffer containing PBS, 2% foetal calf-serum, 1% anti-anti and 0.5mM EDTA (ThermoFisher) before being resuspended in Human TrueStain FcX blocking buffer (Biolegend) diluted 1:10 in FACS buffer and incubated for 10 minutes on ice. Brilliant Violet 711 anti-human CD45 (1:100) and a unique TotalSeq-A hashtag oligo (HTO) (A-0251, A-0252, A-0253, A-0255, A-0256, A-0258, A-0256, A-0259, A-0260) were added directly to each tube and incubated for 30 minutes on ice. Samples were subsequently centrifuged, resuspended in FACS buffer and strained (100µm strainer) into FACS tubes. Cells were sorted into 1.5ml microcentrifuge tubes containing complete RPMI media
Cells were loaded onto a Chromium Controller (10X Genomics) for single-cell partitioning, using Chromium Next GEM Chip G Single Cell Kit (10X Genomics), and single-cell 3’ Reagent Kits v3.1 (10X Genomics).  A library consisting of iMACs and MoMs was sequenced on an Illumina Nextseq 500 at the Glasgow Polyomics facility.

treatment_protocol: iMacs and MoMs were cultured alone and with healthy (3,7 days) or damaged (7 days) iPSC-derived sensory neurons

value: iPSCs/Blood

value: Macrophages

value: Mixes sample

tag: library type

value: HTO

tag: hto


title: SG16374548_253949448103_2_1_0929-009-900_hr60


title: Diversity Outbred mESCs, S/LIF + 2i,B1_A18

value: Serum/LIF +2i culture


title: SG16374548_253949448107_2_2_0928-009-900_hr72


title: SG16374548_253949448105_2_3_0928-009-900_hr60


title: iMacs and MoMs - RNA

description: Library name: Human_macrophages_RNA

value: Mixed sample

value: mRNA


title: Diversity Outbred mESCs, S/LIF + 2i,B1_B46


title: MLL-AF4_rearranged_PDX_2


title: SG16374548_253949448099_1_1_0928-008-900_hr48

value: Male

value: Alive


title: SG16374548_253949447601_2_1_0928-007-900_hr36

value: Agilent's Universal Human Reference RNA


title: SG16374548_253949448098_2_1_0928-005-900_hr12


title: SG16374548_253949448100_1_1_0928-005-900_hr24


title: SG16374548_253949448096_2_1_0928-004-900_hr8


title: Sample 1022 CD45+ cells, TCR

first: Ning

last: Yao

address: 321 E 61st St

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: Sample_1022_TCR
10X Genomics

data_processing:
FASTQ sequencing reads were processed using the Cell Ranger pipeline, which extracts cell barcodes, unique molecular identifiers (UMIs), and cDNA or antibody barcodes. It aligns cDNA reads to the human GRCh38 reference genome and generates gene and antibody UMI count matrices.
Assembly: hg38
Supplementary files format and content: Raw count matrices: matrix.mtx.gz, Barcode files: barcode.tsv.gz , Feature files: features.tsv.gz
Supplementary files format and content: TCR sequencing: TCR_contig.csv
Library strategy: TCR-seq

molecule: polyA RNA

source_name: PBMC

extract_protocol:
Human peripheral blood mononuclear cells (PBMC) from participants of the clinical study were isolated and thawed using prewarmed BD BSA stain buffer (BD Biosciences), washed twice with ice-cold buffer and counted
Single cells were encapsulated into nanoliter-scale Gel Beads-in-emulsion (GEMs) using Chromium Controller (10X Genomics) following manufacture’s protocol. Chromium Single Cell 5’ Library & Gel Bead, Single Cell V(D)J Enrichment Kit, Mouse T Cell, and Single Cell 5' Feature Barcode kits were used to prepare single cell 5’ RNA, single cell TCR, and single cell surface protein libraries following manufacture’s protocol. The quality and quantity of the libraries were assessed with Agilent TapeStation (Agilent Technologies) and Qubit Fluorometer (Thermo Fisher Scientific).

value: PBMC

value: CD45+ cells

value: Mixed timepoints (C16D1 Patient 10909, Day28 Patient 10909)

value: TCR


title: SG16374548_253949446603_2_3_0928-001-900_hr0


title: Sample 1016 CD45+ cells, TCR

description:
Library name: Sample_1016_TCR
10X Genomics

value: Mixed timepoints (C2D1 Patient 11212, C2D8 Patient 11212)


title: Sample 1022 CD45+ cells, GEX

description:
Library name: Sample_1022_GEX
10X Genomics

data_processing:
FASTQ sequencing reads were processed using the Cell Ranger pipeline, which extracts cell barcodes, unique molecular identifiers (UMIs), and cDNA or antibody barcodes. It aligns cDNA reads to the human GRCh38 reference genome and generates gene and antibody UMI count matrices.
Assembly: hg38
Supplementary files format and content: Raw count matrices: matrix.mtx.gz, Barcode files: barcode.tsv.gz , Feature files: features.tsv.gz
Supplementary files format and content: TCR sequencing: TCR_contig.csv
Library strategy: CITE-seq


title: Sample 1016 CD45+ cells, GEX

description:
Library name: Sample_1016_GEX
10X Genomics


title: Sample 1022 CD45+ cells, HTO

description:
Library name: Sample_1022_HTO
10X Genomics

value: Total Seq C Hashtag 2, Total Seq C Hashtag 3


title: Sample 1016 CD45+ cells, HTO

description:
Library name: Sample_1016_HTO
10X Genomics

value: Total Seq C Hashtag 5, Total Seq C Hashtag 6


title: SG16374548_253949448307_1_3_0925-001-900_hr0


title: SG16374548_253949447272_2_4_0928-002-900_hr2


title: Sample 1015 CD45+ cells, TCR

description:
Library name: Sample_1015_TCR
10X Genomics

value: Mixed timepoints (C1D1 Patient 11212, C1D4 Patient 11212)


title: Sample 1015 CD45+ cells, HTO

description:
Library name: Sample_1015_HTO
10X Genomics


title: MLL-AF4_rearranged_patient_1

value: bone marrow

value: bone marrow cells

value: BCP-ALL

value: BM cells isolated at diagnosis


title: SG16374548_253949448094_1_3_0928-003-900_hr4


title: Sample 1015 CD45+ cells, GEX

description:
Library name: Sample_1015_GEX
10X Genomics


title: SG16374548_253949448112_2_3_0924-017-900_hr168


title: Sample 1014 CD45+ cells, HTO

description:
Library name: Sample_1014_HTO
10X Genomics

value: End of treatment Patient 11010

value: HTO

value: Total Seq C Hashtag 1


title: SG16374548_253949448109_1_1_0924-016-900_hr144

value: Male

value: Alive


title: Sample 1014 CD45+ cells, TCR

description:
Library name: Sample_1014_TCR
10X Genomics

value: PBMC


title: SG16374548_253949448111_2_4_0924-017-900_hr156

value: Agilent's Universal Human Reference RNA


title: Sample 1014 CD45+ cells, GEX

description:
Library name: Sample_1014_GEX
10X Genomics

value: CD45+ cells

value: mRNA


title: Sample 1013 CD45+ cells, TCR

description:
Library name: Sample_1013_TCR
10X Genomics

value: Mixed timepoints (C1D1 Patient 10606, Day28 Patient 10606)

value: TCR


title: SG16374548_253949448105_1_1_0924-015-900_hr132


title: SG16374548_253949448107_2_4_0924-014-900_hr120


title: SG16374548_253949448104_1_4_0924-012-900_hr96


title: Sample 1013 CD45+ cells, GEX

description:
Library name: Sample_1013_GEX
10X Genomics

value: Mixed timepoint s(C1D1 Patient 10606, Day28 Patient 10606)


title: Sample 1012 CD45+ cells, TCR

description:
Library name: Sample_1012_TCR
10X Genomics

value: Mixed timepoints (C2D8 Patient 11414, C11D1 Patient 11414)


title: SG16374548_253949448101_2_4_0924-010-900_hr84


title: Sample 1012 CD45+ cells, HTO

description:
Library name: Sample_1012_HTO
10X Genomics

value: Total Seq C Hashtag 1, Total Seq C Hashtag 4


title: SG16374548_253949448332_1_2_0924-008-900_hr48


title: Sample 1012 CD45+ cells, GEX

description:
Library name: Sample_1012_GEX
10X Genomics


title: SG16374548_253949447600_2_2_0924-004-900_hr8


title: SG16374548_253949447594_2_1_0924-004-900_hr12


title: SG16374548_253949447555_2_1_0924-003-900_hr4


title: Sample 1011 CD45+ cells, HTO

description:
Library name: Sample_1011_HTO
10X Genomics

value: Mixed timepoints (C1D4 Patient 11414, C2D1 Patient 11414)


title: SG16374548_253949447272_2_3_0924-007-900_hr36


title: Sample 1011 CD45+ cells, TCR

description:
Library name: Sample_1011_TCR
10X Genomics


title: Sample 1011 CD45+ cells, GEX

description:
Library name: Sample_1011_GEX
10X Genomics


title: SG16374548_253949447270_1_1_0924-001-900_hr0


title: Sample 1010 CD45+ cells, GEX

description:
Library name: Sample_1010_GEX
10X Genomics

value: C1D1 Patient 11414


title: Sample 1010 CD45+ cells, TCR

description:
Library name: Sample_1010_TCR
10X Genomics


title: SG16374548_253949447271_2_4_0924-002-900_hr2


title: Sample 1010 CD45+ cells, HTO

description:
Library name: Sample_1010_HTO
10X Genomics


title: SG16374548_253949448306_1_1_0921-020-900_Day21


title: SG16374548_253949448305_1_2_0921-018-900_hr168


title: Sample 1008 CD45+ cells, HTO

description:
Library name: Sample_1008_HTO
10X Genomics

value: Mixed timepoints (C2D1 Patient 11010, C2D8 Patient 11010)

value: Total Seq C Hashtag 5, Total Seq C Hashtag 6


title: Sample 1008 CD45+ cells, TCR

description:
Library name: Sample_1008_TCR
10X Genomics


title: Sample 1013 CD45+ cells, HTO

description:
Library name: Sample_1013_HTO
10X Genomics

value: HTO


title: Sample 1007 CD45+ cells, TCR

description:
Library name: Sample_1007_TCR
10X Genomics

value: Mixed timepoints (C1D1 Patient 11010, C1D8 Patient 11010)


title: Sample 1008 CD45+ cells, GEX

description:
Library name: Sample_1008_GEX
10X Genomics


title: SG16374548_253949448111_1_2_0921-017-900_hr156

value: Male


title: Sample 1007 CD45+ cells, GEX

description:
Library name: Sample_1007_GEX
10X Genomics


title: Sample 1007 CD45+ cells, HTO

description:
Library name: Sample_1007_HTO
10X Genomics


title: SG16374548_253949448104_1_2_0921-014-900_hr120

value: Alive


title: Sample 1006 CD45+ cells, TCR

description:
Library name: Sample_1006_TCR
10X Genomics

value: PBMC

value: Mixed timepoints (C2D1 Patient 10606, C2D8 Patient 10606)


title: SG16374548_253949448095_1_3_0921-009-900_hr72

value: Agilent's Universal Human Reference RNA


title: SG16374548_253949447556_2_4_0924-004-900_hr24


title: Sample 1006 CD45+ cells, HTO

description:
Library name: Sample_1006_HTO
10X Genomics

value: CD45+ cells


title: SG16374548_253949448101_1_4_0921-009-900_hr108


title: Sample 1006 CD45+ cells, GEX

description:
Library name: Sample_1006_GEX
10X Genomics

value: Mixed timepoins t(C2D1 Patient 10606, C2D8 Patient 10606)

value: mRNA


title: SG16374548_253949448098_2_4_0921-009-900_hr84


title: Sample 1005 CD45+ cells, HTO

description:
Library name: Sample_1005_HTO
10X Genomics

value: Mixed timepoints (C1D1 Patient 10606, C1D8 Patient 10606)


title: Sample 1004 CD45+ cells, TCR

description:
Library name: Sample_1004_TCR
10X Genomics

value: Mixed timepoints (C2D1 Patient 10909, C2D8 Patient 10909)

value: TCR


title: Sample 1005 CD45+ cells, GEX

description:
Library name: Sample_1005_GEX
10X Genomics


title: SG16374548_253949447597_2_2_0921-006-900_hr24


title: SG16374548_253949447594_1_3_0921-005-900_hr12


title: SG16374548_253949448327_2_1_0921-008-900_hr48


title: SG16374548_253949448307_1_4_0921-019-900_Day14


title: SG16374548_253949448108_2_1_0921-016-900_hr144


title: Sample 1005 CD45+ cells, TCR

description:
Library name: Sample_1005_TCR
10X Genomics


title: Sample 1003 CD45+ cells, TCR

description:
Library name: Sample_1003_TCR
10X Genomics

value: Mixed timepoints (C1D1 Patient 10909, C1D8 Patient 10909)


title: SG16374548_253949446603_1_2_0921-003-900_hr4


title: Sample 1003 CD45+ cells, HTO

description:
Library name: Sample_1003_HTO
10X Genomics


title: Sample 1004 CD45+ cells, HTO

description:
Library name: Sample_1004_HTO
10X Genomics


title: SG16374548_253949447556_1_1_0921-004-900_hr8


title: SG16374548_253949446602_2_1_0921-002-900_hr2


title: SG16374548_253949446591_2_1_0921-001-900_hr0


title: Sample 1003 CD45+ cells, GEX

description:
Library name: Sample_1003_GEX
10X Genomics

value: Mixed timepoints (C1D1 Patient 10808, C1D8 Patient 10808)


title: SG16374548_253949447592_2_3_0915-016-900_hr168

value: Female


title: Sample 1002 CD45+ cells, HTO

description:
Library name: Sample_1002_HTO
10X Genomics

value: Mixed timepoints (C2D1 Patient 10808, C2D8 Patient 10808)

value: Total Seq C Hashtag 5, Total Seq C Hashtag 6


title: SG16374548_253949448103_1_3_0915-016-900_hr156


title: Sample 1002 CD45+ cells, TCR

description:
Library name: Sample_1002_TCR
10X Genomics


title: Sample 1002 CD45+ cells, GEX

description:
Library name: Sample_1002_GEX
10X Genomics


title: SG16374548_253949448330_2_4_0921-009-900_hr96


title: SG16374548_253949448106_1_2_0915-016-900_hr144


title: SG16374548_253949447599_1_3_0921-007-900_hr36


title: SG16374548_253949448102_2_2_0915-015-900_hr132


title: Sample 1001 CD45+ cells, TCR

description:
Library name: Sample_1001_TCR
10X Genomics


title: Sample 1001 CD45+ cells, HTO

description:
Library name: Sample_1001_HTO
10X Genomics

value: HTO


title: Sample 1004 CD45+ cells, GEX

description:
Library name: Sample_1004_GEX
10X Genomics


title: SG16374548_253949448100_1_2_0915-013-900_hr108


title: Sample 1001 CD45+ cells, GEX

description:
Library name: Sample_1001_GEX
10X Genomics


title: SG16374548_253949448093_2_4_0915-014-900_hr120


title: COPD_94_K4me3

city: Verona

first: Barbara

last: Mariotti

state: Verona

address: strada le grazie 8

department: Medicine

institute: University of Verona

data_processing:
Sequencing reads were mapped against the reference genome using BWA package, multiple reads mapping to the same location and strand were collapsed to single read and only uniquely placed reads were used for peak-calling.
Peaks/regions were called using MACS (–q 0.01 --extsize 320 --bdg --nomodel), peaks overlapping ENCODE blacklist were removed. Only peaks identified in at least 90% of samples for each condition were further analyzed.
Peaks with differential H3K4me3 occupancy between groups were idnetified using DESEq2
Assembly: GrCh38
Supplementary files format and content: tab delimited file of normilized reads per H3K4me3 peak

source_name: primary cells from peripheral blood

growth_protocol: Neutrophils were purified from peripheral blood of COPD patients and control donors by density gradient centrifugation.

extract_protocol:
2 milions  neutrophils were crosslinked with 1 % formaldehyde for 10 min. Cross-linking reaction was stopped adding 125mM glycine dor 5 min.  After fixation, cells were washed with ice-cold PBS, pelleted by centrifugation and resuspend in 900 ml L1 buffer (50 mM Tris, pH 8.0, 2 mM EDTA, 0.1 % IGEPAL, 10 % glycerol) containing protease inhibitors. Nuclei were pelleted at 1000xg at 4°C and resuspended in 500 ml L2 buffer (50 mM Tris, pH 8.0, 1 % SDS, 5 mM EDTA) supplemented with protease inhibitors. Chromatin was sheared  using a BANDELIN SONOPLUS ultrasonic homogenizers HD 2070 (Bandelin, Berlin, Germany).  Immunoprecipitations were carried out overnight at 4°C using 3ml antibody. Immune complexes were then collected by adding 15 µl of protein A magnetic beads (Thermo Fisher) for 20min at 4°C under gentle rotation. Beads werewashed three times in washing buffer (20 mM Tris, pH 8.0, 0.1 % SDS, 2 mM EDTA, 1% IGEPAL, 500 mM NaCl) and once in TE. Protein complexes were then eluted in TE containing 2 % SDS, and reversed crosslinked by an overnight incubation at 65°C. The DNA was purified by QiaQuick PCR purification kit (Qiagen) according to the manufacturer’s instructions, and eluted in 50-100 µl. Prior to lybrary preparation, ChIP-DNA was cleaned and concentrated using the ChIP DNA Clean & Concentrator kit (Zymo Research).
ChIP DNA libraries were prepared using the NEXTflex Rapid DNA Sequencinf Bundle (BIOO SCIENTIFIC) according to manufacturer protocol.

treatment_protocol: freshly isolated cells

tag: disease state

value: COPD

value: primary cells from peripheral blood

value: neutrophils

tag: chip antibodies

value: H3K4me3 (17-614, Merck Millipore)

value: freshly purifies


title: SG16374548_253949447270_2_3_0915-011-900_hr96

value: Alive

value: Agilent's Universal Human Reference RNA


title: COPD_115_K4me3


title: COPD_110_K4me3


title: SG16374548_253949447552_2_3_0915-009-900_hr60


title: COPD_107_K4me3


title: SG16374548_253949447593_2_4_0915-007-900_hr36


title: SG16374548_253949447271_2_1_0915-010-900_hr72


title: SG16374548_253949448095_1_1_0915-011-900_hr84


title: SG16374548_253949447595_2_2_0915-006-900_hr24


title: SG16374548_253949447553_1_4_0915-008-900_hr48


title: COPD_103_K4me3


title: COPD_106_K4me3


title: COPD_108_K4me3


title: COPD_104_K4me3


title: SG16374548_253949447601_1_2_0915-005-900_hr12


title: COPD_100_K4me3


title: SG16374548_253949448329_2_4_0915-004-900_hr8


title: SG16374548_253949448332_2_3_0915-003-900_hr4


title: HD_95_K4me3

value: control


title: SG16374548_253949448094_1_4_0915-002-900_hr2


title: SG16374548_253949448096_1_2_0915-001-900_hr0


title: US22502722_253949423825_2_3 - 0907-008

description: US22502722_253949423825_2_3 - 0907-008


title: HD_125_5_K4me3


title: US22502722_253949423825_2_2 - 0907-007

description: US22502722_253949423825_2_2 - 0907-007


title: HD_112_K4me3


title: HD_116_K4me3


title: US22502722_253949423825_1_4 - 0907-004

description: US22502722_253949423825_1_4 - 0907-004


title: HD_148_K4me3


title: HD_111_K4me3


title: HD_106_5_K4me3


title: US22502722_253949423825_1_2 - 0907-002

description: US22502722_253949423825_1_2 - 0907-002


title: HD_101_K4me3


title: COPD_102_K4me3


title: SG16374548_253949448309_1_1_0904-001-900_hr0


title: US22502722_253949423825_1_3 - 0907-003

description: US22502722_253949423825_1_3 - 0907-003


title: US22502722_253949423802_2_3 - 0905-019

description: US22502722_253949423802_2_3 - 0905-019

value: Male


title: HD_149_K4me3


title: US22502722_253949423825_1_1 - 0907-001

description: US22502722_253949423825_1_1 - 0907-001


title: COPD_94

data_processing:
Basecalls performed using bcl2fastq2
The quality of sequenced reads obtained from each sample was assessed using FastQC software. UMI sequences were extracted using UMI-Tools (v1.0.1). Raw reads were trimmed to remove low-quality ends, polyA tails, and adapters sequences using bbduk (v38.86).
Trimmed reads were aligned to the reference human genome (GRCh38) using STAR (v2.7.3a).
After mapping, PCR duplicates were removed from the BAM files based on UMI sequence using UMI-tools. The number of reads mapping to each gene was determined using HTSeq-count (v0.11.2). Reads counts were normalized with the FPM normalization method implemented in DESeq2. Batach correction of FPM counts were done with limma.
Assembly: GrCh38
Supplementary files format and content: tab delimited file containing batch adjusted FPM value

source_name: peripheral blood

extract_protocol:
Total RNA was extracted after cell lysis by the RNeasy Mini Kit (Qiagen, Venlo, Limburg, Netherlands). To completely remove any possible contaminating DNA, an on-column DNase digestion with the RNase-free DNase set (Qiagen) was performed during total RNA isolation.
RNA libraries for RNA-seq were prepared using QUANTSEQ 3' mRNA-seq library prep Kit (LEXOGENE) following manufacturer's protocols.

value: peripheral blood

value: primary cells

tag: Sex


title: SG16374548_253949448108_1_2_0903-018-900_hr168

data_processing:
Agilent Feature Extraction Software (v 10.7) was used for background subtraction and GeneSpring v.10.1 (Agilent Technologies, Inc., CA) software was used to conduct the preliminary data filtration and statistical analysis.
processed_data: Logratio (test/reference)


title: COPD_88

tag: cell type


title: SG16374548_253949448105_1_3_0903-017-900_hr156


title: HD_105_K4me3

tag: treatment


title: US22502722_253949423802_2_2 - 0905-018

description: US22502722_253949423802_2_2 - 0905-018

tag: age


title: SG16374548_253949448099_2_2_0903-016-900_hr144

tag: gender


title: COPD_86


title: COPD_82


title: COPD_79


title: US22502722_253949423825_2_1 - 0907-005

description: US22502722_253949423825_2_1 - 0907-005

tag: timepoint


title: HD_109_K4me3


title: SG16374548_253949448098_2_3_0903-015-900_hr132

tag: reference


title: COPD_75


title: SG16374548_253949448097_2_2_0903-014-900_hr120


title: COPD_74


title: SG16374548_253949448096_1_4_0903-013-900_hr108


title: COPD_73


title: SG16374548_253949448330_2_2_0903-012-900_hr96


title: COPD_68


title: SG16374548_253949448329_1_1_0903-011-900_hr84


title: SG16374548_253949447601_2_2_0903-010-900_hr72


title: COPD_63


title: COPD_52


title: SG16374548_253949447600_2_4_0903-009-900_hr60


title: COPD_40


title: SG16374548_253949447598_1_2_0903-008-900_hr48


title: COPD_36


title: SG16374548_253949447271_2_3_0903-004-900_hr8


title: COPD_33


title: SG16374548_253949447596_2_3_0903-007-900_hr36


title: COPD_43


title: COPD_50


title: COPD_22


title: SG16374548_253949446602_2_2_0903-003-900_hr4


title: SG16374548_253949446591_2_4_0903-001-900_hr0


title: COPD_35


title: SG16374548_253949447592_2_1_0903-006-900_hr24


title: SG16374548_253949447551_1_1_0903-002-900_hr2


title: SG16374548_253949447555_1_3_0903-005-900_hr12


title: COPD_18


title: COPD_23


title: COPD_189


title: US22502722_253949423827_1_4 - 0902-017

description: US22502722_253949423827_1_4 - 0902-017

value: Deceased


title: US22502722_253949423827_1_3 - 0902-016

description: US22502722_253949423827_1_3 - 0902-016


title: COPD_185


title: US22502722_253949423827_1_2 - 0902-014

description: US22502722_253949423827_1_2 - 0902-014


title: COPD_184


title: US22502722_253949423827_1_1 - 0902-011

description: US22502722_253949423827_1_1 - 0902-011


title: COPD_16


title: US22502722_253949423826_2_4 - 0902-010

description: US22502722_253949423826_2_4 - 0902-010


title: US22502722_253949423826_2_3 - 0902-009

description: US22502722_253949423826_2_3 - 0902-009


title: US22502722_253949423826_2_2 - 0902-008

description: US22502722_253949423826_2_2 - 0902-008


title: COPD_153


title: US22502722_253949423826_2_1 - 0902-007

description: US22502722_253949423826_2_1 - 0902-007


title: COPD_136


title: COPD_134


title: US22502722_253949423827_2_1 - 0902-018

description: US22502722_253949423827_2_1 - 0902-018


title: COPD_115


title: US22502722_253949423826_1_4 - 0902-005

description: US22502722_253949423826_1_4 - 0902-005


title: US22502722_253949423826_1_2 - 0902-003

description: US22502722_253949423826_1_2 - 0902-003


title: COPD_110


title: US22502722_253949423826_1_1 - 0902-002

description: US22502722_253949423826_1_1 - 0902-002


title: COPD_156


title: COPD_108


title: SG16374548_253949447595_2_3_0901-001-900_hr0


title: COPD_126


title: COPD_104


title: Mouse BMDC 100Q rep 3 (mRNA-seq)

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

description:
Library name: Sample6
100Q_rep3_L1_bc17

data_processing:
Raw sequencing reads were first demultiplexed by barcode sequence using Je demultiplex (PMID: 27717304).
Reads were trimmed using FastP (PMID: 30423086). After trimming, read quality control was assessed with FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc) to confirm the removal of low-quality bases and adapter sequences.
Trimmed reads were aligned to the mm39 (GRCm39) reference genome using STAR (PMID: 23104886).
Once mapped, reads were counted with the RSEM software (PMID: 21816040). Subsequent differential expression analysis was completed using custom scripts in R.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: Murine bone marrow-derived dendritic cells (BMDCs) were generated from 6-8 week-old C57BL/6 female mice. Bone marrow cells were collected from femora and tibiae and cultured at 37°C in RPMI-1640 (Gibco; AM9260G) supplemented with 10% v/v dialyzed fetal bovine serum (Gibco; 26400044), L-glutamine (2 mM; Gibco; 25030081), penicillin-streptomycin (Gibco; 15140122), MEM non-essential amino acids (Corning; MT25025CI), HEPES (10 mM; Gibco; 15630080), sodium pyruvate (1 mM; Corning; MT25000CI), and β-mercaptoethanol (55 µM; Gibco; 21985023). Recombinant murine GM-CSF (Peprotech 315–03-100μg) at 15 ng/mL was added to the complete RPMI medium. Cells were fed at days 2 and 4 with complete RPMI medium containing GM-CSF.

extract_protocol:
On day 5, total RNA was extracted from cells using TRIzol reagent (Thermo Fisher Scientific; 15596026)
RNA-seq (PMID: 28942919)

treatment_protocol: Cells were plated in triplicate with either media alone (0Q) or supplemented with 100 nM queuine (100Q). Cells were fed at days 2 and 4 with complete RPMI medium containing GM-CSF ± queuine to maintain treatment concentration .

value: bone marrow

value: dendritic cell

value: 100 nM queuine supplement


title: COPD_186

value: Female


title: US22502722_253949423804_2_4 - 0900-018

description: US22502722_253949423804_2_4 - 0900-018


title: US22502722_253949423804_2_3 - 0900-017

description: US22502722_253949423804_2_3 - 0900-017


title: COPD_103


title: US22502722_253949423804_2_2 - 0900-016

description: US22502722_253949423804_2_2 - 0900-016


title: US22502722_253949423804_2_1 - 0900-015

description: US22502722_253949423804_2_1 - 0900-015


title: Mouse BMDC 100Q rep 2 (mRNA-seq)

description:
Library name: Sample5
100Q_rep2_L1_bc10


title: COPD_102


title: US22502722_253949423826_1_3 - 0902-004

description: US22502722_253949423826_1_3 - 0902-004


title: US22502722_253949423804_1_4 - 0900-013

description: US22502722_253949423804_1_4 - 0900-013


title: SG16374548_253949447599_1_4_0901-002-900_hr2


title: US22502722_253949423804_1_3 - 0900-012

description: US22502722_253949423804_1_3 - 0900-012


title: Mouse BMDC 0Q rep 3 (mRNA-seq)

description:
Library name: Sample3
0Q_rep3_L1_bc12

value: queuine-depleted media


title: COPD_106

value: COPD


title: Mouse BMDC 100Q rep 1 (mRNA-seq)

description:
Library name: Sample4
100Q_rep1_L1_bc8


title: COPD_100


title: COPD_162


title: US22502722_253949423803_2_3 - 0900-008

description: US22502722_253949423803_2_3 - 0900-008


title: US22502722_253949423803_2_1 - 0900-005

description: US22502722_253949423803_2_1 - 0900-005


title: US22502722_253949423804_1_2 - 0900-011

description: US22502722_253949423804_1_2 - 0900-011


title: Mouse BMDC 0Q rep 1 (mRNA-seq)

description:
Library name: Sample1
0Q_rep1_L1_bc7


title: US22502722_253949423804_1_1 - 0900-010

description: US22502722_253949423804_1_1 - 0900-010


title: US22502722_253949423803_2_4 - 0900-009

description: US22502722_253949423803_2_4 - 0900-009


title: Mouse BMDC 0Q rep 2 (mRNA-seq)

description:
Library name: Sample2
0Q_rep2_L1_bc5


title: HD_93


title: US22502722_253949423803_1_3 - 0900-003

description: US22502722_253949423803_1_3 - 0900-003


title: US22502722_253949423803_1_2 - 0900-002

description: US22502722_253949423803_1_2 - 0900-002


title: HD_84


title: B16-Ats1KO tumor 3, day 21

city: Granada

first: Juan Carlos

last: Rodriguez-Manzaneque

state: Granada

address: Avda de la Ilustración 114

country: Spain

institute: GENYO. Centre for Genomics and Oncological Research

data_processing:
Raw FastQ files were quality filtered using FACSTQC and aligned against the mouse genome GRCm38 by STAR v2.7.0a
Gene expression values were quantified using RSEM v1.2.31
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Murine melanoma

extract_protocol:
Frozen pieces of tumors (approximately 5-8 mg) were mechanically disrupted with metallic beads on TissueLyser LT (Qiagen, Netherlands). Then, total RNA was extracted from tumor samples using NucleoSpin RNAII kit (Macherery-Nagel).
mRNA-seq libraries were generated according to the manufacturer’s instructions of the TruSeq stranded mRNA Library Prep kit (20020595, Illumina)

value: Murine melanoma

value: Murine skin melanoma cells

tag: genotype

value: WT cells in Adamts1-KO C57Bl/6 mice


title: B16-Ats1KO tumor 2, day 21

tag: tissue


title: SG16374548_253949448308_2_4_0897-019-900_Day14


title: B16-Ats1KO tumor 1, day 21

tag: cell line


title: SG16374548_253949448305_2_4_0897-018-900_hr168


title: HD_187

value: neutrophils


title: SG16374548_253949447552_1_4_0897-016-900_hr144

value: Alive


title: HD_95

value: m


title: US22502722_253949423803_2_2 - 0900-007

description: US22502722_253949423803_2_2 - 0900-007

value: Agilent's Universal Human Reference RNA


title: SG16374548_253949447599_1_1_0897-017-900_hr156

value: Male


title: HD_183

value: peripheral blood

value: control


title: SG16374548_253949448307_1_1_0897-014-900_hr120


title: SG16374548_253949448112_1_1_0897-013-900_hr108


title: SG16374548_253949448107_1_1_0897-012-900_hr96


title: B16F1 tumor 3, day 21

value: WT cells in WT C57Bl/6 mice


title: HD_182

value: primary cells


title: SG16374548_253949447598_1_1_0897-015-900_hr132


title: US22502722_253949423803_1_4 - 0900-004

description: US22502722_253949423803_1_4 - 0900-004


title: HD_179


title: SG16374548_253949447600_1_1_0897-011-900_hr84


title: B16Nid1 tumor 3, day 21

value: NID1 Overexpressor cells in WT C57Bl/6 mice


title: US22502722_253949423803_1_1 - 0900-001

description: US22502722_253949423803_1_1 - 0900-001


title: SG16374548_253949447271_1_3_0897-010-900_hr72


title: SG16374548_253949447597_2_1_0897-008-900_hr48


title: B16Nid1 tumor 1, day 21


title: B16Nid1 tumor 2, day 21


title: HD_178


title: HD_38


title: HD_180


title: B16F1 tumor 1, day 21


title: SG16374548_253949447596_1_3_0897-007-900_hr36


title: SG16374548_253949447595_1_4_0897-005-900_hr12


title: SG16374548_253949447594_1_2_0897-002-900_hr2


title: HD_175


title: S2_L002, 120 day, scRNASEQ, pig retinal organoid

city: Madison

first: David

last: Gamm

state: WI

address: 1500 Highland Ave

department: Department of Ophthalmology and Visual Sciences

institute: University of Wisconsin School of Medicine and Public Health

description:
10x Genomics
2_S2_L002

library_source: transcriptomic single cell

data_processing:
Star solo version 2.7.10b with chemistry v.3 was used to align reads to the swine genome (Sscrofa11.1) and obtain count matrices with the following parameters: --soloType= CB_UMI_Simple, --soloMultiMappers= EM, --soloUMIdedup= 1MM_CR, --soloFeatures= Gene GeneFull SJ Velocyto,--soloCellFilter= EmptyDrops_CR.
Assembly: Sus scrofa Berkshire v1.109
Supplementary files format and content: Tab separated values files and matrix files STAR solo output where barcodes are cell IDs, features are genes, and matrix files are the counts.  Filtered files represent counts filtered for empty droplets while raw files are the raw counts.
Supplementary files format and content: RDS files are Seurat objects that include annotations. Sample 2 (day 120) includes both manual annotations and Seurat mapping annotations from human data.
Supplementary files format and content: H5ad files are Anndata objects that include pseudotime calculations.

organism: Sus scrofa

source_name: Porcine iPSC-derived retinal organoid

growth_protocol: Female and male piPSC lines used in this study were obtained from the laboratory of Dr. James Thomson lab at UW-Madison and Dr. Li-Fang Chu at the University of Calgary (Conrad et al., 2023). Porcine iPSCs were maintained in 6-well plates (Fisherbrand 140685) on irradiated MEF feeder layers (Wicell) at a density of 5.4 x 105 MEF/well under humidified conditions at 5% CO2 and 37⁰C using piPSC stem cell media [piPSC SCM; KnockOut DMEM (Gibco 10829-018) containing 15% [v/v] KnockOut Serum Replacement (Gibco 10828028), 0.1% [v/v] Chemically Defined Lipid Concentrate (Gibco 11905031), 1X GlutaMAX (Gibco 35050079), 0.1 mM β-mercaptoethanol (Sigma M3148-100ML), 1X MEM nonessential amino acids (MEM NEAA) (Gibco 11140-076), 1X antibiotic-antimycotic (Gibco 15240-112), 20 ng/mL FGF2 (WiCell), 5 ng/mL Activin A (Peprotech 120-14E-500UG), 1.5 µM CHIR99021 (Peprotech 2520691), and 2.5 µM IWR-1 (Sigma I0161-25MG)]. To passage the piPSC lines, colonies were dissociated into small clumps using 1X TrypLE Select (Gibco 12563011) and plated onto new MEF feeder cells in piPSC SCM containing 10uM Y-27632 (Tocris 1254/10) for 24 hours. Media was changed every 24 hours using piPSC SCM lacking Y-27632, with subculture every 2-3 days.

extract_protocol:
At each designated timepoint or period, 5 piPSC-ROs from 3 independent differentiations were pooled for scRNA-seq analysis. Porcine ROs were dissociated using the Neural Tissue Dissociation Papain Kit (P) at 37°C for 1 hr and the resulting cell suspension was filtered through a pre-wet 37 µm cell strainer to obtain a single cell suspension. Cells were counted on a Countess 3FL Automated Cell Counter.
Libraries were constructed according to the Chromium Single Cell 3’ Reagent Kit v3.1 user guide (10x Genomics, Pleasanton, CA). Briefly, cells in single cell suspension were delivered to the University of Wisconsin-Madison Biotechnology Center on ice where the cell concentration and viability were quantified on the Luna FX-7 automated cell counter (Logos Biosystems, Anyang, Gyeonggi Province, South Korea) using acridine orange/propidium iodide stain (Logos Biosystems). The appropriate volume of cells were loaded onto the Single Cell Chip G required for yielding a targeted cell recovery of 10,000 cells. Following the completion of the Chromium run the GEMs were transferred to emulsion safe strip tubes for GEM-RT using an Eppendorf MasterCycler Pro thermocycler (Eppendorf, Hamburg, Germany). Following RT, GEMs were broken, and the pooled single cell cDNA was amplified. Post-cDNA amplified product was purified using SPRIselect (Beckman Coulter, Brea, CA) and quantified on a Bioanalyzer 2100 (Agilent, Santa Clara, CA) using the High Sensitivity DNA kit. Adapters were then added to the libraries after fragmentation, end repair, A-tailing, and double-sided size selection using SPRIselect. Following adapter ligation, libraries were purified using SPRIselect and sample-specific indexes (Dual Index Plate TT set A, 10x Genomics) were added by sample index PCR. After sample index PCR, samples were double-size selected using SPRIselect yielding final libraries compatible for Illumina sequencing. Final libraries were quantified using the Qubit High Sensitivity DNA Kit (Thermo Fisher Scientific).

treatment_protocol: Retinal differentiation was initiated when piPSC colonies reached 80-90% confluency. On day (d) 0 of differentiation, piPSC colonies from 4 wells of a 6-well plate were lifted with 1 mg/mL dispase (Gibco 17105041) to form a suspension of embryoid bodies (EBs) in 1:1 modified piPSC SCM (piPSC SCM without FGF2, Activin A, CHIR99021, and IWR-1) : Neural Induction Medium [NIM; DMEM/F12 (Gibco 11330-057, 1% [v/v] N2 supplement (Gibco 17502048), 1X MEM NEAA, 1X GlutaMAX, and 2 mg/mL Heparin (Sigma H-3149)] supplemented with 10uM Y-27632, and transferred to a T-75 flask (VWR 353136). On d1, media was replaced with NIM. On d2, media was exchanged for fresh NIM supplemented with 12.5ng/mL BMP4 (R&D Systems 314-BP-01M) and EBs were plated on a 6-well plate coated with Matrigel (Corning 356234). Half of the media was replaced with fresh NIM on d3 and d4, and on d5 the media was changed to Retinal Differentiation Medium [RDM; 3:1 DMEM:F12 (Gibco 11965-118 and 11765070, respectively), 2% B27 supplement (Gibco 17504044), MEM NEAA, 1X Antibiotic-Antimycotic, and 1X GlutaMAX]. Media was replaced every other day until d11-d13, by which time numerous optic vesicle (OV)-like colonies were visible by light microscopy. The OV-like colonies were microdissected using a MSP ophthalmic surgical knife (Surgical Specialties Corporation), transferred as a suspension to poly-HEMA-coated T-25 flasks (Sigma P3932, Falcon 353109), and maintained in 3D-RDM [3:1 DMEM:F12, 2% B27 supplement, 1X MEM NEAA, 1X Antibiotic-Antimycotic, 1X GlutaMAX, 5% FBS (WiCell), 100 μM taurine (Sigma T0625-10G), and 1:1000 Chemically Defined Lipid Concentrate] with twice-weekly media replacement. Live cultures were imaged on a Nikon Ts2-FL equipped with a DS-Fi3 camera or on a Nikon ECLIPSE Ti2-E equipped with a multi-wavelength LED Light Engine.

value: Porcine iPSC-derived retinal organoid

value: piPSC Clone 8

value: Porcine iPSCs

value: 120 days


title: US22502722_253949444820_2_4- 0896-019

description: US22502722_253949444820_2_4- 0896-019

extract_protocol: Total RNA was isolated using the PAXgene Blood RNA kit (Qiagen, Valencia, CA) following manufacturer directions

value: Female


title: HD_173


title: S2_L001, 120 day, scRNASEQ, pig retinal organoid

description:
10x Genomics
2_S2_L001


title: B16F1 tumor 2, day 21

value: Murine melanoma

value: Murine skin melanoma cells


title: SG16374548_253949446603_1_4_0897-001-900_hr0


title: US22502722_253949444820_2_3- 0896-015

description: US22502722_253949444820_2_3- 0896-015


title: HD_171

value: neutrophils


title: US22502722_253949444819_2_2- 0896-012

description: US22502722_253949444819_2_2- 0896-012

value: Alive


title: HD_170


title: US22502722_253949444819_2_1- 0896-010

description: US22502722_253949444819_2_1- 0896-010


title: US22502722_253949444819_2_3- 0896-014

description: US22502722_253949444819_2_3- 0896-014


title: S1_L001, 40 day, scRNASEQ, pig retinal organoid

description:
10x Genomics
1_S1_L001

value: 40 days


title: HD_169


title: US22502722_253949444816_2_4- 0896-009

description: US22502722_253949444816_2_4- 0896-009

value: Agilent's Universal Human Reference RNA


title: S1_L002, 40 day, scRNASEQ, pig retinal organoid

description:
10x Genomics
1_S1_L002


title: SG16374548_253949446602_1_1_0897-006-900_hr24

value: Male


title: HD_168

value: peripheral blood


title: US22502722_253949444820_2_1- 0896-011

description: US22502722_253949444820_2_1- 0896-011