title: RNA_CD34_31_SA2KO_d14

description:
RNAseq_HSPCs_STAG2_KO_d14_counts_raw.txt
RNAseq_HSPCs_STAG2_KO_d14_log.rpkm.batchcorr.donor.txt
qstat.d14.SA2KOvsCTRL.d14.glm.txt
raw data cannot be deposited online

data_processing:
For AML samples, Sequences were trimmed to 100 bp length
Sequences were aligned using STAR v2.5.3a to human reference genome GRCh38.p10 incorporating gene annotation from GENCODE 44 (release 27) and gene-count tables using the --quantMode GeneCounts function were generated.
A combined read count table (counts.raw.txt) was assembled based on STAR reads per gene tables in R for each dataset.
Data was normalized using edgeR 3.32.1 and normalized counts were calculated using the rpkm function of edgeR. For HSPC datasets, pkms were batch corrected for donor-batch using limma removeBatchEffect.
Differential gene expression was tested using the qlf-test in edgeR between CTRL-AML and STAG2mut AML or CTRL-AML and RAD21mut AML using a model accounting for most common co-mutations. For HSPCs, differential gene expression was tested using the qlf-test in edgeR between associated ctrl-HSPCs and depleted samples using a model accounting for donor-batches.
Assembly: GRCh38.p10
Supplementary files format and content: tab-delimited file containing raw counts for each sample of the associated dataset (counts.raw.txt)
Supplementary files format and content: tab-delimited file containing rpkm normalized counts for each sample of the associated dataset
Supplementary files format and content: tab-delimited file containing qstat differential gene expression test results between controls and associated cohesin deficient groups (qstat)

extract_protocol:
For AMLs and adult HSCs, total RNA was is extracted using AllPrep DNA/RNA mini kit (Qiagen), for cord blood HSPCs total RNA was is extracted using RNeasy Mini Kit (Qiagen)
For AMLs and adult HSCs, RNA-seq libriaries were generated using KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche). Libraries for HSPCs with siRNA-based knockdown were generated with  using TruSeq Stranded mRNA library prep kit (Illumina) and for Cas9-edited HSPCs the TruSeq Stranded total RNA library prep kit (Illumina) was utilized.

treatment_protocol: To obtain AML cells, PBMCS were extracted from bone marrow or whole blood samples of patients using Lymphoprep at the timepoint of first diagnosis and viably frozen. To obtain healthy adult CD34+ HSCs, PBMCS were extracted from bone whole blood samples using Lymphoprep from healthy mobilized stem cell donors and enriched for CD34+ expressing cells. For knockdown experiments with healthy cells, HSPCs were transfected using the Neon electroporation system (Invitrogen, 1400V, 20ms, 2 pulses) at a density of 60,000 viable cells/µL with 1.33µg of chemically modified siRNAs (Axiolabs) per mio cells. Depleted HSPCs were kept in antibiotics-free media after transfection and harvested after 4d. For CRISPR/Cas9-mediated knockout of STAG2 HSPCs were transfected using  at a density of 10,000 viable cells/µL with ribonucleoprotein complexes of guide RNA and Cas9 protein ( Cas9 (Alt-R™ S.p. HiFi Cas9 Nuclease V3, IDT)  and Cas9 electroporation enhancer (IDT). Genome-edited Cells were kept in antibiotics-free media after transfection and harvested after 14 d.


title: ChIP_IN_AML_ctr_14094

status: Public on Jun 18 2024

type: SRA

city: Regensburg

first: Alexander

last: Fischer

address: Franz-Josef-Strauß-Allee 11

country: Germany

institute: Leibniz Institute for Immunotherapy

description:
2273
EGAR00003766142

library_source: genomic

data_processing:
Sequences wer aligned to the human reference genome (GRCh38.p10) using bowtie2 (v. 2.4.5) in very sensitive mode
Samtools (v.1.6) was used to remove lower quality alignments with mapQ=<10 and sorting
FREEC (v. 11.0) 41 was run on the generated sam files including mappability filtering (unique match =TRUE) based on a hg38 mappabiltiy track created with the GEM library to optain copy number variations.
Assembly: GRCh38.p10
Supplementary files format and content: tab-delimited files containing  position, copy number and type of CNV (FreeC output)
Library strategy: low pass whole genome DNA-seq

molecule: genomic DNA

organism: Homo sapiens

source_name: hematopoietic

extract_protocol:
DNA was is extracted using AllPrep DNA/RNA mini kit (Qiagen). 32.5ng of DNA was sheared to 200bp using the Covaris S-series sonication device.
DNA libriaries were generated using the NebNext library preparation kit (NEB).

treatment_protocol: PBMCS were extracted from bone marrow or whole blood samples using Lymphoprep at the timepoint of first diagnosis and viably frozen.

tag: tissue

value: hematopoietic

tag: cell type

value: AML blasts

tag: genotype

value: cohesin wt


title: HiC_AML_RAD21_UKR186

description:
UKR186
CohAML_CTRL_RAD21_merged.loop.scores.XYrm.txt
CohAML_CTRL_RAD21_merged.normTotalaverage.loop.scores.txt
RAD21mutvsCTRL.merged.loop.scores.DESeq.norm2Total.loopcoords2.txt
merged_rad21_mut_10kb.hic
EGAR00003764772

data_processing:
Reads were trimmed for GATC sequences using Skewer (v0.2.2)
Sequences wer aligned to the human reference genome (GRCh38.p10) using bowtie2 (v. 2.4.5).
HOMER style tagDirectories were generated using HOMER makeTagDirectory (-checkGC and -unique) and filtered using “-restrictionSite GATC -both -genome hg38 -removePEbg -removeSelfLigation -removeSpikes 10000 5“ options
HOMERs findTADsAndLoops.pl  was run to determine loop positions which were subsetquently merged to obtian consensus positions. Individual tag directories were scored for merged loop positions using findTADsAndLoops.pl -score function in default and normTotal mode. Sex chromosomes (X/Y) were filtered out after this step.
DESeq2 analysis was run on combined loop score tables of CTRL-AMLs vs. Either STAG2 or RAD21-mutant AMLs implementing a normalization factor calculated by dividing total scores from scoring to total counts by total scores derived from the regular interaction normalized scoring
For visualization of interactions, Hi-C data was analyzed using the FAN-C v.0.9.25 suite. The genome was binned at 10kb resolution and Hi-C matrices summarizing the number of valid pairs per bin were constructed and merged by patient group (.hic files)
Assembly: GRCh38.p10
Supplementary files format and content: Tab delimited file containing loop coordinates and loop scores for individual samples generated by HOMER with default HiC normalization (merged.loop.scores)
Supplementary files format and content: Tab delimited file containing loop coordinates and loop scores for individual samples generated by HOMER with normTotal HiC normalization (.normTotalaverage.merged.loop.scores)
Supplementary files format and content: Tab delimited file containing loop coordinates and DESeq2 differnetial loop statistics testing STAG2/RAD21-mutant AMLs vs CTRL-AMLs  or cohesin depleted HSPCs (SA1/SA2/RAD21 KD) vs CTRL HSPCs (DESeq.norm2Total.loopcoords2.txt)
Supplementary files format and content: .hic file generated by FAN-C at 10 kb resolution

growth_protocol: CD34+ HSPCs were enriched from fresh cord blood samples on the day of birth using the CD34 MicroBead kit (Miltenyi biotec). Cells were expanded for 7d in serum-free Stem Span media (Stem Cell Technologies) supplemented with human recombinant cytokines (Peprotech): SCF (0.1ng/mL), FLT3 (0.1ng/mL), IL6 (0.004ng/mL), TPO (0.025ng/mL) and StemRegenin1 (7500nmol/mL, Stem Cell technologies) as well as Penicillin/Streptomycin.

extract_protocol:
2Mio Cells were fixated using 1% formaldehyde. Nuclei were extracted, a restriction digest using DpnII was performed, followed by incorporation of biotin-dATP and in situ proximity ligation using T4 DNA ligase. Ligated fragments were sheared on a Covaris S series sonicator and biotionylated fragments were purified using MyOne Streptavidin T1 Dynabeads.
Libraries were constructed on-bead following an in-house protocol with 12 cycles of PCR amplification using NEBNext High-Fidelity Q5 2x PCR Mix and Bioo Nextflex DNA sequencing adapters .

treatment_protocol: To obtain AML cells, PBMCS were extracted from bone marrow or whole blood samples of patients using Lymphoprep at the timepoint of first diagnosis and viably frozen. For knockdown experiments with healthy cells, HSPCs were transfected using the Neon electroporation system (Invitrogen, 1400V, 20ms, 2 pulses) at a density of 60,000 viable cells/µL with 1.33µg of chemically modified siRNAs (Axiolabs) per mio cells. Cells were kept in antibiotics-free media after transfection and harvested after 4d.

value: RAD21 mut


title: RNA_CD34_29_SA2KO_d14

library_source: transcriptomic

molecule: total RNA

source_name: cord blood

value: cord blood

tag: cell line

value: HSPC

tag: treatment


title: HiC_AML_ctr_19405

description:
3323
CohAML_allpat_merged.loop.scores.XYrm.txt
CohAML_allpat_merged.normTotalaverage.loop.scores.XYrm.txt
SA2mutvsCTRL.merged.loop.scores.DESeq.norm2Total.loopcoords2.txt
merged_aml_ctrl_10kb.hic
EGAR00003764768


title: RNA_CD34_29_NC_d14

value: wt


title: RNA_CD34_27_SA2KO_d14


title: RNA_CD34_27_NC_d14


title: HiC_AML_ctr_18136

description:
1551
CohAML_allpat_merged.loop.scores.XYrm.txt
CohAML_allpat_merged.normTotalaverage.loop.scores.XYrm.txt
SA2mutvsCTRL.merged.loop.scores.DESeq.norm2Total.loopcoords2.txt
merged_aml_ctrl_10kb.hic
EGAR00003764766


title: RNA_CD34_21_NC_d14


title: ChIP_IN_AML_ctr_18367

description:
2305
EGAR00003766147


title: HiC_AML_ctr_18519

description:
1747
CohAML_allpat_merged.loop.scores.XYrm.txt
CohAML_allpat_merged.normTotalaverage.loop.scores.XYrm.txt
SA2mutvsCTRL.merged.loop.scores.DESeq.norm2Total.loopcoords2.txt
merged_aml_ctrl_10kb.hic
EGAR00003764767


title: RNA_CD34_13_d4_8_SA2_529_549_1252

description:
RNAseq_HSPCs_cohesin_KD_counts_raw.txt
RNAseq.HSPCs.cohesinKD.corr.log.rpkm.txt
qstat_SA1_SA2vs.CTRL.glm.extended.txt
raw data cannot be deposited online


title: RNA_CD34_31_NC_d14


title: RNA_adult_CD34_20598

description:
20598
RNAseq_adultHSC_counts.raw.txt
EGAR00002817106

value: HSC

value: healthy


title: HiC_AML_ctr_16911

description:
2236
CohAML_allpat_merged.loop.scores.XYrm.txt
CohAML_allpat_merged.normTotalaverage.loop.scores.XYrm.txt
SA2mutvsCTRL.merged.loop.scores.DESeq.norm2Total.loopcoords2.txt
merged_aml_ctrl_10kb.hic
EGAR00003764765


title: RNA_CD34_13_d4_5_SA2_529


title: HiC_AML_ctr_19416

description:
3488
CohAML_allpat_merged.loop.scores.XYrm.txt
CohAML_allpat_merged.normTotalaverage.loop.scores.XYrm.txt
SA2mutvsCTRL.merged.loop.scores.DESeq.norm2Total.loopcoords2.txt
merged_aml_ctrl_10kb.hic
EGAR00003764769


title: RNA_CD34_28_NC_d14


title: RNA_CD34_d4_8_SA2_1252


title: RNA_CD34_9_d4_9_SA2_529_549_1252


title: RNA_CD34_9_d4_8_SA2_1252


title: RNA_adult_CD34_20447

description:
20447
RNAseq_adultHSC_counts.raw.txt
EGAR00002817105


title: RNA_adult_CD34_20248

description:
20248
RNAseq_adultHSC_counts.raw.txt
EGAR00002817104


title: RNA_CD34_9_d4_6_SA2_529


title: RNA_CD34_28_SA2KO_d14


title: RNA_adult_CD34_19421

description:
19421
RNAseq_adultHSC_counts.raw.txt
EGAR00002817101


title: RNA_CD34_9_d4_10_SA1_2259_SA2_529


title: RNA_adult_CD34_19769

description:
19769
RNAseq_adultHSC_counts.raw.txt
EGAR00002817103


title: RNA_CD34_d4_8_SA2


title: RNA_CD34_13_d4_15_SA1_2259_4094_SA2_529_549_1252


title: RNA_CD34_9_d4_12_SA1_2259_SA2_1252


title: RNA_CD34_13_d4_12_SA1_4094_SA2_529


title: RNA_CD34_9_d4_15_SA1_4094_SA2_1252


title: RNA_CD34_21_SA2KO_d14


title: RNA_CD34_13_d4_7_SA2_1252


title: RNA_adult_CD34_18997

description:
18997
RNAseq_adultHSC_counts.raw.txt
EGAR00002817099


title: RNA_CD34_13_d4_9_SA1_2259_SA2_529


title: RNA_adult_CD34_19212

description:
19212
RNAseq_adultHSC_counts.raw.txt
EGAR00002817100


title: RNA_CD34_13_d4_11_SA1_2259_SA2_1252


title: RNA_CD34_9_d4_13_SA1_4094_SA2_529


title: RNA_CD34_d4_9_SA1_SA2


title: RNA_CD34_13_d4_4_SA1_2259_4094

description:
RNAseq_HSPCs_cohesin_KD_counts_raw.txt
RNAseq.HSPCs.cohesinKD.corr.log.rpkm.txt
qstat_SA1vs.CTRL.glm.extended.txt
raw data cannot be deposited online


title: RNA_CD34_13_d4_3_SA1_4094


title: RNA_adult_CD34_19555

description:
19555
RNAseq_adultHSC_counts.raw.txt
EGAR00002817102


title: RNA_CD34_13_d4_14_SA1_4094_SA2_1252


title: RNA_AML_STAG2_BB007

description:
BB007
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
qstat_STAG2.vs.CTRL.glm.extended.txt
EGAR00003766057

value: STAG2 mut


title: RNA_CD34_9_d4_5_SA1_2259_4094


title: RNA_CD34_13_d4_2_SA1_2259


title: RNA_CD34_9_d4_4_SA1_4094


title: RNA_AML_STAG2_48380

description:
48380
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
qstat_STAG2.vs.CTRL.glm.extended.txt
EGAR00003766056


title: RNA_AML_STAG2_27513

description:
27513
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
qstat_STAG2.vs.CTRL.glm.extended.txt
EGAR00003766054


title: RNA_CD34_d4_5_SA1


title: RNA_CD34_d4_6_SA1


title: RNA_AML_STAG2_36835

description:
36835
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
qstat_STAG2.vs.CTRL.glm.extended.txt
EGAR00003766055


title: RNA_CD34_9_d4_3_SA1_2259


title: RNA_CD34_13_d4_17_RAD21_2031

description:
RNAseq_HSPCs_cohesin_KD_counts_raw.txt
RNAseq.HSPCs.cohesinKD.corr.log.rpkm.txt
qstat_RAD21vs.CTRL.glm.extended.txt
raw data cannot be deposited online


title: RNA_CD34_13_d4_18_RAD21_467_2031


title: RNA_CD34_13_d4_16_RAD21_467


title: RNA_AML_STAG2_24603

description:
24603
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
qstat_STAG2.vs.CTRL.glm.extended.txt
EGAR00003766053


title: RNA_AML_STAG2_12567

description:
12567
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
qstat_STAG2.vs.CTRL.glm.extended.txt
EGAR00003766052


title: RNA_CD34_9_d4_19_RAD21_467_2031


title: RNA_CD34_9_d4_18_RAD21_2031


title: RNA_CD34_d4_12_RAD21


title: RNA_CD34_d4_11_RAD21


title: RNA_CD34_9_d4_2_untreated

description:
RNAseq_HSPCs_cohesin_KD_counts_raw.txt
RNAseq.HSPCs.cohesinKD.corr.log.rpkm.txt
raw data cannot be deposited online

value: untreated


title: RNA_CD34_d4_0_untreated


title: RNA_AML_STAG2_12514

description:
12514
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
qstat_STAG2.vs.CTRL.glm.extended.txt
EGAR00003766051


title: RNA_CD34_13_d4_23_siCtrl2x

value: siCtrl


title: RNA_AML_STAG2_7323

description:
7323
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
qstat_STAG2.vs.CTRL.glm.extended.txt
EGAR00003766050


title: RNA_adult_CD34_17815

description:
17815
RNAseq_adultHSC_counts.raw.txt
EGAR00002817098


title: RNA_AML_STAG2_3481

description:
3481
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
qstat_STAG2.vs.CTRL.glm.extended.txt
EGAR00003766049


title: RNA_CD34_13_d4_22_siCtrl


title: RNA_CD34_d4_3_siCtrl


title: RNA_AML_STAG2_2216

description:
2216
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
qstat_STAG2.vs.CTRL.glm.extended.txt
EGAR00003766047


title: RNA_CD34_d4_4_siCtrl


title: RNA_CD34_9_d4_25_siCtrl2x


title: RNA_CD34_9_d4_23_siCtrl


title: RNA_AML_STAG2_2292

description:
2292
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
qstat_STAG2.vs.CTRL.glm.extended.txt
EGAR00003766048


title: RNA_AML_STAG2_2193

description:
2193
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
qstat_STAG2.vs.CTRL.glm.extended.txt
EGAR00003766046


title: RNA_CD34_13_d4_24_Mock

value: Mock


title: RNA_AML_RAD21_AML0117

description:
AML0117
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
qstat_RAD21.vs.CTRL.glm.extended.txt
EGAR00003766044


title: RNA_CD34_9_d4_26_Mock


title: RNA_CD34_d4_2_Mock


title: RNA_AML_RAD21_UKR186

description:
UKR186
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
qstat_RAD21.vs.CTRL.glm.extended.txt
EGAR00003766045


title: ATAC_CD34_28_5_SA2

description:
CD34_combined.intersect.peaks.CD34.ann.table.txt
raw data cannot be deposited online

data_processing:
Reads were trimmed for NEXTERA adapter sequences using Skewer (v0.2.2)
Sequences wer aligned to the human reference genome (GRCh38.p10) using bowtie2 (v. 2.4.5) in very sensitive mode
Samtools (v.1.6) was used to remove lower quality alignments with mapQ=<10 and sorting. Read positions in sam files were shifted to move the ends proximal to transposase cut sites (for positive strand: start +4 bp and its partner read start −5 bp, for negative strand: start −5 bp and its partner read start +4 bp)
HOMER style tagDirectories were generated using HOMER makeTagDirectory (-checkGC and -unique)
ATAC peaks were called in condition-merged tag directories using HOMER in region mode “-size 150 -minDist 250 -L 2 -fdr 0.00001" and factor mode "-size 250 -minDist 250 -L 2 -fdr 0.00001“. Only those region peaks, overlapping a focal peak using bedtools intersect were kept and used for the downstream analyses. HSPC peak sets were merged to create a common peak set. Individual HSPC tagdirectories were annotated to this combined peak set. AML tagdirectores were instead annotated to the combined AML RAD21 peak set to obtain cohesin-associated ATAC coverage tables.
Bigwig coverage tracks  were generated using HOMER’s makeUCSCfile function. BigWigs of HSPCs were additionally scaled based on median coverage across the top 5% common ATAC peaks detected in all samples
Assembly: GRCh38.p10
Supplementary files format and content: bigWig coverage track files for individual samples
Supplementary files format and content: tab-delimited file containing ATAC or RAD21 peak coordinates and associated ATAC coverage counts for each sample (HOMER annotation output)
Supplementary files format and content: tab-delimited file containing qstat differential peak coverage results between control and either of the cohesin mutant groups (qstat)

extract_protocol:
50k Cells were lysed using 0.1% NP-40 and 0.01% Digitonin. Tagment DNA TDE1 Enzyme (Illumina)  was used to perform the tagmentation. DNA was purified using Monarch PCR & DNA clean-up columns (NEB)
Tagmented DNA was amplified using Phusion polymerase (NEB) and Nextera indexing primers (Illumina) by 11 cycles of PCR.


title: ATAC_CD34_21_3_SA2


title: RNA_AML_RAD21_AML0105

description:
AML0105
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
qstat_RAD21.vs.CTRL.glm.extended.txt
EGAR00003766043


title: RNA_AML_RAD21_27918

description:
27918
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
qstat_RAD21.vs.CTRL.glm.extended.txt
EGAR00003766041


title: ATAC_CD34_17_2_SA2


title: ATAC_CD34_14_2_SA2


title: RNA_AML_RAD21_12557

description:
12557
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
qstat_RAD21.vs.CTRL.glm.extended.txt
EGAR00003766037


title: ATAC_CD34_17_1_SA1


title: ATAC_CD34_28_4_SA1


title: ATAC_CD34_28_2_SA1_SA2


title: ATAC_CD34_27_3_SA1


title: ATAC_CD34_20_4_SA1


title: RNA_AML_RAD21_19733

description:
19733
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
qstat_RAD21.vs.CTRL.glm.extended.txt
EGAR00003766039


title: ATAC_CD34_22_1_RAD21


title: RNA_AML_RAD21_41580a

description:
41580a
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
qstat_RAD21.vs.CTRL.glm.extended.txt
EGAR00003766042


title: RNA_AML_RAD21_19740

description:
19740
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
qstat_RAD21.vs.CTRL.glm.extended.txt
EGAR00003766040


title: ATAC_CD34_20_2_SA1_SA2


title: ATAC_CD34_21_2_SA1


title: ATAC_CD34_18_1_Rad21


title: ATAC_CD34_14_1_SA1


title: ATAC_CD34_22_2_SA2


title: ATAC_CD34_28_1_Rad21


title: ATAC_CD34_20_1_Rad21


title: RNA_CD34_d4_1_Mock

description:
RNAseq_HSPCs_cohesin_KD_counts_raw.txt
RNAseq.HSPCs.cohesinKD.corr.log.rpkm.txt
raw data cannot be deposited online


title: ATAC_CD34_18_2_SA1_SA2


title: RNA_CD34_13_d4_1_untreated


title: RNA_AML_RAD21_7324

description:
7324
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
qstat_RAD21.vs.CTRL.glm.extended.txt
EGAR00003766036


title: RNA_AML_RAD21_2234

description:
2234
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
qstat_RAD21.vs.CTRL.glm.extended.txt
EGAR00003766033


title: ATAC_CD34_27_1_Rad21


title: ATAC_CD34_20_5_SA2


title: RNA_AML_RAD21_19725

description:
19725
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
qstat_RAD21.vs.CTRL.glm.extended.txt
EGAR00003766038


title: RNA_AML_RAD21_7314

description:
7314
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
qstat_RAD21.vs.CTRL.glm.extended.txt
EGAR00003766035


title: ATAC_CD34_27_4_siCtrl


title: RNA_AML_RAD21_6379

description:
6379
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
qstat_RAD21.vs.CTRL.glm.extended.txt
EGAR00003766034


title: ATAC_CD34_24_1_siCtrl


title: ATAC_CD34_14_4_Mock


title: RNA_AML_CTRL_7326

description:
7326
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
EGAR00003766032


title: ATAC_CD34_22_3_siCtrl


title: RNA_AML_CTRL_7308

description:
7308
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
EGAR00003766031


title: ATAC_CD34_19_2_siCtrl


title: RNA_AML_CTRL_6374

description:
6374
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
EGAR00003766030


title: ATAC_CD34_18_4_siCtrl


title: ATAC_CD34_20_6_siCtrl


title: ATAC_CD34_17_3_siCtrl


title: RNA_AML_CTRL_6246

description:
6246
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
EGAR00003766029


title: RNA_AML_CTRL_5286

description:
5286
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
EGAR00003766028


title: ATAC_CD34_21_4_siCtrl

description:
CD34_combined.intersect.peaks.CD34.ann.table.txt
raw data cannot be deposited online


title: ATAC_CD34_28_6_siCtrl


title: ATAC_CD34_14_3_siCtrl


title: ATAC_AML_SA2_27493

description:
48386
ATAC_Cohesin_AML.goodQC.Allpat_mergePeaks_RAD21.filtered.peaks.ann.txt
qstat.ATAC.goodQC.SA2mutvsCTRL.RAD21peak.ann.txt
EGAR00003768395


title: RNA_AML_CTRL_5285

description:
5285
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
EGAR00003766027


title: ATAC_CD34_20_7_Mock


title: ATAC_AML_SA2_24743

description:
12514
ATAC_Cohesin_AML.goodQC.Allpat_mergePeaks_RAD21.filtered.peaks.ann.txt
qstat.ATAC.goodQC.SA2mutvsCTRL.RAD21peak.ann.txt
EGAR00003768394


title: RNA_AML_CTRL_4338

description:
4338
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
EGAR00003766026


title: ATAC_AML_SA2_29728

description:
24603
ATAC_Cohesin_AML.goodQC.Allpat_mergePeaks_RAD21.filtered.peaks.ann.txt
qstat.ATAC.goodQC.SA2mutvsCTRL.RAD21peak.ann.txt
EGAR00003768396


title: RNA_AML_CTRL_3488

description:
3488
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
EGAR00003766024


title: ATAC_AML_RAD21_AML0117

description:
AML0117
ATAC_Cohesin_AML.goodQC.Allpat_mergePeaks_RAD21.filtered.peaks.ann.txt
qstat.ATAC.goodQC.RAD21mutvsCTRL.RAD21peak.ann.txt
EGAR00003768391


title: ATAC_AML_RAD21_27650

description:
19725
ATAC_Cohesin_AML.goodQC.Allpat_mergePeaks_RAD21.filtered.peaks.ann.txt
qstat.ATAC.goodQC.RAD21mutvsCTRL.RAD21peak.ann.txt
EGAR00003768390


title: ATAC_AML_SA2_22525

description:
7325
ATAC_Cohesin_AML.goodQC.Allpat_mergePeaks_RAD21.filtered.peaks.ann.txt
qstat.ATAC.goodQC.SA2mutvsCTRL.RAD21peak.ann.txt
EGAR00003768393


title: RNA_AML_CTRL_4334

description:
4334
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
EGAR00003766025


title: ATAC_AML_ctr_21047

description:
6246
ATAC_Cohesin_AML.goodQC.Allpat_mergePeaks_RAD21.filtered.peaks.ann.txt
qstat.ATAC.goodQC.SA2mutvsCTRL.RAD21peak.ann.txt
EGAR00003768389


title: ATAC_AML_ctr_19416

description:
3488
ATAC_Cohesin_AML.goodQC.Allpat_mergePeaks_RAD21.filtered.peaks.ann.txt
qstat.ATAC.goodQC.SA2mutvsCTRL.RAD21peak.ann.txt
EGAR00003768388


title: RNA_AML_CTRL_3326

description:
3326
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
EGAR00003766023


title: ATAC_AML_ctr_16911

description:
2236
ATAC_Cohesin_AML.goodQC.Allpat_mergePeaks_RAD21.filtered.peaks.ann.txt
qstat.ATAC.goodQC.SA2mutvsCTRL.RAD21peak.ann.txt
EGAR00003768386


title: RNA_AML_CTRL_3323

description:
3323
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
EGAR00003766022


title: ATAC_AML_ctr_10156

description:
2195
ATAC_Cohesin_AML.goodQC.Allpat_mergePeaks_RAD21.filtered.peaks.ann.txt
qstat.ATAC.goodQC.SA2mutvsCTRL.RAD21peak.ann.txt
EGAR00003768385


title: RNA_AML_CTRL_3319

description:
3319
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
EGAR00003766021


title: RNA_AML_CTRL_3313

description:
3313
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
EGAR00003766020


title: H3K4me1 in SK-LMS-1 HDAC4-/- HDAC4-ER 0h from 4-OHT (HDAC4) removal

city: Udine

first: Emiliano

last: Dalla

state: UD

address: Piazzale Kolbe 4

department: Department of Medicine

country: Italy

institute: Università degli Studi di Udine

description: Enhancer identification

data_processing:
Basecalls performed using the FastQC/MultiQC programs
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 version 2.3.4.3 with default configuration for unpaired reads
Duplicate reads were flagged using samtools but no duplicates were removed
Peak calling was performed against input sequences using MACS2 (--nomodel, --extsize 150 and -q 0.05 options). ChIP-seq replicates were compared using the Irreproducibility Discovery Rate (IDR) framework, with MACS2 narrow peaks as input and applying the following settings: --input-file-type narrowPeak, --rank signal.value, --output-file-type narrowPeak. ROSE algorith was used to identify SEs.
Assembly: hg38
Supplementary files format and content: Coverage tracks were generated using the bamCoverage (deepTools) tool, taking an alignment of reads as input (BAM file) and generating a coverage track (bigWig) as output, applying the following parameters: --outFileFormat bigwig --binSize 50 -p 10 --normalizeUsing RPGC

growth_protocol: SK-LMS-1 cells were grown in DMEM without red phenol, supplemented with 10% stripped FBS, 2mM L-glutamine and penicillin–streptomycin (Euroclone, Milan, Italy). For each ChIP, 3.2*10^6 cells were used.

extract_protocol:
Lysates were obtained with a two-step protocol (nuclei were obtained with an hypotonic buffer (20mM TRIS-HCl pH8; 85 mM KCl; 0.5% NP-40), and nuclear membrane was lysed with Lysis buffer (10mM TRIS pH7.5; 1% NP-40, 0.5% Na-deossicholate; 0.1% SDS); then lysates were clarified from sonicated nuclei (30', medium power, Bioruptor Diagenode) and histone-DNA complexes were isolated with protein A/antibodies (2μg of anti-H3K27ac (Abcam ab4729) , 3 μg of anti-H3K4me1 (Diagenode, pAb-194-050) or control IgG. Washes were performed in LOW SALT IMMUNE COMPLEX WASH BUFFER (0.1% SDS, 1% TRITON, 20mM Tris-HCl pH8, 150 mM NaCl), HIGH SALT WASH BUFFER (0.1% SDS, 1% TRITON, 2mM EDTA, 20mM Tris-HCl pH8, 500 mM NaCl), LiCl Immune Complex Wash Buffer (0.25M LiCl, 1% NP40, 0.2% Na-deossicolato, 1mM EDTA, 10Mm Tris-HCl pH8) and TE. RNA was digested with RNAseA (2μg). DNA was de-crosslinked and purified with Zymo DNA columns.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, 5 μg of DNA were used. DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSseq550 following the manufacturer's protocols.
TruSeq ChIP Library

treatment_protocol: Cells were seeded in 200 mm plate three days before the ChIP and 4-OHT (1um, Sigma-Aldrich, Darmstadt, Germany) treated to mantain HDAC4 expresison. 36h or 12h before the harvesting, 4-OHT was washed out from the medium. At the moment of the ChIP, cross-linking was performed for 15' with 1% formaldeyde (Fisher Scientific, Schwerte, Germany) and then blocked with 125 mM Glycine (Sigma-Aldrich, Darmstadt, Germany).

value: Leiomyosarcoma cells

tag: chip antibody

value: H3K4me1 (Diagenode, pAb-194-050)

tag: time


title: H3K4me1 in SK-LMS-1 HDAC4-/- HDAC4-ER 36h from 4-OHT (HDAC4) removal

description: Enhancer identification


title: H3K27ac in SK-LMS-1 HDAC4-/- HDAC4-ER 12h from 4-OHT (HDAC4) removal

description: Open chromatin evaluation

value: H3K27ac (Abcam, ab4729)


title: H3K4me1 in SK-LMS-1 HDAC4-/- HDAC4-ER 12h from 4-OHT (HDAC4) removal

description: Enhancer identification


title: H3K27ac in SK-LMS-1 HDAC4-/- HDAC4-ER 0h from 4-OHT (HDAC4) removal

description: Open chromatin evaluation


title: RNA_AML_CTRL_2273

description:
2273
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
EGAR00003766018


title: H3K27ac in SK-LMS-1 HDAC4-/- HDAC4-ER 36h from 4-OHT (HDAC4) removal

description: Open chromatin evaluation


title: ATAC_AML_RAD21_UKR186

description:
UKR186
ATAC_Cohesin_AML.goodQC.Allpat_mergePeaks_RAD21.filtered.peaks.ann.txt
qstat.ATAC.goodQC.RAD21mutvsCTRL.RAD21peak.ann.txt
EGAR00003768392


title: Input SK-LMS-1 HDAC4-/- HDAC4-ER 36h from 4-OHT (HDAC4) removal

description: Input


title: H4K16ac BJ-hTERT/HRAS/HDAC4 day8 RepA

description: H4K16ac at day 8

data_processing:
Basecalls performed using the FastQC/MultiQC programs
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 version 2.3.4.3 with default configuration for unpaired reads
Duplicate reads were flagged using samtools but no duplicates were removed
Peak calling was performed against input sequences using EDD for H2AX ChIP (--write-log-ratios and --write-bin-scores options) and MACS2 for HDAC4, H2BK120ac and H4K16ac (--nomodel, --extsize 150 and -q 0.05 options). ChIP-seq replicates were compared using the Irreproducibility Discovery Rate (IDR) framework, with MACS2 narrow peaks as input and applying the following settings: --input-file-type narrowPeak, --rank signal.value, --output-file-type narrowPeak.
Assembly: hg38
Supplementary files format and content: Coverage tracks were generated using the bamCoverage (deepTools) tool, taking an alignment of reads as input (BAM file) and generating a coverage track (bigWig) as output, applying the following parameters: --outFileFormat bigwig --binSize 50 -p 10 --normalizeUsing RPKM

source_name: BJ

growth_protocol: BJ cells were grown in EMEM supplemented with 10% FBS, 2mM L-glutamine, penicillin–streptomycin and NEAA (Euroclone, Milan, Italy). For each ChIP, 3.2*10^6 cells were used.

extract_protocol:
Lysates were obtained with a two-step protocol (nuclei were obtained with an hypotonic buffer (20mM TRIS-HCl pH8; 85 mM KCl; 0.5% NP-40), and nuclear membrane was lysed with Lysis buffer (10mM TRIS pH7.5; 1% NP-40, 0.5% Na-deossicholate; 0.1% SDS); then lysates were clarified from sonicated nuclei (30', medium power, Bioruptor Diagenode) and histone-DNA complexes were isolated with the relative antibodies and 8ul protein A Dynabeads (ThermoFisher). Washes were performed in LOW SALT IMMUNE COMPLEX WASH BUFFER (0.1% SDS, 1% TRITON, 20mM Tris-HCl pH8, 150 mM NaCl), HIGH SALT WASH BUFFER (0.1% SDS, 1% TRITON, 2mM EDTA, 20mM Tris-HCl pH8, 500 mM NaCl), LiCl Immune Complex Wash Buffer (0.25M LiCl, 1% NP40, 0.2% Na-deossicolato, 1mM EDTA, 10Mm Tris-HCl pH8) and TE. RNA was digested with RNAseA (2μg). DNA was de-crosslinked and purified with Zymo DNA columns.
Libraries were prepared according to Drmanac et al. (Science 2010, PMID 19892942) with combinatorial probe anchor ligation chemistry generating patterned nanoarrays of self-assembling DNA nanoballs. Briefly, after End repairing, A-tailing and Ad153 index adapter ligation of 50 ng size-selected DNA, DNA was puriefied with Ampure XP beads.  KAPA HiFi Hot Start Ready Mix was used for pre-PCR amlification: 95 °C 3 ', (98 °C 20s, 60 °C 15 s, 72 °C 30s) 8 cycles, 72 °C 10'. 4 °C hold thermal cycles using , the product was purified with 1X Ampure XP beads and quantified with Qubit BR ds DNA kit. For Illumina platform, Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, 5 μg of DNA were used. DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSseq550 following the manufacturer's protocols.    Exome capture  The hybridization of BGISEQ-500 library was performed according to the Agilent SureSelect protocol with the following optimized parameters: 1000 ng purified DNA was used for hybridization, the index block and PCR block of Agilent were replaced by a corresponding Ad153_index block (one for all indexes) and Ad153_PCR block. KAPA HiFi Hot Start Ready Mix was used for Post-PCR following the 95 °C 3 min, (98 °C 20s, 60 °C 15 s, 72 °C 30s) 13 cycles, 72 °C 10 min, 4 °C hold thermal cycle. Post-PCR products were purified and single strand DNA (ssDNA) circle was performed by using adapters; T4 DNA ligae was used for ligation (NEB, Ipswich, Massachusetts). Uncirculated DNA was digested with Exo I and Exo III. The libraries were purified with 168 μL of Ampure XP beads and quantified with Qubit BR ssDNA kit. The resulting ssDNA circle is the final library. Rolling circle amplification (RCA) was performed on ssDNA with Phi29 DNA polymerase (Thermo-Fisher, Waltham, Massachusetts) to generate DNA nanoballs (DNBs).
DNBseq Nanoballs library and TruSeq ChIP Library

treatment_protocol: Cells were seeded in 200 mm plates. 4-OHT was used to induce HRAS (or empty ER) for 2 days or 8 days. At the moment of the ChIP, cross-linking was performed for 15' with 1% formaldeyde (Sigma-Aldrich, Darmstadt, Germany) and then blocked with 125 mM Glycine (Sigma-Aldrich, Darmstadt, Germany).

value: foreskin fibroblasts

tag: passages

value: below 20


title: RNA_AML_CTRL_2236

description:
2236
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
EGAR00003766017

value: hematopoietic

value: AML blasts


title: Input SK-LMS-1 HDAC4-/- HDAC4-ER 12h from 4-OHT (HDAC4) removal

description: Input


title: Input SK-LMS-1 HDAC4-/- HDAC4-ER 0h from 4-OHT (HDAC4) removal

description: Input


title: H4K16ac BJ-hTERT day8 RepA

description: H4K16ac at day 8


title: H4K16ac BJ-hTERT/HRAS day8 RepA

description: H4K16ac at day 8


title: RNA_AML_CTRL_2195

description:
2195
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
EGAR00003766015

value: cohesin wt


title: H2BK120ac BJ-hTERT day8 RepA

description: H2BK120ac at day 8

value: H2BK120ac (Active Motif AB_2615080)


title: ATAC_AML_ctr_18136

description:
1551
ATAC_Cohesin_AML.goodQC.Allpat_mergePeaks_RAD21.filtered.peaks.ann.txt
qstat.ATAC.goodQC.SA2mutvsCTRL.RAD21peak.ann.txt
EGAR00003768387


title: H2BK120ac BJ-hTERT/HRAS day8 RepA

description: H2BK120ac at day 8


title: RNA_AML_CTRL_2194

description:
2194
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
EGAR00003766014


title: RNA_AML_CTRL_1747

description:
1747
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
EGAR00003766013


title: RNA_AML_CTRL_2305

description:
2305
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
EGAR00003766019


title: RNA_AML_CTRL_1551

description:
1551
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
EGAR00003766012


title: OX6_P_S2

city: Thuwal

first: Abdugaffor

last: Ablazov

address: Bld. 2 L3

department: BESE

country: Saudi Arabia

institute: KAUST

data_processing:
The Illumina Novaseq platform was used for sequencing and 150 bp paired-end reads were generated. Paired-end clean reads were mapped to the Nipponbare reference genome (http://rice.uga.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/) by Hisat2 v2.0.5. Gene quantity was calculated by featureCounts v1.5.0-p3, and then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: http://rice.uga.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/
Supplementary files format and content: tab text file inludes raw gene count data as matrix

molecule: polyA RNA

organism: Oryza sativa

source_name: Shoot

extract_protocol:
Total RNA was extracted from rice roots and shoots of the OX6 and WT (NB) lines, using TRI-Reagent with Direct-zol RNA MiniPrep Kit according to the manufacturer’s instruction (Zymo Research).
Library construction, sequencing and data analysis were performed by Novogene Technology (Novogene Co., Ltd., Beijing, China).

value: Shoot

value: genotype


title: gammaH2AX BJ-hTERT/HRAS/HDAC4 day8 RepA

description: Estimation of DSBs at day 8

value: gammaH2AX (Millipore PA5-28778)


title: Input BJ-hTERT/HRAS day8 RepA

description: Input


title: gammaH2AX BJ-hTERT/HRAS day8 RepA

description: Estimation of DSBs at day 8


title: OX6_P_S3


title: gammaH2AX BJ-hTERT day8 RepA

description: Estimation of DSBs at day 8


title: C_19, Control

city: nanjing

first: feifan

last: wang

address: No. 818 Tianyuan East Road

country: China

institute: Nanjing Medical University

data_processing:
The raw reads were processed using Trimmomatic v0.36. The quality of clean reads was evaluated using FastQC v0.11.7. The Star software was utilized to align the clean reads with the reference genome sequence. The HTSeq v0.7.2 was used to statistic the true gene expression level (read counts). The FPKM value was a result of standardizing the read counts.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes raw counts for all Samples
Supplementary files format and content: tab-delimited text file includes FPKM values for all Samples

source_name: peripheral blood

extract_protocol:
Total RNA was extracted using the magnetic bead method (Yuan, Yu-BR02-1, China). 2 µg of total RNA was used for the construction of sequencing libraries.
The rRNA was removed using a Ribo-zero reagent kit. The synthesized double-stranded cDNA fragments were screened and purified several times by VAHTSTM DNA Clean Beads.

value: peripheral blood

tag: disease

value: healthy control


title: OX6_P_R3

source_name: Root

value: Root


title: H2023 PTPRH Overexpression Replicate 2

city: East Lansing

first: Mylena

last: Ortiz

state: Michigan

address: 567 Wilson Road

department: Genetics and Genomics Sciences

country: USA

institute: Michigan State University

data_processing:
The quality of the raw reads was assessed through FastQC 0.11.7 and trimmed using Trimmomatic 0.39. Trimmed reads were aligned against the human genome (grch38) using Hisat2 2.1.0 and a count matrix of raw reads to be used as input for DESeq2 was generated by StringTie 2.1.3 as described in the StringTie documentation.
Assembly: Trimmed reads were aligned against the human genome (grch38) using Hisat2 2.1.0
Supplementary files format and content: gene_count_matrix.csv includes matrix of raw counts for each sample.
Supplementary files format and content: phenodata.csv included phenodata information for each sample.

growth_protocol: Each cell line was seeded in 6-wells plates (n=3/group) and the total RNA was extracted when cells reached ~80% confluency.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen #74104) according to the manufacturer's instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached  magnetic beads. After fragmentation, the first strand cDNA was synthesized  using random hexamer primers, followed by the second strand cDNA  synthesis using either dUTP for directional library. For the directional library, it was ready after end repair, A-tailing, adapter  ligation, size selection, USER enzyme digestion, amplification, and  purification. Paired-end RNA sequencing (Illumina PE150) were conducted using NovaSeq X Plus Series (Illumina) with a minimum coverage of 30M reads per sample

treatment_protocol: Cells were serum starved for 24 hours, followed by FBS stimulation (5% or 10% in complete media for NCI-H2023 and NCI-H23 derived cells, respectively) for 16 hours prior to collection of total RNA.

value: Non-small cell lung cancer

value: PTPRH wild-type Overexpressed

value: FBS stimulation


title: OX6_P_S1


title: H23 Replicate 3

value: PTPRH Endogenous


title: H2023 PTPRH Overexpression Replicate 1


title: NB_P_S3

value: WT


title: C_20, Control


title: NB_P_S2


title: Input BJ-hTERT day8 RepA

description: Input

value: foreskin fibroblasts


title: H23 Replicate 2


title: C_18, Control


title: NB_P_R3


title: RNA_AML_CTRL_2207

description:
2207
RNAseq_AML_STAG2_RAD21_counts.raw.txt
RNAseq_AML_STAG2_RAD21_log.rpkm.txt
EGAR00003766016


title: H2023 PTPRH Overexpression Replicate 3


title: H23 Replicate 1


title: C_17, Control


title: NB_P_S1


title: H2BK120ac BJ-hTERT/HRAS/HDAC4 day8 RepA

description: H2BK120ac at day 8

value: below 20


title: OX6_P_R2


title: C_15, Control


title: C_16, Control


title: OX6_P_R1


title: Input BJ-hTERT/HRAS/HDAC4 day8 RepA

description: Input


title: C_14, Control


title: C_13, Control


title: H2023 Replicate 2


title: H2023 Replicate 1


title: BTZ axn127,RNA-seq,Rep2

city: New Orleans

first: Jun-yuan

last: Ji

state: LA

address: 1700 Tulane Avenue

department: Department of Biochemistry and Molecular Biology

institute: Tulane University

description:
BTZ axn127 2
BTZ count table
BTZ_cts.txt

data_processing:
RNA-Star alignment to dm6 reference with default setting
Gathering counts with FeatureCount with default setting
DESeq2 to normalize counts and generate differential gene expression table with p.adj < 0.05 filter
CUT&Run reads went through nf-core/cutandrun pipeline for trimming, alignment and deduplication
MACS3 for peak calling and normalization
Assembly: dm6
Supplementary files format and content: tab delimited table, count table
Supplementary files format and content: bigwig file, normalized CUT&Run reads

organism: Drosophila melanogaster

source_name: 3rd instar whole larvae

extract_protocol:
Total RNA was extracted by standard protocol with Trizol; 1ug RNA was used for librariy construction
RNA-seq library was prepared by using Illumina TruSeq Stranded Total RNA kit, CUT&Run library was prepared by using illumina TruSeq ChIP library preparation kit

value: 3rd instar whole larvae


title: NB_P_R2


title: H2023 Replicate 3


title: C_9, Control


title: C_12, Control


title: H23 PTPRH KO Replicate 3

value: PTPRH Knockout


title: NB_P_R1


title: BTZ axn127,RNA-seq,Rep1

description:
BTZ axn127 1
BTZ count table
BTZ_cts.txt


title: H23 PTPRH KO Replicate 2


title: C_7, Control


title: DMSO axn127,RNA-seq,Rep3

description:
DMSO axn127 3
BTZ count table
BTZ_cts.txt


title: BTZ axn127,RNA-seq,Rep3

description:
BTZ axn127 3
BTZ count table
BTZ_cts.txt


title: DMSO axn127,RNA-seq,Rep2

description:
DMSO axn127 2
BTZ count table
BTZ_cts.txt


title: C_10, Control


title: H23 PTPRH KO Replicate 1


title: H23 PTPRH Overexpression Replicate 3


title: C_8, Control


title: C_5, Control


title: DMSO w1118,RNA-seq,Rep3

description:
DMSO w1118 3
BTZ count table
BTZ_cts.txt


title: C_6, Control


title: C_4, Control


title: H23 PTPRH Overexpression Replicate 2


title: DMSO axn127,RNA-seq,Rep1

description:
DMSO axn127 1
BTZ count table
BTZ_cts.txt


title: DMSO w1118,RNA-seq,Rep2

description:
DMSO w1118 2
BTZ count table
BTZ_cts.txt


title: H23 PTPRH Overexpression Replicate 1


title: C_3, Control


title: C_2, Control


title: C_11, Control


title: DMSO w1118,RNA-seq,Rep1

description:
DMSO w1118 1
BTZ count table
BTZ_cts.txt


title: RU11/001 ΔldtR- Replicate 3

city: Blacksburg

first: Birgit

middle: E

last: Scharf

state: VA

address: 970 Washington St SW

department: Biological Sciences

institute: Virginia Tech

data_processing:
Onboard adapter trimming was performed.
Sequences were quality-trimmed using the BBDuk plugin in Geneious Prime® 2023.2.1 (base quality score cutoff of 20 and minimum sequence length of 30 nt).
Cleaned reads were mapped to the S. meliloti RU11/001 genome in Geneious Prime® 2023.2.1 using the Geneious RNA mapper with default settings.
Differential expression analysis was performed using the DESeqs2 plugin in Geneious Prime® 2023.2.1.
Assembly: Sinorhizobium meliloti RU11/001 (GenBank accession number GCA_001050915.2)
Supplementary files format and content: Excel (.xls) files containing raw read counts, TPM, RPKM, and TPKM for all six samples, one file per sample
Supplementary files format and content: Excel (.xls) file containing the full DESeqs2 analysis results for all six samples

organism: Sinorhizobium meliloti RU11/001

source_name: Bacterial

growth_protocol: TYC-Sm liquid cultures (24 hours) were subcultured into Bromfield overlay plates at OD600 = 0.002 and incubated at 30C for 17 hours, to an OD600 of 0.20-0.25. Cultures were standardized to 2 ml at an OD600 = 0.20.

extract_protocol:
RNA extraction was performed using the Rneasy Protect Bacteria Mini Kit (Qiagen) according to the manufacturer's protocol. For each sample, 1.25 µg total RNA was provided for rRNA depletion and library preparation.
RNA libraries were prepared with the TruSeq Stranded mRNA library preparation kit (Illumina).

value: Bacterial

value: deltaldtR

value: Bromfield overlay


title: C_1, Control


title: Patient12

city: Solna

first: Felix

last: Haglund de Flon

state: Stockholm

address: Solnavägen 1

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institute

data_processing:
Data processing followed the ‘NGI best practice pipeline’ which included raw quality control by FastQC, alignment to GRCh37 using TOPHAT, alignment to QC using RSeqQC, and calculation of gene counts using HTSeq.
Assembly: Hg19/GRch37
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

growth_protocol: Not applicable

extract_protocol:
Promega Maxwell® RSC RNA FFPE Kit (modified)
Lucigen NxSeq AmpFREE Low Kit

treatment_protocol: Not applicable

value: fresh frozen diagnostic fine-needle aspiration cytology specimen

tag: metastasis

value: No

tag: survival

value: Alive without disease

tag: dead of_disease

tag: response to_chemotherapy

value: Good

tag: salzer-kuntschnik

tag: fusion

tag: gender

value: Male

tag: location

value: Central


title: Patient13

tag: tissue

value: Not available

value: Lost to follow-up

value: Female

value: Peripheral


title: RU11/001 ΔldtR- Replicate 1

tag: cell type


title: Wild type RU11/001- Replicate 3

tag: genotype

value: Wild type


title: Patient11


title: T_8, Schizophrenia

value: peripheral blood

value: Schizophrenia


title: RU11/001 ΔldtR- Replicate 2


title: T_9, Schizophrenia


title: Wild type RU11/001- Replicate 1


title: T_6, Schizophrenia


title: Patient9


title: Patient10


title: Wild type RU11/001- Replicate 2


title: Reactivated, scRNAseq

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

institute: Max-Planck-Institute for Molecular Biomedicine

description: BD Rhapsody Express

library_source: transcriptomic single cell

data_processing:
Sequencing data were processed with UMI-tools (ver1.0.1)
aligned to the mouse reference genome (mm10) with STAR (version 2.7.1a)
quantified with Subread featureCounts (version 1.6.4)
Assembly: mm10
Supplementary files format and content: tsv files include UMI counts for each cell barcode and genes

organism: Mus musculus

source_name: Whole embryo

extract_protocol:
Single cell suspension was obtained by dissociated embryos for 10-15min at 37 °C with TrypLE express enzyme. The cells were then loaded on to a microwell cartridge of BD Rhapsody Express system (BD Biosciences).
Single-cell whole transcriptome analysis libraries were prepared according to the manufacturer’s instructions using a BD Rhapsody WTA Reagent kit (BD Biosciences) and sequenced on the Illumina NextSeq 500 using the Mid Output Kit v2.5 (150 cycles, Illumina).

treatment_protocol: E4.5, EDG7.5, EDG9.5 and reactivated embryos were collected by flushing the uterus. E5.5 embryos were removed from their implantation sites using fine forceps, in PBS. Embryos were then washed in fresh PBS and transferred to M2 medium (Sigma-Aldrich) prior to dissociation by TrypLE express enzyme (no phenol red, Thermo Fisher Scientific).

value: Whole embryo

tag: strain

tag: developmental stage

value: wildtype


title: T_5, Schizophrenia


title: Patient8


title: Patient7


title: EDG9.5, scRNAseq

description: BD Rhapsody Express


title: T_4, Schizophrenia


title: Patient6

value: Yes

value: Dead

value: Poor


title: T_3, Schizophrenia


title: EDG7.5, scRNAseq

description: BD Rhapsody Express


title: T_2, Schizophrenia


title: E5.5, scRNAseq

description: BD Rhapsody Express


title: Patient5

value: fresh frozen diagnostic fine-needle aspiration cytology specimen

value: No

value: Unknown

value: Uknown


title: Patient4

value: Alive without disease

value: Male

value: Central


title: Taz KO_rep3

description: Yap f/f Taz ∆/∆_3

data_processing:
Sequenced reads were aligned to the mouse reference genome (mm10) with TopHat (version 2.1.1)
The aligned reads were used for the transcript quantification by using HTSeq-count (version 0.6.1)
DESeq2 was used to identify differentially expressed genes across the samples
Assembly: mm10
Supplementary files format and content: txt file of FPKM values for each gene and sample

source_name: Mouse embryonic stem cells

growth_protocol: ES cell lines were maintained in N2B27 medium supplemented with 2i/Lif (0.4 µM PD0325901, 3 µM CHIR99021 and 4 ng/ml Lif), on fibronectin coated plate and passaged at 1:6 ratio using 0.05% Trypsin-EDTA.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA (MACHEREY-NAGEL) Mini kit for RNA purification.
In all, 1 μg of the total RNA, with RIN (RNA integrity number) numbers above 7 (Agilent 2100 Bioanalyzer), were used. mRNA was enriched using NEBNext® Poly(A) mRNA Magnetic Isolation Module and cDNA library was prepared with NEBNext® Ultra™ II Directional RNA Library Prep Kit. Sequencing was performed on the NextSeq 500 system (75 cycles, high output, v2.5).

treatment_protocol:
The transposase encoding plasmid (plB1-PyCAG-PBase) and PB transposon vertor containing Cre-ERT2 (plB58-PB-CAG-CreERT2-IRES-Neo) were co-transfected in ESCs.
Cre/loxP recombination was induced using 500 nM 4-OHT treatment.

value: Mouse embryonic stem cells

value: Yapfl/fl/Taz-/-


title: T_1, Schizophrenia


title: Taz KO_rep2

description: Yap f/f Taz ∆/∆_2


title: Patient2


title: sensory neuron, control SFC-856

city: Oxford

first: Kevin

last: Talbot

address: John Radcliffe Hospital, Headley Way

department: Nuffield Department of Clinical Neurosciences

country: United Kingdom

institute: University of Oxford

data_processing:
fastq quality control was performed using fastqc and fastq-screen
Mapping against Ensembl genome version 101 was performed with STAR using the 2-pass method using a standard hg38 genome, with the following options on first pass: “--alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --outFilterMismatchNoverReadLmax 0.04 --outFilterScoreMinOverLread 0.9 --outFilterMatchNminOverLread 0.9”.
Count tables were obtained using featureCounts for the coding subset of the geneset only.
Assembly: hg38
Supplementary files format and content: tab-delimited counts file

source_name: iPSC sensory neuron

extract_protocol:
iPSC-MNs for RNA sequencing were harvested on day in vitro 53, iPSC-SNs were harvested on day in vitro 45. RNA extraction was performed using the QIAGEN RNeasy Micro kit. RNA abundance and quality were assessed using nanodrop and the Bioanalyzer Nano RNA kit.
Library preparation was done using Illumina Truseq and paired-end sequencing with a read length of 150bp was performed on the Illumina NovaSeq 6000.

value: iPSC sensory neuron

value: Healthy Control

tag: Sex

value: f


title: Taz KO_rep1

description: Yap f/f Taz ∆/∆_1


title: motor neuron, control SFC-856

source_name: iPSC motor neuron

value: iPSC motor neuron


title: Patient1

value: Alive with disease

value: Peripheral


title: Yap Taz double KO_rep3

description: Yap ∆/∆ Taz ∆/∆_3


title: T_7, Schizophrenia

value: peripheral blood

value: Schizophrenia


title: Yap Taz double KO_rep2

description: Yap ∆/∆ Taz ∆/∆_2


title: Yap Taz double KO_rep1

description: Yap ∆/∆ Taz ∆/∆_1


title: NAc input

city: Seattle

first: Marta

last: Soden

state: WA

address: 1959 NE Pacific St

institute: University of Washington

description: 10x Genomics

data_processing:
Demultiplexing, genome alignment, and processing of gene expression matrices were carried out using CellRanger v3.1.0
Assembly: mm10

source_name: Ventral tegmental area (VTA)

extract_protocol:
Immediately following stimulation mice were anesthetized and perfused with an ice cold solution containing (in mM): 92 NMDG, 2.5 KCl, 1.25 NaH2PO4, 30 NaHCO3, 20 HEPES, 25 glucose, 2 thiourea, 5 Na-ascorbate, 3 Na-pyruvate, 0.5 CaCl2, 10 MgSO4, pH 7.3-7.4. The following inhibitor cocktail was also included (in mM): 5 actinomycin-D, 37.7 anisomycin, 2 kynurenic acid, 0.5 tetrodotoxin. 500 µm coronal VTA sections were cut in the same solution using a VT1000s vibratome (Leica). The VTA from each section was dissected using a fine scalpel blade under a dissecting microscope, transferred to a 1.5 mL tube, snap-frozen on powdered dry ice, and stored at -80°C. Tissue from 3-4 mice per group was pooled for nuclear isolation. VTA tissue was dounce homogenized in a buffer containing (in mM): 320 sucrose, 5 CaCl2, 3 Mg(C2H3O2)2, 10 Tris (pH 7.8), 0.1 EDTA, 0.1 protease inhibitor cocktail, 1 β-mercaptoethanol, 5 actinomycin-D, 37.7 anisomycin, with 0.1% NP40 and 0.2 U/ul RNase inhibitor. Following a 5 min incubation on ice homogenized samples were mixed with an equal volume of 50% iodixanol solution (50% OptiPrep containing (in mM): 5 CaCl2, 3 Mg(C2H3O2)2, 10 Tris (pH 7.8), 0.1 protease inhibitor cocktail, 1 β-mercaptoethanol, 5 actinomycin-D, 37.3 anisomycin). This mixture was layered on top of an equal volume of 29% iodixanol (OptiPrep) and spun at 7500 RPM for 30 min at 4°C. Pelleted nuclei were resuspended in PBS with 10% BSA and 0.2 U/ul RNAse inhibitor. The concentration of nuclei was determined using a hemocytometer, and was adjusted to 1,000 nuclei/ul.
Approximately 10,000 nuclei per experimental group were captured and single-nucleus cDNA libraries were constructed using the Chromium NextGEM platform (10x Genomics) according to manufacturer’s instructions. Libraries were sequenced using an Illumina 4400 HiSeq platform to a target output of ~ 350,000,000 reads

treatment_protocol: All mice underwent surgery to receive bilateral viral injections into indicated input region and optical fiber implants over the VTA. Mice were allowed to recover for at least 3 weeks and subsequently underwent a 15 min stimulation period with 20 Hz, 5 ms pulse width blue light.

value: Ventral tegmental area (VTA)

tag: age

value: 11-15 weeks

value: Brain

value: Vgat-cre

tag: treatment

value: AAV-FLEX-ChR2-YFP into NAc; 15 min 20 Hz, 5 ms pulse duration


title: PFC input

description: 10x Genomics

value: AAV-FLEX-ChR2-YFP into PFC; 15 min 20 Hz, 5 ms pulse duration


title: Control_rep3

description: Yap f/f Taz f/f_3

value: Yapfl/fl/Tazfl/fl


title: motor neuron, control SFC-180


title: Control_rep2

description: Yap f/f Taz f/f_2

value: Mouse embryonic stem cells


title: LH input

description: 10x Genomics

value: AAV-FLEX-ChR2-YFP into LH; 15 min 20 Hz, 5 ms pulse duration


title: YFP, control

description: 10x Genomics

value: AAV-FLEX-YFP into LH; 15 min 20 Hz, 5 ms pulse duration


title: sensory neuron, patient C9-04, clone 12

value: iPSC sensory neuron

value: m


title: Control_rep1

description: Yap f/f Taz f/f_1


title: Blister leaf Rep3

city: Sutton Bonington

first: Rupert

last: Fray

address: Sutton Bonington Campus

institute: University of Nottingham

data_processing:
QC using fastqc and fastp
Sequence reads were trimmed for adaptor sequence / low-quality sequence using fastp with mean read quality of 20
kallisto used for mapping filtered paired end reads
trimmed sequence reads were mapped using kallisto v0.46.0
quantification and normalization were performed using kallisto software
Assembly: Reference transcriptome: Quercus robur downloaded from urgi.versailles.inra.fr
Supplementary files format and content: tab-delimited text file includes estimeated reads count for each sample calculated using kallisto
Supplementary files format and content: tab-delimited text file includes tpm value for each sample calculated using kallisto

organism: Quercus robur

source_name: Leaf

growth_protocol: Tissue harvested from one mature oak tree

extract_protocol:
RNA was extracted was carried out using a modified CTAB method (Pushkova et al., 2019, Barbier et al., 2019). 0.5ml of CTAB buffer (100mM Tris-HCL, pH9.5, 2% CTAB, 1.4M NaCl, 1% PEG 8000, 20mM EDTA, 2% PVP-40, 40mM DTT) and 2µl proteinase K was added to 50mg of ground tissue. This was incubated for 5 minutes at 65°C. 60µl of 10% SDS was then added, the tube inverted, and 1 volume of chloroform added. The samples were vortexed for 10 seconds, centrifuged (4°C, 5500xg,10 minutes). The aqueous phase was taken and mixed with an equal volume of chloroform. After centrifugation (room temperature, 14,000xg, 5 minutes), the aqueous phase was taken and precipitated overnight with 0.5 volumes of 7.5M Ammonium acetate and 2.5 volumes of ethanol. After extraction the RNA was treated with turbo DNAse (Invitrogen, AM2238) according to the manufacturer instructions.
mRNA library preparation (poly A enrichment)

value: Leaf


title: Wild type KDM3B rep2

city: Seoul

first: Jung-Woong

last: Kim

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

country: South Korea

institute: Chung-Ang University

data_processing:
Illumina Casava software used for basecalling
Sequenced read were trimmed for adaptor sequence, and masked for low-quality sequence using TrimGalore (v.0.6.6)
Alignment to GRCm38.p13.101 or mm10 whole genome with Bowtie2 (v.2.4.4)
Peak calling with EPIC2 (v.0.0.51) with the defualt option
Annotation process and motif finding process with HOMER (v.4.11.1)
genome build: GRCm38.p13.101 (mm10)
processed data files format and content: BigWig for each samples

source_name: mouse retina

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: mouse retina

value: Kdm3b wild type

tag: chip antibody


title: Blister leaf Rep2


title: motor neuron, patient C9-04, clone 12

value: iPSC motor neuron


title: Patient3

value: fresh frozen diagnostic fine-needle aspiration cytology specimen

tag: metastasis

value: Yes

value: Alive without disease

value: No

value: Good

value: Female

value: Central


title: Blister leaf Rep1


title: Wild type KDM3B rep1


title: sensory neuron, control SFC-841

value: Healthy Control


title: Wild type IgG

value: IgG


title: motor neuron, patient C9-02, clone 3

value: f


title: Blister gall Rep3

source_name: Oak Gall

value: Oak Gall


title: motor neuron, control SFC-841


title: sensory neuron, patient C9-01, clone 7

value: iPSC sensory neuron


title: Kdm3b Hetero Input rep2

value: Kdm3b heterogeneous gene


title: Blister gall Rep2


title: Kdm3b Hetero Input rep1


title: sensory neuron, control SFC-180


title: motor neuron, patient C9-01, clone 6

value: m


title: Blister gall Rep1


title: Wild type Input rep2

value: mouse retina


title: Button gall leaf Rep3

value: Leaf


title: Wild type Input rep1

value: Kdm3b wild type


title: Mel0911,conjunctival melanoma

city: Shanghai

first: Hanhan

last: Shi

address: Zhizhaoju road

institute: Shanghai Ninth People’s Hospital

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:  MT% < 40%;   Cell Gene Number < 10000;  Cell Gene Number > 200. PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: GRCh38
Supplementary files format and content: cellname.list file and counts.tsv.gz file contain counts for each barcodes and genes

source_name: conjuntive

extract_protocol:
Cells from each sample were used for single-cell isolation using BD Rhapsody Single-Cell Analysis System (BD Biosciences). Before single-cell isolation, all cells were labeled using a BD Single-Cell Multiplexing Kit.
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.

value: conjuntive

value: male

tag: clinical tumor_stage


title: Button gall leaf Rep2


title: hepatic fibroblasts

city: Nagakute

first: Takashi

last: Kobayashi

state: Aichi

address: 1-1 Yazakokarimata

department: Institute for Molecular Science of Medicine

country: Japan

institute: Aichi Medical University

description:
HFB
10X Genomics

data_processing:
Raw data was processed using CellRanger v6.1.2 and mapped to the pre-built human reference genome hg38.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hiPSC derived fibroblasts

growth_protocol: For DFB differentiation, hiPSC were cultured in FDM1 (3:1 DMEM:F12, 5% FBS, 0.18 mM adenine, 10 ng/ml EGF, and 5 µg/ml human insulin) for 4 days. The cells were then cultured in FDM1 containing 0.5 nM human BMP4 for 3 days. On day 7, the cells were passaged onto Geltrex-coated plates and cultured in FDM2 (1:1 DMEM:F12, 5%FBS and 1% non-essential amino acids) for 7 days. On day 14, the cells were passaged onto uncoated plates and cultured in EDM1 for 7 days. At day21, the cells were passaged onto type I collagen-coated dishes in EDM1 for a few days. For CFB differentiation, hiPSC were treated with 6 µM CHIR99021 in RPMI/B27 (RPMI with B27 supplement minus insulin) for 24 h and then treated with RPMI/B27 for 2 d. On day 3, the cells were treated with 5 µM IWP-2 in 1:1 conditioned media to fresh RPMI/B27. After 2 days (day 5), the cells were treated with RPMI/B27. On day 6, the cardiac progenitors were detached with Accutase and seeded on a Geltrex-coated plate in LaSR medium (Advanced DMEM/F12 containing 1.3% GlutaMax and 0.1 mg/ml ascorbic acid). The cells were then treated with 3 µM CHIR99021 in LaSR medium for 2 days and cultured in LaSR for 3 days. On day 12, the cells were detached with Accutase and seeded onto a Geltrex-coated plate in LaSR medium with 0.5 µM A83-01. For epicardial fibroblast differentiation, the cells were cultured in LaSR with 5 ng/ml bFGF and 0.5 µM A83-01 for 10 days. For HFB differentiation, hiPSC were incubated with Advanced-DMEM/F12 containing 2% B27 supplement, 1% N2 supplement, 10 µM CHIR99021, 10 ng/ml bFGF, 30 ng/ml BMP-4, and 10 ng/ml human activin A for 3 days. The cells were then incubated with Advanced-DMEM/F12 containing 2% B27 supplement, 1% N2 supplement, 100 ng/mL bFGF, and 50 ng/mL BMP-4 for 3 days. These hiPSC-derived fibroblasts were cultured in FibroGRO complete media on collagen I-coated dishes.

extract_protocol:
The cells were dissociated by accutase and frozen in StemSure freezing medium until the analysis. The frozen cells were thawed at 37°C, centrifuged, and resuspened in PBS containing 0.04% BSA. To generate single cell GEM, cells were loaded onto the 10X Chromium Single Cell Platform (10X Genomics).
Libraries were constructed with Chronium Next GEM Chip S Single cell kit, Chronium Next GEM single Cell 3' Kit v3.1, and Dual Index Kit TT Set A.

value: hiPSC derived fibroblasts


title: Kdm3b Hetero H3K9me3 rep1


title: dermal fibroblasts

description:
DFB
10X Genomics


title: Button gall leaf Rep1


title: Kdm3b Hetero H3K9me2 rep2


title: cardiac fibroblasts

description:
CFB
10X Genomics


title: Button gall Rep2


title: Ds_3

city: Dalian

first: Jinsong

last: Yan

state: Liaoning

address: 467 Zhongshan Road, Dalian 116027, Liaoning, P. R. China

department: Department of Hematology

institute: the Second Hospital of Dalian Medical University

data_processing:
For the gene expression, we mapped the sequencing data to reference genome (hg38) using STAR, and defined transcript coordinates according to the gene annotation format file (GTF file) from GENCODE (Release 27, GRCh38).
The Gene abundances are given as Reads Per Kilobase per Million mapped reads (RPKM) with “cuffnorm” command using the Cufflinks package.
Assembly: hg38
Supplementary files format and content: Excel file include RPKM values for each Sample …

source_name: Daudi

extract_protocol:
Total RNA of the wild type and shENO1 Daudi cells were extracted using the QIAamp AllPrep RNA Mini Kit (Cat# 80204, QIAGEN), according to the manufacturer's specifications.
Libraries were constructed using the TruSeq RNA Sample Preparation Kits (Illumina), and the quality of the library was assessed using Bioanalyzer 2100 (Agilent Technologies).

tag: cell line

value: Daudi

value: Burkitt's lymphoma cell

value: ENO1 knockdown


title: Kdm3b Hetero H3K9me2 rep1


title: Ds_1


title: Button gall Rep1


title: Spangle gall leaf Rep3


title: Dp_3

value: wild type


title: Spangle gall leaf Rep2


title: Kdm3b Hetero H3K9me1 rep1


title: Wild type H3K9me3 rep2


title: Spangle gall leaf Rep1


title: Dp_1


title: sensory neuron, patient C9-02, clone 3


title: Wild type H3K9me3 rep1


title: Kdm3b Hetero H3K9me3 rep2


title: Spangle gall Rep3


title: Mel1022,conjunctival melanoma

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:
- MT% < 40%;
- Cell Gene Number < 10000;
- Cell Gene Number > 200.
PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: GRCh38
Supplementary files format and content: cellname.list file and counts.tsv.gz file contain counts for each barcodes and genes

value: female

tag: pathological tumor_stage


title: Wild type H3K9me2 rep2


title: Spangle gall Rep2


title: Button gall Rep3


title: Wild type H3K9me2 rep1


title: Mel0909,conjunctival melanoma


title: Ds_2


title: Spangle gall Rep1


title: Wild type H3K9me1 rep2


title: Mel0722,conjunctival melanoma


title: Currant gall leaf Rep3


title: Wild type H3K9me1 rep1


title: Kdm3b Hetero H3K9me1 rep2


title: Mel0622,conjunctival melanoma


title: Currant gall leaf Rep1


title: Dp_2


title: Mel0618,conjunctival melanoma


title: BL21, Glucose  (G), Replicate3

city: Chicago

last: Mankin

state: Illinois

address: 900 S. Ashland Ave, Rm. 3052,

department: College of Pharmacy

institute: University of Illinois at Chicago

description:
Amplicon Sequencing
NS_aa_table_filtered_raw_counts.txt

library_source: other

data_processing:
The raw reads were trimmed to the size of the peptide gene and those containing internal ambiguous bases or being less than 60 bases in length were discarded. The nucleotide sequences were translated into amino acid sequences and the peptides lacking N-terminal methionine or deviating from the size of the expected sequence were eliminated.
Peptides with less than 100 reads in each of the pApi(Glu) samples were also discarded.
Subsequently, the filtered data underwent differential abundance analysis using the standard workflow of edgeR within the R/Bioconductor package
For Positive selection, raw data was processed with Geneious Prime software (v. 2022.2)
Assembly: Api Ib peptide
Supplementary files format and content: For neagtive selection, tab-delimited text file includes raw counts for each sample
Supplementary files format and content: For Positive selection, spreadsheet include raw counts
Library strategy: Amplicon Sequencing

molecule: other

organism: Escherichia coli

source_name: BL21 (DE3)strain

growth_protocol: E.coli BL21 cells were maintained in lysogeny broth (LB) medium, CA244 strain were grown in LB and M9 minum medium

extract_protocol:
Plasmids were isolated from treated or control samples with Roche High Pure Plasmid Isolation Kit
peptide-coding genes were PCR-amplified from isolated plasmids with Q5 DNA polymerase (New England Biolabs)

treatment_protocol: 0.05% arabinose or 2% Glucose were supplmented with liquid medium or added in agar plates

value: BL21 (DE3)strain

value: E. coliB F- ompT gal

value: Glucose


title: Currant gall Rep3

value: Oak Gall


title: BL21, Glucose  (G), Replicate2


title: Currant gall Rep2


title: BL21, Glucose (G), Replicate1


title: Con0923,benign conjunctival lesion


title: Currant gall Rep1


title: Con0914,benign conjunctival lesion


title: T47D cells, 17e, 12h, biol rep3

city: Wuhan

first: Jian

last: Huang

address: Bayi Road 299

institute: Wuhan University

data_processing:
SeqPrep and Sickle
The raw paired end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
Then clean reads were separately aligned to reference human genome GRCh38 with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software.
The mapped reads of each sample were assembled by StringTie(https://ccb.jhu.edu/software/stringtie/index.shtml? t=example) in a reference-based approach.
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: T47D cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara).
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA.

treatment_protocol: T47D cells were treated with compound 17e at 10 μM for 12 hours.

value: estrogen receptor alpha positive breast cancer cells

value: WT

value: compound 17e

tag: time

value: 12 hours


title: BL21, Arabinose (A), Replicate2

first: Alexander

value: Arabinose


title: Mature Leaf Rep3

value: Leaf


title: BL21, Arabinose (A), Replicate1


title: Mature Leaf Rep2


title: Mature Leaf Rep1


title: LPS

city: Beijing

first: Ziyi

last: Wang

address: Litang Road 168, Changping District, Beijing

institute: Beijing Tsinghua Changgung Hospital

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The clean reads were used for protein binding site analysis. They were mapped to the reference genome of mice from https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001635.20/ using STAR software (version 2.5.3a) with default parameters.
The RSeQC（version 2.6）was used for reads distribution analysis.
The MACS2 software（Version 2.1.1）was used for peak calling. The bedtools（Version 2.25.0）was used for peaks annotation and peak distribution analysis.
bigWig files were generated using deepTools.
Assembly: GRCm38
Supplementary files format and content: bigWig

organism: Mus

extract_protocol:
The tissue/cell was fixed in 1% formaldehyde for 10 min at room temperature by a vacuum pump, after which 0.125 M glycine was added and the mixture was sat for 5 min to terminate the crosslinking reaction. The tissue was then collected and frozen in liquid nitrogen, and grinded by tissue lyser. The grinded powder was treated with lysis buffer and nucleus was collected by centrifuging at 2000g for 5min. Then, nucleus was treated with nucleus lysis buffer and sonicated to fragment chromatin DNA.
The 10% lysis sonicated chromatin was stored and named “input”, and 80% was used in immunoprecipitation reactions with anti-EZH2 antibody（Abcam, EPR20108）and named “IP”, and 10% was incubated with rabbit IgG (Cell Signaling Technology) as a negative control and named “IgG”，respectively. The DNA of input and IP was extracted by phenol-chloroform method. The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3（Catalog NO. ND607, Vazyme）. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

value: macrophage status in sepsis

tag: agent

value: LPS

value: anti-EZH2 antibody (Abcam, EPR20108)


title: Mel0701,conjunctival melanoma

value: conjuntive

value: male


title: T47D cells, 17e, 12h, biol rep1


title: Currant gall leaf Rep2


title: CA244, Arabinose, 1

description:
Amplicon Sequencing
PS_AA_counts.xlsx

source_name: CA244 strain

value: CA244 strain

value: E. coli k12 lacZ125(Am), e14-, trpA49(Am), relA1, spoT1


title: Kdm3b Hetero 12M rep2

data_processing:
Illumina Casava software used for basecalling
Sequenced read were trimmed for adaptor sequence, and masked for low-quality sequence using TrimGalore (v.0.6.6)
Alignment to GRCm38.p13.101 or mm10 whole genome with STAR (v.2.7.1a) and read feature counting with RSEM (v.1.3.3)
FPKM were calculated using a fpkm function from DESeq2 (v.1.32.0) and differential gene expression by edgeR (v.3.36.0)
genome build: GRCm38.p13.101 (mm10)
processed data files format and content: txt files include normalized counts (FPKM)

extract_protocol:
Total RNA was extracted using Trizol reagent and mRNA was extracted by mRNA pull-down using poly-A tagged bead using TruSeq Stranded mRNA Library Prep kit (Illumina, #20020595).
Each 100 ng total RNA from retinas were isolated and an oligo-dT primer including an Illumina-compatible sequence at its 5’ end was hybridized to the RNA and reverse transcription was carried out. After degradation of the RNA template, second strand synthesis was initiated by a random primer containing an Illumina-compatible linker sequence at its 5’ end. The double-stranded library was purified by employing AMPure magnetic beads (A63881, Beckman coulter, CA, USA) to get rid of all reaction components. The library was amplified to add the complete adapter sequences required for cluster generation. The finished library is purified from PCR components.

value: mouse retina

value: Kdm3b heterogeneous gene


title: T47D cells, control, biol rep3

value: DMSO


title: LPS_Input


title: Kdm3b Hetero 12M rep1


title: CK


title: Wild type 12M rep3

value: Kdm3b wild type


title: T47D cells, control, biol rep1

value: estrogen receptor alpha positive breast cancer cells


title: Wild type 12M rep2


title: T47D cells, control, biol rep2

value: WT


title: Nev1013,benign conjunctival lesion


title: CK_Input


title: S36

status: Public on Jun 17 2024

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

description: ~6w old mouse; spleen; CD8 T cells plated for 6h

data_processing:
Samples were trimmed for adapters and low quality bases using Trimmomatic software and aligned with referencemouse mm10genome using STAR software.
Quantification was carried out with RSEM using the transcriptome bam file created by STAR.
Basecalling was performed by RTA (version 1.18.66.3).
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.17) allowing 1 mismatch.
Reads were filtered with a base call quality with 89-94% of pass filter reads having Q30 or above.
Trimming of adapters and low-quality bases was performed using Trimmomatic (version 0.36).
First pass alignment of reads to the mm10 reference genome was performed using STAR (version 2.5.1) with parameters: STAR --genomeDir $star_genome --readFilesIn R1_trimmed.fastq R2_trimmed.fastq --outTmpDir /logs/star --outSAMunmapped Within -- outFilterType BySJout --outFilterMultimapNmax 20 -- outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 -- alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 -- sjdbScore 1 --runThreadN 8 --genomeLoad NoSharedMemory -- outSAMtype BAM Unsorted --quantMode TranscriptomeSAM
Gene-level expression quantificiation and library size normalization in counts-per-million was performed using RSEM (version 1.2.22).
Quantile-normalization and differential expression was performed using limma-voom (version 3.34.5).
Assembly: mm10/M21
Supplementary files format and content: Excel (.xlsx) file containing RSEM raw counts (i.e. expected counts).

source_name: spleen

growth_protocol: CD8 Naïve T cells were isolated from spleen of same litter mate WT and CD47-/- C57Bl/6J background 4–6-week-old mice (n=4).  Cell isolation buffer was prepared using phosphate-buffered saline (PBS), pH 7.2, 0.5% bovine serum albumin (BSA), and 2 Mm EDTA and kept on ice. The buffer was filtered using Corning® 50 mL Tube Top Vacuum Filter System, 0.22 µm Pore 13.6cm² CA Membrane, Sterile (Corning). Dissected spleens were immediately placed in Petri dish containing 1XPBS (Gibco), and homogenized placing spleen on cell strainer (70um) and smashed using back of plastic transfer pipettes (Sigma) with 5 ml of buffer. Mature RBC mixture were lysed using 1 ml of ACK lysis buffer (Quality Biologicals) at room temperature for 5 minutes according to manufactures instructions.

extract_protocol:
Cell pellets from each treatment were washed with PBS, and total RNA was extracted using Trizol. The concentration of RNA and RNA quality was measured via Nanodrop and RNA bioanalyzer.
mRNA sequencing was performed by core facility at Frederick National Laboratory for cancer Research (Leidos Biomedical Research, Inc) using HiSeq3000 with Illumina v4. All the samples have yield from 24 to 38 million reads.

treatment_protocol: The freshly isolated CD8+ T cells were washed with filtered buffer solution containing phosphate-buffered saline (PBS), pH 7.2, 0.5% bovine serum albumin (BSA), and 2 Mm EDTA. The clumps of isolated cells were removed using Pre-Separation Filters (30 µm) and subjected to negative selection of CD8+ T cells. The cells were immediately placed at -80 °C until the RNA was extracted.

value: spleen

value: Primary CD8+T cells

value: mouse CD8+T

value: CD47 null

value: UT


title: S35


title: S33


title: BL21, Arabinose (A), Replicate3

value: BL21 (DE3)strain

value: E. coliB F- ompT gal

value: Arabinose


title: Mouse rep 2

city: New York

first: Sumin

last: Jang

state: NY

institute: Columbia University

data_processing:
Demultiplexing, barcode analysis and gene expression quantification was done using CellRanger v3.1.0
Assembly: mm10 and hg38
Supplementary files format and content: tab-delimited gene expression matrix (UMI)

source_name: mouse ES

extract_protocol:
Embryoid bodies were dissociated with papain and DNase I, followed by FACS to select GFP+ cells.
Library was prepared according to manufacturer's protocol (10X Genomics: single cell 3')

treatment_protocol: Prior to differentiation, human and mouse pluripotent stem cells were transduced with a lentivirus harboring unique 6bp barcode sequences downstream of CAGGS-driven GFP.

tag: mouse strain

value: mouse ES

value: in vitro motor neuron differentiation


title: S34


title: S37


title: T47D cells, 17e, 12h, biol rep2

value: compound 17e

value: 12 hours


title: S39


title: S40


title: S38


title: mccc-1_Coma_biorep1

city: Worcester

first: Yonguk

last: Lee

state: Massachusetts

address: 55 N Lake Avenue

department: Department of Systems Biology

institute: University of Massachusetts Chan Medical School

description: Grown on NGM + Feeding Comamonas aquatica DA1877

data_processing:
BGI internal software "SOAPnuke" was used to remove adaptors and low quality reads with parameters: -n 0.001 -l 20 -q 0.4 -A 0.25. Low quality reads are defined as having greater than 40% bases whose quality is less than 20.
Reads were aligned to the reference genome using Bowtie2 with default parameters.
RSEM was used for estimation of read counts with default parameters
The Ebseq method was used for differential expression analysis.
Assembly: c_elegans.PRJNA13758 (WormBase WS271)
Supplementary files format and content: tab dilimeted file containing FPKM matrix for all samples and all genes

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Animals were maintained on NGM-agar. They were synchronized by an 20 hour L1 arrest post-buffered bleach treatment.

extract_protocol:
A minumum of 200 staged animals were collected and washed thrice in M9 buffer. Total RNA was extracted via Trizol and BCP followed by Dnase I treatment. Zymo Direct-zol RNA miniprep kit was used for clean up.
BGI standard protocol

treatment_protocol: Synchronized animals were grown on NGM-agar fed with Comamonas aquatica DA1877

value: whole animal

value: mccc-1(ww4) IV; wwIs24[acdh-1p::GFP + unc-119(ed3)]

tag: culture condition

value: Nematode Growth Medium (NGM)

value: 70 hours after egg hatching at 20degreeC


title: control_Coma_biorep1

tag: tissue

value: wwIs24[acdh-1p::GFP + unc-119(ed3)]


title: control_Coma_biorep2


title: MLV_K562_GFP

city: Prague

first: Dalibor

last: Miklik

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the Czech Academy of Sciences

description: pooled, barcode-discriminated libraries

data_processing:
Cutadapt was used for the pre-mapping processing of raw reads. Reads were sorted according to the barcodes using the ‘cutadapt -g ^B --overlap 8 --discard-untrimmed’ command, where ‘B’ stands for the barcode sequence (wt: TAGTATCAGC, GCATATGCAC; W390A: CTCGCGTGTC, CAGCTCATCA; CBX: CGTGTCTCTA, TCTCTATGCG). Reads containing LTR sequence  were sequentially selected first using ‘cutadapt -g ^GCTTGCCAAACCTACAGGTG --overlap 20 --discard-untrimmed’ command to select reads containing a sequence targeted by LTR-specific primer. Next, reads containing the last 9 nucleotides of the LTR sequence with residual sequence of the minimal length of 15 bp were selected using ‘cutadapt -g ^GGTCTTTCA --overlap 8 --discard-untrimmed --minimum-length 15’ command. Adapter sequences were then removed from the reads with ‘cutadapt -a ACCACTAGTGTCGAC --overlap 10 --minimum-length 15’ command and the reads containing amplified inner proviral sequence were removed using the ‘cutadapt -g TTCCCCCCTT --overlap 10 --discard-trimmed' command.
Trimmed reads were mapped to both hg19 and hg38 human genome assemblies using the Bowtie 2 with ‘bowtie2 -p 20 -q -x hgX ‘command where the ‘hgX' marks the name of the assembly.
Reads that map from the start of the read (“MD:Z:0” reads) that show single hit in the genome (“XS:i:” reads) were selected and converted to BED file using ‘samtools view -S -b’ and ‘bedtools bamtobed -cigar -i 'commands. Each proviral integration site is recorded as a coordinate of single genomic LTR-proximal position. Integration site coordinates supported by at least 5 reads were selected. If more inegrations site coordinates were present within the distance of 5 bp, only the coordinate supported by the most reads is present in the bed file.
Assembly: hg19, hg38
Supplementary files format and content: BED file with integration site coordinates mapped to hg19 genome assembly
Supplementary files format and content: BED file with integration site coordinates mapped to hg38 genome assembly
Library strategy: ligation mediated PCR

growth_protocol: The cell line K562 was cultivated in RPMI 1640 medium (Sigma) supplemented with 5% fetal calf serum and 5% newborn calf serum (both GIBCO) and antibiotics (#A5955, Antibiotic Antimycotic Solution (100×), Stabilized; Sigma-Aldrich) at 37 °C and in a 5% CO2 atmosphere.

extract_protocol:
Genomic DNA was extracted by a phenol-chloroform extraction.
Genomic DNA was fragmented by DNA fragmentase (NEB) to obtain fragments 100-2000 bp long with the main density between 500-1000 bp on an agarose gel. By purification fragments on SPRI Magnetic beads (Canvax), we selected fragments 300-2000 bp long. Then, we repaired the ends and added 3’polyA overhangs with T4 polymerase, T4 polynucleotide kinase, and Taq DNA polymerase (all NEB). After purification with the High Pure PCR Cleanup Micro Kit (Roche), through T-A ligation, we ligated adaptors with Quick Ligase (NEB). Apart from the standard adaptor oligos Ion-Link-A and Ion-Link-Ba, we added blocking oligo Ion-Link-Bb to prevent adaptor-adaptor amplification. After another purification on columns, DNA was amplified with adaptor-specific and provirus-specific primers. In the PCR reaction mix, we added blocking oligos to prevent the amplification of inner proviral sequences. First, we ran a linear PCR reaction with biotinylated primer MLV-LTR1_F_Bio. After purification of the PCR reaction on the Dynabeads™ MyOne™ Streptavidin C1 beads (Invitrogen), we ran a PCR reaction with the Ion_trP1 primer and the barcoded IonA_MIDx_mlvLTR2 primers. We isolated 300-500-bp-long PCR products from an agarose gel. After purification on columns, the samples were quantified with the KAPA Library Quantification Kit for IonTorrent Platforms (Roche). The quantified samples were pooled in equimolar ratio and mixed with Ion Sphere Particles (Thermo Fisher Scientific).

treatment_protocol: The K562 cells were counted and seeded with fresh cultivation medium on a cultivation plate/dish on the day of transduction. Virus-containing medium was added to the cultivation medium and cells were incubated for 24 hours. The next day, the medium was removed and fresh cultivation medium was added to the cells.

value: 14 dpi

value: vector transduction


title: Huh7_LG_RNA

city: Hong Kong

first: Chi Ho

last: Lin

address: 6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam

department: Centre for PanorOmic Sciences

country: Hong Kong

institute: The University of Hong Kong

data_processing:
To obtain high quality reads for downstream analysis, raw sequencing reads were firstly filtered for adapters sequences and low quality, in which more than 5% of the bases in a read contained unknown bases (‘N’) and more than 50% of the bases having a base quality value of ≤ 10, and were removed using cutadapt (Martin, 2011) and custom scripts. Subsequently, low complexity bases (more than 10bp of continuous bases of “A” and “T”) were trimmed from the 3’ end using prinseq (Schmieder and Edwards, 2011). Reads with length < 40bp were then discarded. Finally, sequencing reads were filtered for rRNA sequence and remaining high quality reads were used for downstream analysis.
The high quality reads were aligned against human transcriptome (hg19) using RSEM package v1.2.21 (Li and Dewey, 2011). Expression estimation and tests for differential expression were accomplished using EBSeq v1.6.0 (Leng at el, 2013) which is part of the RSEM package.
Genome_build: Human genome (hg19)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: HCC cells

growth_protocol: Huh7 cells were cultured in DMEM supplemente with 10% FBS at 37°C in a 5% CO2 setting. Medium was renewed 2-3 times a week and subcultured when cell clonfluency reached 90%.

extract_protocol:
Cells were trypsinized and RNA was extracted using Rneasy Plus Mini Kit (Qiagen cat.no.: 74134).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Huh7 cells were seeded in a 6-well dish on Day 0 (500,000 cells per well). Next day, high glucose (HG; 4.5g/L) and low glucose (LG; 0.45g/L) media were replaced respectively. The treatment lasted for 6 days. Cells were subcultured when cell confluency reached 90% and only live cells were seeded back to the dish everytime.

tag: cell type

value: well differentiated hepatocyt-derived carcinoma cell line

value: low glucose (LG; 0.45g/L) medium


title: Huh7_HG_RNA

value: high glucose (HG; 4.5g/L) medium


title: mccc-1_Coma_biorep2

tag: genotype


title: Alim Diapause 1 Month ATACseq Rep3

city: Stanford

first: Anne

last: Brunet

state: California

address: 290 Jane Stanford Way

department: Genetics

institute: Stanford University

description:
Alim_consensusPeaks_rpkm.txt
Alim_1M_3

data_processing:
Fastq filles underwent read trimming using Trimgalore (v0.4.1)
Fastq files were mapped using --very-sensitve parameter on Bowtie2 (v2.2.5)
Duplicate reads were flagged and removes with Picard tools (v2.22.1) and SAMtools (v1.5)
Tn5 base shifting corrected by alignmentSieve in deepTools (version 3.2.1)
Peaks called using MACS2 (version 2.1.1.20160309)
Assembly: Genomes used: African Turqouise Killifish: GCA_001465895.2 ; Red-Striped & Lyretail Killifish: GCA_006937985.1 MPIBA_Aaus_1.0 scaffolds: 12,236 contigs: 30,782 N50: 119,465 L50: 1,783 ; South American Killifish: GCA_001266775.1
Supplementary files format and content: Concensus Peak files across replicates and timepoints. Columns 1-11 are Bed format entries and all following are RPKM-normalized readcounts within each sample.

organism: Austrofundulus limnaeus

source_name: Dissected Embryo (Whole Body)

growth_protocol: Synchronized killifish embryos for African turquoise and South American killifish were collected within a tight (~5 hour) breeding window. Most collected embryos were at the 1-2 cell stage upon collection. We monitored embryos every day post-collection to observe the visual markers of diapause and development as previously described. Briefly, we used Kupffer’s vesicle (KV), which is a transient embryonic organ present from early to middle somitogenesis as a marker to stage embryos that are about to reach diapause. KV-positive embryos reach the end of somitogenesis in 1-2 days and the loss of KV roughly coincides with the onset of heartbeat in killifish, followed by either diapause or continue development. We counted the number of somites in KV-positive embryos and designated KV-positive embryos at 15-22 somites as our “pre-diapause (Pre-Dia) stage”. Embryo morphology for all the killifish species was similar at this stage. This mid-somitogenesis time point also coincides with the vertebrate phylotypic period (the period of the most conserved gene expression pattern during vertebrate development) with available gene expression and chromatin accessibility data from multiple other fish species. we next monitored the onset of heartbeat, and stage diapause embryos at 6 days (Dia 6d) and 1 month of diapause (Dia 1m) as exhibiting a continuously decreasing heartbeat rate since diapause onset (<45 beat-per-minute (BPM)) as described in Hu et al. For embryos in 1 month diapause (Dia 1m), we additionally made sure that there was no heartbeat by monitoring them for 5 minutes under a stereoscope to verify that they were not prematurely exiting the diapause state. For embryos in development, embryos that had an increase in heartbeat rate 1 day after heartbeat onset (>45 BPM), but before the visual pigmentation in eyes was developed (i.e. before pharyngula stage) were designated as developing embryos (Dev). All the diapause and development stages stage are identical to our previous study, except Pre-Dia stage which is a day before the onset of heartbeat.

extract_protocol:
To generate nuclei-suspension for ATAC-seq libraries, snap frozen embryo samples (~10 embryos per sample) were thawed for 1 minute and resuspended at 4oC in 200ml EZ-lysis buffer (Sigma Aldritch No. 3408). Samples were then transferred to 250 ml mini-douncers (DWK (Kimble) 885300-0000) and dounced 25 times with pestle A and B respectively. After a 2 minute incubation following douncing, samples were spun at 500g for 5 minutes to precipitate nuclei, and the EZ-lysis supernatant was removed. Nuclei were then resuspended in 250ml PBS (ThermoFisher No. AM9624) and an aliquot of 5µl of nuclei was incubated with 5ml of 0.4% trypan blue stain (ThermoFisher No. 15250061) for counting the total intact nuclei counts.
Samples of ~25,000 nuclei were then suspended in a Tn5 transposition mix (65ml of tagmentation DNA buffer (Illumina No. 20034197), 63ml of nuclease-free water, and 2.5ml of tagmentation DNA enzyme I (e.g Tn5 transposase) (Illumina No. 20034197) for 20 minutes at 37oC. Following incubation, the mix was purified using the Qiagen mini-elute kit (Qiagen No. 28206) to isolate tagmented DNA. PCR amplification and subsequent qPCR monitoring was performed as described in the original ATAC-seq protocol (~14-18 cycles of PCR). Amplified DNA from the PCR reaction was purified using the Qiagen mini-elute kit (Qiagen No. 28206), as recommended by the manufacturer. Samples were subsequently pooled and sequenced using next-generation short-read sequencing on an Illumina NEXTseq 550.

treatment_protocol: All collected embryos were wildtype and untrated for the duration of their development.

value: Dissected Embryo (Whole body)

tag: Stage

value: Diapause

tag: timing

value: Diapause 1 Month


title: Alim Diapause 1 Month ATACseq Rep1.5

description:
Alim_consensusPeaks_rpkm.txt
Alim_1M_1.5


title: wt_d6_1

type: RNA

city: St. Louis

first: Vincent

last: Peng

state: MO

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine in St. Louis

description: day 6 post-tamoxifen

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: To determine differentially expressed genes between genotypes over multiple timepoints, gene expression was fit to linear models using the Limma package with R (v3.5)37. For gene signature scoring, z-scores were calculated for each gene per sample and gene signature scores were calculated using the averaged z-scores for genes in each signature.

label: biotin

source_name: jejunum

label_protocol: RNA quality control, amplification and hybridization to Affymetrix Mouse Gene 1.0 ST array was conducted by the Genome Technology Access Center  (GTAC) in the Department of Genetics at Washington University in St Louis.

growth_protocol: For inducible gene ablation, tamoxifen (MilliporeSigma) was dissolved in the corn oil (MilliporeSigma) at final concentration of 20 mg/mL and i.p. injected to mice at the dose of 75 mg/kg body weight for five consecutive days. Mice were sacrificed and intestinal tissues were isolated at days 6, 9, and 12.

extract_protocol: RNA was extracted from the whole tissue small intestinal samples with an RNeasy Micro Kit (Qiagen).

value: wt

tag: time point

value: day 6 post-tamoxifen


title: ko_d12_1

description: day 12 post-tamoxifen

value: Fgfr1op KO

value: day 12 post-tamoxifen


title: wt_d9_2

description: day 9 post-tamoxifen

value: day 9 post-tamoxifen


title: ko_d6_2

description: day 6 post-tamoxifen


title: ko_d9_2

description: day 9 post-tamoxifen


title: wt_d12_2

description: day 12 post-tamoxifen


title: ko_d12_2

description: day 12 post-tamoxifen


title: wt_d9_1

description: day 9 post-tamoxifen


title: ko_d6_1

description: day 6 post-tamoxifen


title: Alim Diapause Day 6 ATACseq Rep3

description:
Alim_consensusPeaks_rpkm.txt
Alim_6D_3

value: Diapause Day 6


title: wt_d6_2

description: day 6 post-tamoxifen


title: Alim Diapause 1 Month ATACseq Rep2

description:
Alim_consensusPeaks_rpkm.txt
Alim_1M_2


title: Alime Development Rep2

description:
Alim_consensusPeaks_rpkm.txt
Alim_Dev_2

value: Development

value: Development (>60BPM)


title: Alim Pre-Diapause ATACseq Rep2

description:
Alim_consensusPeaks_rpkm.txt
Alim_preDia_2

value: Pre-Diapause (K-vesicle)


title: Alim Diapause Day 6 ATACseq Rep2

description:
Alim_consensusPeaks_rpkm.txt
Alim_6D_2


title: Alim Diapause Day 6 ATACseq Rep1

description:
Alim_consensusPeaks_rpkm.txt
Alim_6D_1