title: control, sortChIC with H3K27me3 antibody

value: control


title: 26wk_Mid-Diaphysis_Loaded Limb _24h _Animal24hO4

status: Public on Nov 15 2024

type: SRA

city: Ithaca

first: Carolyn

last: Chlebek

state: NY

address: 110 Hoy Road

department: Biomedical Engineering

country: USA

institute: Cornell University

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for adaptor sequence. 12bp were trimmed from the 5' end for quality assurance.
Trimmed sequence reads were mapped to mm10 using STAR (parameters- outFilterMismatchNmax: 2 - outFilterMultimapNmax: 1)
Fastqc was run for all files and only samples with high quality from both fastqc & RQN were included for analysis
Each sample contained over 1 million reads. Genes with less than 3 counts per million were not included for analysis.
Normalized gene counts were calculated in DESeq2 with Trimmed Mean of M-values correction
Assembly: mm10
Supplementary files format and content: .xlsx file with normalized gene counts and experimental conditions for each samle

molecule: total RNA

organism: Mus musculus

source_name: Mid-Diaphysis

extract_protocol:
Cancellous bone was separated from the cortical shell. The cortical bone was segmented into three sections: metaphyseal cortex, proximal diaphysis, and mid-diaphysis,and the metaphyseal cortex and mid-diaphysis were then analyzed. All tissues were flash frozen in liquid nitrogen. Samples were pulverized and RNA  isolated using a phenol-chloroform extraction followed by the RNeasy kit (Qiagen).
RNA libraries were prepared for 3' mRNA-seq

treatment_protocol: 10- and 26-week-old female C57Bl/6J were subjected to in vivo mechanical loading of the left tibia (9N peak load at 4 Hz for 1200 cycles per day). Mice were euthanized by cervical dislocation at 1-hour, 3-hours, or 24-hours following the completion of one bout of loading. To evaluate long term time points, a final group received 5 consecutive days of loading with euthanasia on the eighth day following the first loading session

tag: sample number

tag: tissue

value: Mid-Diaphysis

tag: loaded

value: L

tag: animal number

tag: timepoint

tag: age

value: Adult

tag: genotype

tag: treatment

value: Loaded _24h


title: Hmga1a OE, sortChIC with H3K9me3 antibody

city: Utrecht

first: Mara

last: Bouwman

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

library_source: genomic

data_processing:
Data preprocessing has been performed using the SingleCellMultiOmics package (https://github.com/BuysDB/SingleCellMultiOmics) and the sequences were mapped to the Zebrafish danRer11 ENSEMBL genome using Burrows-Wheeler Aligner (BWA).
bigwig files were generated in Galaxy.org using mapping quality treshold of 50 and samflag exclude code 1536
reads were normalised to counts per millinon (CPM)
Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation
Supplementary files format and content: bigwigs, CPM normalized, >50 mapping quality, samflag exlude 1536

molecule: genomic DNA

organism: Danio rerio

source_name: adult heart

extract_protocol:
Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. sortChIC protocol was followed as in (Zeller, 2023 nature genetics)
As in (Zeller, 2023 nature genetics).

treatment_protocol: zebrafish were treated with tamoxifen to induce Hmga1a overexpression

value: adult heart

tag: chic antibody

tag: cell type

value: cardiomyocytes

value: Hmga1a overexpression

value: 14 days post tamoxifen


title: wAMD patient, female, sampling age 95, ID=A813

city: Kuopio

first: Kai

last: Kaarniranta

address: Yliopistonrinne 3

department: Department of Ophthalmology

country: Finland

institute: University of Eastern Finland

data_processing:
FIMM-RNAseq 2.0.7 workflow
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing raw counts for each Sample

organism: Homo sapiens

source_name: Blood

extract_protocol:
RNA was extracted using Maxwell® RSC 48 Instrument and Maxwell RSC miRNA Plasma and Serum Kit, including a DNase treatment.
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA with Ribo-Zero Plus.

tag: patient group

value: wAMD

value: Blood

tag: Sex

value: female

tag: bmi

tag: smoking habit

value: no

tag: age at_sampling


title: control patient, male, sampling age 71, ID=C812

value: male


title: 26wk_Metaphyseal Shell_Loaded Limb _24h _Animal24hO4

source_name: Metaphyseal Shell

value: Metaphyseal Shell


title: 26wk_Mid-Diaphysis_Contralateral Control Limb _1h _Animal1h06

value: R

value: Contralateral Control Limb _1h


title: Sec-Cre_ApcNull_Organoid_Rep2

city: Boston

first: Ramesh

middle: A.

last: Shivdasani

state: MA

address: 450 Brookline Ave. SM1060

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Processed with the Viper Pipeline using the default parameters using STAR.
Additional analysis was performed on the STAR counts using DEseq2 (version 1.22.2).
Assembly: mm10
Supplementary files format and content: *.tab: Tab-delimited text files with STAR counts.

molecule: polyA RNA

source_name: Small intestine

extract_protocol:
Epithelium was isolated from the duodenum of adult mice using a 5mM EDTA chelation for 30 minutes at 4°C followed by disaggregation with 4x TrypLE Select for 30 minutes at 37°C for the Lgr5_ApcKO samples while the others were incubated in Type 2 collagenase at 3mg/mL in HBSS for 30 minutes at 37°C. For the primary cells, ISCs were isolated using flow cytometry while the whole organoids were collected for RNA. The RNA was isolated using Trizol extraction followed by column purification using RNeasy Plus micro kit (Qiagen).
Libraries were prepared using the NEBnext Ultra II non-directional library kit (New England Biolabs E7770S).

treatment_protocol: Treated with 2x 1mg tamoxifen followed by plating ileal crypts 10dpi in organoid culture.

value: Small intestine

value: Whole organoid

value: 2x 1mg tamoxifen

tag: time point

value: 10 dpi


title: wAMD patient, female, sampling age 90, ID=A811


title: Hmga1a OE, sortChIC with H3K4me3 antibody


title: control, sortChIC with H3K9me3 antibody

value: control


title: 26wk_Cancellous_Loaded Limb _24h _Animal24hO4

source_name: Cancellous

value: Cancellous

value: L

value: Adult

value: Loaded _24h


title: control, sortChIC with H3K4me3 antibody

value: adult heart

value: cardiomyocytes

value: 14 days post tamoxifen


title: wAMD patient, male, sampling age 71, ID=A810

value: wAMD

value: Blood

value: random


title: 26wk_Metaphyseal Shell_Contralateral Control Limb _1h _Animal1h06

value: Metaphyseal Shell

value: R


title: 26wk_Mid-Diaphysis_Loaded Limb _1h _Animal1h06

value: Mid-Diaphysis

value: Loaded _1h


title: 26wk_Cancellous_Contralateral Control Limb _1h _Animal1h06

value: Contralateral Control Limb _1h


title: 26wk_Mid-Diaphysis_Contralateral Control Limb _1h _Animal1h03


title: wAMD patient, female, sampling age 67, ID=A808

value: female

value: no


title: 26wk_Mid-Diaphysis_Loaded Limb _1h _Animal1h03


title: LYCT2

city: Zhoushan

first: Yang

last: Yang

state: China

address: No. 10,  Tiyu Road

country: China

institute: Zhejiang province marine fisheries research institute

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10× Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells.
Assembly: L_crocea_2.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

organism: Larimichthys crocea

source_name: adult regressed testis

extract_protocol:
Freshed  testicular tissues were washed with 1× PBS twice. The blood and tunica albuginea of testes were removed on ice under microscopic examination. The testes were cut into small pieces via scissor, then incubated in L-15 medium solution (Gibco Invitrogen) containing 0.25% trypsin, 5% fetal bovine serum, 20mg/ml collagenase H and 0.05% DNase I at 25℃ for 3 hours with gentle agitation. The digestions were stopped by adding 10% FBS. The cell suspensions were filtered with strainers with mesh size 150 μm and 50 μm. The cells were pelleted by centrifugation at 200 X g for 5 min, and resuspended in 1× PBS. The cell number were measured using a blood counting chamber with Trypan Blue dying.
Testicular cells were diluted following manufacture recommendations, mixed with 33.4 μl master mixed buffer, and were loaded into a 10× chromium controller using Chromium single cell 3’ library & single cell 3’ v3 solution. Each sequencing library was prepared following the manufacturer’s instructions. The resulting libraries were then sequenced on an IIIumina hiseq 2500 instrument.

value: adult regressed testis

tag: cell line

value: testicular cells


title: control patient, female, sampling age 61, ID=C805

value: control


title: control patient, female, sampling age 93, ID=C802


title: 26wk_Metaphyseal Shell_Loaded Limb _1h _Animal1h06

tag: sample number

value: L

value: Adult


title: 26wk_Cancellous_Loaded Limb _1h _Animal1h06

tag: tissue

value: Cancellous


title: LYCT3

description: 10x Genomics

source_name: juvenile testis

value: juvenile testis


title: 26wk_Cancellous_Loaded Limb _1h _Animal1h03

tag: loaded


title: control patient, male, sampling age 83, ID=C807

value: male

value: active


title: wAMD patient, male, sampling age 66, ID=A801

value: wAMD

value: Blood


title: 26wk_Cancellous_Contralateral Control Limb _1h _Animal1h03

value: R

tag: animal number


title: LYCT1

description: 10x Genomics

source_name: adult differentiating testis

value: adult differentiating testis


title: Y56A3A.28,RW12344,youngadult,Exp1,Input1

city: Seattle

first: Louis

last: Gevirtzman

state: WA

address: 3720 15th Ave NE

department: Genome Science

institute: University of Washington

description: TF

data_processing:
alignment with BWA Version: 0.7.17-r1188
peak calling with SPP Version 1.15.5
Irreproducible Discovery Rate (IDR) Version 2.0.4.2
Signal tracks using macs2 version 2.2.4 for read pileup
Assembly: ce11
Supplementary files format and content: bigWig, narrowPeak, html

organism: Caenorhabditis elegans

extract_protocol:
For the modENCODE and modERN project, worm growth and ChIP were conducted as previously described in Zhong et al. 2010 (PMID: 20174564); Niu et al. 2011 (PMID: 21177963); Kasper et al. 2014(PMID: 25373775); and Kudron et al., 2018(PMID: 29284660) with the following modifications. Embryonic stages were collected after bleaching and arresting in M9 at 20°C with shaking until the desired embryonic stage was visualized by DIC microscopy. Larval and the young adult stages were synchronized by bleaching and L1 starvation and then arrested L1s were plated on peptone-enriched plates seeded with OP50 bacteria and grown for 6 hrs at 20°C for L1 collection, or grown to the desired stage based on visual examination of their development (Brenner 1974 (PMID: 4366476). GFP fluorescent and DIC images were collected immediately before collection. Worm samples were then cross-linked with 2% formaldehyde for 28 min at room temperature and quenched with 1M Tris pH 7.5. The pelleted worms were rinsed with M9 buffer twice and then with 150 mM NaCl FA buffer (50mM HEPES/KOH pH7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150mM NaCl) with one Roche Complete tablet (Catalog number 11697498001) before the pellet was flash frozen in liquid nitrogen and stored at -80°C. Worm pellets resuspended in 150 mM FA Buffer containing one Roche Complete tablet, 25 ul 1M DTT and 125 ul of 100 mM PMSF per 25 mL chilled FA were sonicated using a microtip to achieve mostly 200–800 bp DNA fragments. For a subset of factors (OP662, OP565, OP579, OP638, OP553, OP550, OP658, OP696, OP552, OP563, OP688, OP685, OP707, OR3349, and XIL99), an additional dounce step was added prior to sonication as described in Kudron MM et al., 2018 (PMID: 29284660).    Worm lysate was measured by Bradford assay and extract corresponding to 2.2 or 4.4 mg was resuspended in 150 mM FA Buffer with Complete protease inhibitors along with 20µl 20% N-lauroylsarcosine sodium salt and spun for 5 minutes at 13,000 g at 4℃ in a non-stick Eppendorf tube. Samples were transferred to a fresh tube and 10% of the lysate was removed as input. Input samples were stored at -20℃ until the following day. ChIP samples were immunoprecipitated using 7.5 μg anti-GFP antibodies (gifts of Tony Hyman and Kevin White) overnight at 4℃ with rotation.    The following day, input samples were thawed and 2μl of 10 mg/mL RNase A was added and samples were digested at room temperature for 2 hours. Then input samples were brought up to 300 μl using Elution Buffer (1% SDS in TE pH 8.0 with 250 mM NaCl), and 4 μl of 10 mg/mL Proteinase K (Roche 03115887001) was added and they were incubated at 55℃ for 4 hours.   In the meantime, the ChIP samples were incubated with protein G sepharose beads for 2 hours at 4℃ with rocking (GE Healthcare Cat. # 17-0618-01). Beads were first washed 4 times in 150 mM FA buffer. All subsequent spins were at 2500 x g for 2 minutes each. The beads were then washed 2 times with room temperature 150 mM FA buffer for 5 minutes and then 1 time with 1M NaCl FA (50mM HEPES/KOH pH7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1M NaCl) for 5 minutes. Samples were then transferred to new tubes and washed one time with 500 mM NaCl FA (50mM HEPES/KOH pH7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 500mM NaCl) for 10 minutes, 1 time with TEL buffer (0.25M LiCl, 1% NP40, 1% sodium deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH8.0) for 10 minutes and then 2 times with TE pH 8.0 for 5 minutes. To elute the immunocomplexes, the beads were incubated two times for 15 minutes each with 150 μl Elution Buffer with gentle vortexing every 5 minutes. The two elutions were pooled after spinning down and 1 ul of 20 mg/mL Proteinase K was added to each ChIP sample. Both the eluted ChIP samples and the input samples were incubated overnight at 65℃ to reverse crosslinks. All samples were purified using either a minElute PCR Purification Kit from Qiagen (Catalog number 28006) or in later stages of the modERN project a ChIP DNA Clean and concentrator kit from Zymo (ZD5205).
Library preparation during the modENCODE and early stages of the modERN project were performed as previously described in Zhong et al. 2010 (PMID: 20174564); Niu et al. 2011 (PMID: 21177963); Kasper et al. 2014(PMID: 25373775); and Kudron et al., 2018(PMID: 29284660). More recently, chromatin has been prepared for sequencing using the following methods at the Yale Center for Genome Analysis (Kudron et al., 2024 Supplemental_File_S1). ChIP and input control samples (genomic DNA from the same sample) for two technical replicates for worm and three for fly were used for library construction using approximately 5-10ng of DNA after the samples were end-repaired, A-tailed, adapter ligated and PCR enriched (8 -10 cycles) (KAPA Biosystems, Part#KK8504).  Indexed libraries were quantified by qPCR (KAPA Biosystems, Part#KK4854) and inserts were distributed by size using the Caliper LabChip GX system.  Samples that had a concentration of ≥0.5 ng/ul were used for sequencing.  Samples were normalized to 10 nM and sequenced using 100bp paired-end sequencing on an Illumina HiSeq NovaSeq Sequencer achieving > 5 million reads passing filter clusters.  A positive control provided by Illumina is spiked into every lane at a concentration of 0.3% to monitor quality in real time. Sequencing data that passed internal quality controls at YCGA were transferred to the Waterston Lab for downstream processing.

tag: strain

tag: genetic modification

value: CRISPR

tag: developmental stage

value: youngadult

tag: chip antibody


title: 26wk_Metaphyseal Shell_Contralateral Control Limb _1h _Animal1h03

value: Metaphyseal Shell

tag: timepoint

tag: age

tag: genotype

tag: treatment

value: Contralateral Control Limb _1h


title: 26wk_Cancellous_Contralateral Control Limb _3h _Animal3h04

value: Contralateral Control Limb _3h


title: Y56A3A.28,RW12344,youngadult,Exp1,ChIP2

description: TF


title: control patient, male, sampling age 69, ID=C800

tag: patient group

tag: Sex

tag: bmi


title: wAMD patient, male, sampling age 90, ID=A799

tag: smoking habit

value: no

tag: age at_sampling


title: 26wk_Metaphyseal Shell_Loaded Limb _1h _Animal1h03

tag: sample number

value: Loaded _1h


title: 26wk_Mid-Diaphysis_Contralateral Control Limb _3h _Animal3h04

tag: tissue

value: Mid-Diaphysis


title: Y56A3A.28,RW12344,youngadult,Exp1,ChIP1

description: TF


title: 26wk_Metaphyseal Shell_Loaded Limb _3h _Animal3h04

tag: loaded

value: L

value: Adult

value: Loaded _3h


title: 26wk_Cancellous_Loaded Limb _3h _Animal3h04

value: Cancellous

tag: animal number


title: unc-4,PHX1658,L4larva,Exp1,Input1

description: TF

tag: strain

value: unc-4(syb1658[unc-4::GFP]) II


title: 26wk_Metaphyseal Shell_Contralateral Control Limb _3h _Animal3h03


title: 26wk_Mid-Diaphysis_Loaded Limb _3h _Animal3h04


title: 26wk_Metaphyseal Shell_Contralateral Control Limb _3h _Animal3h04


title: control patient, female, sampling age 74, ID=C798

value: control

value: female


title: unc-4,PHX1658,L4larva,Exp1,ChIP1

description: TF

tag: genetic modification


title: control patient, female, sampling age 77, ID=C795

value: Blood


title: 26wk_Cancellous_Contralateral Control Limb _3h _Animal3h03

value: R


title: 26wk_Mid-Diaphysis_Contralateral Control Limb _3h _Animal3h03


title: unc-4,PHX1658,L4larva,Exp1,ChIP2

description: TF

value: CRISPR

tag: developmental stage


title: 26wk_Mid-Diaphysis_Loaded Limb _3h _Animal3h03


title: ttx-1,PHX1679,lateembryonic,Exp1,Input1

description: TF

value: lateembryonic

tag: chip antibody


title: 26wk_Metaphyseal Shell_Contralateral Control Limb _1h _Animal1h01

value: Metaphyseal Shell

tag: timepoint


title: ttx-1,PHX1679,lateembryonic,Exp1,ChIP2

description: TF


title: wAMD patient, female, sampling age 62, ID=A794

value: wAMD


title: 26wk_Mid-Diaphysis_Contralateral Control Limb _1h _Animal1h01

tag: age

value: Contralateral Control Limb _1h


title: 26wk_Metaphyseal Shell_Loaded Limb _3h _Animal3h03

tag: genotype


title: 26wk_Metaphyseal Shell_Loaded Limb _1h _Animal1h01

tag: treatment


title: 26wk_Cancellous_Loaded Limb _3h _Animal3h03


title: sta-1,RW12332,L4larva,Exp1,Input1

description: TF

value: st12332(sta-1::TY1::EGFP::3xFLAG] IV.


title: 26wk_Mid-Diaphysis_Contralateral Control Limb _3h _Animal3h02

value: Contralateral Control Limb _3h


title: wAMD patient, female, sampling age 88, ID=A793

tag: patient group

value: no


title: wAMD patient, female, sampling age 91, ID=A792

tag: Sex


title: 26wk_Cancellous_Contralateral Control Limb _1h _Animal1h01


title: 26wk_Metaphyseal Shell_Contralateral Control Limb _3h _Animal3h02


title: 26wk_Mid-Diaphysis_Loaded Limb _1h _Animal1h01

value: Mid-Diaphysis

value: L

value: Loaded _1h


title: ttx-1,PHX1679,lateembryonic,Exp1,ChIP1

description: TF


title: control patient, female, sampling age 77, ID=C791

tag: bmi


title: 26wk_Cancellous_Contralateral Control Limb _3h _Animal3h02

value: Cancellous

value: Adult


title: sta-1,RW12332,L4larva,Exp1,ChIP1

description: TF


title: 26wk_Cancellous_Loaded Limb _1h _Animal1h01


title: control patient, male, sampling age 57, ID=C788

value: control

value: male

tag: smoking habit


title: control patient, female, sampling age 73, ID=C789

value: Blood

value: female

value: active

tag: age at_sampling


title: 26wk_Metaphyseal Shell_Loaded Limb _3h _Animal3h02

tag: sample number

value: Loaded _3h


title: sma-4,CS692,youngadult,Exp1,ChIP2

description: TF

value: syb2546[EGFP::sma-4] III.

value: CRISPR

value: youngadult


title: 26wk_Mid-Diaphysis_Loaded Limb _3h _Animal3h02

tag: tissue


title: sma-4,CS692,youngadult,Exp1,Input1

description: TF


title: wAMD patient, female, sampling age 93, ID=A786

value: wAMD


title: h,h-GFP,embryonic,Exp2,ChIP2

description: TF

data_processing:
alignment with BWA Version: 0.7.17-r1188
peak calling with SPP Version 1.15.5
Irreproducible Discovery Rate (IDR) Version 2.0.4.2
Signal tracks using macs2 version 2.2.4 for read pileup
Assembly: dm6
Supplementary files format and content: bigWig, narrowPeak, html

organism: Drosophila melanogaster

source_name: h-GFP

extract_protocol:
Fly growth was performed as described previously for the modENCODE and modERN projects Kudron et al., 2018(PMID: 29284660). Transgenic flies were expanded in vials and bottles containing standard Drosophila media at ~22℃ and larvae, white pre-pupae(WPP) and adults were collected from these expansion vials. Pupae were obtained by collecting WPP and incubating for 1-2 days at ~22℃. For embryonic collections, 0-8 day old adult flies were moved to embryo cages capped with apple juice plates. After a 24 hour hours, apple juice plates were replaced at appropriate intervals, restricting the collected embryos to their desired developmental stages. For late embryonic stages, collection plates were removed and embryos were grown at room temperature until the desired stage was reached prior to chromatin collection.    Chromatin was collected and ChIP was performed using the goat anti-GFP as described previously Kudron et al., 2018 (PMID: 29284660).  However, later experiments were performed using Ab290 (Abcam) and denoted as such in Kudron et al., 2024;
Library preparation during the modENCODE and early stages of the modERN project were performed as previously described in Zhong et al. 2010 (PMID: 20174564); Niu et al. 2011 (PMID: 21177963); Kasper et al. 2014(PMID: 25373775); and Kudron et al., 2018(PMID: 29284660). More recently, chromatin has been prepared for sequencing using the following methods at the Yale Center for Genome Analysis (Kudron et al., 2024 Supplemental_File_S1). ChIP and input control samples (genomic DNA from the same sample) for two technical replicates for worm and three for fly were used for library construction using approximately 5-10ng of DNA after the samples were end-repaired, A-tailed, adapter ligated and PCR enriched (8 -10 cycles) (KAPA Biosystems, Part#KK8504).  Indexed libraries were quantified by qPCR (KAPA Biosystems, Part#KK4854) and inserts were distributed by size using the Caliper LabChip GX system.  Samples that had a concentration of ≥0.5 ng/ul were used for sequencing.  Samples were normalized to 10 nM and sequenced using 100bp paired-end sequencing on an Illumina HiSeq NovaSeq Sequencer achieving > 5 million reads passing filter clusters.  A positive control provided by Illumina is spiked into every lane at a concentration of 0.3% to monitor quality in real time. Sequencing data that passed internal quality controls at YCGA were transferred to the Waterston Lab for downstream processing.

value: h-GFP

value: e/se

value: embryonic


title: 26wk_Cancellous_Loaded Limb _3h _Animal3h02

tag: loaded

value: L


title: sta-1,RW12332,L4larva,Exp1,ChIP2

description: TF

value: st12332(sta-1::TY1::EGFP::3xFLAG] IV.


title: h,h-GFP,embryonic,Exp2,ChIP3

description: TF


title: 26wk_Metaphyseal Shell_Contralateral Control Limb _3h _Animal3h01

value: Metaphyseal Shell

value: R

tag: animal number

value: Contralateral Control Limb _3h


title: control patient, male, sampling age 87, ID=C790

value: control

value: male

value: no


title: sma-3,CS152,youngadult,Exp1,Input1

description: TF

tag: strain

value: bombardment


title: h,h-GFP,embryonic,Exp2,ChIP1

description: TF


title: 26wk_Mid-Diaphysis_Contralateral Control Limb _3h _Animal3h01

value: Mid-Diaphysis

value: Adult


title: sma-4,CS692,youngadult,Exp1,ChIP1

description: TF

value: syb2546[EGFP::sma-4] III.

tag: genetic modification

value: CRISPR


title: sma-3,CS152,youngadult,Exp1,ChIP2

description: TF

tag: developmental stage

value: youngadult


title: control patient, female, sampling age 87, ID=C787

value: Blood

value: female


title: 26wk_Mid-Diaphysis_Loaded Limb _3h _Animal3h01

value: Loaded _3h


title: 26wk_Cancellous_Contralateral Control Limb _3h _Animal3h01

value: Cancellous


title: control patient, male, sampling age 71, ID=C784

value: active


title: control patient, female, sampling age 70, ID=C785

value: random


title: h,h-GFP,embryonic,Exp2,Input1

description: TF

value: h-GFP

value: e/se

value: embryonic

tag: chip antibody


title: Lgr5DTR-GFP_WT_Ileal_InVivo_ISC_Rep1

treatment_protocol: Treated with 2x 1mg tamoxifen and primary ISCs were isolated 21 dpi.

value: Small intestine

tag: cell type

value: Ileal intestinal stem cell

value: 2x 1mg tamoxifen

tag: time point

value: 21 dpi


title: 19069R-01-06_HTseq

city: Detroit

first: Kezhong

last: Zhang

state: MI

address: 540 E Canfield street

department: CMMG

institute: Wayne State University

description: Read 1 fastq file was lost

data_processing:
RNA-seq using an Illumina HiSeq 4000 was performed by Admera Health (South Plainfield, NJ). The criteria for a regulated gene were a Log2(fold change) greater than 1.0 (either direction) and a significant adj p value (<0.05) versus WT. Gene ontology (GO) and pathway enrichment analyses of differentially regulated genes were performed using the bioinformatic platform of Enrichr (https://maayanlab.cloud/Enrichr/) and SRplot (https://www.bioinformatics.com.cn/en). Cluster function was used for comparisons between groups. The regulated GO terms or pathway enrichments were ranked by p values and gene number counts. A volcano plot was generated using R software to summarize both fold-change and measures of statistical significance. A k-mean cluster heatmap was generated using iDEP.96 (http://bioinformatics.sdstate.edu/idep96) to reveal which genes are more closely related in terms of their gene expression profile under the regulation of CREBH.
Assembly: CREBH gene knock out mice and Wild type mice are uses for RNA-seq
Supplementary files format and content: Tab-delimited text files include raw counts for each sample

source_name: Liver

extract_protocol:
For transcriptomics analyses total RNA was isolated from the liver tissues of CREBH-KO and WT control mice after 14-h overnight fasting. Three independent samples per group were analyzed. Paired-end, 40-million reads were obtained from the same sequencing lane. Total RNA was extracted from cells using TRIzol reagent (Life Technologies, Bleiswijk, The Netherlands) and subsequently purified using the RNeasy Micro kit (Qiagen, Venlo, The Netherlands). RNA integrity was verified with RNA 6000 Nano chips on an Agilent 2100 bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands). RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).
RNA-seq using an Illumina HiSeq 4000 was performed by Admera Health (South Plainfield, NJ).

value: Liver

tag: genotype

value: Fasting


title: sma-3,CS152,youngadult,Exp1,ChIP1

description: TF

value: bombardment


title: 26wk_Cancellous_Loaded Limb _3h _Animal3h01

value: L

tag: timepoint

tag: age

value: Adult

tag: treatment


title: control patient, male, sampling age 67, ID=C783

tag: patient group

value: control

value: Blood

tag: Sex

value: male

tag: bmi


title: control patient, female, sampling age 85, ID=C782

value: female

tag: smoking habit

value: no

tag: age at_sampling


title: nhr-40,RW12341,L4larva,Exp1,ChIP2

description: TF

value: CRISPR


title: nhr-40,RW12341,L4larva,Exp1,Input1

description: TF


title: 19069R-01-05_HTseq

description: Read 1 fastq file was lost

tag: tissue


title: nhr-40,RW12341,L4larva,Exp1,ChIP1

description: TF


title: 19069R-01-04_HTseq


title: 10wk_Cancellous_Contralateral Control Limb _1h_Animal1hYD

tag: sample number

value: Cancellous

tag: loaded

value: R

tag: animal number

value: Young

value: Contralateral Control Limb _1h


title: 26wk_Metaphyseal Shell_Loaded Limb _3h _Animal3h01

value: Metaphyseal Shell

value: Loaded _3h


title: wAMD patient, female, sampling age 79, ID=A778

value: wAMD


title: wAMD patient, female, sampling age 85, ID=A779


title: 19069R-01-03_HTseq

value: Liver

value: WT

value: Fasting


title: 10wk_Cancellous_Loaded Limb _1h_Animal1hYE

value: L

value: Loaded _1h


title: wAMD patient, male, sampling age 76, ID=A777

value: Blood

value: random


title: control patient, female, sampling age 84, ID=C776

value: control

value: female


title: 19069R-01-02_HTseq


title: 10wk_Cancellous_Contralateral Control Limb _5d2_Animal5d2E

value: Contralateral Control Limb _5d2


title: 10wk_Cancellous_Contralateral Control Limb _1h_Animal1hYE

value: Cancellous


title: control patient, female, sampling age 79, ID=C775

value: no


title: madf-1,RW12345,youngadult,Exp1,Input1

description: TF

tag: strain

value: st12345[madf-1::TY1::EGFP::3xFLAG] IV.

tag: genetic modification

value: CRISPR

tag: developmental stage

value: youngadult


title: wAMD patient, female, sampling age 79, ID=A781


title: control patient, female, sampling age 72, ID=C774


title: nfyc-1,RW12333,youngadult,Exp1,ChIP1

description: TF

value: st12333(nfyc-1::TY1::EGFP::3xFLAG] II

tag: chip antibody


title: 19069R-01-01_HTseq

tag: genotype


title: 10wk_Cancellous_Loaded Limb _1h_Animal1hYD

tag: timepoint

value: Young


title: madf-1,RW12345,youngadult,Exp1,ChIP1

description: TF


title: nfyc-1,RW12333,youngadult,Exp1,Input1

description: TF


title: 10wk_Cancellous_Loaded Limb _5d2_Animal5d2E

tag: age

value: Loaded _5d2


title: madf-1,RW12345,youngadult,Exp1,ChIP2

description: TF


title: egl-38,OP171,L4larva,Exp1,Input1

description: TF

value: bombardment


title: 10wk_Cancellous_Contralateral Control Limb _5d2_Animal5d2D

value: R

tag: treatment


title: wAMD patient, male, sampling age 82, ID=A780

tag: patient group

value: wAMD

value: male


title: nfyc-1,RW12333,youngadult,Exp1,ChIP2

description: TF


title: 10wk_Cancellous_Loaded Limb _5d2_Animal5d2D

value: L


title: wAMD patient, female, sampling age 75, ID=A771

value: Blood

tag: Sex


title: 10wk_Cancellous_Contralateral Control Limb _1h_Animal1hYC

value: Contralateral Control Limb _1h


title: control patient, male, sampling age 65, ID=C772

value: control

tag: bmi

value: active


title: control patient, female, sampling age 88, ID=C769

value: female

tag: smoking habit


title: 10wk_Cancellous_Loaded Limb _1h_Animal1hYC

value: Cancellous

value: Loaded _1h


title: egl-38,OP171,L4larva,Exp1,ChIP1

description: TF


title: wAMD patient, male, sampling age 70, ID=A770

value: random

tag: age at_sampling


title: 10wk_Cancellous_Contralateral Control Limb _1h_Animal1hYB

tag: tissue


title: wAMD patient, male, sampling age 86, ID=A767


title: 10wk_Cancellous_Loaded Limb _1h_Animal1hYB

tag: sample number


title: crh-1,RW12338,youngadult,Exp1,ChIP2

description: TF

value: CRISPR

value: youngadult


title: pie-1,RW12313,earlyembryonic,Exp1,Input1

description: RNA binding

value: pie-1(ne4301[pie-1::gfp]) III

value: earlyembryonic


title: Control (p2)

city: Shreveport

first: Stephan

middle: N.

last: Witt

state: Louisiana

address: 1501 Kings Highway

department: Biochemistry & Molecular Biology

institute: LSUHSC

data_processing:
STAR-featureCounts
Assembly: UCSC hg38
Supplementary files format and content: Counts/ FPKM/ TPM

source_name: Cell line

growth_protocol: SK-MEL-28 parental cells and SK-MEL-28 SNCA-KO  clones were propagated in DMEM supplemented with 10% fetal bovine serum (FBS) and 1%  penicillin–streptomycin.

extract_protocol:
After harvesting SK-MEL-28 (controls and KOs) cells, the total RNA was  extracted using the E.Z.N.A column-based total RNA kit (Omega BioTek, catalog number  R6834-01) following the manufacturer’s protocol.
KAPA mRNA Hyperprep Kit (KK8581). Dual Index.

value: Cell line

tag: cell line

tag: cell type

value: WT


title: 26wk_Mid-Diaphysis_Loaded Limb_5d2_Animal5dAA

value: Mid-Diaphysis

tag: loaded

tag: animal number

value: Adult


title: pie-1,RW12313,earlyembryonic,Exp1,ChIP2

description: RNA binding

tag: strain

tag: genetic modification

tag: developmental stage


title: egl-38,OP171,L4larva,Exp1,ChIP2

description: TF

tag: genotype

value: bombardment

tag: chip antibody


title: wAMD patient, male, sampling age 58, ID=A768

value: wAMD

value: Blood

value: male

value: no


title: 10wk_Cancellous_Contralateral Control Limb _1h_Animal1hYA

value: R

tag: timepoint

tag: age

value: Young

tag: treatment

value: Contralateral Control Limb _1h


title: crh-1,RW12338,youngadult,Exp1,Input1

description: TF


title: control patient, female, sampling age 83, ID=C773

tag: patient group

value: control

tag: Sex

value: female

tag: bmi


title: Control (p3)

tag: tissue


title: pie-1,RW12313,earlyembryonic,Exp1,ChIP1

description: RNA binding

value: CRISPR


title: 10wk_Cancellous_Loaded Limb _1h_Animal1hYA

tag: sample number

value: Cancellous

value: L

value: Loaded _1h


title: wAMD patient, male, sampling age 78, ID=A764

tag: smoking habit

value: random

tag: age at_sampling


title: 26wk_Metaphyseal Shell_Contralateral Control Limb _24h _Animal24hO3

value: Metaphyseal Shell

tag: loaded

value: Contralateral Control Limb _24h


title: wAMD patient, male, sampling age 91, ID=A765


title: 26wk_Mid-Diaphysis_Contralateral Control Limb _24h _Animal24hO3

value: Mid-Diaphysis

tag: animal number

value: Adult


title: Crispr-Control (p1)

value: Cell line

tag: cell line

tag: cell type

value: Control


title: 26wk_Mid-Diaphysis_Loaded Limb _24h _Animal24hO3

value: Loaded _24h


title: wAMD patient, female, sampling age 75, ID=A761

value: wAMD

value: Blood

value: no


title: 26wk_Metaphyseal Shell_Loaded Limb _24h _Animal24hO3


title: wAMD patient, female, sampling age 86, ID=A762


title: wAMD patient, female, sampling age 88, ID=A763


title: 26wk_Mid-Diaphysis_Contralateral Control Limb_5d2_Animal5dAA

value: R

value: Contralateral Control Limb_5d2


title: crh-1,RW12338,youngadult,Exp1,ChIP1

description: TF

tag: strain

tag: genetic modification

value: CRISPR

tag: developmental stage

value: youngadult


title: wAMD patient, female, sampling age 89, ID=A759

value: female


title: 26wk_Mid-Diaphysis_Contralateral Control Limb _24h _Animal24hO2

tag: timepoint

tag: genotype


title: Crispr 9 (p1)

value: SNCA-KO

tag: treatment


title: wAMD patient, female, sampling age 80, ID=A766

tag: patient group

value: active


title: 26wk_Cancellous_Contralateral Control Limb _24h _Animal24hO3

value: Cancellous

tag: age


title: wAMD patient, female, sampling age 84, ID=A758

tag: Sex

tag: bmi


title: 26wk_Cancellous_Loaded Limb _24h _Animal24hO3

tag: sample number

tag: tissue

value: L


title: wAMD patient, male, sampling age 78, ID=A757

value: male

tag: smoking habit

value: random

tag: age at_sampling


title: 26wk_Metaphyseal Shell_Contralateral Control Limb _24h _Animal24hO2

value: Metaphyseal Shell

tag: loaded

tag: animal number

value: Adult

value: Contralateral Control Limb _24h


title: wAMD patient, female, sampling age 83, ID=A760

value: wAMD


title: Crispr 9 (p3)

value: Cell line

tag: cell line

tag: cell type


title: Crispr 8 (p3)


title: Crispr 6 (p1)


title: Crispr 6 (p3)


title: wAMD patient, female, sampling age 92, ID=A754

value: Blood

value: no


title: 26wk_Cancellous_Contralateral Control Limb _24h _Animal24hO2

value: R


title: wAMD patient, female, sampling age 96, ID=A755


title: Control (p1)

value: WT


title: Crispr 6 (p2)


title: 26wk_Mid-Diaphysis_Loaded Limb _24h _Animal24hO2

value: Mid-Diaphysis

value: Loaded _24h


title: Crispr 9 (p2)

value: SNCA-KO


title: Crispr 8 (p2)


title: Crispr 8 (p1)


title: 26wk_Cancellous_Loaded Limb _24h _Animal24hO2


title: Crispr 3 (passage number 1)


title: wAMD patient, female, sampling age 77, ID=A749

value: female


title: wAMD patient, female, sampling age 66, ID=A753


title: 26wk_Cancellous_Contralateral Control Limb _3h _Animal3hO

value: Cancellous

value: Contralateral Control Limb _3h


title: Crispr 3 (p2)


title: CHEM064.WT.T13C.WNK463

city: Toronto

first: Jason

last: Moffat

state: Ontario

address: 686 Bay Street

department: Genetics and Genome Biology

country: Canada

institute: Hospital for Sick Children

description:
sgRNA amplified from gDNA
CHEM_7894

data_processing:
Reads from each sample were mapped to the TKOv3 reference library using Bowtie (v0.12.8) allowing up to two mismatches and one exact alignment (specific parameters: -v2, -m1, -p4 -sam-nohead).
Successfully aligned reads were counted and combined into a matrix with guide annotations.
Read counts were normalized to 10 million reads per sample and log fold-changes (LFC) of each gRNA between each timepoint and T0 were determined. Guides with fewer than 30 or greater than 10,000 absolute read counts at T0 were removed.
To identify genetic interactions, the qGI algorithm was used to score the differential effects between HAP1 parental (Arreger et. al.) and gene knockout screens, while the Bioconductor package limma was used to examine drug-treated versus DMSO effects. Interactor genes with FDR (or minimum FDR across replication screens) > 0.2 were plotted with GraphPad (PRISM software).
Assembly: hg38
Supplementary files format and content: tab-delimited read count matrix
Library strategy: CRISPR screen

growth_protocol: HAP1 cells (Horizon Discovery, male human) were maintained in IMDM (Wisent) supplemented with 10% FBS (Gibco) and as needed supplemented with 1% penicillin–streptomycin (PS) (Gibco). HAP1 cells were maintained at 37°C with 5% CO2 and passaged regularly and were dissociated with 0.25% trypsin-EDTA (Gibco) for passaging. HAP1 cells were regularly monitored for mycoplasma contamination using the e-Myco PLUS Mycoplasma PCR Detection kit (iNtRON Bio).

extract_protocol:
gRNA abundance was measured at T0 and endpoints of each screen by next-generation sequencing (NGS). Genomic DNA was extracted from cell pellets using the Wizard Genomic DNA Purification kit (Promega).
Sequencing libraries were prepared from 50 µg gDNA (200-fold library coverage of haploid genome) via a 2-step nested PCR using primers that include Illumina TruSeq adapters with i5 and i7 indices. Barcoded libraries were gel purified using PureLink Quick Gel Extraction kit (Thermo Fisher Scientific) and sequenced on an Illumina HiSeq2500 or NovaSeq6000 using single-read sequencing and standard primers for dual-indexing with HiSeq SBS Kit v4 or NovaSeq v1.5 reagents. T0 samples were sequenced at read depths of 500-fold library coverage, while all other samples were sequenced at 200-fold. Amplicons were sequenced using a custom sequencing recipe comprising DC: 21 cycles; R1: 36 cycles; Index read 1: 8 cycles; Index read 2: 8 cycles.

treatment_protocol: The Toronto knockout (TKOv3) genome-scale CRISPR library (Addgene #90294) was used to perform pooled CRISPR knockout screens in HAP1 parental and knockout cell lines to identify genetic interactions. For each screen, a total of 9E7 cells were transduced with TKOv3 lentivirus at an MOI of 0.3 and > 200-fold library coverage. 24 hours after infection, transduced cells were selected with a medium containing 1 μg/ml puromycin for 48 hours. Cells were then harvested, pooled, and split into three replicates of at least 1.5 x 107 cells maintaining 200-fold library coverage. Approximately 3 – 5 x 107 cells were also collected for gRNA extraction and determination of library representation at day 0 (T0 reference). Cells were passaged every 3-4 days at > 200-fold library coverage until 15 population doublings were reached. Cell pellets for gRNA extraction were collected at every cell passage for each replicate. For WNK463 drug-treated screens, replicates were separated into drug or vehicle (DMSO, <0.1% v/v) treatment screening arms at passage T4. Both WNK463-treated and DMSO control replicates were passaged at > 200-fold coverage on the same day until drug dosing at IC50 reached three rounds. Cell pellets for treated and control replicates were also collected at each passage.

value: chronic myelogenous leukemia

value: wild-type

value: Genome-wide CRISPR screen with TKOv3


title: 26wk_Metaphyseal Shell_Loaded Limb _24h _Animal24hO2

value: Metaphyseal Shell

value: L

value: Adult


title: CHEM064.WT.T13A.WNK463

description:
sgRNA amplified from gDNA
CHEM_7892


title: 26wk_Mid-Diaphysis_Contralateral Control Limb _3h _Animal3hO


title: 26wk_Metaphyseal Shell_Contralateral Control Limb _3h _Animal3hO


title: wAMD patient, female, sampling age 77, ID=A748

value: wAMD


title: 26wk_Mid-Diaphysis_Loaded Limb _3h _Animal3hO

value: Loaded _3h


title: CHEM064.WT.T13B.WNK463

description:
sgRNA amplified from gDNA
CHEM_7893

value: Blood


title: wAMD patient, female, sampling age 93, ID=A747

value: no


title: Crispr 3 (p3)

value: Cell line


title: wAMD patient, female, sampling age 62, ID=A744

value: random


title: CHEM064.WT.T13C.DMSO

description:
sgRNA amplified from gDNA
CHEM_7891


title: 26wk_Metaphyseal Shell_Loaded Limb _3h _Animal3hO


title: CHEM064.WT.T13B.DMSO

description:
sgRNA amplified from gDNA
CHEM_7890


title: 26wk_Mid-Diaphysis_Contralateral Control Limb _24h _Animal24hO1

value: Mid-Diaphysis

value: R

value: Contralateral Control Limb _24h


title: wAMD patient, female, sampling age 91, ID=A743

value: female


title: 26wk_Cancellous_Loaded Limb _3h _Animal3hO

value: Cancellous


title: wAMD patient, female, sampling age 73, ID=A752


title: 26wk_Metaphyseal Shell_Contralateral Control Limb _24h _Animal24hO1


title: wAMD patient, female, sampling age 70, ID=A742


title: CHEM064.WT.T0

description:
sgRNA amplified from gDNA
CHEM_8097

value: chronic myelogenous leukemia


title: wAMD patient, female, sampling age 81, ID=A746


title: 26wk_Cancellous_Contralateral Control Limb _24h _Animal24hO1


title: wAMD patient, female, sampling age 85, ID=A741


title: GIN441.WNK2/WNK3-T14C

description:
sgRNA amplified from gDNA
GIN_7189

value: WNK2_WNK3 dual mutant


title: 26wk_Mid-Diaphysis_Loaded Limb _24h _Animal24hO1

value: Loaded _24h


title: wAMD patient, female, sampling age 63, ID=A738


title: 26wk_Metaphyseal Shell_Loaded Limb _24h _Animal24hO1

value: Metaphyseal Shell


title: 26wk_Cancellous_Loaded Limb _24h _Animal24hO1

value: L


title: wAMD patient, male, sampling age 73, ID=A739

value: male

value: active


title: wAMD patient, male, sampling age 81, ID=A737

value: wAMD


title: GIN441.WNK2/WNK3-T0

description:
sgRNA amplified from gDNA
GIN_7141

value: Blood

value: Genome-wide CRISPR screen with TKOv3


title: GIN441.WNK2/WNK3-T14B

description:
sgRNA amplified from gDNA
GIN_7188


title: GIN441.WNK2/WNK3-T14A

description:
sgRNA amplified from gDNA
GIN_7187


title: wAMD patient, female, sampling age 72, ID=A745

value: no


title: 26wk_Metaphyseal Shell_Contralateral Control Limb _1h _Animal1hO

value: Adult

value: Contralateral Control Limb _1h


title: 26wk_Mid-Diaphysis_Contralateral Control Limb _1h _Animal1hO

value: Mid-Diaphysis

value: R


title: GIN440.TSC22D1/TSC22D2.T20C

description:
sgRNA amplified from gDNA
GIN_7195

value: TSC22D1_TSC22D2 dual mutant


title: wAMD patient, male, sampling age 71, ID=A735

value: random


title: GIN440.TSC22D1/TSC22D2.T2B

description:
sgRNA amplified from gDNA
GIN_7194

value: chronic myelogenous leukemia


title: CHEM064.WT.T13A.DMSO

description:
sgRNA amplified from gDNA
CHEM_7889

value: wild-type


title: 26wk_Mid-Diaphysis_Loaded Limb _1h _Animal1hO

value: Loaded _1h


title: GIN440.TSC22D1/TSC22D2.T20A

description:
sgRNA amplified from gDNA
GIN_7193


title: wAMD patient, female, sampling age 73, ID=A733

value: female


title: 26wk_Metaphyseal Shell_Loaded Limb _1h _Animal1hO

value: Metaphyseal Shell

value: L


title: GIN440.TSC22D1/TSC22D2.T0

description:
sgRNA amplified from gDNA
GIN_7051


title: wAMD patient, male, sampling age 76, ID=A731

value: male


title: GIN435.WNK2/WNK3-T15C

description:
sgRNA amplified from gDNA
GIN_6461

value: WNK2_WNK3 dual mutant


title: 10wk_Cancellous_Contralateral Control Limb _5d2_Animal5d2C

value: Cancellous

value: Young

value: Contralateral Control Limb _5d2


title: 26wk_Cancellous_Loaded Limb _1h _Animal1hO

value: Adult


title: wAMD patient, male, sampling age 80, ID=A730

value: wAMD

value: Blood


title: wAMD patient, female, sampling age 89, ID=A736

value: no


title: GIN435.WNK2/WNK3-T15B

description:
sgRNA amplified from gDNA
GIN_6460

value: Genome-wide CRISPR screen with TKOv3


title: wAMD patient, female, sampling age 89, ID=A728


title: 10wk_Cancellous_Contralateral Control Limb _5d2_Animal5d2B

value: R


title: 10wk_Cancellous_Loaded Limb _5d2_Animal5d2C

value: Loaded _5d2


title: GIN435.WNK2/WNK3-T15A

description:
sgRNA amplified from gDNA
GIN_6459

value: chronic myelogenous leukemia


title: GIN435.WNK2/WNK3-T0

description:
sgRNA amplified from gDNA
GIN_6438


title: wAMD patient, female, sampling age 84, ID=A727


title: GIN434.TSC22D1/TSC22D2.T22C

description:
sgRNA amplified from gDNA
GIN_6473

value: TSC22D2 mutant


title: 10wk_Cancellous_Loaded Limb _5d2_Animal5d2B


title: 26wk_Cancellous_Contralateral Control Limb _1h _Animal1hO

value: Contralateral Control Limb _1h


title: wAMD patient, female, sampling age 84, ID=A726

value: female


title: wAMD patient, male, sampling age 74, ID=A725


title: GIN434.TSC22D1/TSC22D2.T22B

description:
sgRNA amplified from gDNA
GIN_6472


title: wAMD patient, female, sampling age 86, ID=A734


title: 10wk_Cancellous_Loaded Limb _5d2 _Animal5d2A

value: L


title: wAMD patient, female, sampling age 77, ID=A724

value: random


title: wAMD patient, male, sampling age 72, ID=A723

value: male


title: GIN434.TSC22D1/TSC22D2.T0

description:
sgRNA amplified from gDNA
GIN_6439


title: 10wk_Cancellous_Contralateral Control Limb _5d2_Animal5d2A

value: Cancellous


title: 10wk_Cancellous_Contralateral Control Limb _24h _Animal24hYD

value: Young

value: Contralateral Control Limb _24h


title: GIN434.TSC22D1/TSC22D2.T22A

description:
sgRNA amplified from gDNA
GIN_6471


title: 10wk_Cancellous_Loaded Limb _24h _Animal24hYD

value: Loaded _24h


title: GIN428.TSC22D1.T13C

description:
sgRNA amplified from gDNA
GIN_6353

value: TSC22D1 mutant


title: wAMD patient, female, sampling age 68, ID=A722

value: wAMD

value: Blood


title: GIN428.TSC22D1.T13B

description:
sgRNA amplified from gDNA
GIN_6352

value: Genome-wide CRISPR screen with TKOv3


title: 10wk_Cancellous_Contralateral Control Limb _3h _Animal3hYD

value: R

value: Contralateral Control Limb _3h


title: GIN428.TSC22D1.T13A

description:
sgRNA amplified from gDNA
GIN_6351

value: chronic myelogenous leukemia


title: wAMD patient, female, sampling age 69, ID=A729

value: no


title: GIN428.TSC22D1.T0

description:
sgRNA amplified from gDNA
GIN_6341


title: wAMD patient, female, sampling age 70, ID=A721


title: 10wk_Cancellous_Contralateral Control Limb _3h _Animal3hYC


title: 10wk_Cancellous_Loaded Limb _3h _Animal3hYD

value: Loaded _3h


title: 10wk_Cancellous_Loaded Limb _3h _Animal3hYC


title: 10wk_Cancellous_Loaded Limb _24h _Animal24hYC


title: scBSseq_H9_P6_B3

city: Hangzhou

first: Shou-Wen

last: Wang

address: No. 18 Shilongshan Road, Xihu District

institute: Westlake University

data_processing:
BS-seq libraries were aligned to the bisulfite-converted hg38 human genome using Bismark (v.0.24.0) in a paired-end, non-directional mode. Then the unmapped reads were aligned again in a single-end, non-directional mode. We used the coverage2cytosine script from Bismark with the –nom-seq option to generate CpG report files containing only A–C–G and T–C–G positions and GpC report files containing only G–C–A, G–C–C, and G–C–T positions. The DNA methylation rate (CpG rate) at a given CpG site was determined by the ratio between the number of methylated CpG reads over unmethylated CpG reads. The accessibility rate or GpC rate was computed similarly.
Assembly: hg38
Supplementary files format and content: Methylation calling tsv.gz files which include the methylation level of covered cytosines, only including CpG contexts

extract_protocol:
Individual cells were directly sorted into 96-well plates containing Buffer RLT Plus (Qiagen, 1053393) and incubated for 5 minutes at 4°C. EZ-96 DNA Methylation-Direct MagPrep Kit (ZYMO, D5045) was then used to process DNA bisulfite conversion.
Bisulfite-converted DNA was amplified with random primer and klenow exo– polymerase (Qiagen, P7010-HC-L) for 5 rounds and excess primer was removed by AMPure XP beads (Beckman, A63881). After second strand synthesis, the library was amplified by KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602) for 14 cycles.

tag: clone id


title: scBSseq_H9_P6_B4


title: GIN425.WNK2.T15C

description:
sgRNA amplified from gDNA
GIN_6314

value: WNK2 mutant


title: scBSseq_H9_P6_A5


title: 10wk_Cancellous_Contralateral Control Limb _24h _Animal24hYC


title: scBSseq_H9_P6_B2


title: GIN426.WNK3.T13B

description:
sgRNA amplified from gDNA
GIN_6326

value: WNK3 mutant


title: scBSseq_H9_P6_B1


title: GIN426.WNK3.T13A

description:
sgRNA amplified from gDNA
GIN_6325


title: scBSseq_H9_P6_A3


title: 10wk_Cancellous_Contralateral Control Limb _3h _Animal3hYB


title: GIN426.WNK3.T0

description:
sgRNA amplified from gDNA
GIN_6315


title: 10wk_Cancellous_Contralateral Control Limb _24h _Animal24hYB


title: GIN425.WNK2.T15A

description:
sgRNA amplified from gDNA
GIN_6312


title: 10wk_Cancellous_Loaded Limb _24h _Animal24hYB

value: L


title: scBSseq_H9_P6_A4


title: scBSseq_H9_P6_A2


title: 10wk_Cancellous_Loaded Limb _3h _Animal3hYB


title: GIN425.WNK2.T15B

description:
sgRNA amplified from gDNA
GIN_6313


title: GIN426.WNK3.T13C

description:
sgRNA amplified from gDNA
GIN_6327


title: scBSseq_H9_P6_B6


title: GIN350-TSC22D2.T15C

description:
sgRNA amplified from gDNA
Moffat_2158

value: TSC22D2 mutant


title: GIN425.WNK2.T0

description:
sgRNA amplified from gDNA
GIN_6302


title: 10wk_Cancellous_Contralateral Control Limb _24h _Animal24hYA

value: Cancellous


title: 10wk_Cancellous_Loaded Limb _24h _Animal24hYA

value: Young


title: GIN350.TSC22D2.T15B

description:
sgRNA amplified from gDNA
Moffat_2157


title: scBSseq_H9_P6_A1


title: 10wk_Cancellous_Contralateral Control Limb _3h _Animal3hYA


title: 10wk_Cancellous_Loaded Limb _3h _Animal3hYA


title: scBSseq_H9_P4_D5


title: scBSseq_H9_P4_D4


title: PHF6KO_ERHOXB8_RNA-Seq_Rep3

city: Philadelphia

first: Vikram

middle: R

last: Paralkar

state: PA

address: 421 Curie Boulevard

department: Division of Hematology and Oncology, Department of Medicine

institute: University of Pennsylvania Perelman School of Medicine

description: clonally expanded and sequence verified

data_processing:
Sequence reads were trimmed for low quality/adapter sequence using Trimmomatic.
Trimmed reads were mapped to mm10 genome using STAR.
Read quantification and feature annotation were performed using featureCounts.
Differential expression analysis was performed using DESeq2.
Assembly: mm10
Supplementary files format and content: text file includes mapped reads to genomic features for all samples

source_name: Hematopoietic

growth_protocol: Cells were transduced with lentiviral vector expressing Cas9 and Phf6 gRNAs. Resultant pools was sorted and selected for individual knockout and wildtype clones. Cells were grown in complete media (RPMI1640 + FBS + 2% SCF + 20uM beta-estradiol) and used for RNA extraction.

extract_protocol:
1 million cells from each clone were used for total RNA extraction using RNeasy mini kit (Qiagen 74106) following the manufacturer recommended protocol. RNA concentration was determined by using Agilent 2200 TapeStation and a high sensitivity RNA Screentape (Agilent 5067-5579). Samples with RIN greater than 8 were used to construct RNA-Seq libraries.
RNA libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB E7530L) using the manufacturer recomended protocol. Concentration and the size of the libraries were detremined using Agilent 2200 Tapestation and KAPA library quantification kit (Roche KK4824). Libraries from all samples were pooled in equimolar concentrations and denatured for paired-end sequencing. Pooled libraries were quantified using KAPA library quantification kit (Roche KK4824).

value: Hematopoietic

value: artificial myeloid progenitor cell line

value: Phf6 knockout


title: GIN350.TSC22D2.T15A

description:
sgRNA amplified from gDNA
Moffat_2156


title: GIN350.TSC22D2.T0

description:
sgRNA amplified from gDNA
Moffat_2155


title: scBSseq_H9_P4_D3


title: GIN349.NRBP1.T15C

description:
sgRNA amplified from gDNA
Moffat_2150

value: NRBP1 mutant


title: GIN349.NRBP1.T15B

description:
sgRNA amplified from gDNA
Moffat_2149

value: Blood


title: PHF6KO_ERHOXB8_RNA-Seq_Rep2

description: clonally expanded and sequence verified


title: GIN349.NRBP1.T15A

description:
sgRNA amplified from gDNA
Moffat_2148

value: Genome-wide CRISPR screen with TKOv3


title: scBSseq_H9_P4_D1


title: GIN349.NRBP1.T0

description:
sgRNA amplified from gDNA
Moffat_2147


title: scBSseq_H9_P4_C6


title: WT_ERHOXB8_RNA-Seq_Rep3

description: clonally expanded and sequence verified

value: Wildtype


title: WT_ERHOXB8_RNA-Seq_Rep4

description: clonally expanded and sequence verified


title: scBSseq_H9_P4_C5


title: WT_ERHOXB8_RNA-Seq_Rep2

description: clonally expanded and sequence verified


title: GIN335.WNK1.T16C

description:
sgRNA amplified from gDNA
Moffat_2058

value: WNK1 mutant


title: scBSseq_H9_P4_D6


title: GIN335.WNK1.T16B

description:
sgRNA amplified from gDNA
Moffat_2057

value: chronic myelogenous leukemia


title: WT_ERHOXB8_RNA-Seq_Rep1

description: clonally expanded and sequence verified


title: GIN335.WNK1.T16A

description:
sgRNA amplified from gDNA
Moffat_2056


title: scBSseq_H9_P4_C4


title: scBSseq_H9_P4_C2


title: Hoxb8 MS5, Cdkn2a-WT MYB-WT, V5 Rep2

first: Christopher

last: Booth

address: 450 Brookline Ave

data_processing:
Cut&Run reads were aligned using Bowtie2 and the following parameters: --very-sensitive-local --soft-clipped-unmapped-tlen --no-unal --no-mixed --no-discordant --dovetail --phred33 -I 10 -X 700
Coverage tracks were generated using Bedtools genomecov -bg on paired-end DNA fragments, then UCSC-tools bedGraphToBigWig
For MYB and V5, peak files were generated using MACS2 and the following parameters: -q 0.01 --keep-dup all
For H3K27ac, peak files were generated using MACS2 and the following parameters: -q 0.01 --keep-dup all --broad
Assembly: mm10
Supplementary files format and content: Coverage tracks: bigWig
Supplementary files format and content: Peak files: narrowPeak or broadPeak
Library strategy: Cut&Run

growth_protocol: Hoxb8 MS5 cells were co-cultured with MS5 stroma in RPMI-1640 + 10% FBS + 1% Pen/Strep + 50 ng/ml mFLT3L.

extract_protocol:
Cut&Run performed as described: Skene et al. Nat Protoc 2018
NEBNext Ultra II DNA Library Prep

treatment_protocol: Hoxb8 leukemia cells were obtained from recipient mouse spleens by FACS

value: Hoxb8-FL co-cultured with MS5

value: Cdkn2a-WT MYB-WT


title: Hoxb8 MS5, Cdkn2a-WT MYB-WT, V5 Rep1


title: PHF6KO_ERHOXB8_RNA-Seq_Rep1

description: clonally expanded and sequence verified


title: GIN307.TSC22D2.T18B

description:
sgRNA amplified from gDNA
Moffat_1993


title: Hoxb8 MS5, Cdkn2a-WT MYB-WT, IgG


title: scBSseq_H9_P4_B6


title: Hoxb8 MS5, Cdkn2a-WT MYB-WT, H3K27ac


title: GIN335.WNK1.T0

description:
sgRNA amplified from gDNA
Moffat_2055


title: scBSseq_H9_P4_C1


title: GIN307.TSC22D2.T18C

description:
sgRNA amplified from gDNA
Moffat_1994


title: scBSseq_H9_P4_D2


title: scBSseq_H9_P4_B5


title: scBSseq_H9_P4_B4


title: GIN307.TSC22D2.T0

description:
sgRNA amplified from gDNA
Moffat_1991


title: GIN307.TSC22D2.T18A

description:
sgRNA amplified from gDNA
Moffat_1992


title: Hoxb8 MS5, Cdkn2a-WT MYB-TR, V5 Rep1

value: Cdkn2a-WT MYB-TR


title: GIN149.WNK1.T18C

description:
sgRNA amplified from gDNA
Moffat_1237

value: WNK4 mutant


title: scBSseq_H9_P4_B3


title: scBSseq_H9_P4_C3


title: scBSseq_H9_P4_B2


title: GIN149.WNK1.T18B

description:
sgRNA amplified from gDNA
Moffat_1236

value: WNK3 mutant


title: Hoxb8 MS5, Cdkn2a-WT MYB-TR, H3K27ac


title: GIN149.WNK1.T18A

description:
sgRNA amplified from gDNA
Moffat_1235

value: WNK2 mutant


title: scBSseq_H9_P4_B1


title: scBSseq_H9_P4_A6


title: Hoxb8 MS5, Cdkn2a-WT MYB-TR, IgG


title: Hoxb8 MS5, Cdkn2a-WT MYB-PLEKHO1, V5 Rep1

value: Cdkn2a-WT MYB-PLEKHO1


title: GIN149.WNK1.T0

description:
sgRNA amplified from gDNA
Moffat_1234


title: scBSseq_H9_P4_A5


title: Hoxb8 MS5, Cdkn2a-WT MYB-TR, V5 Rep2


title: Hoxb8 MS5, Cdkn2a-WT MYB-PLEKHO1, IgG


title: scBSseq_H9_P4_A2


title: scBSseq_H9_P4_A3


title: Hoxb8 MS5, Cdkn2a-WT MYB-PLEKHO1, H3K27ac


title: scBSseq_H9_P4_A4


title: Kcnd3 F227del KI/KI, female, bio rep 3

city: Taipei

first: Ting-Fen

last: Tasi

address: No. 155, Sec. 2, Li-Nong Street, Peitou

department: Department of Life Sciences and Institute of Genome Sciences

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
CLC Genomics Workbench v21.0.5
Assembly: Mus musculus(GRCm38, mm10)_sequence
Supplementary files format and content: tab-delimited text file includes raw count for each sample

source_name: microdissection laser capture to isolate cerebellar tissues enriched with Purkinje cells

extract_protocol:
Total RNA was extracted from the microdissected tissues using the RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (Cat. # AM1975, Invitrogen), following the provided protocol.
Library was constructed using Illumina TruSeq Stranded mRNA Sample Prep Kit

value: Kcnd3 F227del KI/KI

value: Female


title: Kcnd3 F227del KI/KI, female, bio rep 1

value: microdissection laser capture to isolate cerebellar tissues enriched with Purkinje cells


title: Hoxb8 MS5, Cdkn2a-KO MYB-WT, V5 Rep2

value: Hematopoietic

value: Cdkn2a-KO MYB-WT


title: Kcnd3 F227del KI/+, female, bio rep 2

value: Kcnd3 F227del KI/+


title: Hoxb8 MS5, Cdkn2a-WT MYB-PLEKHO1, V5 Rep2


title: scBSseq_H9_P4_A1


title: Kcnd3 F227del KI/+, female, bio rep 3


title: Hoxb8 MS5, Cdkn2a-KO MYB-WT, V5 Rep1


title: Kcnd3 F227del KI/+, female, bio rep 1


title: Kcnd3 F227del KI/KI, female, bio rep 2


title: scBSseq_H9_20231107_D5


title: Hoxb8 MS5, Cdkn2a-KO MYB-WT, V5 IgG


title: Wildtype, female, bio rep 3


title: scBSseq_H9_20231107_D4


title: Hoxb8 MS5, Cdkn2a-KO MYB-TR, V5 Rep1

value: Cdkn2a-KO MYB-TR


title: scBSseq_H9_20231107_D6


title: Wildtype, female, bio rep 2

value: Wildtype


title: scBSseq_H9_20231107_D3


title: Wildtype, female, bio rep 1


title: scBSseq_H9_20231107_D2


title: Hoxb8 MS5, Cdkn2a-KO MYB-TR, IgG


title: Hoxb8 MS5, Cdkn2a-KO MYB-TR, V5 Rep2


title: scBSseq_H9_20231107_D1


title: Hoxb8 MS5, Cdkn2a-KO MYB-TR, H3K27ac


title: Hoxb8 MS5, Cdkn2a-KO MYB-PLEKHO1, V5 Rep2

value: Cdkn2a-KO MYB-PLEKHO1


title: FDS002_Azoxystrobin_T8h_rep-A

city: Piracicaba

first: Paulo

last: Teixeira

state: SP

address: Av. Pádua Dias, 11

department: Biology

country: Brazil

institute: University of São Paulo (ESALQ/USP)

data_processing:
Illumina bcl2fastq v.1.8.4 was used for basecalling
Quality assessment of the sequencing reads was performed using FastQC
Trimmomatic was used to identify and discard reads containing Illumina adapter sequences
Quality-filtered reads were mapped to the M. perniciosa genome using HISAT2
The featureCounts function from the subread package was used to count reads that mapped to protein-coding genes
Assembly: Moniliophthora perniciosa CP02
Supplementary files format and content: tab-delimited text file including read counts per gene for each sample
Supplementary files format and content: tab-delimited text file including normalized gene expression values (TPM) for each sample
Processed data file Gene IDs are publicly available here: lge.ibi.unicamp.br/atlas

organism: Moniliophthora perniciosa

source_name: Mycelium

growth_protocol: The M. perniciosa isolates FA553 and its derivatives FDS01 (FA553-derived sector 01; insensitive to azoxystrobin) and FDS02 (FA553-derived sector 02; parental phenotype) were used in this study. Fungal cultures were regularly maintained in Malt Yeast Extract Agar (MYEA) plates (17 g/L malt extract, 5 g/L yeast extract and 20 g/L agar) in an incubator at 28oC. Liquid cultures in Malt light medium (2 g/L malt extract, 5 g/L yeast extract and 50 mL/L glycerol) were maintained in Erlenmeyer flasks under 150 rpm agitation at 28oC.

extract_protocol:
RNA isolation was performed using the RNeasy Plant Kit (Qiagen) following the manufacturer’s instructions. RNA integrity and concentration were evaluated using the Lab Chip RNA high sensitivity assay (Caliper).
A total of 90 RNA-seq libraries (30 for each isolate) were prepared from 1 µg of total RNA per sample, according to the TruSeq mRNA Stranded Sample Prep Kit protocol (Illumina). The Sciclone G3 Automated Liquid Handling Workstation (PerkinElmer) was used to prepare all libraries simultaneously. Quality control and final library concentrations were assessed using the DNA 1K Lab Chip high sensitivity assay (Caliper).

treatment_protocol: Three biological replicates of each M. perniciosa isolate (FA553 and its derivatives FDS01 and FDS02) were cultivated separately in MYEA medium for 28 days. Fungal mycelia were then transferred to liquid cultures and incubated at 28oC under 150 rpm agitation. After seven days, two grams of wet mycelium were transferred to 20 mL of Malt light liquid medium, either without fungicide (control condition) or supplemented with 50 mg/L azoxystrobin (treated condition). Samples were harvested for RNA extraction at five time points: 0 minutes (i.e., immediately after fungal inoculation into the culture media), 30 minutes, 2 hours, 4 hours, and 8 hours.

value: Mycelium

tag: time

value: Azoxystrobin

tag: replicate

value: A


title: scBSseq_H9_20231107_C6


title: FDS002_Azoxystrobin_T8h_rep-C

tag: genotype

value: C


title: FDS002_Azoxystrobin_T8h_rep-B

tag: treatment

value: B


title: Hoxb8 MS5, Cdkn2a-KO MYB-WT, H3K27ac

value: Hoxb8-FL co-cultured with MS5


title: Hoxb8 MS5, Cdkn2a-KO MYB-PLEKHO1, V5 Rep1


title: FDS002_Mock_T8h_rep-C

value: Mock


title: scBSseq_H9_20231107_C4


title: Hoxb8 MS5, Cdkn2a-KO MYB-PLEKHO1, IgG


title: FDS002_Mock_T8h_rep-B


title: Hoxb8 MS5, Cdkn2a-KO MYB-PLEKHO1, H3K27ac


title: scBSseq_H9_20231107_C3


title: FDS002_Mock_T8h_rep-A


title: scBSseq_H9_20231107_C2


title: FDS002_Azoxystrobin_T4h_rep-B


title: Hoxb8 leukemia, Cdkn2a-KO MYB-PLEKHO1, H3K27ac

value: Hoxb8-FL derived leukemia


title: FDS002_Azoxystrobin_T4h_rep-C


title: scBSseq_H9_20231107_C1


title: scBSseq_H9_20230913_F6_5


title: scBSseq_H9_20230913_F6_9


title: WT_LSK, RNA-seq, rep4

city: Münster

first: Frank

last: Rosenbauer

address: Robert-Koch-Str. 43

department: Institut of Molecular Tumor Biology

country: Germany

institute: University Hospital Münster

data_processing:
Reads were quantified with salmon (options --validateMappings --gcBias --seqBias -l A) against a genome-decoyed (GRCm38) transcriptome (GENCODE vM25). Transcript abundance estimates were then summarized to gene level with tximport and its lengthScaledTPM option. This matrix of gene-level counts corrected for average transcript length bias is provided in the supplement of this submission as "raw_counts.txt.gz".
Assembly: GRCm38
Supplementary files format and content: Matrix of raw counts created by tximport with lengthScaledTPM option based on transcript abundance estimates from salmon

source_name: bone marrow

extract_protocol:
Total RNA was extracted with the Macherey Nagel RNA Plus XS kit.
Either up to 10ng (if available) or all total RNA was used to construct low input RNA-seq libraries for Illumina using the NEBNext Single Cell/Low Input RNA Library Prep followed by paired-end sequencing.

value: bone marrow

value: LSK

value: WT


title: Hoxb8 leukemia, Cdkn2a-KO MYB-PLEKHO1, IgG

value: Hematopoietic


title: FDS002_Azoxystrobin_T4h_rep-A


title: WT_LSK, RNA-seq, rep3


title: FDS002_Mock_T4h_rep-C


title: scBSseq_H9_20230913_F6_2


title: FDS002_Mock_T4h_rep-B


title: scBSseq_H9_20231107_C5


title: WT_LSK, RNA-seq, rep2


title: FDS002_Mock_T4h_rep-A


title: WT_LSK, RNA-seq, rep1


title: FDS002_Azoxystrobin_T2h_rep-C


title: scBSseq_H9_20230913_F6_1


title: Hoxb8 leukemia, Cdkn2a-KO MYB-PLEKHO1, V5


title: FDS002_Azoxystrobin_T2h_rep-B


title: WT_GMP, RNA-seq, rep3

value: GMP


title: FDS002_Azoxystrobin_T2h_rep-A


title: HCT116_SETDB1_KO_H3K14ac_bio-rep1

city: Stuttgart

first: Thyagarajan

last: Thiruvanmiyur Chandrasekaran

address: Allmandring 31

department: Biochemistry

institute: University of Stuttgart

description: HCT116_SETDB1_KO_H3K14ac_bio-rep1_rep2_merge.bigwig

data_processing:
The quality of the raw reads was assessed using FastQC (v0.72) and adaptors were trimmed using Trim Galore! (v0.4.3.1) with default settings
High-quality reads were mapped to latest version of human genome build T2T-CHM13 v2.0 using HISAT2 (v2.1.0) with --no-spliced-alignment set to true
using bamcoverage (v3.2.0.0.0) in 25bp bins and normalized by reads per kilobase per million mapped reads (RPKM)
Bam files were used to call peak using MACS2 (v2.1.1.20160309.6). Two biological ChIP-seq replicates along with Input as a background were used. Statistically significant peaks were called with effective genome size of 3.03 x 10^9 for T2T-CHM13 v2.0 and rest with default settings.
Assembly: T2T-CHM13 v2.0
Supplementary files format and content: bigWig (for all ChIP-seq samples including replicates and merged)and BED file (for H3K9me3)

growth_protocol: McCoy’s 5A, 10% Fetal Bovine Serum, 20 mM L-glutamate and 100 U/ml penicillin/streptomycin and cells were grown at 37°C and 5% CO2

extract_protocol:
Native Chromatin immunoprecipitation was performed for both H3K9me3 and H3K14ac and were performed in biological replicates. Briefly, cells were resuspended in lysis buffer and digested with MNase to yield mononucleosomes. H3K9me3 antibody (Diagenode, C15200146) was incubated with DynabeadsG for 2 h and then with precleared chromatin for overnight at 4°C. In the case of H3K14ac, H3K14ac antibody (Millipore‐Sigma, 07‐353) was incubated with the precleared chromatin overnight and then pulled-down by incubating with DynabeadsG for 2 h. Beads were then washed twice each with low salt buffer (20 mM Tris/HCl pH 8.0, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100, 0.1% SDS) and with high salt buffer (20 mM Tris/HCl pH 8.0, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% SDS) and then followed by two rinses with TEN buffer (20 mM Tris/HCl pH 8.0, 2 mM EDTA, 150 mM NaCl). Chromatin was eluted with ChIP elution buffer (1% SDS, 100 mM NaHCO3), digested with Proteinase K, and purified with ChIP DNA Purification Kit (Active Motif).
NGS libraries were prepared with 15 to 27 ng DNA using the NEBNext® Ultra™ II DNA Library Prep Kit according to the manufacturer’s instructions

treatment_protocol: No Treatment

value: colorectal carcinoma

tag: antibody


title: WT_GMP, RNA-seq, rep2


title: FDS002_Mock_T2h_rep-C


title: WT_GMP, RNA-seq, rep1


title: FDS002_Mock_T2h_rep-B


title: HCT116_WT_H3K14ac_Input


title: URE_LSK, RNA-seq, rep3

value: URE


title: URE_LSK, RNA-seq, rep4


title: FDS002_Mock_T2h_rep-A


title: URE_LSK, RNA-seq, rep2


title: FDS002_Azoxystrobin_T30min_rep-C


title: HCT116_WT_H3K14ac_bio-rep1

description: HCT116_WT_H3K14ac_bio-rep1_rep2_merge.bigwig


title: HCT116_WT_H3K14ac_bio-rep2


title: HCT116_HBO1_KO_H3K9me3_Input


title: scBSseq_H9_20230913_F6_11


title: URE_LSK, RNA-seq, rep1


title: WT_GMP, RNA-seq, rep4


title: HCT116_SETDB1_KO_H3K14ac_Input


title: HCT116_HBO1_KO_H3K9me3_bio-rep2


title: FDS002_Azoxystrobin_T30min_rep-A


title: URE_GMP, RNA-seq, rep3


title: HCT116_SETDB1_F332A_H3K9me3_Input


title: FDS002_Mock_T30min_rep-B


title: FDS002_Azoxystrobin_T30min_rep-B


title: URE_GMP, RNA-seq, rep4


title: HCT116_HBO1_KO_H3K9me3_bio-rep1

description:
HCT116_HBO1_KO_H3K9me3_bio-rep1_rep2_merge.bigwig
HCT116_HBO1_KO_H3K9me3_bio-rep1_rep2_over_Input.bed


title: HCT116_SETDB1_KO_H3K14ac_bio-rep2


title: URE_GMP, RNA-seq, rep2


title: FDS002_Mock_T30min_rep-A


title: URE_GMP, RNA-seq, rep1


title: FDS002_Mock_T30min_rep-C


title: HCT116_SETDB1_F332A_H3K9me3_bio-rep1

description:
HCT116_SETDB1_F332A_H3K9me3_bio-rep1_rep2_merge.bigwig
HCT116_SETDB1_F332A_H3K9me3_bio-rep1_rep2_over_Input.bed


title: HCT116_SETDB1_F332A_H3K9me3_bio-rep2


title: FDS002_Azoxystrobin_T0_rep-C


title: HCT116_SETDB1_WT_H3K9me3_Input


title: FDS002_Mock_T0_rep-C


title: ISC-Cre_ApcNull_InVivo_ISC_Rep3

treatment_protocol: Treated with 2x 1mg tamoxifen and primary ISCs were isolated 14 dpi.

value: Small intestine

value: Duodenum intestinal stem cell

tag: age

value: Adult

value: 2x 1mg tamoxifen

tag: time point

value: 14 dpi


title: HCT116_SETDB1_WT_H3K9me3_bio-rep2


title: ISC-Cre_ApcNull_InVivo_ISC_Rep1


title: ISC-Cre_ApcNull_InVivo_ISC_Rep2


title: HCT116_SETDB1_WT_H3K9me3_bio-rep1

description:
HCT116_SETDB1_WT_H3K9me3_bio-rep1_rep2_merge.bigwig
HCT116_SETDB1_WT_H3K9me3_bio-rep1_rep2_over_Input.bed


title: HCT116_SETDB1_H1224K_H3K9me3_Input


title: FDS002_Mock_T0_rep-B

value: Mycelium


title: FDS002_Mock_T0_rep-A

value: A


title: mouse 14dpi_heart2

description: 14dpi mouse heart 2 tomoseq

data_processing:
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2) with default parameters.
The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike-ins in sense direction. Reads mapping equally to multiple loci were discarded.
Mapped reads were assigned to sections based on barcodes according to the CEL-seq protocol (Hashimshony et al., Cell Reports, 2012)
processed data files contain transcript read counts normalized against spike-in read count and total read count per section
Assembly: GRCm38 for mouse, danrer9 for zebrafish
Supplementary files format and content: csv file containing transcript counts per gene (rows) and section (columns)
Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish

extract_protocol:
Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL-seq protocol (Hashimshony et al., Cell Reports, 2012) see also: Junker et al., 2014, Cell
CEL-seq protocol (Hashimshony et al., Cell Reports, 2012); also  see: Junker et al., 2014, Cell

treatment_protocol: Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned, and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. (2014) Cell.

value: adult heart

tag: transgenic background

tag: section thickness

value: Took 20um section, then skipped 80um, took the next 20um section, etc

tag: section direction

value: from injured area into the remote myocardium

value: permanent LAD ligation

tag: timepoint


title: mouse 14dpi_heart1

description: 14dpi mouse heart 1 tomoseq

tag: tissue


title: HCT116_SETDB1_H1224K_H3K9me3_bio-rep2


title: FDS001_Azoxystrobin_T8h_rep-C

value: Azoxystrobin

value: C


title: HCT116_SETDB1_H1224K_H3K9me3_bio-rep1

description:
HCT116_SETDB1_H1224K_H3K9me3_bio-rep1_rep2_merge.bigwig
HCT116_SETDB1_H1224K_H3K9me3_bio-rep1_rep2_over_Input.bed


title: mouse 7dpi_heart2

description: 7dpi mouse heart 2 tomoseq


title: HCT116_SETDB1_KO_H3K9me3_Input


title: HCT116_SETDB1_KO_H3K9me3_bio-rep2


title: FDS001_Azoxystrobin_T8h_rep-B

value: B


title: FDS001_Azoxystrobin_T8h_rep-A


title: HCT116_WT_H3K9me3_Input


title: BM_GS-KO_ERY-V-VI_rep3

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

data_processing:
Sequencing reads from all RNA-seq experiments were aligned to mm10 reference genome by STAR v. 2.5.2b with the following parameters: --runThreadN 28 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1 --outWigStrand Unstranded  --quantMode TranscriptomeSAM.
Genic read counts were derived using HTSeq with parameter "-s no".
Assembly: mm10
Supplementary files format and content: raw read count

source_name: Retic/RBC

extract_protocol: RNA-seq libraries were prepared using the SMARTer Stranded Total RNA-seq Pico Input kit (Takara)

value: Bone Marrow


title: FDS002_Azoxystrobin_T0_rep-B


title: FDS001_Mock_T8h_rep-B

value: Mock


title: mouse 3dpi_heart1

description: 3dpi mouse heart tomoseq


title: FDS002_Azoxystrobin_T0_rep-A


title: BM_GS-KO_ERY-V-VI_rep2


title: HCT116_WT_H3K9me3_bio-rep2

value: colorectal carcinoma


title: BM_WT_ERY-V-VI_rep3


title: BM_WT_ERY-V-VI_rep2


title: FDS001_Azoxystrobin_T4h_rep-C


title: FDS001_Azoxystrobin_T4h_rep-B


title: scBSseq_293T_P9_B5

description: Clone ID: P9_1

source_name: HEK 293T

value: HEK 293T


title: scBSseq_293T_P9_B6

description: Clone ID: P9_1


title: mouse 7dpi_heart1

description: 7dpi mouse heart 1 tomoseq

source_name: adult heart


title: FDS001_Azoxystrobin_T4h_rep-A


title: BM_WT_ERY-V-VI_rep1


title: FDS001_Mock_T4h_rep-C


title: scBSseq_293T_P9_B3

description: Clone ID: P9_1


title: BM_GS-KO_ERY-III-VI_rep3

source_name: PolyE/OrthoE


title: FDS001_Mock_T4h_rep-B


title: BM_GS-KO_ERY-III-VI_rep2


title: scBSseq_293T_P9_B4

description: Clone ID: P9_1


title: HCT116_SETDB1_KO_H3K9me3_bio-rep1

description:
HCT116_SETDB1_KO_H3K9me3_bio-rep1_rep2_merge.bigwig
HCT116_SETDB1_KO_H3K9me3_bio-rep1_rep2_over_Input.bed


title: FDS001_Mock_T8h_rep-C


title: scBSseq_293T_P9_B2

description: Clone ID: P9_1


title: BM_GS-KO_ERY-III-VI_rep1


title: scBSseq_293T_P9_B1

description: Clone ID: P9_1


title: FDS001_Mock_T4h_rep-A


title: FDS001_Azoxystrobin_T2h_rep-C


title: FDS001_Azoxystrobin_T2h_rep-B


title: scBSseq_293T_P9_A6

description: Clone ID: P9_1


title: BM_WT_ERY-III-VI_rep3


title: FDS001_Mock_T8h_rep-A


title: BM_GS-KO_ERY-V-VI_rep1


title: HCT116_WT_H3K9me3_bio-rep1

description:
HCT116_WT_H3K9me3_bio-rep1_rep2_merge.bigwig
HCT116_WT_H3K9me3_bio-rep1_rep2_over_Input.bed


title: BM_WT_ERY-III-VI_rep2


title: FDS001_Azoxystrobin_T2h_rep-A


title: FDS001_Mock_T2h_rep-C


title: BM_WT_ERY-III-VI_rep1


title: scBSseq_293T_P9_A4

description: Clone ID: P9_1


title: FDS001_Mock_T2h_rep-B


title: BM_GS-KO_ERY-I-II_rep3

source_name: ProE/BasoE


title: scBSseq_293T_P9_A2

description: Clone ID: P9_1


title: scBSseq_293T_P9_A1

description: Clone ID: P9_1


title: BM_GS-KO_ERY-I-II_rep2


title: BM_GS-KO_ERY-I-II_rep1


title: FDS001_Azoxystrobin_T30min_rep-C


title: BM_WT_ERY-I-II_rep3


title: FDS001_Azoxystrobin_T30min_rep-B


title: scBSseq_293T_P8_F6

description: Clone ID: P8_3


title: scBSseq_293T_P8_F5

description: Clone ID: P8_3


title: BM_WT_ERY-I-II_rep1


title: FDS001_Azoxystrobin_T30min_rep-A


title: scBSseq_293T_P9_A5

description: Clone ID: P9_1


title: FDS001_Mock_T30min_rep-C


title: FDS001_Mock_T30min_rep-A


title: scBSseq_293T_P8_F4

description: Clone ID: P8_3


title: BM_WT_ERY-I-II_rep2


title: BM_GS-KO_CFU-E_rep2

source_name: CFU-E


title: scBSseq_293T_P8_F3

description: Clone ID: P8_3


title: FDS001_Mock_T30min_rep-B


title: BM_GS-KO_CFU-E_rep3


title: scBSseq_293T_P8_F2

description: Clone ID: P8_3


title: BM_GS-KO_CFU-E_rep1


title: scBSseq_293T_P9_A3

description: Clone ID: P9_1


title: scBSseq_293T_P8_F1

description: Clone ID: P8_3


title: FDS001_Mock_T2h_rep-A


title: FDS001_Azoxystrobin_T0_rep-C


title: BM_WT_CFU-E_rep3


title: scBSseq_293T_P8_E6

description: Clone ID: P8_3


title: FDS001_Azoxystrobin_T0_rep-B


title: BM_WT_CFU-E_rep2


title: scBSseq_293T_P8_E5

description: Clone ID: P8_3


title: scBSseq_293T_P8_E4

description: Clone ID: P8_3


title: BM_WT_CFU-E_rep1


title: FDS001_Mock_T0_rep-C


title: scBSseq_293T_P8_E3

description: Clone ID: P8_3


title: FDS001_Mock_T0_rep-B


title: scBSseq_293T_P8_E1

description: Clone ID: P8_3


title: FA553_Azoxystrobin_T8h_rep-C


title: scBSseq_293T_P8_E2

description: Clone ID: P8_3


title: BM_GS-KO_BFU-E_rep1

source_name: BFU-E


title: FA553_Azoxystrobin_T8h_rep-B


title: BM_GS-KO_BFU-E_rep2


title: FDS001_Mock_T0_rep-A


title: scBSseq_293T_P8_D4

description: Clone ID: P8_2


title: BM_WT_BFU-E_rep3


title: FA553_Azoxystrobin_T8h_rep-A


title: BM_ERY-VI_rep4

source_name: RBC


title: scBSseq_293T_P8_D6

description: Clone ID: P8_2


title: BM_WT_BFU-E_rep1


title: FA553_Mock_T8h_rep-C


title: BM_ERY-VI_rep3


title: BM_GS-KO_BFU-E_rep3


title: scBSseq_293T_P8_D3

description: Clone ID: P8_2


title: FDS001_Azoxystrobin_T0_rep-A


title: FA553_Mock_T8h_rep-A


title: scBSseq_293T_P8_D1

description: Clone ID: P8_2


title: BM_ERY-VI_rep1


title: FA553_Azoxystrobin_T4h_rep-C


title: scBSseq_293T_P8_C5

description: Clone ID: P8_2


title: BM_ERY-VI_rep2


title: FA553_Azoxystrobin_T4h_rep-B


title: scBSseq_293T_P8_C6

description: Clone ID: P8_2


title: BM_WT_BFU-E_rep2


title: scBSseq_293T_P8_D5

description: Clone ID: P8_2


title: FA553_Azoxystrobin_T4h_rep-A


title: scBSseq_293T_P8_C3

description: Clone ID: P8_2


title: scBSseq_293T_P8_C2

description: Clone ID: P8_2


title: FA553_Mock_T4h_rep-C


title: BM_ERY-V_rep6

source_name: Retic


title: BM_ERY-V_rep7


title: BM_ERY-V_rep5


title: scBSseq_293T_P8_C4

description: Clone ID: P8_2


title: FA553_Mock_T8h_rep-B


title: FA553_Mock_T4h_rep-B


title: BM_ERY-V_rep3


title: scBSseq_293T_P8_C1

description: Clone ID: P8_2


title: BM_ERY-V_rep4


title: FA553_Azoxystrobin_T2h_rep-C


title: BM_ERY-V_rep2


title: scBSseq_293T_P8_B6

description: Clone ID: P8_1


title: FA553_Azoxystrobin_T2h_rep-B


title: scBSseq_293T_P8_B5

description: Clone ID: P8_1


title: BM_ERY-V_rep1


title: BM_ERY-IV_rep4

source_name: OrthoE


title: scBSseq_293T_P8_B3

description: Clone ID: P8_1


title: FA553_Mock_T2h_rep-C


title: BM_ERY-IV_rep3


title: scBSseq_293T_P8_B4

description: Clone ID: P8_1


title: FA553_Mock_T2h_rep-B


title: scBSseq_293T_P8_B2

description: Clone ID: P8_1


title: BM_ERY-IV_rep2


title: scBSseq_293T_P8_B1

description: Clone ID: P8_1


title: BM_ERY-IV_rep1


title: FA553_Azoxystrobin_T30min_rep-C


title: FA553_Mock_T2h_rep-A


title: BM_ERY-III_rep4

source_name: PolyE


title: BM_ERY-III_rep3


title: scBSseq_293T_P8_A5

description: Clone ID: P8_1


title: FA553_Mock_T4h_rep-A


title: FA553_Azoxystrobin_T30min_rep-B


title: scBSseq_293T_P8_A6

description: Clone ID: P8_1


title: scBSseq_293T_P8_A4

description: Clone ID: P8_1


title: scBSseq_293T_P8_A2

description: Clone ID: P8_1


title: FA553_Mock_T30min_rep-C


title: BM_ERY-III_rep2


title: scBSseq_293T_P8_A3

description: Clone ID: P8_1


title: BM_ERY-III_rep1


title: FA553_Mock_T30min_rep-B


title: FA553_Azoxystrobin_T2h_rep-A


title: FA553_Mock_T30min_rep-A


title: BM_ERY-II_rep4

source_name: BasoE


title: FA553_Azoxystrobin_T0_rep-C


title: scBSseq_293T_P10_B6

description: Clone ID: P10_1


title: scBSseq_293T_P8_A1

description: Clone ID: P8_1


title: BM_ERY-II_rep2


title: scBSseq_293T_P10_B4

description: Clone ID: P10_1


title: BM_ERY-II_rep3


title: FA553_Azoxystrobin_T0_rep-B


title: BM_ERY-II_rep1


title: scBSseq_293T_P10_B3

description: Clone ID: P10_1


title: BM_ERY-I_rep7

source_name: ProE


title: FA553_Mock_T0_rep-C


title: FA553_Azoxystrobin_T30min_rep-A


title: scBSseq_293T_P10_B2

description: Clone ID: P10_1


title: BM_ERY-I_rep6


title: BM_ERY-I_rep5


title: scBSseq_293T_P10_B1

description: Clone ID: P10_1


title: FA553_Mock_T0_rep-B


title: BM_ERY-I_rep4


title: scBSseq_293T_P10_A5

description: Clone ID: P10_1


title: BM_ERY-I_rep3


title: FA553_Azoxystrobin_T0_rep-A


title: BM_ERY-I_rep2


title: scBSseq_293T_P10_A4

description: Clone ID: P10_1


title: Embryoid bodies, day16, experiment3, sample1

city: Planegg

first: Ines

last: Hellmann

address: Großhaderner Straße 2

department: Anthropology and Human Genomics, Faculty of Biology

institute: Ludwig-Maximilians-Universität München

description: 10x Genomics

data_processing:
Reads were processed using the 10x CellRanger software (Version 7.0.0)
All samples were aligned to 4 reference genomes: GRCh38 (Homo sapiens), Susie_PABv2/ponAbe3 (Pongo abelii), macFas6 (Macaca fascicularis), rheMac10 (Macaca mulatta)
For non-human primate genomes, custom GTF files were created by transferring the hg38 annotation via the tool Liftoff
Assembly: GRCh38, ponAbe3, macFas6, rheMac10
Supplementary files format and content: Cellranger output: 4 filtered count matrices per sample (one per genome) in HDF5 matrix format

organism:
Macaca fascicularis
Macaca mulatta
Pongo abelii
Homo sapiens

source_name: Embryoid bodies

extract_protocol:
For dissociation, floating EBs (on day8) / attached EBs (on day16) were washed with DPBS and incubated with Accumax (Sigma-Aldrich, SCR006) for 10-20 min at 37°C. Next, EBs were pipetted up and down with a p1000 pipette until they were completely dissociated to single cells and DFK20 medium was added. Cells were pelleted at 300 xg for 5 min and then resuspended in 1 mL DPBS. If remaining cell clumps were observed, the cell suspension was filtered through a 40 µm cell strainer, then cells were counted using a Countess II automated cell counter (Thermo Fisher Scientific, C10228). Equal cell numbers from each cell line were pooled, washed with DPBS + 0.04% BSA and resuspended in an appropriate volume of DPBS + 0.04 % BSA leading to a final concentration of 800 - 1000 cells/µL. The pooled cells were kept on ice and loaded on a 10x Chromium Controller Chip within 15 min.
scRNA-seq libraries were generated using the 10x Genomics Chromium Next GEM Single Cell 3´Kit V3.1 workflow in three replicates. Each time, evenly pooled single cells from the different clones were loaded on 2 to 6 lanes of a 10x chip, with a targeted cell recovery of 16,000 cells per lane.

value: Embryoid bodies


title: Embryoid bodies, day8, experiment3, sample4

description: 10x Genomics


title: Embryoid bodies, day16, experiment3, sample2

description: 10x Genomics


title: BM_ERY-I_rep1


title: BM_CFU-E_rep5


title: Embryoid bodies, day8, experiment3, sample3

description: 10x Genomics


title: scBSseq_293T_P10_A1

description: Clone ID: P10_1


title: Embryoid bodies, day8, experiment3, sample2

description: 10x Genomics


title: scBSseq_293T_P10_A3

description: Clone ID: P10_1


title: Embryoid bodies, day8, experiment3, sample1

description: 10x Genomics


title: Hypertrophic scar, scRNA-seq

city: Shanghai

first: Jia

last: Zhou

state: --- Select One ---

address: 639 Zhizaoju Road, Shanghai

institute: Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

description: 10x Genomics

data_processing:
Gel Beads-in-emulsion (GEMs) are generated by combining Barcoded Single Cell 3ʹ v3 Gel Beads, a Master Mix containing cells, and Partitioning Oil onto Chromium Chip B.
GEM generation: the Gel Bead is dissolved, primers are released, and any co- partitioned cell is lysed. Primer than contains an Illumina TruSeq Read 1 (Read 1 sequencing primer), 16 nt 10x Barcode, 12 nt unique molecular identifier (UMI) and 30 nt poly(dT) sequence are mixed with the cell lysate and a Master Mix containing reverse transcription (RT) reagents. Incubation of the GEMs produces Barcoded, fulllength cDNA from poly-adenylated mRNA.
Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size.
The libraries were sequenced on an NovaSeq platform (Illumia) to generate 150 bp paired-end Reads, according to the manufacturer’s instructions.
Raw data (Raw Reads) of fastq files were assembled from the Raw BCL files using Illumina’s bcl2fastq converter.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Skin (Lower abdomen)

extract_protocol:
The skin tissue were excised and immediately transferred to a 50-ml centrifuge tube and washed with precooled PBS at 4 °C. The tissues were placed in a precooled dish on ice, cut into 2 to 4-mm pieces, and then all transferred to an Eppendorf tube containing an enzyme mix [Collagenase I (1 mg/ml) + Collagenase IV (0.5 mg/ml) + Collagenase V (0.5 mg/ml) (Solarbio) + Collagenase-neutral protease (Roche) + DNase I (Solarbio)]. A gentleMACSTM Octo Dissociates with Heaters was used for 4 h for dissociation and digestion.
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3ʹ Reagent Kits v3 (10x Genomics) , according to the manufacturer’s instructions.

value: Skin (Lower abdomen)

tag: gender

value: female

value: 34 years


title: BM_CFU-E_rep3


title: scBSseq_293T_P10_A6

description: Clone ID: P10_1


title: BM_CFU-E_rep2


title: Keloid, scRNA-seq

description: 10x Genomics

source_name: Skin (Anterior chest)

value: Skin (Anterior chest)


title: Embryoid bodies, day16, experiment2, sample1

description: 10x Genomics


title: FA553_Mock_T0_rep-A

source_name: Mycelium

value: Mycelium

value: A


title: N2

first: yue

last: li

state: None Selected

address: No.639 Zhi Zao Ju Road, 200011, Shanghai, P.R. China

institute: Shanghai Jiaotong University

data_processing:
Off-Line Base Caller software, version 1.8 used for basecalling.
Hisat2 was used to align the sequencing reads of each lacrimal sac tissue sample with reference genome to generate Sequence Alignment/Map (SAM) files
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Ballgown.
STAR software was used to align the sequencing reads of each lacrimal sac tissue sample with reference genome
CircRNA Identifier (CIRI) software was used to scan paired chiastic clipping (PCC) signals in SAM files, and circRNA sequences were predicted based on junction reads and GT-AG splicing signals.
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: lacrimal sac

extract_protocol:
Total RNA was isolated from lacrimal sac samples of chronic dacryocystitis patients and control individuals using Trizol (Invitrogen, Carlsbad, CA, United States) according to the manufacturer's instructions. The quantity and quality of total RNA samples were measured on the Nanodrop 2000 (Thermo Scientific, Wilmington, DE).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease

value: normal control

tag: Sex


title: Embryoid bodies, day16, experiment1, sample2

description: 10x Genomics

tag: cell type


title: BM_CFU-E_rep1


title: BM_BFU-E_rep3


title: N3


title: Embryoid bodies, day16, experiment1, sample1

description: 10x Genomics


title: N1

value: male


title: CD3

value: chronic dacryocystitis


title: I/R-30min+7.5mg/kgNAT5

city: Nanjing

first: Ning

last: Shi

address: No.639 Longmian Road

institute: State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China.

data_processing:
RNA-Seq
Assembly: mm9
Supplementary files format and content: FPKM

source_name: KIdney

growth_protocol: C57BL/6J male mice aged 6-8 weeks were used.

extract_protocol:
Total RNA was extracted and reverse transcription to cDNA. Each cDNA library was sequenced in a single lane of the BGISEQ platform
GCF_000001635.26_GRCm38.p6

treatment_protocol: The renal ischemia-reperfusion injury models were established by bilateral renal pedicle clamping for 30 minutes, followed by reperfusion.GroupL were treated with NAT

value: KIdney


title: I/R-30min+7.5mg/kgNAT4


title: BM_BFU-E_rep1


title: scBSseq_293T_P10_A2

description: Clone ID: P10_1

source_name: HEK 293T

tag: cell line


title: BM_BFU-E_rep2


title: BM_CFU-E_rep4


title: lipid-laden DCs isolated from western-type diet fed mice, rep2

city: Maastricht

first: Han

last: Jin

address: P. Debyelaan 25

institute: Maastricht University

data_processing:
After de-multiplexing and adapter removal, per sample sequence quality was assessed with FastQC
Good quality samples were aligned to the murine genome (mm10) using the Bowtie2/TopHat2 alignment tools
The aligned files were sorted and indexed using SAMtools
Feature counts (gene level) were computed using the htseq tool
Assembly: mm10
Supplementary files format and content: dc_exp_count.tsv (tab-delimited text file includes read count values for each Sample)

source_name: Spleen

extract_protocol:
Total RNA was extracted from the samples using the Direct-zol RNA MiniPrep Plus Kit (Zymo Research), including an in-column DNase I treatment. RNA was quantified with a NanoDrop 8000 UV-Vis Spectrophotometer (Thermo Scientific) and quality was assessed using the Bioanalyzer RNA 6000 Nano Kit (Agilent). Samples of sufficient quantity and quality (minimum RNA integrity number = 6.4) were retained for sequencing.
The NEBNext Poly(A) mRNA Magnetic Isolation Module was then used to select poly-A tailed (including most messenger RNA) molecules from total RNA. The purified mRNA was used to prepare a cDNA library for sequencing using the NEBNext Ultra RNA Library Prep Kit for Illumina. Quality control before and after library preparation was done using the Bioanalyzer HighSens DNA Kit (Agilent) and the molarity was checked using the Kapa qPCR quantification kit. Single-end 80 base pair sequence was generated using an Illumina NextSeq500, with the version 2 chemistry.

value: Spleen

value: Dendritic cells (lipid-laden)

value: LDLR knockout

value: 3w HFD


title: CD2


title: I/R-30min+7.5mg/kgNAT2


title: CD1


title: I/R-30min+7.5mg/kgNAT3


title: I/R-30min+7.5mg/kgNAT1


title: lipid-laden DCs isolated from western-type diet fed mice, rep1


title: lipid-free DCs isolated from western-type diet fed mice, rep2

value: Dendritic cells (lipid free)


title: I/R-30min-5


title: ENZA_day91_rep_2

city: San Francisco

first: Xiaolin

last: Zhu

state: CA

institute: UCSF

data_processing:
RNA-seq data was generated in FASTQ format. We quantified the gene-level expression using kallisto and then used the abundance calls for downstream analysis.
Assembly: hg38
Supplementary files format and content: Length-scaled TPM generated by tximport.

extract_protocol:
RNA extraction was performed using the Zymo Quick-RNA MiniPrep Kit (R1054) and sent to the QB3 Genomics Sequencing Facility at UC Berkeley for library preparation and sequencing.
Sequencing libraries were constructed per Illumina protocol.

value: prostate cancer

value: wildtype

value: enzalutamide


title: ENZA_day91_rep_1


title: lipid-free DCs isolated from western-type diet fed mice, rep1


title: I/R-30min-3


title: I/R-30min-4


title: ENZA_day49_rep_2


title: ENZA_day28_rep2


title: DCs isolated from chow fed mice, rep2

value: Dendritic cells

value: Chow fed


title: ENZA_day49_rep_1


title: ENZA_day28_rep1


title: FOXA M3

city: Houston

first: Jayhun

last: Lee

state: TX

address: 6431 Fannin St. MSE R222

department: Microbiology and Molecular Genetics

institute: The University of Texas Health Science Center at Houston

description: FOXA M3

data_processing:
CLC Genomics Workbench 23 (Qiagen)
Adapter and low quality reads were trimmed using default settings (Quality limit = 0.05)
Quality passed reads were mappped to S. mansoni genome (SM_V10) using default settings (Spike-in controls = No; mismatch cost = 2; Insertion cost = 3; Deletion cost = 3; Length fraction = 0.8)
Assembly: SM_V10 (PRJEA36577 WBPS18)
Supplementary files format and content: Excel file containing differential expression of males and females and total counts, RPKM, TPM, and CPM values for each gene for all samples.

organism: Schistosoma mansoni

source_name: Whole worm

growth_protocol: Adult S. mansoni parasites were cultuered for 2 weeks in ABC media without the red blood cells. ~15 paired worms were cultured in 5-10 mL of media with daily change of media.

extract_protocol:
Total RNA was extracted using TRIzol/chloroform follwed by precipitation/wash using isopropanol/high salt (sodium citrate+sodium chloride) and 75% ethanol.
TruSeq Stranded mRNA Sample Preparation

treatment_protocol: During the two-week culture period, parasites were treated with 15-20 µg/mL of dsRNA against foxA (Smp_331700) at day 1, 2, 3, 6, 9, and 12. Parasites were unpaired using tricane and males and females were collected separately.

value: Whole worm

tag: developmental stage

value: Adult

value: Male

value: foxA knockdown

value: foxA RNAi


title: ENZA_day7_rep_2


title: SHAM5

value: SHAM


title: SHAM4

value: KIdney


title: ENZA_day7_rep_1


title: SHAM3


title: DMSO_day91_rep1

value: DMSO


title: CTRL M1

description: CTRL M1

value: WT

value: control RNAi


title: I/R-30min-2


title: SHAM1


title: FOXA F3

description: FOXA F3

value: Female


title: DMSO_day49_rep1


title: I/R-30min-1


title: CTRL M3

description: CTRL M3


title: FOXA M2

description: FOXA M2


title: FOXA M1

description: FOXA M1


title: DMSO_day49_rep2


title: DCs isolated from chow fed mice, rep1

value: Spleen

value: LDLR knockout


title: DMSO_day28_rep2

value: prostate cancer

value: wildtype


title: SHAM2


title: FOXA F2

description: FOXA F2


title: DMSO_day7_rep2


title: DRG, cKO-3

city: Shenzhen

first: Jun

last: Yu

state: Guangdong

address: Xue Yuan, Nanshan

department: Department of Neuroscience

institute: SUSTech

data_processing:
The raw data was filtered with SOAPnuke (v1.6.5) , afterwards clean reads were obtained and stored in FASTQ format.
The clean data were mapped to the reference genome GRCm38/mm10 by HISAT (v2.2.1)
The clean data were mapped to the assembled unique gene by Bowtie2 (v2.4.5). The expression level of genes was calculated by RSEM (v1.3.1).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Tab-delimited text file include FPKM, TPM, read_count values for each Sample

source_name: DRG

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen,15596026)
Optimal Dual-mode mRNA Library Prep Kit

value: DRG


title: DRG, cKO-2


title: FOXA F1

description: FOXA F1


title: DRG, Ctrl-2


title: CTRL F3

description: CTRL F3


title: CTRL F2

description: CTRL F2


title: DMSO_day7_rep1


title: DMSO_day91_rep2


title: DRG, Ctrl-1


title: CTRL F1

description: CTRL F1


title: CTRL M2

description: CTRL M2


title: DMSO_day28_rep1


title: DRG, Ctrl-3


title: DRG, cKO-1


title: R_DRN_15

status: Public on Nov 14 2024

first: Chun-Xiao

last: Huang

address: 65 Chifeng Road, Yangpu District

department: School of Medcine, Tongji University

data_processing:
Sequencing was carried out using Illumina NovaSeq 6000 with 150 bp paired-end reads. Gene expression level analysis was performed using R (Version 4.3.1) package Seurat (Version 5.0.2), and the mean gene expression matrix of all samples was obtained after processing by NormalizeData function. For marker gene analysis of each subpopulation, FindAllMarkers function in Seurat was used, with parameters set as min.pct=0.1 and logfc.threshold=0.25.
Assembly: danRer11
Supplementary files format and content: Excel file include readcounts values for each Sample.

source_name: brain

growth_protocol: Tg(tph2:GFP) fish at 7 dpf were used.

extract_protocol:
For each sample, 10-12 neurons were collected and transferred to lysis buffer solution. Total RNA was extracted for construction of cDNA libraries, involving fragmentation, PCR enrichment, N7 index linking, and purification.
A total of 71 QuantSeq libraries (N=9-12 samples for each subpopulation) were prepared using the Lexogen’s QuantSeq 3′ mRNA-Seq Library Prep Kit for Illumina according to the manufacturer’s instructions.

treatment_protocol: Tg(tph2:GFP) fish at 7 dpf were fixed in a recording chamber containing extracellular solution. The somata of 5-HT neurons from seven subpopulations (PT, SR-R, SR-M, SR-C, IR-R, IR-C, MO) were visualized under a fluorescence microscopy, then targeted and collected separately using glass electrode.

value: brain

tag: strain

value: 5-HT neurons


title: R_DRN_11


title: R_DRN_12


title: R_DRN_9


title: R_DRN_8


title: R_DRN_6


title: R_DRN_5


title: PT_21


title: R_DRN_4


title: PT_20


title: PT_15


title: PT_4


title: PT_14


title: PT_5


title: PT_3


title: MO_12


title: MO_14


title: MO_11


title: PT_9


title: MO_9


title: MO_8


title: MO_6


title: MO_4


title: MO_5


title: MO_3


title: R_DRN_7


title: MO_1


title: MO_2


title: PT_23


title: M_DRN_17


title: M_DRN_20


title: M_DRN_14


title: M_DRN_19


title: M_DRN_15


title: PT_12


title: M_DRN_10


title: M_DRN_13


title: IN_62_A


title: IN_55_A


title: M_DRN_12


title: IN_56_A


title: IN_49_A


title: IN_44_A


title: IN_43_A


title: IN_34_A


title: IN_32_A


title: IN_33_A


title: IN_35_A


title: IN_7_A


title: IN_42_P


title: IN_41_P


title: IN_40_P


title: IN_37_P


title: IN_12_P


title: IN_11_P


title: day_0

tag: genotype


title: IN_9_P


title: IN_3_P


title: IN_2_P


title: M_DRN_5


title: M_DRN_6


title: C_DRN_12


title: C_DRN_11


title: IN_36_A


title: C_DRN_9


title: C_DRN_7


title: C_DRN_5


title: C_DRN_4


title: embryo, HIRA mislocalized mutant, 5.5-6h, rep2

city: Kunming

first: Liangliang

last: Wang

state: Yunnan

address: South Section, East Outer Ring Road, Chenggong District

institute: Yunnan University

description: 5.5_6h_embryo_HIRA_mislocalized_mutant_RNAseq_replicate_2

data_processing:
Sequence reads were trimmed by trimmomatic (v0.39).
Clean reads were mapped to dm6 using STAR (v2.7.10a).
Read count extraction were performed using RSEM (v1.3.1).
Reads normalization and differentially-expressed gene calling were performed using DESeq2 (v1.40.2).
Assembly: dm6
Supplementary files format and content: tab-delimited text files include gene expression for each Sample.

source_name: embryo

extract_protocol:
Total RNAs were extracted from embryos at specific stages utilizing TRIzol reagent. Each RNA sample (0.5 µg total RNA) underwent rRNA depletion.
Strand-specific libraries were constructed using the VAHTS Universal V8 RNA-seq Library Prep Kit for MGI, following the manufacturer's instructions.

value: embryo

value: HIRA mislocalized mutant


title: embryo, M-Z+ HIRA mutant, 5.5-6h, rep1

description: 5.5-6h_embryo_M-Z+_HIRA_mutant_RNAseq_replicate_1

value: M-Z+ HIRA mutant


title: embryo, HIRA mislocalized mutant, 5.5-6h, rep1

description: 5.5_6h_embryo_HIRA_mislocalized_mutant_RNAseq_replicate_1


title: embryo, wild type for M-Z+ HIRA mutant, 2.5-3h, rep2

description: 2.5-3h_embryo_wild_type_for_M-Z+_HIRA_mutant_RNAseq_replicate_2

value: wild type


title: embryo, wild type for M-Z+ HIRA mutant, 2.5-3h, rep1

description: 2.5-3h_embryo_wild_type_for_M-Z+_HIRA_mutant_RNAseq_replicate_1