title: RNA-seq - Human breast cancer (stageIIIC)

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

description:
mRNA_stageIIIC
TPMMatrix_breastcancer.csv.gz

data_processing:
Gene expression quantification (TPM estimation) was performed by Salmon "quant" with the default option.
The reads of ChIL-seq were mapped against the GRCm38 or GRCh38 reference genome using Bowtie2 with the default option.
Duplicated reads were discarded using samtools (rmdup) and the uniquely mapped reads were used for further analysis.
The bigWig files were generated using deepTools (version 3.4.1) with the command: bamCoverage -p 36 --binSize 100 --normalizeUsing CPM --smoothLength 1000.
Genome_build: GRCm38, GRCh38
Supplementary_files_format_and_content: CSV files include comma-delimited gene expression (TPM) matrices

source_name: Human breast cancer

extract_protocol:
Each cryo-tissue section (10 um) was placed onto u-plate 96 well bottom (Ibidi #89626) and the plate was stored at -80ºC freezer without backing to room temperature until use. Tissue section was fixed with 4%PFA in 0.3% TritonX-100/PBS for five minutes and washed with 0.3% TritonX-100/PBS. Double blocking were performed using blocking one (Nacalai #03953) and M.O.M blocking reagent (Vector Laboratories #BMK-2202) as instructed. The sections were incubated with primary antibody in M.O.M. protein concentrate/PBS at 4ºC overnight, followed by incubating with ChIL probe at same condition but in addition of NaCl at 0.5 M concentration.
ChIL-seq was performed according to ChIL (Harada et al., 2018) with some modifications. Longer incubation time is used for some steps (Extended Tn5 binding 1hr and fill-in step 2hrs),  Thermo T7 RNA polymerase (100 U per well; Toyobo), and 15 cycles of PCR amplification. Column purification (Zymo #D4013) and x0.5 volume of AMpure beads (Beckman Coulter) selection were performed to obtain 200-500 bp average of library.  For RNA-seq, total RNA was extracted from the cryo sections (up to five serial sections) using Direct-Zol kit (Zymo #R2063). The total of 10 ng RNA was used for library preparation using SMART-Seq Stranded Kit (Takara) as instructed.

treatment_protocol: Muscle regeneration studies were performed as previously reported (Ono et al., 2011), except for the injection of cardiotoxin (CTX) into the tibialis anterior (TA) muscle. Injured and intact TA muscles were sampled from five mice at day 0, 3, 5, 7 and 14 from mice after CTX injury. Day 0 mice were by needle injured controls.

value: Breast cancer  (stage IIIC)


title: RNA-seq - Human breast cancer (stageI)

status: Public on Oct 25 2021

type: SRA

country: Japan

description:
mRNA_stageI
TPMMatrix_breastcancer.csv.gz

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

value: Breast cancer  (stage I)


title: MFA_CD723

city: Kunming

first: Tianqing

last: Li

state: Yunnan

address: 727 South Jingming Road, Chenggong District

department: Yunnan Key Laboratory of Primate Biomedical Research & Institute of Primate Translational Medicine

country: China

institute: Kunming University of Science and Technology

data_processing:
The sequencing qualities of 166 scRNA-seq profiles were examined with the FASTQC.
The scRNA-seq data were aligned to Macaca fascicularis genome (macFas5) with HISAT2 (v 2.1.0).
The alignment results of HISAT2 in the SAM format were converted to BAM format and sorted with SAMTools (v 1.1).
Quantified transposable element (TEs) and gene expression of single-cell sequencing data using scTE software.And annoted wtih http://ftp.ensembl.org/pub/release-102/gtf/macaca_fascicularis/Macaca_fascicularis.Macaca_fascicularis_5.0.102.gtf.gz  http://hgdownload.soe.ucsc.edu/goldenPath/macFas5/database/rmsk.txt.gz
Single cell dimensionality reduction and visualization use R package seurat (v4.0.1)
Genome_build: macFas5
Supplementary_files_format_and_content: transposable element (TEs) and gene expression (Counts) of single-cell sequencing data were stored in seurat object cymonkeyshRNAdim15r3dim15TrBEPIPrE.rds.

organism: Macaca fascicularis

source_name: embryo

growth_protocol: Oocytes were collected by laparoscopic follicular aspiration approximately 32–35 h after rhCG administration. Follicular contents were added to HEPES-buffered Tyrode’s albumin lactate pyruvate (TALP) medium containing 0.3% bovine serum albumin (BSA) (Sigma-Aldrich, USA) at 37°C. Oocytes were stripped of cumulus cells by pipetting after a brief exposure (< 1 min) to hyaluronidase (0.5 mg/mL) in TALP-HEPES to visually select nuclear-based mature metaphase II (MII; first polar body present) oocytes. The mature oocytes were immediately subjected to intracytoplasmic sperm injection and then cultured in  Connaught Medical Research Laboratories (CMRL) -1066 media (Thermo Fisher Scientific, USA) containing 10\% fetal bovine serum (FBS, Gibco, USA) at 37°C in 5% CO2. Fertilization was confirmed by the presence of a second polar body and two pronuclei. Zygotes were then cultured in chemically defined hamster embryo culture medium-9 containing 10% FBS at 37°C in 5% CO2 to allow embryo development. The culture medium was replaced every other day until the blastocyst stage.

extract_protocol:
Isolation of single cells. The embryos were washed in PBS for 3 times, washed in 0.25% trypsin (T4799; SigmaAldrich) 2 times, incubated with 0.25% trypsin for around 15 min at 37 °C, and terminated by DFBS. Embryo was dissociated into single cells by repeated pipetting and dispersed in 1% DFBS/PBS. A single cell was pipetted into a PCR tube. All operations above were performed under the Nikon SMZ645 microscopy.
The synthesis and amplification of full-length cDNAs were performed following Smart-seq2 protocol4. Briefly, single cells were washed in DPBS (Gibco 14190-144) and picked into lysis buffer using Pasteur pipettes under a dissecting microscope. Reversetranscription reactions and pre-amplification were performed using SuperScript II (Invitrogen 18064-014) and KAPA HiFi HotStart ReadyMix (KAPA Biosystems KK2601), respectively. The quality of the cDNAs were evaluated by Bioanalyzer 2100. Library construction and sequencing were performed by Annoroad Gene Technology (http://www.annoroad.com/). Pair-end sequencing was performed on Illumina X-ten platform.

tag: day

value: embryo invitro day 7

tag: shRNA

tag: embryotag

tag: celltype

value: TrB


title: RNA-seq - Human breast cancer (stageIIIBl)

description:
mRNA_stageIIIB
TPMMatrix_breastcancer.csv.gz

value: Breast cancer  (stage IIIB)


title: MFA_CD722


title: MFA_CD720

value: EPI


title: MFA_CD719


title: RNA-seq - Human breast cancer (normal)

description:
mRNA_normal
TPMMatrix_breastcancer.csv.gz

value: Normal/Non-neoplastic Breast


title: PSM alpha 3 plus FLIPr time 120 rep 3

type: RNA

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

country: USA

institute: NIH

description:
PSM alpha 3 plus FLIPr time 120 rep 3_PSM alpha 3 from Staphylococcus aureus plus FLIPr
4044_KMR-1_Human_84_51-81-PSM-a3+FLIPr-3-120_01_4107

hyb_protocol: Labeled samples were hybridized to GeneChip® Human HG-U133 plus 2 Arrays.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 7Gplus scanner

data_processing:
The data were analyzed with Expression Console (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console
program-id = 1.3.0.187

label: biotin

source_name: neutrophils_PSM alpha 3 plus FLIPr time 120

label_protocol: RNA amplification and labeling was carried out in accordance with the manufacturer’s protocol (Affymetrix/ThermoFisher, Santa Clara, CA).

growth_protocol: Human neutrophils were isolated from fresh heparinized venous blood using standard dextran sedimentation coupled with Hypaque-Ficoll gradient centrifugation

extract_protocol: Total RNA was purified using a Direct-zol RNA MiniPrep kit according to the manufacturer’s protocol (Zymo Research Corp., Irvine, CA)

treatment_protocol: all samples were incubated to designated time point of 0,30,60 and up to 120min at 37 °C with 5% CO2.

tag: cell type

value: Neutrophils

tag: treatment

tag: time (min)


title: time 120 human PMN control rep 3

description:
time 120 human PMN control rep 3_no treatment, control
4038_KMR-1_Human_78_57-84-PMNcontrol-3-120_01_4097

source_name: neutrophils_time 120 human PMN control

value: no treatment, control


title: LAC time 120 rep 3

description:
LAC time 120 rep 3_Staphylococcus aureus
4032_KMR-1_Human_72_34-76-LAC-3-120_01_2010

source_name: neutrophils_LAC time 120

value: Staphylococcus aureus


title: MFA_CD718


title: LAC time 120 rep 1

description:
LAC time 120 rep 1_Staphylococcus aureus
4030_KMR-1_Human_70_52-58-LAC-1-120_01_1877


title: LAC and FLIPr time 120 rep 1

description:
LAC and FLIPr time 120 rep 1_Staphylococcus aureus and FLIPr- (formyl peptide receptor-like 1 inhibitor)
4033_KMR-1_Human_73_4-59-LAC+FLIPr-1-120_01_9032

source_name: neutrophils_LAC and FLIPr time 120


title: RNA-seq - Human breast cancer (stageIIA)

description:
mRNA_stageIIA
TPMMatrix_breastcancer.csv.gz

value: Breast cancer (stage IIA)


title: LAC and FLIPr time 120 rep 2

description:
LAC and FLIPr time 120 rep 2_Staphylococcus aureus and FLIPr- (formyl peptide receptor-like 1 inhibitor)
4034_KMR-1_Human_74_71-68-LAC+FLIPr-2-120_01_0140


title: LAC time 120 rep 2

description:
LAC time 120 rep 2_Staphylococcus aureus
4031_KMR-1_Human_71_41-67-LAC-2-120_01_1937


description:
knock-out psm, psm-alpha, beta-hld time 120 rep 1_Staphylococcus aureus knock out psm, psm-alpha, and beta hld
4027_KMR-1_Human_67_74-61-Dtriple-1-120_01_1918

source_name: neutrophils_knock-out psm, psm-alpha, beta-hld time 120


title: PSM alpha 3 plus FLIPr time 120 rep 2

description:
PSM alpha 3 plus FLIPr time 120 rep 2_PSM alpha 3 from Staphylococcus aureus plus FLIPr
4043_KMR-1_Human_83_81-72-PSM-a3+FLIPr-2-120_01_4119


title: ChIL-Pol2S5P - Human breast cancer (stageI)

library_source: genomic

molecule: genomic DNA

tag: antibody


title: time 120 human PMN control rep 2

description:
time 120 human PMN control rep 2_no treatment, control
4037_KMR-1_Human_77_49-75-PMNcontrol-2-120_01_4116


title: PSM alpha 3 time 120 rep 3

description:
PSM alpha 3 time 120 rep 3_PSM alpha 3 from Staphylococcus aureus
4041_KMR-1_Human_81_61-80-PSM-a3-3-120_01_4099

source_name: neutrophils_PSM alpha 3 time 120

value: PSM alpha 3 from Staphylococcus aureus


title: LAC and FLIPr time 120 rep 3

description:
LAC and FLIPr time 120 rep 3_Staphylococcus aureus and FLIPr- (formyl peptide receptor-like 1 inhibitor)
4035_KMR-1_Human_75_12-77-LAC+FLIPr-3-120_01_4118


description:
knock-out psm, psm-alpha, beta-hld time 120 rep 2_Staphylococcus aureus knock out psm, psm-alpha, and beta hld
4028_KMR-1_Human_68_64-70-Dtriple-2-120_01_1927


title: delta- toxin time 120 rep 3

description:
delta- toxin time 120 rep 3_delta toxin from Staphylococcus aureus
4023_KMR-1_Human_63_83-82-d-toxin-3-120_01_4122

source_name: neutrophils_delta- toxin time 120

value: delta toxin from Staphylococcus aureus


title: PSM alpha 3 time 120 rep 1

description:
PSM alpha 3 time 120 rep 1_PSM alpha 3 from Staphylococcus aureus
4039_KMR-1_Human_79_59-62-PSM-a3-1-120_01_4125


title: ChIL-Pol2S5P - Human breast cancer (stageIIIC)


title: delta- toxin and FLIPr time 120 rep 3

description:
delta- toxin and FLIPr time 120 rep 3_delta toxin from Staphylococcus aureus and FLIPr- (formyl peptide receptor-like 1 inhibitor)
4026_KMR-1_Human_66_18-83-d-toxin+FLIPr-3-120_01_5761

source_name: neutrophils_delta- toxin and FLIPr time 120


title: PSM alpha 3 time 120 rep 2

description:
PSM alpha 3 time 120 rep 2_PSM alpha 3 from Staphylococcus aureus
4040_KMR-1_Human_80_6-71-PSM-a3-2-120_01_4101


title: MFA_CD716


title: delta- toxin time 120 rep 2

description:
delta- toxin time 120 rep 2_delta toxin from Staphylococcus aureus
4022_KMR-1_Human_62_40-73-d-toxin-2-120_01_4127


title: delta- toxin time 120 rep 1

description:
delta- toxin time 120 rep 1_delta toxin from Staphylococcus aureus
4021_KMR-1_Human_61_65-64-d-toxin-1-120_01_4123


title: ChIL-Pol2S5P - Human breast cancer (stageIIIB)


title: MFA_CD717


title: MFA_CD715


title: MFA_CD714


title: knock-out psm alpha time 120 rep 3

description:
knock-out psm alpha time 120 rep 3_Staphylococcus aureus knock out psm alpha
4020_KMR-1_Human_60_53-78-Dpsm-a-3-120_01_4132

source_name: neutrophils_knock-out psm alpha time 120


title: HUVECs senescent-3

city: Bunkyo-ku

first: Goro

last: Katsuumi

state: Tokyo

address: Hongo 2-1-1

institute: Juntendo University

description: HUVECs senescent-3

data_processing:
libraries were analyzed on a Highseq1500(Illumina).
TopHat 2 (version 2.0.13) was used for mapping reads to the reference genome (Ensembl GRCh38/hg38) with annotation data downloaded from the Ensembl Asia website (URL https://asia.ensembl.org/).
Expression of each transcript was quantified as the number of fragments per kilobase of transcript per million fragments mapped (FPKM), and expression was compared among 3 groups by Cuffdiff (included in Cufflinks version 2.2.1).
Genome_build: Ensembl GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: HUVECs

growth_protocol: Human umbilical vein endothelial cells(HUVECs) were cultured in Endothelial Cell Growth Medium-2(Lonza)

extract_protocol:
Total RNA was extracted from young and senescent HUVECs using RNeasy Plus Micro Kit (Quiagen)
cDNA libraries were generated using a NEBNext Ultra RNA Library Prep Kit (New England BioLabs)

treatment_protocol: We prepared two kinds of HUVECs; one under proliferation as "young", the other that underwent replicative senescence as "senescent",

value: umbilical vein endothelial cells

tag: condition

value: senescent


title: HUVECs senescent-2

description: HUVECs senescent-2


title: delta- toxin and FLIPr time 120 rep 1

description:
delta- toxin and FLIPr time 120 rep 1_delta toxin from Staphylococcus aureus and FLIPr- (formyl peptide receptor-like 1 inhibitor)
4024_KMR-1_Human_64_17-65-d-toxin+FLIPr-1-120_01_4095


title: ChIL-Pol2S5P - Human breast cancer (normal)

source_name: Normal/Non-neoplastic Breast


title: ChIL-Pol2S5P - Human breast cancer (stageIIA)


title: HUVECs senescent-1

description: HUVECs senescent-1


title: MFA_CD707


title: MFA_CD711


title: MFA_CD712


title: MFA_CD713


title: MFA_CD710


title: L1_SETD5_96h

city: Akita

first: Yoshihiro

last: Matsumura

state: Akita

address: Hondo 1-1-1

department: Biochemistry and Metabolic Science

institute: Akita University Graduate School of Medicine

hyb_protocol: Biotinylated cRNA was hybridized  according to the standard Affymetrix protocol.

scan_protocol: Scanned by Affymetrix GeneChip scanner 3000 (Affymetrix).

data_processing: GeneChip Analysis Suite software program version 5.0 was (Affymetrix) was used.

label: Biotin

organism: Mus musculus

source_name: 3T3-L1 cells transduced with SETD5 at 96 hr

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: 3T3-L1 preadipocytes were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum at 37 °C. 3T3-L1 preadipocytes were transduced with control empty virus or SETD5.

extract_protocol: Total RNA was extracted using ISOGEN (Nippongene) following manufacturer's protocol.

treatment_protocol: Two days after reaching confluent (day 0), 3T3-L1 preadipocytes were treated with differentiation medium containing insulin (1 μg/ml), 0.25 μM dexamethasone (DEX), and 0.5 mM isobutylmethylxanthine (MDI mixture) for 48 h followed by treatment with insulin (1 μg/ml) alone with medium replacement every 2 days.

tag: viral

tag: hour of differentiation

value: 96 hr

tag: cell line


title: L1_SETD5_48h

source_name: 3T3-L1 cells transduced with SETD5 at 48 hr

value: 48 hr


title: PSM alpha 3 plus FLIPr time 60 rep 3

description:
PSM alpha 3 plus FLIPr time 60 rep 3_PSM alpha 3 from Staphylococcus aureus plus FLIPr
4017_KMR-1_Human_57_82-54-PSM-a3+FLIPr-3-60_01_8996

source_name: neutrophils_PSM alpha 3 plus FLIPr time 60


title: L1_SETD5_24h

source_name: 3T3-L1 cells transduced with SETD5 at 24 hr

value: 24 hr


title: HUVECs young-3

description: HUVECs young-3

value: young


title: L1_SETD5_36h

source_name: 3T3-L1 cells transduced with SETD5 at 36 hr

value: 36 hr


title: knock-out psm alpha time 120 rep 1

description:
knock-out psm alpha time 120 rep 1_Staphylococcus aureus knock out psm alpha
4018_KMR-1_Human_58_55-60-Dpsm-a-1-120_01_4129


title: knock-out psm alpha time 120 rep 2

description:
knock-out psm alpha time 120 rep 2_Staphylococcus aureus knock out psm alpha
4019_KMR-1_Human_59_62-69-Dpsm-a-2-120_01_4140


title: PSM alpha 3 plus FLIPr time 60 rep 1

description:
PSM alpha 3 plus FLIPr time 60 rep 1_PSM alpha 3 from Staphylococcus aureus plus FLIPr
4015_KMR-1_Human_55_58-36-PSM-a3+FLIPr-1-60_01_4106


title: PSM alpha 3 time 60 rep 3

description:
PSM alpha 3 time 60 rep 3_PSM alpha 3 from Staphylococcus aureus
4014_KMR-1_Human_54_60-53-PSM-a3-3-60_01_4117

source_name: neutrophils_PSM alpha 3 time 60


title: HUVECs young-1

description: HUVECs young-1


title: MFA_CD706

source_name: embryo

value: embryo invitro day 7

value: TrB


title: PSM alpha 3 plus FLIPr time 60 rep 2

description:
PSM alpha 3 plus FLIPr time 60 rep 2_PSM alpha 3 from Staphylococcus aureus plus FLIPr
4016_KMR-1_Human_56_27-45-PSM-a3+FLIPr-2-60_01_4131


title: MFA_CD705


title: L1_SETD5_192h

source_name: 3T3-L1 cells transduced with SETD5 at 192 hr


title: HUVECs young-2

description: HUVECs young-2


title: L1_E_192h

source_name: 3T3-L1 cells transduced with control empty virus at 192 hr

value: Empty


title: L1_SETD5_12h

source_name: 3T3-L1 cells transduced with SETD5 at 12 hr

value: 12 hr


title: L1_E_96h

source_name: 3T3-L1 cells transduced with control empty virus at 96 hr


title: time 60 human PMN control rep 2

description:
time 60 human PMN control rep 2_no treatment, control
4010_KMR-1_Human_50_68-48-PMNcontrol-2-60_01_1943

source_name: neutrophils_time 60 human PMN control

value: Neutrophils


title: PSM alpha 3 time 60 rep 1

description:
PSM alpha 3 time 60 rep 1_PSM alpha 3 from Staphylococcus aureus
4012_KMR-1_Human_52_43-35-PSM-a3-1-60_01_4113


title: L1_SETD5_0h

source_name: 3T3-L1 cells transduced with SETD5 at 0 hr

value: 0 hr


title: N2L1IPrep1

city: Birmingham

first: HaoSheng

last: Sun

state: AL

address: 1918 University Blvd, MCLM 916

department: Cell, Developmental and Integrative Biology

institute: University of Alabama at Birmingham

data_processing:
Alignment to WS220 using BWA and filtered using SAMtools.
Samples from respective conditions were merged, and peaks were called using MACS2.
Differential binding analysis between L1 and L2 was done using Diffbind.
The ChIP-seq peak distribution was annotated using ChIPseeker.
Bam: Bam files are the raw fastq files, aligned to WS220 using BWA, filtered for 20+ MAPQ quality score, and merged with the replicates from their respective conditions using MergeSamFiles.
Genome_build: WS220
Supplementary_files_format_and_content: LIN14L1mergedPeaks.bed and LIN14L2mergedPeaks.bed files are peaks files from MACS2 called using the merged bam files above.
Supplementary_files_format_and_content: LIN14L1mergedPeaksannotated.tabular.txt and LIN14L2mergedPeaksannotated.tabular.txt files are annotated from the peak bed files above using ChIPSeeker.
Supplementary_files_format_and_content: LIN14L2vsL1DiffBind.tabular.txt file is obtained through differential analysis between L2 and L1 samples using DiffBind, and the LIN14L2vsL1DiffBindannotated.tabular.txt file is the annotated file using ChIPSeeker.

organism: Caenorhabditis elegans

source_name: whole worm ChIP

growth_protocol: The C-terminally GFP tagged lin-14 (lin14(cc2841[lin-14::gfp]) and N2 strains were used for the ChIP. ~600,000 animals were collected for each L1/L2 replicate. Worms were grown on large plates (150mm) with enriched peptone media coated with NA22 bacteria to allow for the growth of large quantities of worms. Animals were egg prepped according to standard protocol and synchronized at the L1 stage. They were then plated on food and collected after 8 +/-1 hrs and 21 +/-1 hrs for L1 and L2 stages, respectively.

extract_protocol:
Worms were fixed with 2% formaldehyde for 15 minutes at room temperature (RT). ChIP assay was performed as previously described with the following modifications (Li et al., 2020). After fixation, worms were resuspended in FA buffer supplemented with protease inhibitors (150 mM NaCl, 10 μl 0.1 M PMSF, 100 μl 10% SDS, 500 μl 20% N-Lauroyl sarcosine sodium, 1 tablets of cOmplete ULTRA Protease Inhibitor Cocktail in 10 ml FA buffer). The sample was sonicated using a Covaris S220 at the following settings: 200 W Peak Incident Power, 20% Duty Factor, 200 Cycles per Burst for 6 min. Samples were transferred to centrifuge tubes and spun at the highest speed for 15 min. The supernatant was transferred to a new tube, and 5% of the material was saved as input. The remainder was incubated with 25 μl GFP-Trap Magnetic Beads (Chromotek gtd) at 4°C overnight. Wild-type (N2) worms do not carry the GFP tag and serve as negative control. The next day, the beads were washed at 4°C twice with 150 mM NaCl FA buffer (5 min each), once with 1M NaCl FA buffer (5 min), twice with 500 mM NaCl FA buffer (10 min each), once with TEL buffer (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, pH 8.0) for 10 min, and twice with TE buffer (5 min each). The immunocomplex was then eluted in 200 μl elution buffer (1% SDS in TE with 250 mM NaCl) by incubating at 65°C for 20 min. The input and ChIP samples were then treated with 1μl of 20 mg/ml proteinase K, incubated at 55°C for 2 hr, and then 65°C overnight to reverse cross-link. The immunoprecipitated DNA was purified with Ampure XP beads (A63881) according to manufacturer’s instructions.
ChIP-seq libraries were prepped using the Ovation UltralowSystem V2 kit (Tecan) according to manufacturer’s protocol.

tag: strain/genotype

tag: developmental stage

value: Whole body

tag: chip antibody

value: GFP

tag: sample type

value: ChIP


title: LIN14L2IPrep5

description:
LIN14L2mergedPeaks.bed
LIN14L2mergedPeaksannotated.tabular.txt
LIN14L2vsL1DiffBind.tabular.txt
LIN14L2vsL1DiffBindannotated.tabular.txt

tag: tissue


title: LIN14L2IPrep4


title: MFA_CD702

tag: day


title: MFA_CD703

tag: shRNA

value: EPI


title: MFA_CD704

tag: embryotag


title: LIN14L2IPrep3


title: L1_D2_H3K4me1

data_processing:
All bound DNA fragments were mapped UCSC build mm9 assembly of the mouse genome by the mapping program Bowtie2 based on the 5'-side 36-bp sequences.
Signals of ChIP-seq occupancy are presented as counts per million mapped reads (CPM) by using deepTools bamCoverage.
SICER2 program was used under the following parameters: window size 200 bp; gap size 400 bp (for H3K27ac and H3K4me1) and 600 bp (for SETD5-V5 and SETD5); E-value threshold, 100. SICER program was used under the following parameters: window size 200 bp; gap size 600 bp; E-value threshold, 100 for SETD5.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files

source_name: 3T3-L1 preadipocytes

growth_protocol: 3T3-L1 preadipocytes were maintained in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum at 37 °C. For adipocyte differentiation, two days after reaching confluence (day 0), 3T3-L1 preadipocytes were treated with differentiation medium containing insulin (1 μg/ml), 0.25 μM dexamethasone, and 0.5 mM isobutylmethylxanthine (MDI cocktail).

extract_protocol:
Sonicated nuclear fraction was incubated with each antibody and protein-DNA complexes were isolated.
Libraries were prepared according to Illumina's instructions.

tag: day of hour of differentiation

value: Day 2


title: time 60 human PMN control rep 3

description:
time 60 human PMN control rep 3_no treatment, control
4011_KMR-1_Human_51_44-57-PMNcontrol-3-60_01_0085

tag: cell type

value: no treatment, control


title: LIN14L2IPrep1


title: MFA_C25

value: shscramble

tag: celltype


title: LAC and FLIPr time 60 rep 3

description:
LAC and FLIPr time 60 rep 3_Staphylococcus aureus and FLIPr- (formyl peptide receptor-like 1 inhibitor)
4008_KMR-1_Human_48_38-50-LAC+FLIPr-3-60_01_0096

source_name: neutrophils_LAC and FLIPr time 60

tag: treatment

tag: time (min)


title: L1_E_36h

source_name: 3T3-L1 cells transduced with control empty virus at 36 hr


title: LIN14L2INrep3

source_name: whole worm Input

value: Input


title: LIN14L2IPrep2


title: MFA_CD701


title: LIN14L2INrep4


title: L1_D0_H3K4me1

value: Day 0


title: time 60 human PMN control rep 1

description:
time 60 human PMN control rep 1_no treatment, control
4009_KMR-1_Human_49_70-39-PMNcontrol-1-60_01_1907


title: MFA_7CN32


title: L1_E_24h

source_name: 3T3-L1 cells transduced with control empty virus at 24 hr

value: 24 hr


title: LS191591

city: Dalian

first: Wenqian

last: Song

address: Yan'an Road

institute: Dalian Blood Center

description: Y-chromosome

data_processing:
Library strategy: DNA-Seq
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole genome.
Returning a fastq file (raw data) of reads associated with each of the 288 barcoded primer pairs.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.xlsx: Excel files include raw counts.

source_name: cffDNA

extract_protocol:
Plasma was isolated from the whole blood sample using two-step centrifugation at 1500 ×g for 10 min and 13,000 ×g for 10 min. The supernatant was collected and stored at -80°C. Plasma DNA was extracted from 2 mL cell-free maternal plasma using the MagPure Circulating DNA Maxi Kit (Angen Biotech, Guangzhou, China) and eluted with 60 µL water.
1µL of DNA extract from cell-free maternal plasma was amplified using the barcoding primers of the following 12 Y-chromosome mini-STR loci: DYS439, DYS437, DYS643, DYS393, DYS570, DYS392, DYS549, DYS460, DYS458, DYS576, DYS438 and DYS533. The DNA library was prepared using KAPA Library Amplification Kit (Illumina, San Diego, CA, USA) according to the standard Illumina instructions, which mainly includes addition of specialized adapters and indexes to both ends of barcoding sequences.

tag: y-chr str loci

tag: Sex

value: Male

value: Maternal plasma


title: L1_E_12h

source_name: 3T3-L1 cells transduced with control empty virus at 12 hr

tag: viral

tag: hour of differentiation


title: L1_E_48h

source_name: 3T3-L1 cells transduced with control empty virus at 48 hr

value: 48 hr

tag: cell line


title: LS191997

description: Y-chromosome


title: LAC time 60 rep 2

description:
LAC time 60 rep 2_Staphylococcus aureus
4004_KMR-1_Human_44_69-40-LAC-2-60_01_4138

source_name: neutrophils_LAC time 60

value: Staphylococcus aureus


title: LAC time 60 rep 3

description:
LAC time 60 rep 3_Staphylococcus aureus
4005_KMR-1_Human_45_56-49-LAC-3-60_01_1893


title: LS191398

description: Y-chromosome


title: LAC time 60 rep 1

description:
LAC time 60 rep 1_Staphylococcus aureus
4003_KMR-1_Human_43_3-31-LAC-1-60_01_4074


title: L1_E_0h

source_name: 3T3-L1 cells transduced with control empty virus at 0 hr

value: Empty


title: MFA_7CN30

source_name: embryo

value: embryo invitro day 7


description:
knock-out psm, psm-alpha, beta-hld time 60 rep 1_Staphylococcus aureus knock out psm, psm-alpha, and beta hld
4000_KMR-1_Human_40_47-34-Dtriple-1-60_01_8995

source_name: neutrophils_knock-out psm, psm-alpha, beta-hld time 60

value: Neutrophils


description:
knock-out psm, psm-alpha, beta-hld time 60 rep 3_Staphylococcus aureus knock out psm, psm-alpha, and beta hld
4002_KMR-1_Human_42_9-52-Dtriple-3-60_01_9019


title: LS191231

description: Y-chromosome


title: LS191208

description: Y-chromosome


title: MFA_7CN22


title: MFA_7CN33


title: LIN14L2INrep1

tag: strain/genotype

tag: developmental stage

value: Whole body


title: MFA_7CN20


title: LIN14L1IPrep4

description:
LIN14L1mergedPeaks.bed
LIN14L1mergedPeaksannotated.tabular.txt
LIN14L2vsL1DiffBind.tabular.txt
LIN14L2vsL1DiffBindannotated.tabular.txt

tag: chip antibody

value: GFP

tag: sample type


title: LAC and FLIPr time 60 rep 2

description:
LAC and FLIPr time 60 rep 2_Staphylococcus aureus and FLIPr- (formyl peptide receptor-like 1 inhibitor)
4007_KMR-1_Human_47_20-41-LAC+FLIPr-2-60_01_1913


description:
knock-out psm, psm-alpha, beta-hld time 60 rep 2_Staphylococcus aureus knock out psm, psm-alpha, and beta hld
4001_KMR-1_Human_41_42-43-Dtriple-2-60_01_8986


title: LAC and FLIPr time 60 rep 1

description:
LAC and FLIPr time 60 rep 1_Staphylococcus aureus and FLIPr- (formyl peptide receptor-like 1 inhibitor)
4006_KMR-1_Human_46_72-32-LAC+FLIPr-1-60_01_1914


title: LIN14L2INrep2

tag: tissue


title: MFA_7CN19

tag: day

tag: shRNA


title: MFA_7CN21

tag: embryotag

value: PrE


title: LIN14L1IPrep5

value: ChIP


title: MFA_7CN25

value: EPI


title: LIN14L1IPrep2


title: LS190889

description: Y-chromosome


title: delta- toxin and FLIPr time 60 rep 3

description:
delta- toxin and FLIPr time 60 rep 3_delta toxin from Staphylococcus aureus and FLIPr- (formyl peptide receptor-like 1 inhibitor)
3999_KMR-1_Human_39_14-56-d-toxin+FLIPr-3-60_01_8954

source_name: neutrophils_delta- toxin and FLIPr time 60

tag: cell type


title: LS190960

description: Y-chromosome


title: LIN14L1INrep4


title: MFA_7CN18

tag: celltype


title: delta- toxin time 60 rep 3

description:
delta- toxin time 60 rep 3_delta toxin from Staphylococcus aureus
3996_KMR-1_Human_36_67-55-d-toxin-3-60_01_8949

source_name: neutrophils_delta- toxin time 60

tag: treatment

value: delta toxin from Staphylococcus aureus


title: LIN14L1IPrep3


title: LS191025

description: Y-chromosome


title: LS190838

description: Y-chromosome


title: LIN14L1IPrep1


title: LS190445

description: Y-chromosome


title: delta- toxin and FLIPr time 60 rep 2

description:
delta- toxin and FLIPr time 60 rep 2_delta toxin from Staphylococcus aureus and FLIPr- (formyl peptide receptor-like 1 inhibitor)
3998_KMR-1_Human_38_48-47-d-toxin+FLIPr-2-60_01_4094

tag: time (min)


title: MFA_3N10

value: shscramble

value: TrB


title: MFA_3N16


title: LIN14L1INrep1

value: Input


title: LIN14L1INrep2


title: LS190235

description: Y-chromosome

tag: y-chr str loci


title: delta- toxin time 60 rep 2

description:
delta- toxin time 60 rep 2_delta toxin from Staphylococcus aureus
3995_KMR-1_Human_35_29-46-d-toxin-2-60_01_8969


title: LS182090

description: Y-chromosome

tag: Sex


title: delta- toxin time 60 rep 1

description:
delta- toxin time 60 rep 1_delta toxin from Staphylococcus aureus
3994_KMR-1_Human_34_31-37-d-toxin-1-60_01_2009


title: delta- toxin and FLIPr time 60 rep 1

description:
delta- toxin and FLIPr time 60 rep 1_delta toxin from Staphylococcus aureus and FLIPr- (formyl peptide receptor-like 1 inhibitor)
3997_KMR-1_Human_37_73-38-d-toxin+FLIPr-1-60_01_4060


title: LS190054

description: Y-chromosome


title: knock-out psm alpha time 60 rep 3

description:
knock-out psm alpha time 60 rep 3_Staphylococcus aureus knock out psm alpha
3993_KMR-1_Human_33_39-51-Dpsm-a-3-60_01_9123

source_name: neutrophils_knock-out psm alpha time 60


title: ChIL-H3K27ac - Heart - rep. 3

data_processing:
Gene expression quantification (TPM estimation) was performed by Salmon "quant" with the default option.
The reads of tsChIL-seq were mapped against the GRCm38 reference genome using Bowtie2 with the default option.
Duplicated reads were discarded using samtools (rmdup) and the uniquely mapped reads were used for further analysis.
The bigWig files were generated using deepTools (version 3.4.1) with the command: bamCoverage -p 36 --binSize 100 --normalizeUsing CPM --smoothLength 1000.
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV files include comma-delimited gene expression (TPM) matrices

source_name: left ventricle

extract_protocol:
Each cryo-tissue section (10 um) was placed onto u-plate 96 well bottom (Ibidi #89626) and the plate was stored at -80ºC freezer without backing to room temperature until use. Tissue section was fixed with 4%PFA in 0.3% TritonX-100/PBS for five minutes and washed with 0.3% TritonX-100/PBS. Double blocking were performed using blocking one (Nacalai #03953) and M.O.M blocking reagent (Vector Laboratories #BMK-2202) as instructed. The sections were incubated with primary antibody in M.O.M. protein concentrate/PBS at 4ºC overnight, followed by incubating with ChIL probe at same condition but in addition of NaCl at 0.5 M concentration.
ChIL-seq was performed according to ChIL (Harada et al., 2018) with some modifications. Longer incubation time is used for some steps (Extended Tn5 binding 1hr and fill-in step 2hrs),  Thermo T7 RNA polymerase (100 U per well; Toyobo), and 15 cycles of PCR amplification. Column purification (Zymo #D4013) and x0.5 volume of AMpure beads (Beckman Coulter) selection were performed to obtain 200-500 bp average of library.  For RNA-seq, 10 ng of total RNA was used for library preparation using SMART-Seq Stranded Kit (Takara) as instructed.

tag: strain

value: left ventricle

tag: antibody


title: LIN14L1INrep3


title: RNA-seq - Testis - rep. 2

description:
Testis-m2
Tissues_TPMMatrix.csv.gz

source_name: testis

value: testis


title: RNA-seq - Testis - rep. 3

description:
Testis-m3
Tissues_TPMMatrix.csv.gz


title: AINrep4

data_processing:
Alignment to WS220 using Subread
Assignment to gene feature using Featurecounts
Compare neuronal IP to input(total nuclei) for neuronal enrichment using DESeq2-> 7974 neuronally enriched genes (padj<0.05)
Take only the read count for these 7974 neuronally enriched genes, and adjust for library size -> use these adjusted counts for developmental and mutant comparison using DESeq2
Genome_build: WS220
Supplementary_files_format_and_content: neuronalIPvsinput_Rawcounts.txt is raw read counts of control neuronal IP and input samples used for calculation of neuronal enrichment in DESeq2
Supplementary_files_format_and_content: neuronalIPsizeadjustedcounts.txt contain the counts, adjusted for library size, of only the 7974 neuronally enriched genes in all control and mutant samples across developmental stages
Supplementary_files_format_and_content: neuronalIPdevelopmentalDESeq2normalizedcounts.txt is the normalized read counts outputted from DESeq2 after developmental comparison of control samples
Supplementary_files_format_and_content: neuronalIPL1AdultmutantDESeq2normalizedcounts.txt is the normalized read counts outputted from DESeq2 after comparison of control and heterochronic mutants at L1 and adult stages

source_name: input(total nuclei)

growth_protocol: UPN::INTACT control worms (otIs790) as well as mutants were grown on large plates (150mm) with enriched peptone media coated with NA22 bacteria to allow for the growth of large quantities of worms.  Animals were egg prepped according to standard protocol and synchronized at the L1 stage. They were then plated on food and collected after 8 +/-1 hrs, 21 +/-1 hrs, 40 +/- 2hrs, and 53 +/- 2hrs for L1, L2, L4, and adult stages. lin-4(e912) null and lin-14(ot1087) gain of function animals are slower in their developmental progression compared to controls, and adult lin-4(e912) and lin-14(ot1087) animals were collected 57 +/- 2 hrs after plating (~4 hrs after the control and lin-28(ot1088) gain of function adult animals were collected).

extract_protocol:
Animals were collected at the respective stage as described above.  ~600,000 animals were collected for each L1/L2 replicates while ~200,000 animals were collected for each L4/A replicates. At the time of collection, animals were washed off the plate with M9, washed 3x with M9, lightly fixed with cold RNAse-free DMF for 2 minutes before washing with 1xPBS 3x. Modification were made from previous INTACT protocol to optimize pulldown of neuronal nuclei (Steiner et al., 2012). All steps following were done in cold rooms (4°C) to minimized RNA degradation. The animals were homogenized mechanically using disposable tissue grinder (Fisher) in 1x hypotonic buffer (1x HB: 10mM Tris pH 7.5, 10mM NaCl, 10mM KCl, 2mM EDTA, 0.5mM EGTA, 0.5mM Spermidine, 0.2mM Spermine, 0.2mM DTT, 0.1% Triton X-100, 1x protease inhibitor). After each round of mechanical grinding (60 turns of the grinder), the grinder was washed with 1mL 1x HB and the entire homogenate was centrifuged at 100xg for 3 min. The supernatant was collected for later nuclei extraction and the pellet was put under mechanical grinding and centrifugation for 4 additional rounds. The supernatant collected from each round were pooled, dounced in a glass douncer, and gently passed through an 18 gauge needle 20x to further break down small clumps of cells. The supernatant was then centrifuged at 100xg for 10 min to further remove debris and large clumps of cells. Nuclei was isolated from the supernatant using Optiprep (Sigma): supernatant after centrifugation was collected in a 50mL tube, added with nuclei purification buffer (1x NPB: 10mM Tris pH 7.5, 40mM NaCl, 90mM KCl, 2mM EDTA, 0.5mM EGTA, 0.5mM Spermidine, 0.2mM Spermine, 0.2mM DTT, 0.1% Triton X-100, 1x protease inhibitor) to 20mL, and layered on top of 5mL of 100% Optiprep and 10mL of 40% Optiprep. The layered solution was centrifuged at 5000xg for 10 min in a swinging bucket centrifuge at 4°C. The nuclei fraction was collected at the 40/100% Optiprep interface. After removal of the top and bottom layers, leaving a small volume containing the nuclei, the process was repeated 2 additional times. After final collection of the crude nuclei fraction, the volume was added to 4mL with 1xNPB and precleared with 10µl of Protein-G Dynabeads and 10 µl of M270 Carboxylated beads for 30min to 1hr (Invitrogen). The precleared nuclei extract was then removed, and 50 µl was taken out as input samples (total nuclei). The rest was incubated with 30µl of Protein G Dynabeads and 3 µl of anti-FLAG M2 antibody (Sigma) overnight to immmunoprecipiate (IP) the neuronal nuclei. The following day, the IPed neuronal nuclei was washed 6-8 times with 1xNPB for 10-15 min each time. The resulting neuronal nuclei IPed beads were resuspended in 50 ul 1xNPB and a small aliquot was used to check with DAPI staining to ensure the qualities of the procedure: 1) sufficient quantities of nuclei was immunoprecipiated; 2) nuclei are intact and not broken; 3) the majority of bound nuclei are single, mCherry-labelled neuronal nuclei and minimal nuclei clumps and large tissue chunks were immunoprecipiated. Anything not satisfying these quality checks were not used for downstream processing. The resulting input and neuronal IP samples were used for isolation of total RNA using Nucleospin RNA XS kit according to manufacturer’s protocol (Takara).
RNA-seq libraries were prepped using the Universal RNA-seq kit (Tecan) according to manufacter’s protocol.

tag: type

value: total Input

value: UPN INTACT (otIs790)

value: Adult


title: LS182031

description: Y-chromosome

value: Male

value: Maternal plasma


title: AINrep5

tag: strain/genotype


title: AINrep3

tag: developmental stage


title: RNA-seq - Testis - rep. 1

description:
Testis-m1
Tissues_TPMMatrix.csv.gz


title: Drug-treated SK-BR-3 multi-omics sample protein _rep2

city: Xiamen

first: Xing

last: Xu

state: Fujian

address: 422 Road, Siming District, Xiamen, China

institute: Xiamen University

description: Protein

data_processing:
multi-Paired-seq sequencing libraries produce paired-end reads: Read 1 contained a cell barcode (12 bases) and a UMI (8 bases); Read 2 contained mRNA/protein barcode information.
The reads would be preprocessed with the following steps: correcting bead, filtering low-quality reads, trimming read 2 including polyA, adapter and primer, alignment, assigning gene tags, generating digital gene expressing.
The beads with the twenty-first base as A, C or G only were used in our experiments. If the number of continuous T bases at the end of read 1 was less than or equal to 12, we inserted “N” bases before T bases. Otherwise, the pair of reads was dropped. Filtering low-quality reads was based on the base quality of the cell barcode and UMI. Respectively, cell barcode and UMI should have only one base with quality lower than 20 at most. Otherwise, the read pair was discarded. At least 5 contiguous bases of TSO and at least 6 contiguous bases of A with no mismatch were examined for read 2 and were hard clipped off the read. At least 6 contiguous bases of primer with one mismatch allowed considered for read 2 and hard clipped off read.
The read pair was discarded, if the length of read 2 was less than 26 after trimmed. STAR alignment tool was used to align read 2 with the reference genome.
For human and mouse mixed cells, we used hg19_mm10 mentioned in Drop-seq as reference genome. This program from Drop-seq added a tag “GE”. We kept the unique mapping with gene tags. Then unique UMIs for each gene of each cell were counted to generate digital gene expression.
Genome_build: hg19 (GRCh37), mm10 (GRCm38)
Supplementary_files_format_and_content: Digital gene/protein expression in text files.

source_name: breast cancer cells

growth_protocol: Cells are all cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
Cells were lyzed and RNAs/Proteins were captured, reverse transcribed and amplified.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Drug-treated group was treated by Trastuzumab for 72h.

value: breast cancer cells

tag: human cell line

value: Trastuzumab

value: anti-human Epcam antibody, anti-human HER2 antibody and anti-human EGFR antibody


title: Drug-treated SK-BR-3 multi-omics sample RNA _rep2

description: RNA


title: AINrep2


title: RNA-seq - Heart - rep. 3

description:
LV-m3
Tissues_TPMMatrix.csv.gz


title: RNA-seq - Heart - rep. 2

description:
LV-m2
Tissues_TPMMatrix.csv.gz


title: Drug-treated SK-BR-3 multi-omics sample protein _rep1

description: Protein


title: AINrep1


title: RNA-seq - Liver - rep. 3

description:
Liver-m3
Tissues_TPMMatrix.csv.gz

source_name: liver

value: liver


title: knock-out psm alpha time 60 rep 2

description:
knock-out psm alpha time 60 rep 2_Staphylococcus aureus knock out psm alpha
3992_KMR-1_Human_32_10-42-Dpsm-a-2-60_01_8935

value: Neutrophils


title: Drug-treated SK-BR-3 multi-omics sample RNA _rep1

description: RNA


title: PSM alpha 3 plus FLIPr time 30 rep 2

description:
PSM alpha 3 plus FLIPr time 30 rep 2_PSM alpha 3 from Staphylococcus aureus plus FLIPr
3989_KMR-1_Human_29_33-16-PSM-a3+FLIPr-2-30_01_5760

source_name: neutrophils_PSM alpha 3 plus FLIPr time 30


title: PSM alpha 3 plus FLIPr time 30 rep 1

description:
PSM alpha 3 plus FLIPr time 30 rep 1_PSM alpha 3 from Staphylococcus aureus plus FLIPr
3988_KMR-1_Human_28_36-6-PSM-a3+FLIPr-1-30_01_1952


title: MDA-MB-231 multi-omics sample protein _rep2

description: Protein


title: L4INrep4


title: PSM alpha 3 plus FLIPr time 30 rep 3

description:
PSM alpha 3 plus FLIPr time 30 rep 3_PSM alpha 3 from Staphylococcus aureus plus FLIPr
3990_KMR-1_Human_30_66-26-PSM-a3+FLIPr-3-30_01_1925


title: knock-out psm alpha time 60 rep 1

description:
knock-out psm alpha time 60 rep 1_Staphylococcus aureus knock out psm alpha
3991_KMR-1_Human_31_76-33-Dpsm-a-1-60_01_8957


title: PSM alpha 3 time 30 rep 3

description:
PSM alpha 3 time 30 rep 3_PSM alpha 3 from Staphylococcus aureus
3987_KMR-1_Human_27_46-25-PSM-a3-3-30_01_1848

source_name: neutrophils_PSM alpha 3 time 30

value: PSM alpha 3 from Staphylococcus aureus


title: L4INrep3


title: L4INrep2


title: RNA-seq - Liver - rep. 1

description:
Liver-m1
Tissues_TPMMatrix.csv.gz


title: MDA-MB-231 multi-omics sample protein _rep1

description: Protein


title: RNA-seq - Liver - rep. 2

description:
Liver-m2
Tissues_TPMMatrix.csv.gz


title: MDA-MB-231 multi-omics sample RNA _rep2

description: RNA


title: RNA-seq - Heart - rep. 1

description:
LV-m1
Tissues_TPMMatrix.csv.gz


title: L4INrep1


title: MDA-MB-231 multi-omics sample RNA _rep1

description: RNA


title: L2INrep4


title: 174341: Bhlhe40-/- lymphoma from mouse 3

city: Solna

first: Taras

last: Kreslavsky

address: Nks Bioclinicum, J7:30, Visionsgatan 4

department: Department of Medicine, Solna (MedS)

country: Sweden

institute: Karolinska Institutet

description: Bhlhe40-/- lymphoma cells sorted from sick secondary recipient mouse (Rag2-/-)

data_processing:
Sequence reads that passed the Illumina quality filtering were considered for alignment. Reads corresponding to mouse ribosomal RNAs (BK000964.1 and NR046144.1) were removed. The remaining reads were cut down to a read length of 44 bp and aligned to the mouse transcriptome (genome assembly version of July 2007 NCBI37/mm9) using RNA STAR (Dobin et al., 2012). The calculation of RNA expression values was all based on the RefSeq database, which was downloaded from UCSC on January 10th, 2014. The annotation of immunoglobulin and T cell receptor genes was incorporated from the Ensembl release 67 (Cunningham et al, 2015). Genes with overlapping exons were flagged and double entries (i.e. exactly the same gene at two different genomic locations) were renamed. Genes with several transcripts were merged to consensus-genes consisting of a union of all underlying exons using the fuge software (I. Tamir, unpublished), which resulted in 25,726 gene models.  For analysis of differential gene expression, the number of reads per gene was counted using HTseq version 0.5.3 (Anders et al, 2014) with the overlap resolution mode set to 'union'. Transcripts per million (TPM) were calculated from RNA-seq data, as described (Wagner et al, 2012).
Genome_build: MM9
Supplementary_files_format_and_content: text tab delim = count, RPKM, genelength, and TPM values in ASCII text format tab delimited

molecule: polyA RNA

source_name: B cell lymphoma cells

extract_protocol:
Rneasy Plus Mini Kit, Dynabeads mRNA purification kit
NEBNext Ultra II

tag: genotype

tag: cell preparation

value: Ex vivo, FACS-sorted from spleens tumor

tag: cell sorting strategy

value: B cell lymphoma cells


title: 174340: Bhlhe40-/- lymphoma from mouse 7

description: Bhlhe40-/- lymphoma cells sorted from a sick Bhlhe40-/- mouse

value: Ex vivo, FACS-sorted from spleen tumor


title: 174339: Bhlhe40-/- lymphoma from mouse 6

value: Ex vivo, FACS-sorted from lung tumor


title: 174338: Bhlhe40-/- lymphoma from mouse 5

extract_protocol:
Trizol extraction, Rneasy Plus Mini Kit, Dynabeads mRNA purification kit
NEBNext Ultra II

value: Ex vivo, FACS-sorted from mesenteric LN tumor


title: SK-BR-3 multi-omics sample protein _rep2

description: Protein


title: SK-BR-3 multi-omics sample RNA _rep2

description: RNA


title: L2INrep1


title: SK-BR-3 multi-omics sample protein _rep1

description: Protein


title: time 30 human PMN control rep 3

description:
time 30 human PMN control rep 3_no treatment, control
3984_KMR-1_Human_24_75-29-PMNcontrol-3-30_01_9152

source_name: neutrophils_time 30 human PMN control

value: no treatment, control


title: 174337: Bhlhe40-/- lymphoma from mouse 4


title: PSM alpha 3 time 30 rep 2

description:
PSM alpha 3 time 30 rep 2_PSM alpha 3 from Staphylococcus aureus
3986_KMR-1_Human_26_50-15-PSM-a3-2-30_01_1912


title: SK-BR-3 multi-omics sample RNA _rep1

description: RNA


title: L1INrep4

value: total Input


title: time 30 human PMN control rep 1

description:
time 30 human PMN control rep 1_no treatment, control
3982_KMR-1_Human_22_45-9-PMNcontrol-1-30_01_8951


title: L1INrep3

value: UPN INTACT (otIs790)


title: LAC and FLIPr time 30 rep 1

description:
LAC and FLIPr time 30 rep 1_Staphylococcus aureus and FLIPr- (formyl peptide receptor-like 1 inhibitor)
3979_KMR-1_Human_19_30-2-LAC+FLIPr-1-30_01_4036

source_name: neutrophils_LAC and FLIPr time 30


title: LAC and FLIPr time 30 rep 3

description:
LAC and FLIPr time 30 rep 3_Staphylococcus aureus and FLIPr- (formyl peptide receptor-like 1 inhibitor)
3981_KMR-1_Human_21_26-22-LAC+FLIPr-3-30_01_8974


title: LAC and FLIPr time 30 rep 2

description:
LAC and FLIPr time 30 rep 2_Staphylococcus aureus and FLIPr- (formyl peptide receptor-like 1 inhibitor)
3980_KMR-1_Human_20_1-12-LAC+FLIPr-2-30_01_4104


title: LAC time 30 rep 3

description:
LAC time 30 rep 3_Staphylococcus aureus
3978_KMR-1_Human_18_28-21-LAC-3-30_01_4077

source_name: neutrophils_LAC time 30

value: Staphylococcus aureus


title: PSM alpha 3 time 30 rep 1

description:
PSM alpha 3 time 30 rep 1_PSM alpha 3 from Staphylococcus aureus
3985_KMR-1_Human_25_16-5-PSM-a3-1-30_01_0074


title: L1INrep2


title: L2INrep2


title: MCF7 multi-omics sample RNA _rep2

description: RNA


title: MCF7 multi-omics sample protein _rep2

description: Protein


title: LAC time 30 rep 1

description:
LAC time 30 rep 1_Staphylococcus aureus
3976_KMR-1_Human_16_23-1-LAC-1-30_01_4128


title: L1INrep1


title: Cdh5-Cre;Angptl2fl/fl

city: shanghai

first: wenqian

last: yang

address: 280 South Chongqing Road

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Illumina Casava2.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads FPKM(expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) were calculated using a protocol from Trapnell, Cole, et al., 2010.
Differential expression analysis,Gene Ontology (GO) and KEGG enrichment analysis.
Genome_build: mmp10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: HSCs

extract_protocol:
Cells were lysed by TRIzol reagent for extraction of RNA. RNA was prepared using RNasey Mini Kit(Qiagen p/n 74104) according to the manufacturer's recommendations. After clean-up, RNA purity was detected by NanoDrop® spectrophotometers (Thermo Fihser, MA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 3.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
The clustering of the index-coded samples was performed on a cBot Cluster Generation System (Illumia, USA) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq X Ten platform and 150bp pired-end module.

value: HSCs from endothelial cell-specific Angptl2-deficient mice

value: hematopoietic stem cells

tag: tissue

value: bone marrow


title: MCF7 multi-omics sample RNA _rep1

description: RNA

value: breast cancer cells


title: Alin28gofIPrep3

description:
neuronalIPsizeadjustedcounts.txt
neuronalIPL1AdultmutantDESeq2normalizedcounts.txt

source_name: neuronal nuclei IP

value: neuronal IP

value: UPN INTACT (otIs790); lin-14(e1088)

value: Adult


title: MCF7 multi-omics sample protein _rep1

description: Protein

value: anti-human Epcam antibody, anti-human HER2 antibody and anti-human EGFR antibody


title: Angptl2fl/fl

value: control HSCs


description:
knock-out psm, psm-alpha, beta-hld time 30 rep 3_Staphylococcus aureus knock out psm, psm-alpha, and beta hld
3975_KMR-1_Human_15_37-24-Dtriple-3-30_01_4109

source_name: neutrophils_knock-out psm, psm-alpha, beta-hld time 30

value: Neutrophils


title: Alin28gofIPrep2


title: Gene expression Sample 1

city: GuangZhou

first: bian

last: zhenhua

state: GuangDong

address: Panyu University Town

institute: South China University of Technology

data_processing:
The BD Rhapsody analysis pipeline (version 1.9.2beta) provided by BD Biosciences was used to demultiplex cellular barcodes, map reads to the reference genome
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: dnTGFβRII mice and IFN-γ ARE-Del-/- mice liver

extract_protocol:
Beads with oligonucleotide barcodes were added to saturation to pair the beads with the cell in the microwells. Cell-lysis buffer was added to lysis the cell and allow barcode conjugated beads to capture poly-adenylated molecules, including mRNA, AbSeq targets and sample tag.
Ab-Oligos/Sample Tag with cell barcode and UMI information were denatured off of the Cell Capture Beads and saved for AbSeq/Sample Tag amplification. For WTA library Preparation, random priming extension was performed on cDNA archived on Cell Capture Beads.

treatment_protocol: liver immune cells  were fully resuspended in cell stain buffer and co-labelled with AbSeq Ab-Oligos and Sample Tags on ice for 45 minutes. Post-labeling cells were washed 3 times to remove noise that comes from free residual.

tag: age

value: 10 weeks

value: dnTGF[beta]RII and IFN-[gamma] ARE-Del-/-

value: CD45+ cells

tag: feature type

value: gene expression


title: Alin28gofIPrep1


title: Gene expression Sample 2

source_name: P40-/-IL-2Ra-/- mice and wild type mice liver

value: P40-/-IL-2Ra-/- and wild type

tag: cell type


title: Alin14gofIPrep5

value: UPN INTACT (otIs790); lin-14(e1087)


title: Male_Tg_Vehicle (merged_SS-HBD61_S53)

city: Chicago

first: Priyam

last: Patel

state: IL

address: 750 North Lake Shore Drive, Rubloff 11-146

department: Quantitative Data Science Core

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file with read counts per gene

source_name: Short-term ABX Tg mice study_sacrificed at PND24

extract_protocol:
Total RNA was isolated using Trizol, phase separated by chloroform, and extracted by alcohol
RNA quality and quantity was assessed using the Agilent bio-analyzer. Strand-specific RNA-SEQ libraries were prepared using an TruSEQ mRNA RNA-SEQ library protocol (Illumina provided). Library quality and quantity was assessed using the Agilent bio-analyzer and libraries were sequenced using an Illumina NovaSEQ6000 (illumina provided reagents and protocols). Raw data was demultiplexed using Illumina’s bcl2fastq software and fastq.gz files were provided for analysis.

value: Cerebral cortex

tag: tissue dissection anatomy

value: dorsal side of the right hemisphere

value: Male

tag: treatment

value: Vehicle


title: Alin14gofIPrep4


title: Male_Tg_Vehicle (merged_SS-HBD60_S52)


title: Male_Tg_Vehicle (merged_SS-HBD62_S54)


title: NK S20 S21 S22

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

data_processing:
The Cell Ranger Single Cell Software Suite 3.1.1 was used to perform sample demultiplexing, barcode processing, and single cell 5’ gene counting for transcriptome wirh refdata-cellranger-hg19-1.2.0 as reference and expected-cells number of 3000 for each sample; polymorphisms removed.
Genome_build: hg19
Supplementary_files_format_and_content: Barcoded BAM, with Chromium cellular and molecular barcodes for each read, stored as TAG fields; h5: aggregated gene count matrix in hdf5 format. txt: annotation of cellular barcodes with disease state, day after symptom onset or stimulation, if applicable.

extract_protocol:
Frozen Peripheral Blood Mononuclear Cells were thawed and incubated with Fc Blocking Reagent following manufacturer’s instructions. Cells were subsequently incubated with barcoded (hashtagging) and fluorochrome-conjugated antibodies and NK cells were sorted by FACS as live CD3-CD14-CD19-CD45+CD56+ lymphocytes. Sorted cells were then applied to the 10X Genomics platform using the Single Cell 5’ Library & Gel Bead Kit (10x Genomics) following the manufacturer’s instructions. The purified cDNA was amplified using 12 or 13 cycles of PCR and then used for 5’ gene expression (GEX) and cell-surface hashtagging library preparation. Through fragmentation, adapter ligation and index PCR the final libraries were obtained. The quality of single cell 5’ GEX was assessed by Qubit quantification and Bioanalyzer fragment analysis (HS DNA Kit, Agilent).
The sequencing was performed on a NextSeq500 device (Illumina) using High Output v2 Kits (150 cycles) with the recommended sequencing conditions for 5’ GEX and cell-surface hashtagging libraries (read1: 26nt, read2: 98nt, index1: 8nt, index2: n.a.).

value: Peripheral Blood

tag: patient id

tag: sample detail

value: patient S20 #1 d12, #2 d21, patient S21 #3 d2, patient S22 #4 d35


title: NK S13 S10

source_name: NK S13 S10


title: NK S11 S18

source_name: NK S11 S18


title: Male_Tg_Vehicle (merged_SS-HBD59_S51)

tag: strain

tag: Sex


title: Alin14gofIPrep3

tag: type

value: neuronal IP


title: LAC time 30 rep 2

description:
LAC time 30 rep 2_Staphylococcus aureus
3977_KMR-1_Human_17_25-11-LAC-2-30_01_8938

value: Staphylococcus aureus

tag: time (min)


description:
knock-out psm, psm-alpha, beta-hld time 30 rep 1_Staphylococcus aureus knock out psm, psm-alpha, and beta hld
3973_KMR-1_Human_13_22-4-Dtriple-1-30_01_9006


title: Male_Tg_Vehicle (merged_SS-HBD58_S50)


title: delta- toxin and FLIPr time 30 rep 3

description:
delta- toxin and FLIPr time 30 rep 3_delta toxin from Staphylococcus aureus and FLIPr- (formyl peptide receptor-like 1 inhibitor)
3972_KMR-1_Human_12_84-28-d-toxin+FLIPr-3-30_01_8989

source_name: neutrophils_delta- toxin and FLIPr time 30


title: Alin14gofIPrep2

tag: strain/genotype

tag: developmental stage

value: Adult


description:
knock-out psm, psm-alpha, beta-hld time 30 rep 2_Staphylococcus aureus knock out psm, psm-alpha, and beta hld
3974_KMR-1_Human_14_24-14-Dtriple-2-30_01_9020


title: NK stimulated H4 H7 H8 H18

source_name: NK stimulated H4 H7 H8 H18

extract_protocol:
Sorted NK cells from Peripheral Blood Mononuclear Cells of healthy donors were cultured in RPMI containing rh-IL12 and rh-IL15 with or without additional rh-TGF-beta. After stimulation, cells were incubated with Fc Blocking Reagent following manufacturer’s instructions. Cells were subsequently incubated with barcoded (hashtagging) and fluorochrome-conjugated antibodies and NK cells were re-sorted by FACS as live CD3-CD14-CD19-CD45+CD56+ lymphocytes. Sorted cells were then applied to the 10X Genomics platform using the Single Cell 5’ Library & Gel Bead Kit (10x Genomics) following the manufacturer’s instructions. The purified cDNA was amplified using 12 or 13 cycles of PCR and then used for 5’ gene expression (GEX) and cell-surface hashtagging library preparation. Through fragmentation, adapter ligation and index PCR the final libraries were obtained. The quality of single cell 5’ GEX was assessed by Qubit quantification and Bioanalyzer fragment analysis (HS DNA Kit, Agilent).
The sequencing was performed on a NextSeq500 device (Illumina) using High Output v2 Kits (150 cycles) with the recommended sequencing conditions for 5’ GEX and cell-surface hashtagging libraries (read1: 26nt, read2: 98nt, index1: 8nt, index2: n.a.).


title: MFA_3N3

source_name: embryo

extract_protocol:
Isolation of single cells. The embryos were washed in PBS for 3 times, washed in 0.25% trypsin (T4799; SigmaAldrich) 2 times, incubated with 0.25% trypsin for around 15 min at 37 °C, and terminated by DFBS. Embryo was dissociated into single cells by repeated pipetting and dispersed in 1% DFBS/PBS. A single cell was pipetted into a PCR tube. All operations above were performed under the Nikon SMZ645 microscopy.
The synthesis and amplification of full-length cDNAs were performed following Smart-seq2 protocol4. Briefly, single cells were washed in DPBS (Gibco 14190-144) and picked into lysis buffer using Pasteur pipettes under a dissecting microscope. Reversetranscription reactions and pre-amplification were performed using SuperScript II (Invitrogen 18064-014) and KAPA HiFi HotStart ReadyMix (KAPA Biosystems KK2601), respectively. The quality of the cDNAs were evaluated by Bioanalyzer 2100. Library construction and sequencing were performed by Annoroad Gene Technology (http://www.annoroad.com/). Pair-end sequencing was performed on Illumina X-ten platform.

tag: day

value: embryo invitro day 7

tag: shRNA

value: shscramble

tag: embryotag

tag: celltype

value: TrB


title: delta- toxin time 30 rep 2

description:
delta- toxin time 30 rep 2_delta toxin from Staphylococcus aureus
3968_KMR-1_Human_8_35-17-d-toxin-2-30_01_8956

source_name: neutrophils_delta- toxin time 30

extract_protocol: Total RNA was purified using a Direct-zol RNA MiniPrep kit according to the manufacturer’s protocol (Zymo Research Corp., Irvine, CA)

value: Neutrophils

value: delta toxin from Staphylococcus aureus


title: delta- toxin time 30 rep 1

description:
delta- toxin time 30 rep 1_delta toxin from Staphylococcus aureus
3967_KMR-1_Human_7_63-7-d-toxin-1-30_01_1942


title: delta- toxin time 30 rep 3

description:
delta- toxin time 30 rep 3_delta toxin from Staphylococcus aureus
3969_KMR-1_Human_9_21-27-d-toxin-3-30_01_9026


title: delta- toxin and FLIPr time 30 rep 1

description:
delta- toxin and FLIPr time 30 rep 1_delta toxin from Staphylococcus aureus and FLIPr- (formyl peptide receptor-like 1 inhibitor)
3970_KMR-1_Human_10_32-8-d-toxin+FLIPr-1-30_01_8924


title: NK A6 A9 A1 A12

source_name: NK A6 A9 A1 A12

tag: tissue

value: patient A6 #5 d21, patient A9 #6 d15, patient A1 #7 d22, patient A12 #8 d13


title: Alin4IPrep4

value: UPN INTACT (otIs790); lin-4(e912)


title: NK A3 A26 A5 H8

source_name: NK A3 A26 A5 H8

value: patient A3 #2 d11, patient A26 #4 d68, patient A5 #6 d50, donor H8 #8 healthy


title: knock-out psm alpha time 30 rep 2

description:
knock-out psm alpha time 30 rep 2_Staphylococcus aureus knock out psm alpha
3965_KMR-1_Human_5_54-13-Dpsm-a-2-30_01_8953

source_name: neutrophils_knock-out psm alpha time 30


title: Male_Tg_Abx (merged_SS-HBD47_S40)

value: Cerebral cortex

value: Abx


title: MMLV N1mYAC

city: St Louis

first: Hani

last: Zaher

state: MO

address: 1 Brookings Drive

department: Biology

institute: Washington University in St. Louis

description: M-MLV reverse transcribed cDNA product of synthetic RNA

data_processing:
Reads were checked for initial quality using FastQC v0.11.9
Overhanging bases were removed and only consensus sequence retained using NGmerge v 0.3
Consensus reads were merged together to generate a single read with merged quality scores using NGmerge
Merged reads were processed to remove the DNA linker oligo sequence and to filter any reads not containing the linker sequence using Cutadapt v 3.4; minimum adapter overlap of 15 and maximum 10% error
Reads were mapped to the unmodified synthetic RNA sequence using BBmap v 38.94 in local mode with "very slow" settings
Mapped reads were sorted into bam files and indexed using Samtools v1.13
Sequence variants were detected and tested by comparing reads from the modified RNA to its matched unmodified RNA using deepSNV v3.13; only reads with mapping score >= 20 and bases with quality score of >=30 were used; Deletions were ignored as they appeared to be a sequencing artifact -- deletions completely disappeared at MAPQ >= 25
Genome_build: Fasta file of the unmodified synthetic RNA sequence and samtools indexed file
Supplementary_files_format_and_content: deepSNV output combined into an Excel file

organism: synthetic construct

source_name: N1mYAC Synthetic RNA

extract_protocol: An adenylated DNA oligo was ligated to the synthetic RNA. cDNA was amplified using a primer containing the Illumina TruSeq indexed adapter and a sequence complementary to the ligated sequence. cDNA was circularized and then PCR amplified using barcoded primers to generate library sequences.

tag: modification


title: MMLV YAC 2

source_name: YAC Synthetic RNA

value: Pseudouridine


title: NK A2 A11 A28 H6

source_name: NK A2 A11 A28 H6

value: patient A2 #1 d12, patient A11 #3 d13, patient A28 #5 d53, donor H6 #7 healthy


title: Male_Tg_Vehicle (merged_SS-HBD57_S49)

value: dorsal side of the right hemisphere

value: Male

value: Vehicle


title: Alin14gofIPrep1

source_name: neuronal nuclei IP

value: neuronal IP

value: UPN INTACT (otIs790); lin-14(e1087)


title: MMLV YAC 1


title: Alin4IPrep3

value: Adult


title: NK S5

source_name: NK S5

value: Peripheral Blood


title: Male_Tg_Abx (merged_SS-HBD49_S42)


title: Male_Tg_Abx (merged_SS-HBD48_S41)


title: NK H21 H18 H2 A7

source_name: NK H21 H18 H2 A7

value: donor H21 #1 healthy, donor H18 #2 healthy, donor H2 #3 healthy, patient A7 #4 d24


title: knock-out psm alpha time 30 rep 1

description:
knock-out psm alpha time 30 rep 1_Staphylococcus aureus knock out psm alpha
3964_KMR-1_Human_4_11-3-Dpsm-a-1-30_01_9105

tag: cell type

value: Neutrophils


title: time 0 human PMN control rep 2

description:
time 0 human PMN control rep 2_no treatment, control
3962_KMR-1_Human_2_80-20-t=0PMNcontrol-2-0_01_8999

source_name: neutrophils_time 0 human PMN control

value: no treatment, control


title: time 0 human PMN control rep 1

description:
time 0 human PMN control rep 1_no treatment, control
3961_KMR-1_Human_1_78-10-t=0PMNcontrol-1-0_01_1851


title: NK S2 S4

source_name: NK S2 S4


title: Male_Tg_Abx (merged_SS-HBD46_S39)

source_name: Short-term ABX Tg mice study_sacrificed at PND24

tag: tissue dissection anatomy


title: Alin4IPrep2


title: Alin4IPrep1


title: Male_Tg_Abx (merged_SS-HBD45_S38)

tag: treatment


title: MMLV UAC 2

source_name: UAC Synthetic RNA


title: Male_Tg_Abx (merged_SS-HBD44_S37)


title: MMLV UAC 3


title: AMV YAC

description: AMV reverse transcribed cDNA product of synthetic RNA


title: MMLV UAC 1


title: Male_NonTg_Abx (merged_SS-HBD40_S34)

value: C57BL/6 (WT littermates from APPPS1-21 breedings)


title: AMV N1mYAC


title: L1lin4IPrep3

value: UPN INTACT (otIs790); lin-4(e912)


title: NK S3

source_name: NK S3

tag: patient id


title: Male_NonTg_Abx (merged_SS-HBD42_S36)


title: NK S1 S4

source_name: NK S1 S4

tag: sample detail


title: Male_NonTg_Abx (merged_SS-HBD41_S35)

tag: strain


title: L1lin4IPrep2


title: Male_NonTg_Abx (merged_SS-HBD37_S32)

tag: Sex


title: Male_NonTg_Abx (merged_SS-HBD38_S33)


title: AMV UAC 1


title: AIPrep7

description:
neuronalIPvsinput_Rawcounts.txt
neuronalIPsizeadjustedcounts.txt
neuronalIPdevelopmentalDESeq2normalizedcounts.txt
neuronalIPL1AdultmutantDESeq2normalizedcounts.txt

tag: type

value: UPN INTACT (otIs790)


title: AIPrep5


title: CUTLL1_CRISPR_brunello_valine-2V_day_7

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

institute: Helmholtz Centre for Infection Research

description:
CUTLL1_CRISPR_Brunello_normalized-results.tsv
CUTLL1_CRISPR_Brunello_CERES-scores.tsv

data_processing:
Library strategy: CRISPR sgRNA screen
Trimming: Adapter sequences were first trimmed off using cutadapt, removing all untrimmed reads (parameters -e 0.1 -O 10 -m 20 –discard-untrimmed)
Counting: Trimmed 20bp reads were counted by exact matches with the sgRNA library sequences.
Normalization: Raw reads were intra-sample normalized with edgeR function cpm.
Differential analysis: First, log2 fold-changes based on CPM values between different valine conditions and repsective treatment days were calculated with a pseudocount of 0.1.
Gene summary: To summarize individual sgRNAs on a gene-level, we executed the R-package "ceres" to report essentiality scores per gene, using log2 fold-changes..
Genome_build: hg19
Supplementary_files_format_and_content: tsv file - per-sample CPM and differential CERES scores

source_name: CUTLL1 T-ALL cell line

extract_protocol:
Genomic DNA was isolated using Qiagen DNA purfication kit for tRNA screen and Takara Nucleospin Blood XL kit.
Libraries were prepared by amplification of the sgRNA with primers compatible for Illumina sequencing.

treatment_protocol: For the whole genome screen, the infected cells were cultured in standard or low valine media.

tag: cell line

tag: crispr library

value: whole-genome Brunello

tag: valine concentration

value: low - 2V

tag: time point

value: 7 days post passage into differential valine media

tag: molecule subtype

value: CRISPR sgRNA


title: AIPrep6

tag: strain/genotype

tag: developmental stage


title: NK S6

source_name: NK S6

tag: tissue


title: AIPrep4


title: L1lin4IPrep1

description:
neuronalIPsizeadjustedcounts.txt
neuronalIPL1AdultmutantDESeq2normalizedcounts.txt


title: AMV UAC 2

tag: modification


title: Male_NonTg_Abx (merged_SS-HBD36_S31)

value: Cerebral cortex

value: dorsal side of the right hemisphere

value: Abx


title: 4T1-MCF7 mixed single-omics sample RNA

description: RNA

organism:
Homo sapiens
Mus musculus

source_name: breast cancer cells

tag: cell type

value: breast cancer cells

tag: human cell line

tag: mouse cell line


title: AIPrep3

value: neuronal IP


title: CUTLL1_CRISPR_brunello_valine-20V_day_4

value: high - 20V

value: 4 days post passage into differential valine media


title: 4T1-MCF7 mixed multi-omics sample protein

description: Protein

tag: treatment

tag: antibody

value: anti-human Epcam antibody and anti-mouse Epcam antibody


title: Male_NonTg_Vehicle (merged_SS-HBD33_S29)

tag: tissue dissection anatomy

tag: strain

value: Male

value: Vehicle


title: AIPrep1

tag: type

value: Adult


title: CUTLL1_CRISPR_brunello_valine-20V_day_7

tag: cell line


title: CUTLL1_CRISPR_brunello_valine-2V_day_4

tag: crispr library


title: KOPTK1_rep2

data_processing:
Adapter trimming: Adapters were trimmed off on both sides of the sgRNA in the read sequence using cutadapt. This left a 20bp potential sgRNA sequence.
Counting: Trimmed reads were matched exactly to the library's sgRNA sequences and counted.
Normalization: Raw counts were processed in edgeR, using the functions “calcNormFactors” and “estimateTagwiseDisp” functions for intra- and inter-sample normalization, reporting CPM values per tRNA and sample. Additional length normalization, such as FPKM, is not applicable because all sequencing read fragments reflecting tRNAs are of the same length.
Genome_build: hg19
Supplementary_files_format_and_content: tsv-table of CPM values

source_name: human T-ALL cell line

extract_protocol:
Small RNA was extracted using the MicroRNA purification kit from Norgen (Catalog no: 21300) folllowing manufacturer's guidelines.
Library construction was performed using universal primers compatible with Illumina platform. Primers are unqiely matching annotated human tRNA genes.
custom tRNA-specific sequencing

treatment_protocol: CUTLL1 cells were treated with either DMSO or gamma-secretase inhibitor (Compound E, Alexis Bioscience, ALX-270-415-C250) for 72 hours.


title: KOPTK1_rep1


title: HPBALL_rep2

value: HPBALL


title: L4IPrep6

description:
neuronalIPvsinput_Rawcounts.txt
neuronalIPsizeadjustedcounts.txt
neuronalIPdevelopmentalDESeq2normalizedcounts.txt

value: UPN INTACT (otIs790)


title: Male_NonTg_Vehicle (merged_SS-HBD31_S27)

value: C57BL/6 (WT littermates from APPPS1-21 breedings)

tag: Sex


title: Male_NonTg_Vehicle (merged_SS-HBD30_S26)


title: Male_NonTg_Vehicle (merged_SS-HBD32_S28)


title: KOPTK1_gSI_72h_rep1

data_processing:
Alignment: Sequencing reads were aligned against the reference genome sequences hg19 for human and mm10 for mouse using the STAR aligner. Only uniquely mapped reads were kept.
Read counting: STAR integrated function --quantMode GeneCounts was applied using Ensembl Genes V75 for human and Ensembl Genes V85 gene annotations. Only reverse-mapping read counts (RF) were utilized for downstream analyses.
Normalization: FPKM normalization was applied using edgeR after intra- and inter-sample normalization (“calcNormFactors” and “estimateTagwiseDisp”).
Genome_build: hg19 for human; mm10 for mouse
Supplementary_files_format_and_content: tsv-table of FPKM values

extract_protocol:
RNA was extracted using the RNeasy Mini Kit using Qiagen kit (Catalog no: 74106) folllowing manufacturer's guidelines.
The libraries were prepared using NEXTflex Rapid Directional RNA-Seq Kit from Bioo Scientific (Catalog no: 5138-07) folllowing manufacturer's guidelines.

treatment_protocol: Human cell line KOPTK1 was either treated with DMSO control or gamma-secretase inhibitor (Compound E, Alexis Bioscience, ALX-270-415-C250) for 72h. For the in vivo experiments, mice secondrary transplanted with NOTCH-delta E tumors were fed either valine proficient control diet or valine deficient diet or valine defiecinet diet substituted with either 0.8g/L or 0.4g/L valine in drinking water. Mice were sacrificed after 3 weeks in different diets and leuekmic cells were sorted from spleen using GFP as a marker and used for RNA isolation.

value: gSI


title: Jurkat_rep2

value: Jurkat


title: HPBALL_rep1


title: L4IPrep4


title: KOPTK1_gSI_72h_rep2


title: Male_NonTg_Vehicle (merged_SS-HBD29_S25)


title: AIPrep2


title: KOPTK1_DMSO_72h_rep2

value: DMSO


title: L4IPrep5


title: KOPTK1_DMSO_72h_rep1


title: L4IPrep3


title: Male_NonTg_Abx (merged_SS-HBD28_S24)

source_name: Short-term ABX Tg mice study_sacrificed at 9 weeks

value: Cerebral cortex


title: Jurkat_rep1


title: cytoplasmic_vcp_rep2

city: London

first: Oliver

last: Ziff

state: London

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using trimomatic. Reads were aligned to hg38 human reference genome using splice-aware aligner, STAR v2.6.1. Aligned reads were quantified with HTSeq(Anders et al., 2014) using intersection-strict mode to enable counting of spliced transcripts at gene-level based on Ensembl GRCh 38.99 annotation.
Differential gene expression was measured using DESeq2, using a design model by “~ Mutation” and “~ Fraction”. Results were generated by comparing the mutant versus control and a gene was considered significantly differentially expressed if FDR < 0.05.
Genome_build: hg38
Supplementary_files_format_and_content: Gene counts as obtained from htseq.

growth_protocol: iPSCs were maintained using standard protocols and were differentiated into astrocytes, generating highly enriched (>90%) populations of astrocytes and maintained on Geltrex (Life Technologies) with serum-free Essential 8 Medium media (Life Technologies), and passaged using EDTA.

extract_protocol:
Subcellular fractionation was achieved using the Ambion PARIS kit (ThermoFisher Scientific). The cytosolic fraction was obtained by lysing cells in ice-cold cell fractionation buffer for 5 minutes, disrupting plasma membranes whilst leaving nuclear membranes intact. Lysates were centrifuged for 3 minutes at 500 x g at 4°C. Supernatant was further centrifuged at maximum speed at 4°C for 1 minute, and the resulting supernatant was processed as the cytosolic fraction. Nuclear pellets from the first centrifugation step were gently washed with cell fractionation buffer and then lysed on ice for 30 minutes in 8M Urea Nuclear Lysis Buffer. The resulting nuclear fraction was homogenised using a QIAshredder (Qiagen) to shred chromatin and reduce viscosity. Both lysis buffers were supplemented with 0.1 U/μl RiboLock RNase Inhibitor (ThermoFisher Scientific) and HALT Protease Inhibitor Complex (ThermoFisher Scientific).
Poly(A)+ selected reverse stranded RNAseq libraries were prepared from whole astrocyte and their nuclear and cytoplasmic fractions obtained from astrocyte differentiation from two control and two VCP mutant cell lines using the KAPA mRNA HyperPrep Library kit for Illumina®, with 50ng of total RNA as input.

treatment_protocol: After neural conversion (7 days in a chemically defined medium containing 1 μM Dorsomorphin (Millipore), 2 μM SB431542 (Tocris Bioscience) and 3.3 μM CHIR99021 (Miltenyi Biotec) neural precursors were patterned for 7 days with 0.5 μM retinoic acid and 1 μM purmorphamine, followed by a 4-day treatment with 0.1 μM purmorphamine. After a propagation phase (>60 days) with 10 ng/ml FGF-2 (Peprotech) astrocytes were terminally differentiated in presence of BMP4 (10 ng/ml, R&D) and LIF (10 ng/ml, Sigma-Aldrich).

tag: individual

tag: genotype

tag: rna fraction

value: polyA cytoplasmic RNA


title: L4IPrep2

tag: strain/genotype

tag: developmental stage


title: Male_NonTg_Vehicle (merged_SS-HBD34_S30)

tag: tissue

value: dorsal side of the right hemisphere


title: 4T1-MCF7 mixed multi-omics sample RNA

description: RNA

tag: cell type

value: breast cancer cells


title: cytoplasmic_vcp_rep1

value: glia


title: L2IPrep5

value: neuronal IP


title: L4IPrep1


title: TALL_rep4

source_name: primary T-ALL

value: primary T-ALL


title: TALL_rep5


title: Male_NonTg_Abx (merged_SS-HBD24_S21)

value: Abx


title: cytoplasmic_ctrl_rep2


title: L2IPrep4


title: cytoplasmic_ctrl_rep1


title: nuclear_vcp_rep2

value: polyA nuclear RNA


title: TALL_rep2


title: CD4_Tcells_rep2

source_name: human CD4 T-cells

value: healthy CD4 T-cells


title: L2IPrep3


title: nuclear_ctrl_rep2


title: Male_NonTg_Abx (merged_SS-HBD27_S23)

value: Male


title: Male_NonTg_Abx (merged_SS-HBD25_S22)


title: Male_NonTg_Abx (merged_SS-HBD23_S20)


title: nuclear_vcp_rep1


title: Male_NonTg_Vehicle (merged_SS-HBD20_S18)

value: Vehicle


title: CUTLL1_gSI_rep2


title: Male_NonTg_Abx (merged_SS-HBD22_S19)


title: CUTLL1_gSI_rep1


title: Male_NonTg_Vehicle (merged_SS-HBD19_S17)


title: TALL_rep1


title: Male_NonTg_Vehicle (merged_SS-HBD18_S16)


title: nuclear_ctrl_rep1


title: L1IPrep4

value: UPN INTACT (otIs790)


title: TALL_rep3


title: Male_NonTg_Vehicle (merged_SS-HBD16_S14)

value: C57BL/6 (WT littermates from APPPS1-21 breedings)


title: CD4_Tcells_rep1


title: Male_NonTg_Vehicle (merged_SS-HBD17_S15)


title: L1IPrep3


title: whole_vcp_rep2

source_name: iPSC_derived_astrocyte, whole astrocyte

value: polyA whole cell RNA


title: L1IPrep2

source_name: neuronal nuclei IP


title: whole_ctrl_rep2


title: L2IPrep2


title: Cultured mammary cells with DDR1 inhibition, followed by release

city: Boston

first: Charlotte

last: Kuperwasser

address: 136 Harrison Ave

institute: Tufts University

data_processing:
Paired-end fastq files were merged into a single bam using Picard version 1.12 FastqToSam with default parameters
Cell barcodes were tagged using TagBamWithReadSequenceExtended from Drop-seq_tools-1.12 with parameters BASE_RANGE=1-12 BARCODED_READ=1 TAG_NAME=XC NUM_BASES_BELOW_QUALITY=1
UMI were tagged using TagBamWithReadSequenceExtended from Drop-seq_tools-1.12 with parameters BASE_RANGE=13-20 BASE_QUALITY=10 BARCODED_READ=1 DISCARD_READ=True TAG_NAME=XM NUM_BASES_BELOW_QUALITY=1
Low quality barcodes were filtered using FilterBAM from Drop-seq_tools-1.12 with TAG_REJECT=XQ
Trimmed adapters using TrimStartingSequence from Drop-seq_tools-1.12 with parameters SEQUENCE=AAGCAGTGGTATCAACGCAGAGTGAATGGG MISMATCHES=0 NUM_BASES=5
Trimmed polyA using PolyATrimmer from Drop-seq_tools-1.12 with parameters MISMATCHES=0 NUM_BASES=6
Converted bam to fastq usign SamToFastq from Picard version 1.12 with default parameters
Aligned to homo sapiens GRCh38.85 using STAR with parameters --limitOutSJcollapsed 10000000 --limitIObufferSize 300000000
Merged tags with mapped output using MergeBamAlignment from Picard version 1.12 with parameters INCLUDE_SECONDARY_ALIGNMENTS=false PAIRED_RUN=false
Tagged with TagReadWithGeneExon from Drop-seq_tools-1.12 using homo sapiens GRCh38.85 with parameters TAG=GE
Used DetectBeadSynthesisErrors from Drop-seq_tools-1.12 with parameters NUM_BARCODES=2000 PRIMER_SEQUENCE=AAGCAGTGGTATCAACGCAGAGTAC (NUM_CORE_BARCODES=1500 in MEGM sample)
Built digital gene expression matrix using DigitalExpression from Drop-seq_tools-1.12 with parameters NUM_CORE_BARCODES=1000 (NUM_CORE_BARCODES=750 in MEGM sample)
Genome_build: GRCh38.85
Supplementary_files_format_and_content: DGE files represent digital gene expression matrices. Rows represent genes and columns represent cells. The file is tab-delimited.

source_name: Cultured mammary cells

growth_protocol: Cultured as described in Sokol et al. Breast Cancer Research, 2016, https://doi.org/10.1186/s13058-016-0677-5

extract_protocol:
Mammary glands were released from hydrogel pads and dissociated to single cells. The single-cell suspension was subjected to Seq-Well.
Single-cell libraries were generated as described in Gierahn et al. Nature Methods, 2017 and sequenced using the Illumina Nextseq500 in paired-end mode.

value: Treated with DDR1 inhibitor for 12 days followed by 2 days without DDR1 inhibitor

value: mammary cels


title: L1IPrep1

extract_protocol:
Animals were collected at the respective stage as described above.  ~600,000 animals were collected for each L1/L2 replicates while ~200,000 animals were collected for each L4/A replicates. At the time of collection, animals were washed off the plate with M9, washed 3x with M9, lightly fixed with cold RNAse-free DMF for 2 minutes before washing with 1xPBS 3x. Modification were made from previous INTACT protocol to optimize pulldown of neuronal nuclei (Steiner et al., 2012). All steps following were done in cold rooms (4°C) to minimized RNA degradation. The animals were homogenized mechanically using disposable tissue grinder (Fisher) in 1x hypotonic buffer (1x HB: 10mM Tris pH 7.5, 10mM NaCl, 10mM KCl, 2mM EDTA, 0.5mM EGTA, 0.5mM Spermidine, 0.2mM Spermine, 0.2mM DTT, 0.1% Triton X-100, 1x protease inhibitor). After each round of mechanical grinding (60 turns of the grinder), the grinder was washed with 1mL 1x HB and the entire homogenate was centrifuged at 100xg for 3 min. The supernatant was collected for later nuclei extraction and the pellet was put under mechanical grinding and centrifugation for 4 additional rounds. The supernatant collected from each round were pooled, dounced in a glass douncer, and gently passed through an 18 gauge needle 20x to further break down small clumps of cells. The supernatant was then centrifuged at 100xg for 10 min to further remove debris and large clumps of cells. Nuclei was isolated from the supernatant using Optiprep (Sigma): supernatant after centrifugation was collected in a 50mL tube, added with nuclei purification buffer (1x NPB: 10mM Tris pH 7.5, 40mM NaCl, 90mM KCl, 2mM EDTA, 0.5mM EGTA, 0.5mM Spermidine, 0.2mM Spermine, 0.2mM DTT, 0.1% Triton X-100, 1x protease inhibitor) to 20mL, and layered on top of 5mL of 100% Optiprep and 10mL of 40% Optiprep. The layered solution was centrifuged at 5000xg for 10 min in a swinging bucket centrifuge at 4°C. The nuclei fraction was collected at the 40/100% Optiprep interface. After removal of the top and bottom layers, leaving a small volume containing the nuclei, the process was repeated 2 additional times. After final collection of the crude nuclei fraction, the volume was added to 4mL with 1xNPB and precleared with 10µl of Protein-G Dynabeads and 10 µl of M270 Carboxylated beads for 30min to 1hr (Invitrogen). The precleared nuclei extract was then removed, and 50 µl was taken out as input samples (total nuclei). The rest was incubated with 30µl of Protein G Dynabeads and 3 µl of anti-FLAG M2 antibody (Sigma) overnight to immmunoprecipiate (IP) the neuronal nuclei. The following day, the IPed neuronal nuclei was washed 6-8 times with 1xNPB for 10-15 min each time. The resulting neuronal nuclei IPed beads were resuspended in 50 ul 1xNPB and a small aliquot was used to check with DAPI staining to ensure the qualities of the procedure: 1) sufficient quantities of nuclei was immunoprecipiated; 2) nuclei are intact and not broken; 3) the majority of bound nuclei are single, mCherry-labelled neuronal nuclei and minimal nuclei clumps and large tissue chunks were immunoprecipiated. Anything not satisfying these quality checks were not used for downstream processing. The resulting input and neuronal IP samples were used for isolation of total RNA using Nucleospin RNA XS kit according to manufacturer’s protocol (Takara).
RNA-seq libraries were prepped using the Universal RNA-seq kit (Tecan) according to manufacter’s protocol.


title: Female_NonTg_Vehicle (merged_SS-HBD14_S12)

value: Cerebral cortex

value: Female


title: CUTLL1_DMSO_rep2

value: DMSO


title: L2IPrep1


title: Female_NonTg_Vehicle (merged_SS-HBD09_S8)

value: dorsal side of the right hemisphere


title: matched_FL_control_H3K79me2_input

city: Oxford

first: Siobhan

last: Rice

address: Room 320, WIMM, JR Hospital/Headley Way

institute: Weatherall Institute of Molecular Medicine

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Genome_build: hg19
bigWig files made using HOMER v4.7 (tag directories made using command "makeTagDirectory"; bigWigs made using command "makeBigWig.pl")

source_name: human CD45+CD19+ FL cells sorted from the bone marrow of engrafted NSG mouse

growth_protocol: crisprMLL-AF4 cells were maintained in StemLine II supplemented with 100ng/mL each of SCF, FLT3L and TPO during editing protocol and immediately transplanted into NSG mice via tail vein injection. Matched control FL cells were derived from primary human FL and never maintained in culture. SEM cells were continuously grown in IMDM with 10% FBS, split when they reached a density of 1-2x10e6 cells/ml down to 5x10e5 cells/ml

extract_protocol:
Cells were washed with PBS and fixed in either 1% FA for 10 minutes (histones) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (other, non-histone). Cells were sonicated to give fragments of 100-300bp followed by IP.
DNA libraries were made using the NEBnext ultra DNA library preparation kit for Illumina (Cat no. E7370).

treatment_protocol: crisprMLL-AF4 FL cells were electrporated with Cas9-MLL and Cas9-AF4 ribonucleoproteins (RNP) to induce an MLL-AF4 chromosomal translocation. Matched control FL cells were untreated. SEM cells were electroporated with NT or MLL-AF4-specific siRNA at 0h and again at 48h, then harvested 96h after initial transfection.

value: primary human FL CD34+ cells were CRISPR-Cas9 edited to induce an MLL-AF4 chromosomal translocation and engrafted into an NSG mouse

value: human CD19+ cells MACS bead selected from the bone marrow of engrafted NSG mouse

tag: chip antibody


title: CUTLL1_DMSO_rep1


title: Female_NonTg_Vehicle (merged_SS-HBD12_S11)


title: BACO-6-Undiff

city: Cincinnati

first: Jorge

middle: A

last: Bezerra

state: OH

address: 3333 Burnet Ave.

department: Gastroenterology, Hepatology & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Organoids derived from biliary atresia liver obtained from a 9 month old child

data_processing:
RNA-Seq analysis is based on the HiSat2 / Kallisto pipeline.
First, the sequences were aligned to the human reference genome hg19 using HiSat2 (http://daehwankimlab.github.io/hisat2/).
Data was then processed using the Kallisto tool (https://pachterlab.github.io/kallisto/) for quantifying transcript abundance.
The annotated transcripts were obtained from Ensembl annotations and gene levels measured in Transcripts Per Million (TPM).
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited files containing gene levels in Transcripts Per Million (TPM).

source_name: Organoids derived from Liver

growth_protocol: Organoids were generated from human liver tissues. Cultures were maintained in expansion medium.

extract_protocol:
Organoids cultured in either expansion or differentiation media were harvested into Trizol to isolate RNA. Total RNA was isolated from organoids and liver tissue using miRNeasy mini Kit, according to the manufacturer’s protocol (QIAGEN, Valencia, CA).
The samples were checked for quality and quantity using the Nanodrop 1000 spectrophotometer, Qubit fluorometer (Thermo Fisher Scientific, Waltham, MA), and Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA).
Total RNA was reverse transcribed using Illumina’s TruSeq RNA library preparation kit V2. Each sample was fitted with one of the 24 adapters containing a different 6 base molecular barcode for high level multiplexing. After 12 cycles of PCR amplification, completed libraries were sequenced on an Illumina instrument.

treatment_protocol: Organoids were cultured in differentiation medium for 14 days.

tag: age

value: 9 mo

tag: diagnosis

value: Biliary atresia

tag: differentiated

value: No


title: Cultured mammary cells with DDR1 inhibition

tag: treatment

value: Treated with DDR1 inhibitor for 14 days


title: BACO-1-Diff

description: Differentiated organoids derived from biliary atresia liver obtained from a 6 month old child

value: 6 mo

value: Yes


title: Female_NonTg_Abx (merged_SS-HBD06_S5)

tag: tissue dissection anatomy

tag: strain

value: Abx


title: BACO-2-Diff

description: Differentiated organoids derived from biliary atresia liver obtained from a 2 year old child

value: 2 yr


title: BACO-11-Undiff

description: Organoids derived from biliary atresia liver obtained from a 8 month old child

value: 8 mo


title: BACO-3-Diff

description: Differentiated organoids derived from biliary atresia liver obtained from a 7 year old child

value: 7 yr


title: BACO-10-Undiff

description: Organoids derived from biliary atresia liver obtained from a 2 year old child


title: whole_vcp_rep1

tag: cell line

value: glia

value: polyA whole cell RNA


title: whole_ctrl_rep1


title: crisprMLL-AF4_H3K79me2


title: Female_NonTg_Vehicle (merged_SS-HBD10_S9)

value: Cerebral cortex

value: C57BL/6 (WT littermates from APPPS1-21 breedings)

value: Female

value: Vehicle


title: BACO-8-Undiff

description: Organoids derived from biliary atresia liver obtained from a 9 week old child

value: 9 wk


title: BACO-4-Undiff

description: Organoids derived from biliary atresia liver obtained from a 5 week old child

value: 5 wk


title: Female_NonTg_Vehicle (merged_SS-HBD08_S7)

value: dorsal side of the right hemisphere


title: matched_FL_control_H3K79me2

value: primary human FL CD34+ cells were CRISPR-Cas9 edited to induce an MLL-AF4 chromosomal translocation and engrafted into an NSG mouse

value: human CD19+ cells MACS bead selected from the bone marrow of engrafted NSG mouse


title: BACO-7-Undiff

description: Organoids derived from biliary atresia liver obtained from a 22 month old child

value: 22 mo

value: Biliary atresia

value: No


title: Cultured mammary cells

value: Vehicle-treated control for 14 days

value: mammary cels


title: BACO-3-Undiff

description: Organoids derived from biliary atresia liver obtained from a 6 week old child

value: 6 wk


title: Female_NonTg_Vehicle (merged_SS-HBD11_S10)


title: crisprMLL-AF4_input

source_name: human cells from the spleen of engrafted NSG mouse

value: human cells isolated from the spleen of engrafted NSG mouse


title: BACO-2-Undiff

description: Organoids derived from biliary atresia liver obtained from a 12 week old child

value: 12 wk


title: crisprMLL-AF4_H3K79me2_input


title: NCO-1-Undiff

description: Organoids derived from healthy donor liver obtained from a 13 year old child

value: 13 yr

value: Healthy Donor


title: NCO-2-Undiff

description: Organoids derived from Urea cycle defect liver obtained from a 10 month old child

value: 10 mo

value: Urea cycle defect


title: BACO-5-Undiff

description: Organoids derived from biliary atresia liver obtained from a 7 year old child

value: 7 yr


title: BACO-9-Undiff

description: Organoids derived from biliary atresia liver obtained from a 6 month old child

value: 6 mo


title: crisprMLL-AF4_MLL-N


title: NCO-3-Undiff

description: Organoids derived from healthy donor liver obtained from a 17 year old child

value: 17 yr


title: LIV-1-NC

description: Healthy donor liver tissue obtained from a 3.5 year old child

source_name: Liver


title: FL_CBP_rep2

data_processing:
RNA-seq reads were aligned to the hg38 genome using STAR
Read counts were determined using featureCounts (Subread package)
Genome_build: hg38

source_name: primary human FL

growth_protocol: crisprMLL-AF4 and control FL cells were maintained in StemLine II supplemented with 100ng/mL each of SCF, FLT3L and TPO during editing protocol and immediately transplanted into NSG mice via tail vein injection. Sorted FL cells were derived from primary human FL and never maintained in culture.

extract_protocol: RNA was extracted using the RNEasy mini kit (QIAGEN 74134). Poly A purification was conducted using the NEB Poly(A) mRNA magnetic isolation module as per the manufacturer’s protocol.

treatment_protocol: crisprMLL-AF4 FL cells were electrporated with Cas9-MLL and Cas9-AF4 ribonucleoproteins (RNP) to induce an MLL-AF4 chromosomal translocation, Control FL cells were electroporated with Cas9 or Cas9-MLL RNP only. Sorted FL cells were untreated

tag: sample type

value: primary human FL

value: primary human FL cells were FACS sorted to isolate hematopoietic subpoulations


title: BACO-1-Undiff

description: Organoids derived from biliary atresia liver obtained from a 2 month old child

value: 2 mo


title: THP1_CRISPR_tRNA_day_20

description:
CRISPR_tRNA_library_normalized-results.tsv
CRISPR_tRNA_library_CERES-scores.tsv

source_name: THP1 AML cell line

tag: crispr library

value: tRNA-specific

tag: valine concentration

tag: time point

value: 20 days post transduction

tag: molecule subtype

value: CRISPR sgRNA


title: FL_CBP_rep1


title: Female_NonTg_Abx (merged_SS-HBD04_S4)

value: Cerebral cortex

value: dorsal side of the right hemisphere

value: C57BL/6 (WT littermates from APPPS1-21 breedings)

tag: Sex

value: Female

value: Abx


title: LIV-2-NC

description: Healthy donor liver tissue obtained from a 17 year old child

value: Healthy Donor

value: No


title: Female_NonTg_Abx (merged_SS-HBD01_S1)


title: Female_NonTg_Abx (merged_SS-HBD03_S3)


title: THP1_CRISPR_tRNA_day_4

value: 4 days post transduction


title: crisprMLL-AF4_AF4-C

value: primary human FL CD34+ cells were CRISPR-Cas9 edited to induce an MLL-AF4 chromosomal translocation and engrafted into an NSG mouse

value: human cells isolated from the spleen of engrafted NSG mouse


title: Female_NonTg_Abx (merged_SS-HBD02_S2)


title: FL_LMPP_rep1


title: ChIL-H3K27ac - CTX injurured TA - Day 14 - rep. 3

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

data_processing:
Gene expression quantification (TPM estimation) was performed by Salmon "quant" with the default option.
The reads of ChIL-seq were mapped against the GRCm38 or GRCh38 reference genome using Bowtie2 with the default option.
Duplicated reads were discarded using samtools (rmdup) and the uniquely mapped reads were used for further analysis.
The bigWig files were generated using deepTools (version 3.4.1) with the command: bamCoverage -p 36 --binSize 100 --normalizeUsing CPM --smoothLength 1000.
Genome_build: GRCm38, GRCh38
Supplementary_files_format_and_content: CSV files include comma-delimited gene expression (TPM) matrices

source_name: tibialis anterior muscle

extract_protocol:
Each cryo-tissue section (10 um) was placed onto u-plate 96 well bottom (Ibidi #89626) and the plate was stored at -80ºC freezer without backing to room temperature until use. Tissue section was fixed with 4%PFA in 0.3% TritonX-100/PBS for five minutes and washed with 0.3% TritonX-100/PBS. Double blocking were performed using blocking one (Nacalai #03953) and M.O.M blocking reagent (Vector Laboratories #BMK-2202) as instructed. The sections were incubated with primary antibody in M.O.M. protein concentrate/PBS at 4ºC overnight, followed by incubating with ChIL probe at same condition but in addition of NaCl at 0.5 M concentration.
ChIL-seq was performed according to ChIL (Harada et al., 2018) with some modifications. Longer incubation time is used for some steps (Extended Tn5 binding 1hr and fill-in step 2hrs),  Thermo T7 RNA polymerase (100 U per well; Toyobo), and 15 cycles of PCR amplification. Column purification (Zymo #D4013) and x0.5 volume of AMpure beads (Beckman Coulter) selection were performed to obtain 200-500 bp average of library.  For RNA-seq, total RNA was extracted from the cryo sections (up to five serial sections) using Direct-Zol kit (Zymo #R2063). The total of 10 ng RNA was used for library preparation using SMART-Seq Stranded Kit (Takara) as instructed.

value: tibialis anterior muscle

tag: antibody


title: FL_LMPP_rep2

value: primary human FL


title: ChIL-H3K27ac - CTX injurured TA - Day 14 - rep. 4

tag: tissue


title: ChIL-H3K27ac - CTX injurured TA - Day 14 - rep. 5


title: ChIL-H3K27ac - CTX injurured TA - Day 14 - rep. 2


title: LIV-3-NC

description: Healthy donor liver tissue obtained from a 13 year old child

value: 13 yr


title: Jurkat_CRISPR_tRNA_day_4

source_name: Jurkat T-ALL cell line

value: Jurkat


title: CUTLL1_CRISPR_tRNA_day_20

source_name: CUTLL1 T-ALL cell line

value: tRNA-specific


title: ChIL-H3K27ac - CTX injurured TA - Day 14 - rep. 1


title: FL_MPP_rep3

value: primary human FL cells were FACS sorted to isolate hematopoietic subpoulations

tag: cell type


title: CUTLL1_CRISPR_tRNA_day_4

value: CRISPR sgRNA


title: ChIL-H3K27ac - CTX injurured TA - Day 7 - rep. 4


title: FL_LMPP_rep3