title: Th17 cells, Control cohort, Biol rep 11

description: Library name: EDCV040_Th17_S2

value: Th17 Cells

value: Other


title: Th17 cells, Control cohort, Biol rep 12

status: Public on Dec 15 2025

type: SRA

city: Kingston

first: Chandrakant

last: Tayade

state: Ontario

address: 18 Stuart Street

country: Canada

institute: Queen's University

description: Library name: EDCV045_Th17_S4

library_source: transcriptomic

data_processing:
Reads were trimmed to remove adaptor sequences and low-quality bases using Trimmomatic. Trimmed reads were aligned to the human reference genome (GENCODE/GRCh38) using STAR. Gene-level read counts were generated using HTSeq. The resulting raw counts for each sample are provided in the matrix (tsv file).
Assembly: Homo_sapiens:GRCh38
Supplementary files format and content: tsv file includes raw counts for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral Blood/PBMCs

growth_protocol: Prior to sorting cells (FACS), PBMCs were briefly thawed in a water bath at 37C. Cell suspensions were added to warm RPMI media with 10% FBS and centrifuged at 400RCF for 10mins at 20C prior to resuspending in 2% FACS buffer and counting cells. CD4+ T cells were then isolated using a commercially available kit (17952, StemCell, Canada), as per manufacturer’s protocol. CD4+ T cells were washed and resuspended in warm TexMACS media (130-097-196, Miltenyi Biotec, USA) prior to seeding in 96-well plates at 1x10^6 cells/well.

extract_protocol:
RNA was isolated using RNeasy Micro Kit (74004, Qiagen, Canada), as per manufacturer’s guidelines. RNA purity was assessed using the Nanodrop Spectrophotometer (ThermoFisher, Canada) prior to storage at -80C.
Total RNA purity was assessed prior to library preparation. RNA samples were processed at the McGill Genome Centre (Quebec, Canada) using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) with poly (A) mRNA enrichment. Libraries were generated according to standard NEBNext protocols including mRNA capture, fragmentation, first- and second-strand cDNA synthesis, end repair, adaptor ligation, and PCR amplification. Libraries underwent Ampure XP bead clean-up and quality assessment (LibQC), including removal of primer dimer fragments, before pooling and sequencing on an Illumina NovaSeq X Plus platform using paired-end reads.

treatment_protocol: Cells were re-stimulated prior to FACS staining using 30ng/mL of PMA and 1ug/mL of ionomycin and incubated for 4h at 37C with 5% CO2. Following incubation, IFNg-secreting and IL-17-secreting cells were fluorescently labelled using IFNg Secretion Assay – Detection Kit (FITC; 130-090-433, Miltenyi Biotec, Canada) and IL-17 Secretion Assay – Detection Kit (PE; 130-094-537, Miltenyi Biotec, Canada), as per manufacturer’s protocol. This was conducted to avoid permeabilizing cells to allow for downstream analysis. During staining, cells were also labelled with CD3 (300312) and CD4 (300511) extracellular Abs, as well as the viability dye (423102), all products were purchased from BioLegend unless otherwise stated. Following washing, cells were resuspended in 2% FACS buffer for FACS sorting. Cells were sorted into viable populations of Th17 (CD3+CD4+IFNg-IL-17+), Th1/17 (CD3+CD4+IFNg+IL-17+), and Th1 cells (CD3+CD4+IFNg+IL-17-) in collection media, consisting of 50% FBS and 50% phenol-free RPMI 1640 medium (11835030, ThermoFisher, Canada). Samples were stored on ice, added to respective DNA LoBind Tubes (EP022431021, Millipore Sigma, Canada), and centrifuged at 400RCF for 10mins at 4C before resuspending pellets in 300uL of RNAprotect Cell Reagent (76526, Qiagen, Canada). Cells were stored at -80C prior to RNA isolation.

tag: tissue

value: Peripheral Blood/PBMCs

tag: cell line

value: Primary CD4+ T cells

tag: cell type

tag: Sex

value: Female

tag: rasrm disease_stage_(1-4)

value: Control

tag: age

tag: race

value: Caucasian

tag: bmi

tag: education

value: Post secondary


title: Cse4-mNG ChIP tagged sample

city: Dortmund

first: Max

last: Haase

address: Otto-Hahn-Str. 11

country: Germany

institute: Max Planck Institute of Molecular Physiology

description: Library name: H_uvarum_Cse4-ChIP-mNG

library_source: genomic

data_processing:
Data was processed first by removal of sequencing adaptors with Trimmomatic (v0.39). Then reads were aligned to the H. uvarum HuvaT2T genome build using the Burrows Wheeler aligner (BWA) mem algorithm (v0.7.7). Cse4-enriched regions were determined by taking the ratio of reads mapping from the tagged sample (Cse4-mNeonGreen) to the input control (WT, untagged). Further, Cse4-mNG nucleosome dyads were determined using the deeptools program (v3.5.2).
Assembly: HuvaT2T
Supplementary files format and content: Each process file is provided as a BigWig file

molecule: genomic DNA

organism: Hanseniaspora uvarum

source_name: HHO4 (yMAH1509)

growth_protocol: Cells of H. uvarum were grown in YPD at 30˚C until reaching mid-log phase

extract_protocol:
DNA to be sequenced were extracted by digestion of crosslinked chromatin by MNase and Cse4-bound DNA was eneriched by IP of Cse4 using a mNeonGreen Nanobody.
Libraries were made using the NEBNext® Ultra™ II Illumina kit

treatment_protocol: Cells were cross-linked prior to DNA extraction

value: HHO4 (yMAH1509)

tag: genotype


title: Th1/17 cells, Control cohort, Biol rep 11

description: Library name: EDCV040_Th1-17_S1

value: Th1/17 Cells


title: HA807HWZ-09

type: RNA

city: Portland

first: Julie

middle: A

last: Saugstad

state: Oregon

address: 3181 SW Sam Jackson Park Road

department: Anesthesiology & Perioperative Medicine

country: USA

institute: Oregon Health & Science University

description:
Quantstudio 7K Flex
JSAUG1R01_057

scan_protocol: Each card was assayed on a QuantStudio 7K Flex (Thermo Fisher) by automatic loading of the cards using an Orbitor R2 robot to increase throughput and to ensure that each participants matching CSF and plasma were assayed on the same day.

data_processing:
Wells were considered adequately measured if the AmpScore was ≥ 1 and the CqConf was ≥ 0.8. Wells that did not meet this standard ("acceptable QC") or were labeled "Undetermined" by QuantStudio were considered missing measurements, regardless of Cq value. Wells with acceptable QC but Cq > 34 (in CSF) or Cq > 35 (in plasma) were considered censored values and given special handling using censoring-aware methods in the analysis
miRNAs hsa-miR-499a-3p-478948 and hsa-miR-647-479126 were preselected as negative control probes and not expected to amplify with acceptable QC (see below) in any well; this was fulfilled in the data
The spike-in positive control miRNA cel-miR-39-3p-478293 and primary endogenous normalization reference control miRNA hsa-miR-16-5p-477860 were both required to be completely observed with acceptable QC in all wells for all samples; this was fulfilled in the data. Moreover, miRNAs hsa-miR-24-3p-477992, hsa-miR-92a-3p-477827, and hsa-miR-204-5p-478491 were preselected as positive control normalizer probes and expected to amplify with acceptable QC in at least 90% of wells and show no association with Alzheimer's disease status; this was also fulfilled in the data, with complete observation meeting acceptable QC for miR-24-3p and near-complete observation for miR-92a-3p (complete in plasma, 8% dropout in CSF) and miR-204-5p (4% dropout in plasma, 1% dropout in CSF)
32 (10% of 320) samples displaying one or more of three types of aberrant measurement profile were excluded for a final count of 288 samples (from 156 donors) in the study. The aberrant profile types were: 1) low miRNA yield associated with large or missing Cq values across the entire array (n=9; 2.8%), defined as > 15% missing Cq values; 2) an abnormal Cq distribution shift away from the cohort center of all miRNAs that was inconsistent with the spike-in measurements and suggested RNA concentration irregularities that occurred prior to the spike-in (n=17; 5.3%), defined as a divergence for the global median Cq of > 3.3 spike-in standard deviations from the spike-in median for the sample; and 3) large Cq values for spike-in wells only with no corresponding shift in the Cq values for the human miRNAs assayed (n=11; 3.4%), defined as a sample with a studentized residual > 2 and DFITS > 0.112 (= 2 x sqrt(1/320)) for the sample in a regression of the spike-in mean on the RT-qPCR run order. 4 of the 160 donors had both their CSF and plasma samples excluded by these criteria. The excluded samples were: JSAUG1R01_014 (CSF), JSAUG1R01_023 (Plasma), JSAUG1R01_026 (CSF), JSAUG1R01_033 (CSF), JSAUG1R01_040 (CSF) + JSAUG1R01_045 (Plasma) for donor 5275, JSAUG1R01_046 (Plasma), JSAUG1R01_082 (CSF), JSAUG1R01_091 (CSF) + JSAUG1R01_095 (Plasma) for donor 4802, JSAUG1R01_110 (CSF), JSAUG1R01_113 (Plasma) + JSAUG1R01_119 (CSF) for donor 4075, JSAUG1R01_116 (Plasma), JSAUG1R01_122 (CSF), JSAUG1R01_125 (Plasma), JSAUG1R01_126 (CSF), JSAUG1R01_127 (Plasma), JSAUG1R01_146 (CSF), JSAUG1R01_189 (Plasma), JSAUG1R01_191 (Plasma), JSAUG1R01_200 (CSF), JSAUG1R01_211 (CSF), JSAUG1R01_242 (CSF), JSAUG1R01_270 (Plasma), JSAUG1R01_280 (CSF), JSAUG1R01_282 (Plasma), JSAUG1R01_286 (Plasma), JSAUG1R01_304 (Plasma) + JSAUG1R01_308 (CSF) for donor 4598, JSAUG1R01_315 (Plasma), JSAUG1R01_320 (CSF)
Censored Cq values are viewed as quantitatively unreliable because their measurement falls outside the linear range of the assay, so we treated these as interval observations, defined as an unobserved value falling between an upper and a lower limit. Non-censored Cq values with acceptable QC were used as exact measurements (both bounds of the interval are the same normalized Cq value). Censored Cq values with acceptable QC were treated as falling between the biofluid-specific censoring threshold (lower bound) and the average (upper bound) of the normalized Cq value and the maximum normalized Cq value across all observations on all miRNAs (the "observed maximum", a value that will be strictly less than the maximum cycle number of 40, specified as a machine setting). Fully missing Cq values (marked as "Undetermined" by QuantStudio) were treated as falling between the observed maximum (lower bound) and the maximum cycle number (upper bound of 40). Non-missing Cq values with unacceptable QC were treated as missing measurements except that the recorded Cq (with all normalization adjustments; see value definition below) was used instead of the observed maximum as the lower bound. All the interval bounds were subtracted from the maximum cycle number of 40 to invert the Cq scale so that positive values mark higher expression
The triplicate wells for each sample for each miRNA were summarized into a single most-likely value on the expression (inverted normalized Cq) scale using a Bayesian multilevel interval regression model that considers all replicate wells for the sample jointly and naturally accounts for the different character of censored values in the context of non-censored values for the same miRNA when making predictions. For the Bayesian prior distribution on the biofluid-specific mean level for the miRNA we used a Student's t distribution with 4 degrees of freedom and a (wide and uninformative) scale of 10, and for the log of the root mean square error we used a (similarly uninformative) half-Cauchy distribution with the same scale of 10. Random effects for individual samples were assigned a zero-centered prior normal distribution with default conjugate inverse-gamma hyperprior (shape and scale parameters both 1/100) for the random-effect variance. The imputed value for a missing or censored observation was taken as the posterior biofluid-specific grand mean for the miRNA plus the posterior mean of the random effect, based on 10000 Markov chain Monte Carlo draws from the posterior distribution, following a burn-in run of 2500 draws. Note that the rank correlation between the predictions from this model and the naïve means of the corresponding replicate wells was 0.99, reflecting almost complete preservation of rank ordering among samples, but the model prediction is less biased because it accounts for censoring, which prevents it from overestimating the expression level. This bias correction was very necessary for CSF, where censoring was common, but less so for plasma, which had only small amounts of censoring
Cq measurement variance caused by RNA isolation variance was adjusted via median-alignment of the cel-miR-39-3p-478293 spike‑in control reactions as an exogenous calibration factor .For further endogenous calibration of Cq distributions across samples we identified 17 miRNAs in CSF and 53 in plasma that were always present with acceptable QC in 100% of the samples and used these to align the Cq distributions across all donors. For each biofluid, we calculated the median over the per-biofluid always-observed miRNAs and modeled both biofluid medians as a function of a 7-knot restricted cubic spline of the RT-qPCR run order using a linear mixed-effects regression model including random intercepts per donor. Residuals from this model were subtracted from the corresponding Cq values for all miRNAs to align the Cq distributions across all donors. Following this, batch calibration was performed to remove residual technical artifacts in the Cq measurements attributable to processing order. Each paired biofluid RNA (CSF and plasma from same donor) was run on separate cards (to ensure appropriate thresholding and baselining for each biofluid separately) but on the same day to minimize any potential batch effects, so order-related processing effects were expected to affect both biofluids similarly. To account for these, biofluid differences were subtracted out using an absorbing linear regression, which enforced a grand mean of zero across the Cq distribution, and then we fit a linear mixed-effects regression model including the same 7-knot restricted cubic spline of the RT-qPCR run order as above, interacted with a biofluid selector to allow for biofluid-specific adjustments to the fit, and additionally including indicators for known abnormal events or conditions noted during processing, with isolation batches entered as random intercepts. Fitted values from this regression were subtracted from the corresponding Cq values for all miRNAs as the adjustment for batch and order-related effects. Finally, we performed a Cq normalization using a mixed-effects model on the endogenous miRNA normalizer (hsa-miR-16-5p-477860, hsa-miR-24-3p-477992, hsa-miR-92a-3p-477827, and hsa-miR-204-5p-478491) Cq values only. The model included quadratic effects of age, fully-interacted indicators for sex and AD diagnosis , and crossed random effects to model the miRNA-sample interaction. We used this model to estimate the residual differences between different samples (irrespective of biofluid) as BLUPs (best linear unbiased predictions); the BLUP values were subtracted from the fully calibrated Cq values as endogenous normalizer level effects across samples, normalizing the Cq values to those levels. Note that the two biofluids are also normalized by this step, so that miRNA expression is now relative to the normalizer specific to each biofluid. The resulting normalized Cq values were then recentered to the global median of the input Cq value distribution

label: FAM

source_name: Cerebral Spinal Fluid

label_protocol: MiRNA was converted to cDNA using the TaqMan Advanced miRNA cDNA Synthesis kit (A28007, Thermo Fisher). 3 μL of RNA was 3’ poly-adenylated, followed by a 5’ adaptor ligation step and reverse transcription (RT). 5 μL of the RT mix was added to a 14 cycle universal miR-amplification step (miR-amp). The miR-amp reaction was diluted 1:10 with nuclease free water, then 110 μL of the diluted cDNA was mixed with 220 μL of TaqMan Fast Advanced master mix (4444556, Thermo Fisher) and 110 μL of nuclease free water. 100 μL of the qPCR mix from one sample was loaded into the first 4 ports of a 384-well custom TaqMan Advanced Human miRNA Card (Thermo Fisher), then 100 μL of the qPCR mix from a second sample was loaded into the last 4 ports.

extract_protocol: Each RNA isolation batch consisted of 24 samples processed on the same day: 12 pairs of donor- and date-matched CSF and plasma samples, grouped to keep individual donor samples together to avoid any potential effect due to RNA isolation batch. Biofluid samples were thawed on ice and total RNA was isolated from 250 μL of CSF and 250 μL of plasma using the Urine miRNA Purification kit (Norgen, Thorold, ON) following the manufacturers protocol. Following addition of lysis buffer to the sample, an exogenous cel-miR-39-3p spike-in (Thermo Fisher, Waltham, MA) was added at a final concentration of 3 pM. CSF and plasma RNA were eluted with 30 μL and 50 μL of nuclease free water, respectively. The miRNA concentration of each sample was measured using the Qubit miRNA Assay kit (Thermo Fisher) and read using a Qubit 4.0 fluorometer (Thermo Fisher).

tag: donor id

tag: subject status

value: Healthy Control

tag: anatomical location

value: Structure of nervous tissue

tag: sample collection method

value: Lumbar Puncture

value: Cerebral Spinal Fluid

tag: starting amount

tag: holding temperature

tag: molecule type

value: total cell-free biofluid RNA


title: Th1 cells, Control cohort, Biol rep 11

description: Library name: EDCV040_Th1_S5

tag: tissue

value: Th1 Cells


title: GA808SS2-09

description:
Quantstudio 7K Flex
JSAUG1R01_058

value: Alzheimer's Disease

value: Male


title: Th17 cells, Control cohort, Biol rep 10

description: Library name: EDCV039_Th17_S33

tag: cell line

value: Th17 Cells


title: HA807XR3-06

description:
Quantstudio 7K Flex
JSAUG1R01_056

source_name: Plasma

value: Circulating blood

value: Venous

value: Plasma


title: CA808W2B-04

description:
Quantstudio 7K Flex
JSAUG1R01_054


title: Th1 cells, Control cohort, Biol rep 10

description: Library name: EDCV039_Th1_S31

value: Peripheral Blood/PBMCs

value: Primary CD4+ T cells

tag: cell type

value: Female

value: Control


title: Th17 cells, Control cohort, Biol rep 9

description: Library name: EDCV038_Th17_S4

tag: Sex

value: Caucasian

value: Post secondary


title: Cse4-mNG ChIP untagged sample

description: Library name: H_uvarum_Cse4-ChIP-WT


title: HA807L75-06

description:
Quantstudio 7K Flex
JSAUG1R01_052

value: Healthy Control


title: JA80B644-01

description:
Quantstudio 7K Flex
JSAUG1R01_051


title: Th1 cells, Control cohort, Biol rep 9

description: Library name: EDCV038_Th1_S3

tag: rasrm disease_stage_(1-4)


title: Th1 cells, Control cohort, Biol rep 12

description: Library name: EDCV045_Th1_S3

tag: age


title: HA8087W7-09

description:
Quantstudio 7K Flex
JSAUG1R01_053

value: Structure of nervous tissue

value: Lumbar Puncture


title: DA807JHG-12

description:
Quantstudio 7K Flex
JSAUG1R01_050

value: Cerebral Spinal Fluid

value: total cell-free biofluid RNA


title: AA807GVW-03

description:
Quantstudio 7K Flex
JSAUG1R01_060


title: Th1/17 cells, Control cohort, Biol rep 8

description: Library name: EDCV037_Th1-17_S28

value: Th1/17 Cells

tag: race


title: BA809J14-08

description:
Quantstudio 7K Flex
JSAUG1R01_049

value: Alzheimer's Disease

value: Male


title: KA807L88-11

description:
Quantstudio 7K Flex
JSAUG1R01_048

value: Circulating blood


title: Th17 cells, Control cohort, Biol rep 8

description: Library name: EDCV037_Th17_S29

value: Th17 Cells

tag: bmi


title: HA80B4CX-02

description:
Quantstudio 7K Flex
JSAUG1R01_046

value: Venous

value: Plasma


title: KA808JYB-11

description:
Quantstudio 7K Flex
JSAUG1R01_047


title: Th1 cells, Control cohort, Biol rep 7

description: Library name: EDCV036_Th1_S1

value: Peripheral Blood/PBMCs

value: Primary CD4+ T cells

value: Th1 Cells

tag: education


title: Th1/17 cells, Control cohort, Biol rep 7

description: Library name: EDCV036_Th1-17_S26

value: Female

value: Control

value: Caucasian


title: EA80B4DT-02

description:
Quantstudio 7K Flex
JSAUG1R01_044

value: Healthy Control


title: Th17 cells, Control cohort, Biol rep 6

description: Library name: EDCV035_Th17_S25

value: Post secondary


title: Th1/17 cells, Control cohort, Biol rep 6

description: Library name: EDCV035_Th1-17_S24


title: JA807T8R-09

description:
Quantstudio 7K Flex
JSAUG1R01_043

value: Structure of nervous tissue

value: Lumbar Puncture

value: Cerebral Spinal Fluid


title: HA809SPF-09

description:
Quantstudio 7K Flex
JSAUG1R01_055

value: Alzheimer's Disease

value: total cell-free biofluid RNA


title: Th1 cells, Control cohort, Biol rep 6

description: Library name: EDCV035_Th1_S23


title: Th1/17 cells, Control cohort, Biol rep 10

description: Library name: EDCV039_Th1-17_S32

value: Th1/17 Cells


title: JA8092VX-11

description:
Quantstudio 7K Flex
JSAUG1R01_042

value: Male


title: CA80B3LQ-08

description:
Quantstudio 7K Flex
JSAUG1R01_041


title: Th17 cells, Control cohort, Biol rep 5

description: Library name: EDCV034_Th17_S22

value: Th17 Cells


title: Th1/17 cells, Control cohort, Biol rep 9

description: Library name: EDCV038_Th1-17_S30


title: Th1/17 cells, Control cohort, Biol rep 5

description: Library name: EDCV034_Th1-17_S21


title: KA80B3KX-08

description:
Quantstudio 7K Flex
JSAUG1R01_039


title: Th1 cells, Control cohort, Biol rep 5

description: Library name: EDCV034_Th1_S20


title: AA80D23M-08

description:
Quantstudio 7K Flex
JSAUG1R01_040


title: Th1 cells, Control cohort, Biol rep 8

description: Library name: EDCV037_Th1_S2


title: GA808G3D-03

description:
Quantstudio 7K Flex
JSAUG1R01_038

value: Circulating blood

value: Venous

value: Plasma


title: Th17 cells, Control cohort, Biol rep 4

description: Library name: EDCV033_Th17_S10

value: Peripheral Blood/PBMCs

value: Primary CD4+ T cells


title: Th17 cells, Control cohort, Biol rep 7

description: Library name: EDCV036_Th17_S27

value: Female

value: Control


title: Th1/17 cells, Control cohort, Biol rep 4

description: Library name: EDCV033_Th1-17_S9

value: Caucasian


title: FA809072-04

description:
Quantstudio 7K Flex
JSAUG1R01_037


title: DA80CH8J-02

description:
Quantstudio 7K Flex
JSAUG1R01_045


title: JA8089PX-09

description:
Quantstudio 7K Flex
JSAUG1R01_036

value: Healthy Control


title: JA80C8G7-02

description:
Quantstudio 7K Flex
JSAUG1R01_035


title: Th1 cells, Control cohort, Biol rep 4

description: Library name: EDCV033_Th1_S8

value: Th1 Cells

value: Post secondary


title: Th1/17 cells, Control cohort, Biol rep 3

description: Library name: EDCV032_Th1-17_S18


title: FA80CJ72-08

description:
Quantstudio 7K Flex
JSAUG1R01_034

value: Structure of nervous tissue

value: Lumbar Puncture

value: Cerebral Spinal Fluid


title: Th1 cells, Control cohort, Biol rep 3

description: Library name: EDCV032_Th1_S17


title: DA80D2WG-08

description:
Quantstudio 7K Flex
JSAUG1R01_032

value: Alzheimer's Disease

value: total cell-free biofluid RNA


title: EA8086SD-04

description:
Quantstudio 7K Flex
JSAUG1R01_031


title: FA809Y17-10

description:
Quantstudio 7K Flex
JSAUG1R01_033


title: Th1/17 cells, Control cohort, Biol rep 2

description: Library name: EDCV031_Th1-17_S15

value: Th1/17 Cells


title: EA807Q06-03

description:
Quantstudio 7K Flex
JSAUG1R01_030

value: Circulating blood


title: Th17 cells, Control cohort, Biol rep 2

description: Library name: EDCV031_Th17_S16

value: Th17 Cells


title: DA80B3X3-02

description:
Quantstudio 7K Flex
JSAUG1R01_029

value: Venous

value: Plasma


title: GA8082HH-12

description:
Quantstudio 7K Flex
JSAUG1R01_028


title: Th17 cells, Control cohort, Biol rep 1

description: Library name: EDCV030_Th17_S13

value: Peripheral Blood/PBMCs

value: Primary CD4+ T cells


title: Th1 cells, Control cohort, Biol rep 1

description: Library name: EDCV030_Th1_S11

value: Female

value: Control


title: HA80884K-03

description:
Quantstudio 7K Flex
JSAUG1R01_027

value: Healthy Control

value: Male


title: EA808B50-09

description:
Quantstudio 7K Flex
JSAUG1R01_026


title: Th17 cells, Endometriosis cohort, Biol rep 10

description: Library name: EDCV026_Th17_S33

value: Caucasian

value: Post secondary


title: KA80C2DK-02

description:
Quantstudio 7K Flex
JSAUG1R01_025


title: DA80C2YS-01

description:
Quantstudio 7K Flex
JSAUG1R01_024


title: Th1/17 cells, Endometriosis cohort, Biol rep 10

description: Library name: EDCV026_Th1-17_S32


title: Th17 cells, Endometriosis cohort, Biol rep 9

description: Library name: EDCV025_Th17_S12


title: Th17 cells, Control cohort, Biol rep 3

description: Library name: EDCV032_Th17_S19


title: Th1 cells, Endometriosis cohort, Biol rep 10

description: Library name: EDCV026_Th1_S31

value: Th1 Cells


title: EA80C9RP-08

description:
Quantstudio 7K Flex
JSAUG1R01_022

value: Structure of nervous tissue

value: Lumbar Puncture

value: Cerebral Spinal Fluid


title: Th1 cells, Control cohort, Biol rep 2

description: Library name: EDCV031_Th1_S14


title: Th1/17 cells, Endometriosis cohort, Biol rep 9

description: Library name: EDCV025_Th1-17_S11

value: Th1/17 Cells


title: Th1 cells, Endometriosis cohort, Biol rep 9

description: Library name: EDCV025_Th1_S10


title: Th17 cells, Endometriosis cohort, Biol rep 8

description: Library name: EDCV024_Th17_S30


title: FA80BYR6-02

description:
Quantstudio 7K Flex
JSAUG1R01_020

value: Alzheimer's Disease

value: Circulating blood

value: total cell-free biofluid RNA


title: Th1/17 cells, Endometriosis cohort, Biol rep 8

description: Library name: EDCV024_Th1-17_S29


title: AA809Q5S-10

description:
Quantstudio 7K Flex
JSAUG1R01_021


title: EA8084PM-10

description:
Quantstudio 7K Flex
JSAUG1R01_019


title: HA807YXW-07

description:
Quantstudio 7K Flex
JSAUG1R01_018

value: Venous

value: Plasma


title: KA80CGCF-08

description:
Quantstudio 7K Flex
JSAUG1R01_017


title: Th1 cells, Endometriosis cohort, Biol rep 8

description: Library name: EDCV024_Th1_S28

value: Peripheral Blood/PBMCs

value: Primary CD4+ T cells


title: Th1/17 cells, Endometriosis cohort, Biol rep 7

description: Library name: EDCV023_Th1-17_S26

value: Female

value: Unknown


title: Th17 cells, Endometriosis cohort, Biol rep 7

description: Library name: EDCV023_Th17_S27

value: Th17 Cells


title: Th1/17 cells, Control cohort, Biol rep 1

description: Library name: EDCV030_Th1-17_S12

value: Control

value: Caucasian


title: HA807TKK-03

description:
Quantstudio 7K Flex
JSAUG1R01_016

value: Male


title: Th1 cells, Endometriosis cohort, Biol rep 7

description: Library name: EDCV023_Th1_S25

value: Th1 Cells

value: Post secondary


title: AA8083N8-09

description:
Quantstudio 7K Flex
JSAUG1R01_014

value: Structure of nervous tissue

value: Lumbar Puncture

value: Cerebral Spinal Fluid


title: AA809W8M-02

description:
Quantstudio 7K Flex
JSAUG1R01_013

value: Alzheimer's Disease

value: Circulating blood


title: Th1/17 cells, Endometriosis cohort, Biol rep 6

description: Library name: EDCV022_Th1-17_S23

value: Th1/17 Cells


title: Th17 cells, Endometriosis cohort, Biol rep 6

description: Library name: EDCV022_Th17_S24


title: EA8099MG-10

description:
Quantstudio 7K Flex
JSAUG1R01_012

value: Healthy Control

value: Venous

value: Plasma

value: total cell-free biofluid RNA


title: Th1 cells, Endometriosis cohort, Biol rep 6

description: Library name: EDCV022_Th1_S22

value: Peripheral Blood/PBMCs

value: Primary CD4+ T cells

value: Female


title: KA807X8D-03

description:
Quantstudio 7K Flex
JSAUG1R01_023


title: Th17 cells, Endometriosis cohort, Biol rep 5

description: Library name: EDCV019_Th17_S21

value: Th17 Cells

value: Caucasian


title: GA808S1W-10

description:
Quantstudio 7K Flex
JSAUG1R01_010

value: Male


title: EA808TV0-03

description:
Quantstudio 7K Flex
JSAUG1R01_009


title: JA80BKH0-08

description:
Quantstudio 7K Flex
JSAUG1R01_011


title: Th1/17 cells, Endometriosis cohort, Biol rep 5

description: Library name: EDCV019_Th1-17_S20

value: Post secondary


title: Th1 cells, Endometriosis cohort, Biol rep 5

description: Library name: EDCV019_Th1_S19

value: Th1 Cells


title: EA809X27-08

description:
Quantstudio 7K Flex
JSAUG1R01_007

value: Structure of nervous tissue

value: Lumbar Puncture


title: FA809X56-09

description:
Quantstudio 7K Flex
JSAUG1R01_008

value: Cerebral Spinal Fluid


title: BA80BNCB-02

description:
Quantstudio 7K Flex
JSAUG1R01_006

value: Alzheimer's Disease

value: Circulating blood


title: Th17 cells, Endometriosis cohort, Biol rep 3

description: Library name: EDCV015_Th17_S15


title: Th1 cells, Endometriosis cohort, Biol rep 4

description: Library name: EDCV016_Th1_S16


title: Th17 cells, Endometriosis cohort, Biol rep 4

description: Library name: EDCV016_Th17_S18


title: GA809VMP-02

description:
Quantstudio 7K Flex
JSAUG1R01_004


title: DA80BLGC-08

description:
Quantstudio 7K Flex
JSAUG1R01_005


title: HA808PZ0-04

description:
Quantstudio 7K Flex
JSAUG1R01_003

value: Healthy Control


title: Th1/17 cells, Endometriosis cohort, Biol rep 3

description: Library name: EDCV015_Th1-17_S14

value: Th1/17 Cells


title: Th1/17 cells, Endometriosis cohort, Biol rep 4

description: Library name: EDCV016_Th1-17_S17


title: HA8086P0-10

description:
Quantstudio 7K Flex
JSAUG1R01_015


title: Th1/17 cells, Endometriosis cohort, Biol rep 2

description: Library name: EDCV014_Th1-17_S8

value: Other


title: AA808TF9-08

description:
Quantstudio 7K Flex
JSAUG1R01_002

value: total cell-free biofluid RNA


title: Th17 cells, Endometriosis cohort, Biol rep 2

description: Library name: EDCV014_Th17_S9

value: Peripheral Blood/PBMCs


title: Th1 cells, Endometriosis cohort, Biol rep 3

description: Library name: EDCV015_Th1_S13

value: Primary CD4+ T cells


title: Th1 cells, Endometriosis cohort, Biol rep 2

description: Library name: EDCV014_Th1_S7

value: Female


title: HA80BRX9-03

description:
Quantstudio 7K Flex
JSAUG1R01_001

value: Venous

value: Plasma


title: Th1/17 cells, Endometriosis cohort, Biol rep 1

description: Library name: EDCV009_Th1-17_S5

value: Caucasian


title: Th17 cells, Endometriosis cohort, Biol rep 1

description: Library name: EDCV009_Th17_S6

value: Th17 Cells

value: Post secondary


title: H3K37A_Rap_biol rep 3

city: Memphis

first: R.

middle: Nicholas

last: Laribee

state: TN

address: 19 South Manassas

department: Pathology

institute: University of Tennessee Health Science Center

description: Library name: Sample 14

data_processing:
Samples were aligned to yeast reference using RNA STAR 2.0
Count tables were generated using FeatureCounts
Counts were normalized using TMM and log2 transformed
Assembly: Saccharomyces cerevisiae (Saccharomyces cerevisiae S288c) · Genome assembly: R64-1-1
Supplementary files format and content: raw count table in excel

organism: Saccharomyces cerevisiae

growth_protocol: nutrient-defined SC media formulated with 0.2% yeast nitrogen base devoid of amino acids, 0.5% ammonium sulfate, 2% glucose, and 0.19% amino acids. Cells were cultivated in an incubated shaker at 30°C.

extract_protocol:
RNA was isolated using the hot-acid phenol method. Briefly, yeast cells were grown in 10 mL of SC media to OD600=0.8 - 1.0, pelleted, and the supernatant discarded. Pellets were resuspended in 1 mL of ice-cold water, transferred to a clean 1.5 mL microcentrifuge tube, pelleted again, and then the supernatant was removed. Cells were resuspended in 400 μL of TES solution (10 mM Tris HCl (pH 7.5), 10 mM EDTA, and 0.5% SDS), and then 400 μL of acid phenol was added before vortexing vigorously for 10 seconds. Samples were then incubated for 45 minutes at 65 °C with occasional brief vortexing, and then they were placed on ice for five minutes before centrifuging at 4 °C at 15000×rpm for five minutes. The aqueous phase was transferred to a clean 1.5 mL microcentrifuge tube, and the acid phenol treatment was repeated. After isolating the aqueous phase from the second acid phenol extraction, 400 μL of chloroform was added, the samples were vortexed vigorously, and then centrifuged for five minutes at 15,000×rpm at 4 °C. The aqueous phase was transferred to a new tube, ethanol precipitated for 30 minutes and then pelleted at 4 °C. Pellets were washed with ice-cold 70% ethanol, pelleted again, and then resuspended in 40 μL of RNase-free water and incubated at 65 °C for 3-5 minutes to dissolve the RNA pellets. All RNAs were digested with RQ1 DNase (Promega) in a 50 μL total reaction volume, incubated at 37 °C for 45 minutes. RNA was purified by phenol/chloroform extraction, precipitated, and then resuspended in 80 µL of nuclease-free water.
QIAseq FastSelect –rRNA Yeast Kit

treatment_protocol: Yeast cells were grown  to OD600=0.8 and treated with rapamycin 20 nM for 1 hour

value: H3K37A mutation

tag: genotype

value: MATa his3 200 leu2 0 lys2 0 trp1 63 ura3 0met15 0 can1::MFA1pr-HIS3 hht1-hhf1::NatMX4 hht2-hhf2::[HHTS-HHFS]- ura3 H3WT

tag: treatment

value: Rapamycin

tag: time

value: 1 hour


title: KO, male, HFD diet, Rep4

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

institute: Helmholtz Zentrum München

description: Library name: A39

data_processing:
Fastq files were trimmed for adaptors and low-quality reads using the Fastp v0.22.0. Alignment was done towards the Ensembl assembly/build mm39 by using STAR v2.7.10b and FeatureCounts were summed by applying featureCounts v2.0.6
Assembly: mm39
Supplementary files format and content: One feature count file for each sample in csv format

organism: Mus musculus

source_name: Liver

growth_protocol: All mice were kept at room temperature with ad libitum excess to food and water till the age of 22-24 weeks. Mice were sacrificed 2–4,5 h after the lights went on, and serum and tissue samples were collected.

extract_protocol:
RNA was extracted from liver using Qiazol according to the manufacturer’s instructions (Qiazol Lysis Reagent, Qiagen).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: At the age of 11-13 weeks, half of the mouse cohort (female as well as male mice) were switched from chow to a 45 kcal% Fat (ssniff E15744-347, according to research diets D12451). After 11 weeks of HFD feeding, mice were sacrificed 2–4,5 h after the lights went on, and serum and tissue samples were collected.

value: Liver

value: KO

value: male

value: high fat diet

tag: strain


title: H3K37A_Rap_biol rep 2

description: Library name: Sample 13


title: KO, male, HFD diet, Rep3

description: Library name: A38


title: H3K37A_Rap_biol rep 1

description: Library name: Sample 12


title: H3K37A_Control_biol rep 4

description: Library name: Sample 11

value: Control

value: 0 hour


title: KO, male, HFD diet, Rep1

description: Library name: A36


title: RBC-Ve2-5E-r3

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)

description: Library name: RBC-Ve2-5E-r3

data_processing:
nfcore/atac-seq
Assembly: GRCh38
Supplementary files format and content: bigWig

source_name: differentiating HSPCs

growth_protocol: G-CSF-mobilized human peripheral blood CD34+ cells (Stem Cell Technologies) were differentiated into immature erythroid cells utilizing a three-phase culture protocol. Briefly, cells were thawed and cultured overnight at a density of 104 cells/ml in X-VIVO 10 serum-free haematopoietic cell medium (Lonza) supplemented with 100 ng/mL recombinant human SCF (Biotechne), 100 ng/mL recombinant human TPO and 50 ng/mL recombinant human FLT3 Ligand (PeproTech). The next day, cells were washed and resuspended at a density of 1-2,5 x 104 cells/ml into erythroid differentiation medium 1 (EDM1) consisting of IMDM supplemented with 100 ng/ml hSCF, 330 μg/ml human holo-Transferrin, 10 μg/ml recombinant human insulin, 2 IU/ml heparin, 5% heat-inactivated human serum (Sigma), 3 IU human recombinant EPO (Stem Cell Technologies), 1 μM hydrocortisone (Sigma), recombinant human IL-3 (PeproTech) 1% penicillin/streptomycin. From day 7 to day 11, cells were cultured at a concentration of 105 cells/mL in EDM2 (EDM1 without hIL-3 hydrocortisone). From day 11 to day 14, cells were cultured in EDM3 (EDM2 without hSCF) at a concentration of 0.75-1.5 × 106 cells/ml. Cells were cultured at 37°C and 5% CO2.

extract_protocol:
20,000 to 50,000 cells were washed in cold PBS and resuspended in 50ul Lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal) and immediately spun at 500 xg for 10 min at 4 C. The supernatant was then discarded and the nuclei resuspended in the transposase reaction mix (25 ul 2x TD Buffer, 2.5 ul Transposase (Illumina), 22,5 ul nuclease-free water) and incubated for 30 min at 37C. Immediately after, DNA is purified using a MinElute Kit (Qiagen).
Tagmented DNA was PCR amplified to amend sequencing barcodes and qPCR was used to estimate the number of PCR cycles for exponential amplification. Libraries were pooled and sequenced at 150bp paired-end at Azenta.

value: differentiating HSPCs

tag: batch

value: validation

tag: flowcell


title: WT, male, HFD diet, Rep5

description: Library name: A35

value: WT

value: chow diet


title: TIG-3 cells, DXR-Sen cells, ARV825, day7

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description:
Library name: TD8
10x Genomics

library_source: transcriptomic single cell

data_processing:
Libraries were sequenced on an Illumina NovaSeq X Plus platform with 151 bp paired-end reads.
Demultiplexing, alignment, and gene expression quantification were performed using Cell Ranger v8.0.1 (10x Genomics), aligned to the custom human reference genome (GRCh38_hervk).
Filtered feature-barcode matrices were generated for downstream transcriptomic analyses.
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5 format files including filtered counts data for each gene and cell (barcode) combination
Supplementary files format and content: raw_feature_bc_matrix.h5: HDF5 format files including raw counts data for each gene and cell (barcode) combination

growth_protocol: TIG-3 cells were maintained in Dulbecco's Modified Eagle's medium supplumented with 10% fetal bovine serum and 100 U ml^-1 penicillin-streptomycin.

extract_protocol:
Total RNA was extracted using TRIzol.
Approximately 10⁶ fixed TIG-3 cells were hybridized with whole-transcriptome probe pairs for 18 hours at 42 °C. Following post-hybridization washes, the cells were encapsulated into gel beads-in-emulsion (GEMs) using the Chromium X system. Within each GEM, ligated probe pairs were barcoded with 10x GEM Barcodes and Unique Molecular Identifiers (UMIs), followed by heat denaturation and recovery. Barcoded products were pre-amplified and purified using SPRIselect beads. Final libraries were generated by sample index PCR with the Dual Index Kit TS Set A and purified by size selection. Library quality and size distribution were assessed using an Agilent Bioanalyzer, and concentrations were determined with the KAPA Library Quantification Kit (Roche).

treatment_protocol: For induction of cellular senescence, TIG-3 cells were incubated with doxorubicin at 250 ngper ml for 10 days. DXR-Sen TIG-3 cells were incubated with ABT263 (0.5µM) or ARV825 (25 nM) for 7 days.

value: fibroblast


title: TIG-3 cells, DXR-Sen cells, ABT263, day7

description:
Library name: TDA
10x Genomics


title: TIG-3 cells, Control cells

description:
Library name: T
10x Genomics

value: DMSO


title: RBC-Ve2-5E-r2

description: Library name: RBC-Ve2-5E-r2


title: H3K37A_Control_biol rep 3

description: Library name: Sample 10


title: RBC-Ve2-5E-r1

description: Library name: RBC-Ve2-5E-r1


title: H3K37A_Control_biol rep 2

description: Library name: Sample 9


title: RBC-Ve2-TGF-2-r2

description: Library name: RBC-Ve2-TGF-2-r2


title: RBC-Ve2-TGF-1-r2

description: Library name: RBC-Ve2-TGF-1-r2


title: KO, male, HFD diet, Rep5

description: Library name: A40


title: RBC-Ve2-TGF-2-r1

description: Library name: RBC-Ve2-TGF-2-r1


title: WT, male, HFD diet, Rep3

description: Library name: A33


title: WT, male, HFD diet, Rep4

description: Library name: A34


title: H3WT_Rap_biol rep 3

description: Library name: Sample 7

value: Wild Type


title: RBC-Ve2-TGF-1-r3

description: Library name: RBC-Ve2-TGF-1-r3


title: H3K37A_Control_biol rep 1

description: Library name: Sample 8

value: H3K37A mutation


title: TIG-3 cells, DXR-Sen cells, Vehicle(DMSO), day7

description:
Library name: TD
10x Genomics


title: RBC-Ve2-IL4-2-r3

description: Library name: RBC-Ve2-IL4-2-r3


title: RBC-Ve2-IL4-2-r2

description: Library name: RBC-Ve2-IL4-2-r2


title: WT, male, HFD diet, Rep2

description: Library name: A32


title: RBC-Ve2-IL4-2-r1

description: Library name: RBC-Ve2-IL4-2-r1


title: H3WT_Rap_biol rep 2

description: Library name: Sample 6

value: MATa his3 200 leu2 0 lys2 0 trp1 63 ura3 0met15 0 can1::MFA1pr-HIS3 hht1-hhf1::NatMX4 hht2-hhf2::[HHTS-HHFS]- ura3 H3WT


title: KO, male, HFD diet, Rep2

description: Library name: A37


title: WT, male, HFD diet, Rep1

description: Library name: A31


title: RBC-Ve2-IL4-1-r3

description: Library name: RBC-Ve2-IL4-1-r3


title: RBC-Ve2-IL4-1-r2

description: Library name: RBC-Ve2-IL4-1-r2


title: KO, male, chow diet, Rep5

description: Library name: A30


title: RBC-Ve2-IL4-1-r1

description: Library name: RBC-Ve2-IL4-1-r1


title: H3WT_Control_biol rep 4

description: Library name: Sample 4


title: S9,Time1,Rep2

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

description: Library name: S9_Time2_Rep2

data_processing:
Samples were demultiplexed based on the index sequence identified in Read 2. To isolate the sgRNA, fastx_trimmer from FASTX-Toolkit v0.0.14 was used to extract the first 20 bp from Read 1. The trimmed reads were then aligned to the reference library FASTA file using Bowtie v1.3.1. Read counts for each sgRNA in each sample were then extracted from SAM files generated by Bowtie using custom Python scripts.
Significant changes in sgRNA abundance between different conditions were determined using MAGeCK-RRA algorithm v0.5.9.5
Assembly: sgRNA library fasta
Supplementary files format and content: Tab delimited files with the counts for each sgRNA
Library strategy: CRISPR Screen

growth_protocol: Cas9-expressing LN229 cells were maintained in 5% CO2, 20% O2, and humidified in a 37°C incubator and grown in complete DMEM (DMEM (Gibco) + 10% fetal bovine serum.

extract_protocol:
Multiple pellets consisting of 3 million cells were collected for each sample and washed with PBS. PBS was aspirated and cells were flash-frozen and stored at -80°C. gDNA was extracted with Blood and Tissue kit (QIAGEN) according to the manufacturer's protocol.
sgRNA sequences were amplified using NGS Prep Kits from CELLECTA according to the manufacturer's protocol (NGS Prep Kit for sgRNA, shRNA, and DNA Barcode Libraries; version 1).

treatment_protocol: Cells were plated at desired coverage and then immediately treated with the chemical agent or vehicle control while still in suspension. Each condition was performed in duplicate. After 3 days, cells were trypsinized, counted with a hemocytometer (BioRad), replated at desired coverage and retreated. This procedure was repeated on Days 6 and 9. On Day 12, cells were trypsinized and counted.

value: glioma

value: WT (Cas9-expressing)

value: Screen 9


title: H3WT_Control_biol rep 3

description: Library name: Sample 3


title: KO, male, chow diet, Rep3

description: Library name: A28

value: Liver

value: KO


title: KO, male, chow diet, Rep4

description: Library name: A29

value: male

value: high fat diet


title: S9,Bleomycin_Dose2,Rep2

description: Library name: S9_Bleomycin_Dose2_Rep2

value: Bleomycin


title: RBC-Ve2-TGF-1-r1

description: Library name: RBC-Ve2-TGF-1-r1

value: differentiating HSPCs


title: H3WT_Control_biol rep 2

description: Library name: Sample 2

value: Control

value: 0 hour


title: S9,Bleomycin_Dose1,Rep2

description: Library name: S9_Bleomycin_Dose1_Rep2


title: KO, male, chow diet, Rep2

description: Library name: A27


title: S9,Bleomycin_Dose1,Rep1

description: Library name: S9_Bleomycin_Dose1_Rep1


title: S9,Bleomycin_Dose2,Rep1

description: Library name: S9_Bleomycin_Dose2_Rep1


title: S9,Dactinomycin_Dose2,Rep2

description: Library name: S9_Dactinomycin_Dose2_Rep2

value: Dactinomycin


title: Th1 cells, Endometriosis cohort, Biol rep 1

description: Library name: EDCV009_Th1_S7

value: Peripheral Blood/PBMCs

value: Primary CD4+ T cells

value: Th1 Cells

value: Female

value: Caucasian

value: Post secondary


title: H3WT_Control_biol rep 1

description: Library name: Sample 1

value: Wild Type

value: MATa his3 200 leu2 0 lys2 0 trp1 63 ura3 0met15 0 can1::MFA1pr-HIS3 hht1-hhf1::NatMX4 hht2-hhf2::[HHTS-HHFS]- ura3 H3WT


title: KO, male, chow diet, Rep1

description: Library name: A26

value: Liver


title: S9,Dactinomycin_Dose2,Rep1

description: Library name: S9_Dactinomycin_Dose2_Rep1

value: glioma

value: WT (Cas9-expressing)

value: Screen 9


title: Untagged Rpb3 , KY5949 , Input_Sp , Rep2

city: Pittsburgh

first: Karen

middle: M.

last: Arndt

state: Pennsylvania

address: 4249 Fifth Avenue

department: Biological Sciences

institute: University of Pittsburgh

description:
Library name: Untagged_Rpb3_KY5949_Input_Sp_Rep2
MATalpha lys2-128∂ leu2∆1 ura3-52 3XHSV-PAF1

data_processing:
Reads were aligned to the hydrid genome of S. cerevisiae and the corresponding spike-in (either S. pombe or K. lactis) with bowtie2 version 2.4.5.
Mapped reads were filtered with Sambamba view and Samtools markdup to remove multi-mapped reads and PCR duplicates, respectively.
The filtered hybrid alignment was split into separate S. cerevisiae and spike-in files. Normalization factors were calculated using S. cerevisiae and spike-in read counts in the input and IP.
Spike-in normalization was applied and bigWig files were generated using bamCoverage.
Assembly: S. cerevisiae SacCer3
Assembly: K. lactis ASM251v1
Assembly: S. pombe ASM294v2
Supplementary files format and content: bigWig, spike-in normalized ChIP-seq signal

growth_protocol: All yeast cultures, including spike-in cells, were grown to mid-log phase in 250 mL YPD+Trp media at 30ºC.

extract_protocol:
Cells were fixed with 1% formaldehyde for 20 minutes. After quenching and cell lysis, chromatin was sheared using a Bioruptor® (Diagenode B01060010) for 25 cycles with 30 seconds on and 30 seconds off.
ChIP-seq libraries were prepared with the NEB Next II Ultra DNA library kit (NEB, E7645S/L) and multiplex oligos (NEB, E6440S/L) using 0.5-1 ng of DNA input and following manufacturer's protocols. Libraries were purified using AMPure XP beads (Beckman Coulter, A63881) and verified using fragment analyzer (Fragment Analyzer, Advanced Analytics).

treatment_protocol:
For auxin inducible degron, the mid-log culture was treated with 5 µM 5-phenyl-indole-3-acetic acid (5-Ph-IAA) or equivalent amount of vehicle (DMSO) for 45 minutes.
For anchor-away experiments, the mid-log culture was treated with 1 µg/mL rapamycin or equivalent amount of vehicle (DMSO) for 1 hour.

tag: chip antibody


title: WT, male, chow diet, Rep5

description: Library name: A25

value: WT

value: male

value: chow diet


title: Untagged Rpb3 , KY5949 , Input_Sp , Rep1

description:
Library name: Untagged_Rpb3_KY5949_Input_Sp_Rep1
MATalpha lys2-128∂ leu2∆1 ura3-52 3XHSV-PAF1


title: H3WT_Rap_biol rep 1

description: Library name: Sample 5

value: Rapamycin

value: 1 hour


title: S9,Control,Rep6

description: Library name: S9_Control_Rep6

value: DMSO


title: WT, male, chow diet, Rep4

description: Library name: A24


title: S9,Dactinomycin_Dose1,Rep1

description: Library name: S9_Dactinomycin_Dose1_Rep1

value: Dactinomycin


title: S9,Time1,Rep1

description: Library name: S9_Time1_Rep1


title: WT, male, chow diet, Rep3

description: Library name: A23


title: S9,Time0,Rep1

description: Library name: S9_Time0_Rep1


title: S9,Etoposide,Rep2

description: Library name: S9_Etoposide_Rep2

value: Etoposide


title: S9,Control,Rep5

description: Library name: S9_Control_Rep5


title: WT , KY5937 , Input_Sp , Rep2

description:
Library name: WT_KY5937_Input_Sp_Rep2
MATalpha his4-912δ  lys2-128∂ leu2Δ1 ura3-52 RPB3-3xFLAG::KanMX 3xHA-GLC7


title: S9,Topotecan_Dose2,Rep2

description: Library name: S9_Topotecan_Dose2_Rep2

value: Topotecan


title: S9,Etoposide,Rep1

description: Library name: S9_Etoposide_Rep1


title: WT, male, chow diet, Rep2

description: Library name: A22


title: rtf1del , KY5936 , Input_Sp , Rep2

description:
Library name: rtf1del_KY5936_Input_Sp_Rep2
MATalpha his4-912δ  lys2-128∂ leu2∆1 ura3-52 RPB3-3xFLAG::KanMX 3xHA-GLC7 rtf1Δ101::LEU2


title: WT , KY5937 , Input_Sp , Rep1

description:
Library name: WT_KY5937_Input_Sp_Rep1
MATalpha his4-912δ  lys2-128∂ leu2Δ1 ura3-52 RPB3-3xFLAG::KanMX 3xHA-GLC7


title: WT, male, chow diet, Rep1

description: Library name: A21


title: S9,Topotecan_Dose1,Rep1

description: Library name: S9_Topotecan_Dose1_Rep1


title: S9,Topotecan_Dose2,Rep1

description: Library name: S9_Topotecan_Dose2_Rep1


title: KO, female, HFD diet, Rep5

description: Library name: A20

value: KO

value: female

value: high fat diet


title: S9,Topotecan_Dose1,Rep2

description: Library name: S9_Topotecan_Dose1_Rep2


title: rtf1del , ref2del , swd2del , KY5931 , Input_Sp , Rep2

description:
Library name: rtf1del_ref2del_swd2del_KY5931_Input_Sp_Rep2
MATa his4-912δ  lys2-128∂ leu2∆1 RPB3-3xFLAG::KanMX 3xHA-GLC7 rtf1Δ101::LEU2 swd2∆::hphMX ref2∆::KanMX


title: S9,Dactinomycin_Dose1,Rep2

description: Library name: S9_Dactinomycin_Dose1_Rep2


title: S9,Control,Rep4

description: Library name: S9_Control_Rep4


title: KO, female, HFD diet, Rep4

description: Library name: A19


title: rtf1del , KY5936 , Input_Sp , Rep1

description:
Library name: rtf1del_KY5936_Input_Sp_Rep1
MATalpha his4-912δ  lys2-128∂ leu2∆1 ura3-52 RPB3-3xFLAG::KanMX 3xHA-GLC7 rtf1Δ101::LEU2


title: S9,Control,Rep3

description: Library name: S9_Control_Rep3


title: KO, female, HFD diet, Rep3

description: Library name: A18


title: S9,MMS,Rep1

description: Library name: S9_MMS_Rep1

value: MMS


title: S9,MMS,Rep2

description: Library name: S9_MMS_Rep2


title: WT , KY5942 , Input_Sp , Rep2

description:
Library name: WT_KY5942_Input_Sp_Rep2
MATalpha lys2-128∂ leu2Δ1 ura3-52 RPB3-3xFLAG::KanMX 3xHSV-PAF1


title: rtf1del , ref2del , swd2del , KY5931 , Input_Sp , Rep1

description:
Library name: rtf1del_ref2del_swd2del_KY5931_Input_Sp_Rep1
MATa his4-912δ  lys2-128∂ leu2∆1 RPB3-3xFLAG::KanMX 3xHA-GLC7 rtf1Δ101::LEU2 swd2∆::hphMX ref2∆::KanMX


title: S9,Time0,Rep2

description: Library name: S9_Time0_Rep2


title: S9,Control,Rep2

description: Library name: S9_Control_Rep2


title: KO, female, HFD diet, Rep2

description: Library name: A17

value: Liver


title: S9,Control,Rep1

description: Library name: S9_Control_Rep1

value: glioma


title: S8,Time0,Rep2

description: Library name: S8_Time0_Rep2

value: WT (Cas9-expressing)

value: Screen 8


title: WT , KY5942 , Input_Sp , Rep1

description:
Library name: WT_KY5942_Input_Sp_Rep1
MATalpha lys2-128∂ leu2Δ1 ura3-52 RPB3-3xFLAG::KanMX 3xHSV-PAF1


title: S8,Cisplatin_Dose1,Rep2

description: Library name: S8_Cisplatin_Dose1_Rep2

value: Cisplatin


title: S8,Cisplatin_Dose2,Rep1

description: Library name: S8_Cisplatin_Dose2_Rep1


title: S8,Cisplatin_Dose1,Rep1

description: Library name: S8_Cisplatin_Dose1_Rep1


title: spt5delCTR , KY5923 , Input_Sp , Rep1

description:
Library name: spt5_delCTR_KY5923_Input_Sp_Rep1
MATa lys2-128∂ leu2Δ1 ura3-52 RPB3-3xFLAG::KanMX 3XHSV-PAF1 spt5∆CTR::NatMX


title: WT, female, HFD diet, Rep5

description: Library name: A15

value: WT


title: WT, female, HFD diet, Rep4

description: Library name: A14

value: chow diet


title: spt5del5 , KY5917 , Input_Sp , Rep1

description:
Library name: spt5_del5_KY5917_Input_Sp_Rep1
MATalpha lys2-128∂ leu2∆1 RPB3-3xFLAG::KanMX 3xHSV-PAF1 spt5∆5::NatMX


title: WT, female, HFD diet, Rep3

description: Library name: A13


title: FSD1+ human testicular cells, Rep3

city: La Jolla

first: Kun

last: Tan

state: CA

address: 9500 Gilman Drive # 0695

department: Dept. of Obstetrics, Gynecology & Reproductive Science

institute: UCSD

description:
Library name: FSD1_3
Column name in raw_counts.txt: FSD1_3

data_processing:
Reads were filtered for quality and aligned with STAR (2.5.2b) against Homo sapiens, release-106, Ensembl genome (GRCh38). The exon counts were aggregated for each gene to build a read count table using SubRead function featureCounts. DEGs were defined using DESeq2 using the following threshold: q <0.01, fold-change >2. The R package program, pheatmap, was used for clustering and generating heatmap plots. The Metascape platform was used for gene functional annotation using the following parameters: p < 0.01, minimum count of 3, and enrichment factor >1.5.
Assembly: Homo sapiens, release-106, Ensembl genome (GRCh38)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: human testicular cells

extract_protocol:
Total RNA was extracted using the RNeasy Plus Micro Kit (Qiagen), following the manufacturer’s protocol.
10 ng of total RNA was used to make the library using the SMART-Seq Total RNA Pico Input (Takara Bio USA), as per manufacturer's instructions.

treatment_protocol: Single testicular cells were isolated using a two-step enzymatic digestion protocol. Briefly, testicular tissue was mechanically minced and digested with 1 mg/ml collagenase type IV (Worthington Biochemical) in Hanks' Balanced Salt Solution (HBSS; GIBCO) at 37 °C. Following sedimentation and washing with HBSS, the tubules were subjected to a second digestion in 0.25% Trypsin-EDTA (ThermoFisher) supplemented with Deoxyribonuclease I (Worthington Biochemical). The cell suspension was triturated vigorously ten times, incubated at 37 °C for 5 mins, and the trituration/incubation cycle was repeated once. Digestion was stopped by adding an equal volume of αMEM containing 10% FBS. The cell suspension was filtered through 40 μm strainer (ThermoFisher), and cells were pelleted by centrifugation at 300 g for 5 mins. Single cells were then resuspended in staining buffer (PBS + 3% FBS), incubated with the FSD1 primary antibody on ice for 20 mins, washed, and incubated with a species-specific fluorophore-conjugated secondary antibody for 20 mins on ice. After a final wash, cells were resuspended in staining buffer and sorted by FACS. Small debris and doublets were excluded based on forward and side scatter parameters. Unstained cells and cells stained with secondary antibody alone were used as negative controls to define background fluorescence and set gates for FSD1-positive populations.

value: human testicular cells


title: FSD1+ human testicular cells, Rep4

description:
Library name: FSD1_4
Column name in raw_counts.txt: FSD1_4


title: S8,Control,Rep1

description: Library name: S8_Control_Rep1


title: spt5-S1-15D , KY5907 , Input_Sp , Rep2

description:
Library name: spt5_S1_15D_KY5907_Input_Sp_Rep2
MATalpha lys2-128∂ leu2Δ1 ura3-52 RPB3-3xFLAG::KanMX 3xHSV-PAF1 spt5-S1-15D


title: S8,Control,Rep2

description: Library name: S8_Control_Rep2


title: WT, female, HFD diet, Rep2

description: Library name: A12


title: Unfractionated human testicular cells, Rep4

description:
Library name: Unfraction_4
Column name in raw_counts.txt: Unfraction_4

value: Unfractionated


title: FSD1+ human testicular cells, Rep2

description:
Library name: FSD1_2
Column name in raw_counts.txt: FSD1_2


title: spt5-S1-15D , KY5907 , Input_Sp , Rep1

description:
Library name: spt5_S1_15D_KY5907_Input_Sp_Rep1
MATalpha lys2-128∂ leu2Δ1 ura3-52 RPB3-3xFLAG::KanMX 3xHSV-PAF1 spt5-S1-15D


title: FSD1+ human testicular cells, Rep1

description:
Library name: FSD1_1
Column name in raw_counts.txt: FSD1_1


title: WT, female, HFD diet, Rep1

description: Library name: A11


title: KO, female, chow diet, Rep5

description: Library name: A10


title: Unfractionated human testicular cells, Rep2

description:
Library name: Unfraction_2
Column name in raw_counts.txt: Unfraction_2


title: spt5del5 , KY5917 , Input_Sp , Rep2

description:
Library name: spt5_del5_KY5917_Input_Sp_Rep2
MATalpha lys2-128∂ leu2∆1 RPB3-3xFLAG::KanMX 3xHSV-PAF1 spt5∆5::NatMX


title: Unfractionated human testicular cells, Rep3

description:
Library name: Unfraction_3
Column name in raw_counts.txt: Unfraction_3


title: S8,Cisplatin_Dose2,Rep2

description: Library name: S8_Cisplatin_Dose2_Rep2


title: KO, female, HFD diet, Rep1

description: Library name: A16


title: spt5-S1-15A , KY5901 , Input_Sp , Rep2

description:
Library name: spt5_S1_15A_KY5901_Input_Sp_Rep2
MATalpha lys2-128∂ leu2∆1 ura3-52 RPB3-3xFLAG::KanMX 3xHSV-PAF1 spt5-S1-15A


title: spt5delCTR , KY5923 , Input_Sp , Rep2

description:
Library name: spt5_delCTR_KY5923_Input_Sp_Rep2
MATa lys2-128∂ leu2Δ1 ura3-52 RPB3-3xFLAG::KanMX 3XHSV-PAF1 spt5∆CTR::NatMX


title: Unfractionated human testicular cells, Rep1

description:
Library name: Unfraction_1
Column name in raw_counts.txt: Unfraction_1


title: KO, female, chow diet, Rep4

description: Library name: A9


title: Telo-HUVECs, KRAS G12V, doxycycline induction, SL327 treatment, replicate 2

city: Toronto

first: Ruilin

last: Wu

address: 101 College Street

institute: University of Toronto

description: Library name: dox_SL327_2

data_processing:
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GRCh38/hg38
Supplementary files format and content: tab delimited text files include raw counts and fpkm for each sample

molecule: polyA RNA

source_name: HUVEC

growth_protocol: Telomerase-immortalized human umbilical vein endothelial cells (Telo-HUVECs) were cultured in complete ScienCell Endothelial Cell Media (ECM) under standard cell culture conditions. Mutant KRAS G12V construct was stably incorporated into the genome of these cells using a transposon system and expression was induced with 5μg/mL doxycycline for two days prior to RNA collection.

extract_protocol:
RNA extraction was done using the TRIzol reagent and followed standard RNA extraction protocol. RNA samples (1μg/μL; 10μL) were submitted to Novogene Corporation Inc. for sequencing and downstream processing.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: Cells were treated with various inhibitors for 24 hours prior to RNA collection, including 2mM 2-DG (glycolysis inhibitor), 5μM BAY876 (glucose transporter inhibitor), 10μM 3-PO (glycolysis inhibitor) and 10μM SL327 (MEK inhibitor).

value: HUVEC

value: Endothelial Cells

value: KRAS G12V


title: Telo-HUVECs, KRAS G12V, doxycycline induction, SL327 treatment, replicate 1

description: Library name: dox_SL327_1


title: KO, female, chow diet, Rep3

description: Library name: A8


title: Telo-HUVECs, KRAS G12V, doxycycline induction, BAY876 treatment, replicate 3

description: Library name: dox_BAY876_3

value: 5μM BAY876


title: Untagged Rpb3 , KY5949 , FLAG , Rep2

description:
Library name: Untagged_Rpb3_KY5949_FLAG_Rep2
MATalpha lys2-128∂ leu2∆1 ura3-52 3XHSV-PAF1

value: FLAG (Millipore, #A2220)


title: KO, female, chow diet, Rep2

description: Library name: A7

value: KO

value: female


title: Telo-HUVECs, KRAS G12V, doxycycline induction, BAY876 treatment, replicate 1

description: Library name: dox_BAY876_1


title: KO, female, chow diet, Rep1

description: Library name: A6

value: high fat diet


title: Telo-HUVECs, KRAS G12V, doxycycline induction, 3-PO treatment, replicate 3

description: Library name: dox_3PO_3

value: 10μM 3-PO


title: Untagged Rpb3 , KY5949 , FLAG , Rep1

description:
Library name: Untagged_Rpb3_KY5949_FLAG_Rep1
MATalpha lys2-128∂ leu2∆1 ura3-52 3XHSV-PAF1


title: WT , KY5937 , FLAG , Rep2

description:
Library name: WT_KY5937_FLAG_Rep2
MATalpha his4-912δ  lys2-128∂ leu2Δ1 ura3-52 RPB3-3xFLAG::KanMX 3xHA-GLC7


title: Telo-HUVECs, KRAS G12V, doxycycline induction, 3-PO treatment, replicate 2

description: Library name: dox_3PO_2


title: WT, female, chow diet, Rep5

description: Library name: A5

value: Liver


title: Telo-HUVECs, KRAS G12V, doxycycline induction, 2-DG treatment, replicate 3

description: Library name: dox_2DG_3

value: 2mM 2-DG


title: WT, female, chow diet, Rep4

description: Library name: A4


title: Telo-HUVECs, KRAS G12V, doxycycline induction, 2-DG treatment, replicate 2

description: Library name: dox_2DG_2


title: WT , KY5937 , FLAG , Rep1

description:
Library name: WT_KY5937_FLAG_Rep1
MATalpha his4-912δ  lys2-128∂ leu2Δ1 ura3-52 RPB3-3xFLAG::KanMX 3xHA-GLC7


title: Telo-HUVECs, KRAS G12V, doxycycline induction, 3-PO treatment, replicate 1

description: Library name: dox_3PO_1


title: Telo-HUVECs, KRAS G12V, doxycycline induction, 2-DG treatment, replicate 1

description: Library name: dox_2DG_1


title: rtf1del , KY5936 , FLAG , Rep2

description:
Library name: rtf1del_KY5936_FLAG_Rep2
MATalpha his4-912δ  lys2-128∂ leu2∆1 ura3-52 RPB3-3xFLAG::KanMX 3xHA-GLC7 rtf1Δ101::LEU2


title: WT, female, chow diet, Rep3

description: Library name: A3


title: Telo-HUVECs, KRAS G12V, doxycycline induction, SL327 treatment, replicate 3

description: Library name: dox_SL327_3


title: rtf1del , KY5936 , FLAG , Rep1

description:
Library name: rtf1del_KY5936_FLAG_Rep1
MATalpha his4-912δ  lys2-128∂ leu2∆1 ura3-52 RPB3-3xFLAG::KanMX 3xHA-GLC7 rtf1Δ101::LEU2


title: Telo-HUVECs, KRAS G12V, doxycycline induction, no treatment, replicate 3

description: Library name: dox_con_3

value: No Treatment


title: WT, female, chow diet, Rep2

description: Library name: A2


title: spt5-S1-15A , KY5901 , Input_Sp , Rep1

description:
Library name: spt5_S1_15A_KY5901_Input_Sp_Rep1
MATalpha lys2-128∂ leu2∆1 ura3-52 RPB3-3xFLAG::KanMX 3xHSV-PAF1 spt5-S1-15A


title: Telo-HUVECs, KRAS G12V, doxycycline induction, no treatment, replicate 2

description: Library name: dox_con_2


title: Telo-HUVECs, KRAS G12V, doxycycline induction, no treatment, replicate 1

description: Library name: dox_con_1


title: rtf1del , ref2del , swd2del , KY5931 , FLAG , Rep2

description:
Library name: rtf1del_ref2del_swd2del_KY5931_FLAG_Rep2
MATa his4-912δ  lys2-128∂ leu2∆1 RPB3-3xFLAG::KanMX 3xHA-GLC7 rtf1Δ101::LEU2 swd2∆::hphMX ref2∆::KanMX


title: Telo-HUVECs, KRAS G12V, no doxycycline, no treatment, replicate 3

description: Library name: no_dox_3


title: Telo-HUVECs, KRAS G12V, no doxycycline, no treatment, replicate 2

description: Library name: no_dox_2


title: Telo-HUVECs, KRAS G12V, doxycycline induction, BAY876 treatment, replicate 2

description: Library name: dox_BAY876_2


title: rtf1del , ref2del , swd2del , KY5931 , FLAG , Rep1

description:
Library name: rtf1del_ref2del_swd2del_KY5931_FLAG_Rep1
MATa his4-912δ  lys2-128∂ leu2∆1 RPB3-3xFLAG::KanMX 3xHA-GLC7 rtf1Δ101::LEU2 swd2∆::hphMX ref2∆::KanMX


title: Telo-HUVECs, KRAS G12V, no doxycycline, no treatment, replicate 1

description: Library name: no_dox_1


title: RBC-step2-8H-r2

description: Library name: RBC-step-2--8H-r2

value: differentiating HSPCs

value: full


title: Nr5a2_8C_Klf5_KD_TIPseq_rep2

city: Martinsried

first: Siwat

last: Ruangroengkulrith

state: Bavaria

address: Am Klopferspitz 18

department: Totipotency

institute: Max Planck Institute of Biochemistry

description: Library name: TIP seq Sample 4

data_processing:
Low quality reads were trimmed out using TrimGalore (version 0.6.2) (https://github.com/FelixKrueger/TrimGalore) using parameters: --paired --quality 20 --length 20.
Read mapping to mm10 genome was done using Bowtie2 (version 2.3.5.1) using parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant.
Unmapped reads and reads with low mapping quality (Q<30) were removed. PCR duplicated reads were identified and discarded using the MarkDuplicates command from Picard (version 2.18.27) (http://broadinstitute.github.io/picard/) with parameters: VALIDATION_STRINGENCY=LENIENT. T7 duplicated reads (i.e., reads originated from the same T7 promoter tagmentation event) were removed using custom scripts (https://github.com/TotipotencyLab/TIP_tools)
The bigwig files were generated using bamCoverage command from deepTools (version 3.5.4) using parameters: --normalizeUsing RPKM --binSize 1 --ignoreForNormalization chrM. Peak calling was done using MACS2’s callpeak function (version 2.2.9) with default parameters.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: preimplantation embryo

growth_protocol: Zygotes from natural mating were used for siRNA knockdown experiment. Females mice (3-5 weeks old B6129F1 strain) were injected with PMSG (5IU) followed by hCG injection 46-48 hours later for superovulation, before mating with B6CBAF1 male mice. Zygotes were after 19 hours post hCG injection. Embryos were then cultured in KSOM with Lumox dish (Sarstedt).

extract_protocol:
TIP-seq was performed according to the original protocol (Bartlett et al., 2021). Embryos with intact zona pellucida were incubated with ice-cold extraction buffer (25 mM HEPES-NaOH (pH 7.4), 50 mM NaCl, 3 mM MgCl2, 300 mM sucrose, and 0.5% Triton X-100) on ice for 6-7 min and were washed three times with ice-cold extraction buffer without Triton X-100. Pre-extracted embryos were immediately lightly fixed in Dulbecco’s phosphate-buffered saline (DPBS) with 0.1% formaldehyde for 2 min at room temperature. Embryos were incubated in antibody buffer (20 mM HEPES-NaOH (pH7.5), 150 mM NaCl, 0.5 mM Spermidine, 0.1% BSA, 2 mM EDTA and 1x Protease inhibitor cocktail (Roche) with primary antibody (1:100 dilution, NR5A2 (R&D Systems, PP-H2325-00)) overnight at 4°C on nutator. Embryos were washed three times through antibody buffer and further incubated with secondary antibody (1:100 dilution, rabbit anti-mouse IgG H&L (ab46540, abcam)) for 1.5 hours at room temperature. Cells were washed three times with Wash buffer (20 mM HEPES-NaOH (pH 7.5), 150 mM NaCl, 0.5 mM Spermidine, and 1x Protease inhibitor cocktail (Roche)) and further incubated with homemade pA-Tn5 or pAG-Tn5 adaptor complex (1:250 dilution) for 1.5 hours at room temperature. Embryos were washed three times through Wash-300 buffer (20 mM HEPES-NaOH (pH 7.5), 300 mM NaCl, 0.5 mM Spermidine, and 1x Protease inhibitor cocktail (Roche)). Embryos were transferred into a Axygen 0.2 mL Maxymum Recovery Thin Wall PCR Tubes with 50 µl of Tagmentation buffer (10 mM MgCl2 in Wash-300) and incubated at 37°C for 1 hour. The samples were then deproteinized and reverse-crosslinked by adding 1.7 μl of 0.5 M EDTA, 1 μl of 10% SDS (0.2% final) and 0.5 μl of 20 mg/ml proteinase K (Roche #03115887001) and incubating for 2 hours at 50°C, followed by overnight incubation at 65°C. After adding 2 μl of homemade spike-in Drosophila DNA, tagmented gDNA was purified using 2x volume of AMPure XP magnetic beads (Beckman Coulter), and DNA and beads were resuspended in 8 μl of RNase-free water. The further steps involving gap filling, in vitro transcription, cDNA synthesis and cDNA tagmentation were performed according to the original TIP-seq protocol (Bartlett et al., 2021). The tagmented DNA was amplified 50 µl of reaction with 1×Q5 High-Fidelity Master mix (NEB) and 0.25 µM barcoded primers using the following PCR program: 72 °C for 5 min; 98°C for 30 sec; 12 cycles of 98°C for 10 sec and 63°C for 10 sec; final extension at 72 °C for 1 min and hold at 4°C. After the PCR reaction, libraries were purified by 1.1×AMPure XP magnetic beads (Beckman Coulter) and were eluted in 20 µl of RNase-free water.
Purified DNA libraries were sequenced on a NextSeq 500 (Illumina), Novaseq 6000 (Illumina), or AVITI (Element Biosciences) with paired-end reads.

treatment_protocol: For siRNA knockdown, isolated zygotes (8-9 hpf) were microinjected with siRNAs against targets Klf5 (10 µM) or control (15 µM). As a control of successful injection 150 ng/µl H2B-EGFP was co-injected. The siRNA targeting control was ordered as Silencer select from Life technologies. Predesigned siRNAs were obtained from following vendors: Klf5 (#160900, Silencer pre-designed siRNA, Life technologies). The injected embryos were cultured in KSOM using lumox dishes (35 mm, Sarstedt) under 5% O2, 5% CO2, 90% N2.

value: preimplantation embryo

value: 8-cell embryo

value: Klf5 KD

value: R&D Systems, PP-H2325-00


title: RBC-step2-8G-r2

description: Library name: RBC-step-2--8G-r2


title: Nr5a2_8C_Klf5_KD_TIPseq_rep1

description: Library name: TIP seq Sample 3


title: RBC-step2-8H-r1

description: Library name: RBC-step-2--8H-r1


title: Nr5a2_8C_NT_ctrl_TIPseq_rep2

description: Library name: TIP seq Sample 2

value: NT siRNA control KD


title: RBC-step2-8F-r2

description: Library name: RBC-step-2--8F-r2


title: RBC-step2-8G-r1

description: Library name: RBC-step-2--8G-r1


title: RBC-step2-8E-r1

description: Library name: RBC-step-2--8E-r1


title: Nr5a2_8C_NT_ctrl_TIPseq_rep1

description: Library name: TIP seq Sample 1


title: RBC-step2-8F-r1

description: Library name: RBC-step-2--8F-r1


title: spt5delCTR , KY5923 , FLAG , Rep1

description:
Library name: spt5_delCTR_KY5923_FLAG_Rep1
MATa lys2-128∂ leu2Δ1 ura3-52 RPB3-3xFLAG::KanMX 3XHSV-PAF1 spt5∆CTR::NatMX


title: RBC-step2-8E-r2

description: Library name: RBC-step-2--8E-r2


title: spt5del5 , KY5917 , FLAG , Rep2

description:
Library name: spt5_del5_KY5917_FLAG_Rep2
MATalpha lys2-128∂ leu2∆1 RPB3-3xFLAG::KanMX 3xHSV-PAF1 spt5∆5::NatMX


title: RBC-step2-8C-r1

description: Library name: RBC-step-2--8C-r1


title: Tat_2

city: Kodaira

first: Lili

last: Quan

state: Tokyo

address: 4-1-1 Ogawa-Higashi

department: National Institute of Neuroscience

institute: National Center of Neurology and Psychiatry

description: Library name: Ms_HIV1_ Tat_2

data_processing:
Sequencing reads were mapped to the mouse reference genome sequence (mm10) using Hista2 version 2.2.1, SAMtools version 1.3.1, and Stringtie version 2.1.7.
Assembly: mm10
Supplementary files format and content: Ms_Tat_raw_count.tsv
Supplementary files format and content: Ms_Tat_FPKM.tsv

source_name: Mouse prefrontal cortex

extract_protocol:
Total RNAs were isolated from HIV-1 Tat-treated mouse Ecs using TRIzol reagent (Thermo Fisher Scientific) and purified using the RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions.
Library preparation was performed using SMART-Seq HT Kit (Takara) and Nextera XT DNA Library Preparation Kit (Illumina). Whole transcriptome sequencing was performed in 100-base single-ended mode on the Illumina NovaSeq 6000 platform (Illumina).

value: Mouse prefrontal cortex

value: primary cell

value: endothelial cells

value: WT


title: Tat_3

description: Library name: Ms_HIV1_ Tat_3


title: RBC-step2-8C-r2

description: Library name: RBC-step-2--8C-r2


title: spt5del5 , KY5917 , FLAG , Rep1

description:
Library name: spt5_del5_KY5917_FLAG_Rep1
MATalpha lys2-128∂ leu2∆1 RPB3-3xFLAG::KanMX 3xHSV-PAF1 spt5∆5::NatMX

value: FLAG (Millipore, #A2220)


title: RBC-step2-8D-r2

description: Library name: RBC-step-2--8D-r2


title: RBC-step2-8B-r2

description: Library name: RBC-step-2--8B-r2


title: RBC-step2-8B-r1

description: Library name: RBC-step-2--8B-r1


title: WT, female, chow diet, Rep1

description: Library name: A1

value: female

value: chow diet


title: WT , KY5942 , FLAG , Rep2

description:
Library name: WT_KY5942_FLAG_Rep2
MATalpha lys2-128∂ leu2Δ1 ura3-52 RPB3-3xFLAG::KanMX 3xHSV-PAF1


title: WT , KY5942 , FLAG , Rep1

description:
Library name: WT_KY5942_FLAG_Rep1
MATalpha lys2-128∂ leu2Δ1 ura3-52 RPB3-3xFLAG::KanMX 3xHSV-PAF1


title: spt5-S1-15D , KY5907 , FLAG , Rep2

description:
Library name: spt5_S1_15D_KY5907_FLAG_Rep2
MATalpha lys2-128∂ leu2Δ1 ura3-52 RPB3-3xFLAG::KanMX 3xHSV-PAF1 spt5-S1-15D


title: RBC-step2-8A-r2

description: Library name: RBC-step-2--8A-r2


title: RBC-step2-8A-r1

description: Library name: RBC-step-2--8A-r1


title: RBC-step2-7H-r2

description: Library name: RBC-step-2--7H-r2


title: RBC-step2-7H-r1

description: Library name: RBC-step-2--7H-r1


title: Ctrl_2

description: Library name: Ms_Ctrl_2


title: Ctrl_3

description: Library name: Ms_Ctrl_3


title: spt5-S1-15D , KY5907 , FLAG , Rep1

description:
Library name: spt5_S1_15D_KY5907_FLAG_Rep1
MATalpha lys2-128∂ leu2Δ1 ura3-52 RPB3-3xFLAG::KanMX 3xHSV-PAF1 spt5-S1-15D


title: Tat_1

description: Library name: Ms_HIV1_ Tat_1


title: spt5delCTR , KY5923 , FLAG , Rep2

description:
Library name: spt5_delCTR_KY5923_FLAG_Rep2
MATa lys2-128∂ leu2Δ1 ura3-52 RPB3-3xFLAG::KanMX 3XHSV-PAF1 spt5∆CTR::NatMX


title: RBC-step2-7G-r2

description: Library name: RBC-step-2--7G-r2


title: spt5-S1-15A , KY5901 , FLAG , Rep1

description:
Library name: spt5_S1_15A_KY5901_FLAG_Rep1
MATalpha lys2-128∂ leu2∆1 ura3-52 RPB3-3xFLAG::KanMX 3xHSV-PAF1 spt5-S1-15A


title: GLC7-3xHA , KY5236 , Rapa , Input_Sp , Rep2

description:
Library name: GLC7_3xHA_KY5236_Rapa_Input_Sp_Rep2
MATalpha his3∆1 lys2∆0 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA

value: Rapamycin

value: 1 hour


title: Ctrl_1

description: Library name: Ms_Ctrl_1


title: RBC-step2-7F-r2

description: Library name: RBC-step-2--7F-r2


title: RBC-step2-7E-r2

description: Library name: RBC-step-2--7E-r2


title: RBC-step2-7F-r1

description: Library name: RBC-step-2--7F-r1


title: RBC-step2-7E-r1

description: Library name: RBC-step-2--7E-r1


title: A2023 5XFAD IDOL cKO

city: Indianapolis

first: Luke

middle: Child

last: Dabin

state: Indiana

department: Medical and Molecular Genetics

institute: Indiana University

description:
Library name: A2023
10X Genomics

data_processing:
Processing of the sequencing data was performed with the cellranger pipeline (v7.1.0, 10X Genomics).
Assembly: mm10-2020-A
Supplementary files format and content: CellRangerOutputs.tar.gz folder contains cellranger outputs necessary for SoupX loading, each sample has its own subfolder within the main directory.

source_name: Brain (cortex)

extract_protocol:
Nuclei from frozen posterior cortical tissue from female WT and Neu cKO (N=2/genotype) were isolated using the Singulator 100 (S2 Genomics)20. Briefly, frozen brain samples were added to precooled Nuclei Isolation Cartridges (S2 Genomics, 100-063-623) along with RNAse inhibitor (Roche, 03335402001) and loaded into the Singulator 100 to run on Standard Nuclei Isolation Protocol v2. The nuclei suspensions were transferred to conical tubes and pelleted at 500 g for 5 minutes at 4 °C. Once pelleted, the supernatant was aspirated, and the pellets were resuspended in 20% Percoll (100-253-628; S2 Genomics) diluted in Nuclear Storage Reagent (NSR; 100-063-623; S2 Genomics). The samples were centrifuged at 700 g for 8 minutes at 4 °C with the brake off. The nuclei were washed with the Resuspension Buffer (2% BSA in NSR), spun down at 500 g for 5 min at 4 °C, and resuspended in the Resuspension Buffer. The number and viability of the cells were measured using trypan blue staining and observed with an EVOS XL Core microscope.
Nuclei suspensions were processed in a single batch by the 10X Chromium. Each single cell mix was loaded into a Chip G and run on the Chromium Controller for GEM generation and barcoding. Sample processing and library preparation were performed according to the manufacturer’s instructions using the Chromium Next GEM Single Cell 3’ v3.1 dual index kit (10X Genomics) and SPRIselect paramagnetic bead-based chemistry (Beckman Coulter Life Sciences). The cDNA and library quality were assessed using the 2100 Bioanalyzer and a High Sensitivity DNA kit (Agilent Technologies). The final library concentration was determined using a QuBit Fluorometer and the dsDNA HS assay kit (Thermo Fisher Scientific). Sequencing was carried out on a NovaSeq 6000 (v1.5 S2; Illumina) with 28-10-10-91 read setup.

value: Brain (cortex)

value: IDOL KO


title: A1444 5XFAD IDOL cKO

description:
Library name: A1444
10X Genomics


title: A2022 5XFAD IDOL WT

description:
Library name: A2022
10X Genomics

value: IDOL WT


title: RBC-step2-7D-r2

description: Library name: RBC-step-2--7D-r2

value: differentiating HSPCs

value: full


title: RBC-step2-7C-r2

description: Library name: RBC-step-2--7C-r2


title: GLC7-3xHA , KY5235 , Rapa , Input_Sp , Rep1

description:
Library name: GLC7_3xHA_KY5235_Rapa_Input_Sp_Rep1
MATalpha his3∆1 lys2∆0 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA


title: A1331 5XFAD IDOL WT

description:
Library name: A1331
10X Genomics


title: RBC-step2-7C-r1

description: Library name: RBC-step-2--7C-r1


title: RBC-step2-7B-r2

description: Library name: RBC-step-2--7B-r2


title: GLC7-3xHA-FRB , KY5319 , DMSO , Input_Sp , Rep2

description:
Library name: GLC7_3xHA_FRB_KY5319_DMSO_Input_Sp_Rep2
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB

value: DMSO


title: RBC-step2-7B-r1

description: Library name: RBC-step-2--7B-r1


title: RBC-step2-7A-r2

description: Library name: RBC-step-2--7A-r2


title: GLC7-3xHA-FRB , KY5318 , Rapa , Input_Sp , Rep1

description:
Library name: GLC7_3xHA_FRB_KY5318_Rapa_Input_Sp_Rep1
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: mouse LSK(Lin−Sca-1+c-Kit+) cells, Afg3l2-WT, rep1

first: Bin

last: Guo

address: 950 W. Walnut Street

department: Microbiology & Immunology

description: Library name: Afg3l2_WT_1

data_processing:
The sequence reads were aligned to GRCm38/M25 using STAR (2.7.10a).
Uniquely mapped sequencing reads were assigned to Gencode M25 gene using featureCounts (v2.0.1)
Assembly: GRCm38.p6
Supplementary files format and content: Excel files (.xlsx) include CPM values for all samples

source_name: Bone Marrow

growth_protocol: Fresh samples

extract_protocol:
Total RNA was isolated from WT control or Afg3l2-KO LSK(Lin−Sca-1+c-Kit+) cells using FastPure Cell/Tissue Total RNA Isolation Kit (Vazyme).
mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then RNA was digested with RNase H. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. Each group was sequenced in replicates by Illumina NovaSeq 6000 with single end 150 bp read length.

treatment_protocol: PBS wash

value: Bone Marrow

value: Primary cells

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

value: Afg3l2 WT

value: Fresh separation


title: mouse LSK(Lin−Sca-1+c-Kit+) cells, Afg3l2-WT, rep2

description: Library name: Afg3l2_WT_2


title: GLC7-3xHA-FRB , KY5318 , DMSO , Input_Sp , Rep1

description:
Library name: GLC7_3xHA_FRB_KY5318_DMSO_Input_Sp_Rep1
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: spt5-S1-15A , KY5901 , FLAG , Rep2

description:
Library name: spt5_S1_15A_KY5901_FLAG_Rep2
MATalpha lys2-128∂ leu2∆1 ura3-52 RPB3-3xFLAG::KanMX 3xHSV-PAF1 spt5-S1-15A


title: RBC-step2-6H-r2

description: Library name: RBC-step-2--6H-r2


title: RBC-step2-7G-r1

description: Library name: RBC-step-2--7G-r1


title: mouse LSK(Lin−Sca-1+c-Kit+) cells, Afg3l2-KO, rep2

description: Library name: Afg3l2_KO_2

value: Afg3l2 KO


title: RBC-step2-6H-r1

description: Library name: RBC-step-2--6H-r1


title: mouse LSK(Lin−Sca-1+c-Kit+) cells, Afg3l2-KO, rep1

description: Library name: Afg3l2_KO_1


title: GLC7-3xHA , KY5236 , Rapa , Input_Kl , Rep2

description:
Library name: GLC7_3xHA_KY5236_Rapa_Input_Kl_Rep2
MATalpha his3∆1 lys2∆0 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA


title: GLC7-3xHA-FRB , KY5319 , Rapa , Input_Sp , Rep2

description:
Library name: GLC7_3xHA_FRB_KY5319_Rapa_Input_Sp_Rep2
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: RBC-step2-6F-r1

description: Library name: RBC-step-2--6F-r1


title: GLC7-3xHA , KY5235 , Rapa , Input_Kl , Rep1

description:
Library name: GLC7_3xHA_KY5235_Rapa_Input_Kl_Rep1
MATalpha his3∆1 lys2∆0 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA


title: GLC7-3xHA-FRB , KY5319 , Rapa , Input_Kl , Rep2

description:
Library name: GLC7_3xHA_FRB_KY5319_Rapa_Input_Kl_Rep2
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: RBC-step2-6E-r2

description: Library name: RBC-step-2--6E-r2


title: RNA_8C_Nr5a2_Klf5_dKD_rep3

description: Library name: RNA Sample 11

data_processing:
Adaptor sequences were trimmed from the reads using TrimGalore (version 0.6.2) (https://github.com/FelixKrueger/TrimGalore) using parameters: --paired --quality 10 --length 10.
Reads were then mapped to the custom reference transcriptome based on GRCm30 (version 102) with addition of H2B-EGFP and ERCC spike-in reference using STAR with default setting.
Expression for individual gene were quantify using featureCounts (version 2.0.1) with the additional parameters: -t exon -g gene_id -p -O --fraction.
To identify differential expressed genes (DEGs), expression data were imported to R. Genes with low counts across all samples were identified and removed using HTSFilter package. DEGs were identified using DESeq2 package. Only genes with p-value cut-off of 0.05 and have at least 2-fold change compared with the control condition will further be considered as DEGs.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files includes raw read count per gene for each sample

growth_protocol: Females mice (3-5 weeks old B6129F1 strain) were injected with PMSG (5IU) followed by hCG injection 46-48 hours later for superovulation, before mating with B6CBAF1 male mice. Zygotes were after 19 hours post hCG injection. Embryos were then cultured in potassium-supplemented simplex-optimized medium (KSOM) with Lumox dish (Sarstedt).

extract_protocol:
The zona pellucida was removed by treatment with acidic Tyrode. 10 x 8-cell embryos were washed five times in M2 medium and then quickly washed in PBS. Embryos were lysed in lysis buffer containing RNase inhibitor and ERCC spike-in on ice for 15min and then snap frozen with liquid nitrogen.
cDNA was prepared using a SMART-seq v4 Ultra-Low-Input RNA kit for Sequencing (Takara, 634888). Library was prepared by a Nextera XT DNA Library Prep Kit (Illumina, FC-131-1024) according to the manufacturer’s protocol. Purified DNA libraries were sequenced on a Novaseq 6000 (Illumina), or AVITI (Element Biosciences) with paired-end reads.

treatment_protocol: For siRNA knockdown, isolated zygotes (8-9 hpf) were microinjected with siRNAs against targets Nr5a2 (5 µM), Klf5 (10 µM) or control (15 µM). As a control of successful injection 150 ng/µl H2B-EGFP was co-injected. The siRNA targeting control and Nr5a2 were ordered as Silencer select from Life technologies. Predesigned siRNAs were obtained from following vendors: Klf5 (#160900, Silencer pre-designed siRNA, Life technologies); To test Gata6 KD efficiency, 100 M of siRNA targeting Gata6 (#158651, Silencer pre-designed siRNA, Life technologies) was injected into zygotes. The injected embryos were cultured in KSOM using lumox dishes (35 mm, Sarstedt) under 5% O2, 5% CO2, 90% N2.

value: preimplantation embryo

value: 8-cell embryo

value: Nr5a2 and Klf5 KD


title: RBC-step2-6D-r2

description: Library name: RBC-step-2--6D-r2


title: RBC-step2-6E-r1

description: Library name: RBC-step-2--6E-r1


title: GLC7-3xHA-FRB , KY5319 , DMSO , Input_Kl , Rep2

description:
Library name: GLC7_3xHA_FRB_KY5319_DMSO_Input_Kl_Rep2
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: RBC-step2-6C-r2

description: Library name: RBC-step-2--6C-r2


title: RBC-step2-6C-r1

description: Library name: RBC-step-2--6C-r1


title: RBC-step2-7A-r1

description: Library name: RBC-step-2--7A-r1


title: RNA_8C_Nr5a2_Klf5_dKD_rep2

description: Library name: RNA Sample 10


title: RNA_8C_Nr5a2_Klf5_dKD_rep1

description: Library name: RNA Sample 9


title: RBC-step2-6B-r2

description: Library name: RBC-step-2--6B-r2


title: GLC7-3xHA-FRB , KY5318 , DMSO , Input_Kl , Rep1

description:
Library name: GLC7_3xHA_FRB_KY5318_DMSO_Input_Kl_Rep1
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: RNA_8C_Klf5_KD_rep3

description: Library name: RNA Sample 8

value: Klf5 KD


title: RBC-step2-6G-r2

description: Library name: RBC-step-2--6G-r2


title: RBC-step2-6A-r2

description: Library name: RBC-step-2--6A-r2


title: GLC7-3xHA-FRB , KY5319 , DMSO , Myc , Rep2

description:
Library name: GLC7_3xHA_FRB_KY5319_DMSO_Myc_Rep2
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB

value: 1 hour

value: Myc


title: RBC-step2-6A-r1

description: Library name: RBC-step-2--6A-r1


title: RNA_8C_Klf5_KD_rep2

description: Library name: RNA Sample 7


title: RNA_8C_Nr5a2_Klf5_dKD_rep4

description: Library name: RNA Sample 12


title: RBC-step2-6F-r2

description: Library name: RBC-step-2--6F-r2


title: RBC-step2-5H-r2

description: Library name: RBC-step-2--5H-r2


title: RBC-step2-5H-r1

description: Library name: RBC-step-2--5H-r1


title: RBC-step2-5G-r2

description: Library name: RBC-step-2--5G-r2


title: RNA_8C_Klf5_KD_rep1

description: Library name: RNA Sample 6


title: RBC-step2-5G-r1

description: Library name: RBC-step-2--5G-r1


title: RBC-step2-5F-r2

description: Library name: RBC-step-2--5F-r2


title: GLC7-3xHA-FRB , KY5318 , Rapa , Input_Kl , Rep1

description:
Library name: GLC7_3xHA_FRB_KY5318_Rapa_Input_Kl_Rep1
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB

value: Rapamycin


title: GLC7-3xHA , KY5236 , Rapa , HA , Rep2

description:
Library name: GLC7_3xHA_KY5236_Rapa_HA_Rep2
MATalpha his3∆1 lys2∆0 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA

value: HA (Santa Cruz, #sc-7392 AC)


title: RBC-step2-5F-r1

description: Library name: RBC-step-2--5F-r1

value: differentiating HSPCs


title: GLC7-3xHA , KY5235 , Rapa , HA , Rep1

description:
Library name: GLC7_3xHA_KY5235_Rapa_HA_Rep1
MATalpha his3∆1 lys2∆0 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA


title: RBC-step2-6G-r1

description: Library name: RBC-step-2--6G-r1

value: full


title: RBC-step2-5E-r2

description: Library name: RBC-step-2--5E-r2


title: RNA_8C_Nr5a2_KD_rep2

description: Library name: RNA Sample 4

value: Nr5a2 KD


title: RBC-step2-5D-r2

description: Library name: RBC-step-2--5D-r2


title: RBC-step2-6B-r1

description: Library name: RBC-step-2--6B-r1


title: RBC-step2-5E-r1

description: Library name: RBC-step-2--5E-r1


title: GLC7-3xHA-FRB , KY5318 , DMSO , Myc , Rep1

description:
Library name: GLC7_3xHA_FRB_KY5318_DMSO_Myc_Rep1
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB

value: DMSO


title: RNA_8C_Nr5a2_KD_rep1

description: Library name: RNA Sample 3


title: GLC7-3xHA-FRB , KY5319 , Rapa , HA , Rep2

description:
Library name: GLC7_3xHA_FRB_KY5319_Rapa_HA_Rep2
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: GLC7-3xHA-FRB , KY5319 , DMSO , HA , Rep2

description:
Library name: GLC7_3xHA_FRB_KY5319_DMSO_HA_Rep2
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: RBC-step2-5C-r1

description: Library name: RBC-step-2--5C-r1


title: RNA_8C_NT_ctrl_rep2

description: Library name: RNA Sample 2

value: NT siRNA control KD


title: RBC-step2-5C-r2

description: Library name: RBC-step-2--5C-r2


title: GLC7-3xHA-FRB , KY5318 , Rapa , HA , Rep1

description:
Library name: GLC7_3xHA_FRB_KY5318_Rapa_HA_Rep1
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: RBC-step2-5B-r1

description: Library name: RBC-step-2--5B-r1


title: RNA_8C_NT_ctrl_rep1

description: Library name: RNA Sample 1


title: RBC-step2-5A-r1

description: Library name: RBC-step-2--5A-r1


title: RBC-step2-5A-r2

description: Library name: RBC-step-2--5A-r2


title: GLC7-3xHA-FRB , KY5318 , DMSO , HA , Rep1

description:
Library name: GLC7_3xHA_FRB_KY5318_DMSO_HA_Rep1
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: Gata6_Morula_rep2

description: Library name: CUT and Tag Sample 17

data_processing:
Low quality reads were trimmed out using TrimGalore (version 0.6.2) (https://github.com/FelixKrueger/TrimGalore) using parameters: --paired --quality 20 --length 20.
Read mapping to mm10 genome was done using Bowtie2 (version 2.3.5.1) using parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant.
Unmapped reads and reads with low mapping quality (Q<30) were removed. PCR duplicated reads were identified and discarded using the MarkDuplicates command from Picard (version 2.18.27) (http://broadinstitute.github.io/picard/) with parameters: VALIDATION_STRINGENCY=LENIENT.
The bigwig files were generated using bamCoverage command from deepTools (version 3.5.4) using parameters: --normalizeUsing RPKM --binSize 1 --ignoreForNormalization chrM. Peak calling for CUT&Tag, ATAC-seq, and ChIP-seq datasets were done using MACS2’s callpeak function (version 2.2.9) with default parameters.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

growth_protocol: Frozen zygotes from B6CBAF1 mouse strain (Janvier-lab) were used for CUT&Tag experiments of NR5A2, KLF5 GATA6, and H3K27ac. Zygotes were thawed according to a manual of kits of frozen zygotes and cultured in potassium-supplemented simplex-optimized medium (KSOM) with Lumox dish (Sarstedt). Two-cell, four-cell, eight-cell, morula were collected after thawing at 22-24 hours (34-36 hpf), 29-31 hours (41-43 hpf), 44-46 hours (56-58 hpf), and 61-61 hours (71-72 hpf), respectively. Zygotes from natural mating were used for siRNA knockdown experiment. Females mice (3-5 weeks old B6129F1 strain) were injected with PMSG (5IU) followed by hCG injection 46-48 hours later for superovulation, before mating with B6CBAF1 male mice. Zygotes were after 19 hours post hCG injection. Embryos were then cultured in KSOM with Lumox dish (Sarstedt).

extract_protocol:
CUT&Tag was performed as described previously with few modifications (Kaya-Okur, H.S., Wu, S.J., Codomo, C.A. et al. CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat Commun 10, 1930 (2019)). Embryos with intact zona pellucida were incubated with ice-cold extraction buffer (25 mM HEPES-NaOH (pH 7.4), 50 mM NaCl, 3 mM MgCl2, 300 mM sucrose and 0.5% Triton X-100) on ice for 6-7 min and were washed three times through with ice-cold extraction buffer without TritonX-100. Pre-extracted embryos were immediately lightly fixed by Dulbecco’s phosphate- buffered saline (DPBS) with 0.1% formaldehyde for 2 min at room temperature. Embryos were incubated in antibody buffer (20 mM HEPES-NaOH (pH7.5), 150 mM NaCl, 0.5 mM Spermidine, 0.1% BSA, 2 mM EDTA and 1x Protease inhibitor cocktail (Roche) with primary antibody (1:100 dilution) overnight at 4°C on nutator. Embryos were washed three times through antibody buffer and further incubated with secondary antibody (1:100 dilution) for 1.5 hours at room temperature. Cells were washed three times through Wash buffer (20 mM HEPES-NaOH (pH7.5), 150 mM NaCl, 0.5 mM Spermidine and 1x Protease inhibitor cocktail (Roche)) and further incubated with homemade pA-Tn5 or pAG-Tn5 adaptor complex (1:250 dilution) for 1.5 hours at room temperature. Embryos were washed three times through Wash-300 buffer (20 mM HEPES-NaOH (pH7.5), 300 mM NaCl, 0.5 mM Spermidine and 1x Protease inhibitor cocktail (Roche)). Embryos were transferred into 1.5 ml of DNA LoBind Tube (Eppendorf) with 200 µl of Tagmentation buffer (10 mM MgCl2 in Wash-300) and incubated at 37°C for 1 hour. The samples were then deproteinized and reverse-crosslinked. The DNA was purified by phenol-chloroform and followed by ethanol precipitation. The DNA was amplified 50 µl of reaction with 1×Q5 High-Fidelity Master mix (NEB) and 0.25 µM barcoded primers using the following PCR program: 72 °C for 5 min; 98°C for 30 sec; 15 cycles of 98°C for 10 sec and 63°C for 10 sec; final extension at 72 °C for 1 min and hold at 4°C. After PCR reaction, libraries were purified by 1.1×AMPure XP magnetic beads (Beckman Coulter) and were eluted in 20 µl of RNase-free water.
Purified DNA libraries were sequenced on a NextSeq 500 (Illumina), Novaseq 6000 (Illumina), or AVITI (Element Biosciences) with paired-end reads.

value: Morula

value: R&D Systems, AF1700


title: RBC-step2-4H-r2

description: Library name: RBC-step-2--4H-r2


title: RNA_8C_Nr5a2_KD_rep3

description: Library name: RNA Sample 5


title: GLC7-3xHA , KY5236 , Rapa , 8WG16 , Rep2

description:
Library name: GLC7_3xHA_KY5236_Rapa_8WG16_Rep2
MATalpha his3∆1 lys2∆0 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA


title: RBC-step2-4H-r1

description: Library name: RBC-step-2--4H-r1


title: RBC-step2-4G-r2

description: Library name: RBC-step-2--4G-r2


title: Gata6_8C_rep3

description: Library name: CUT and Tag Sample 15


title: Gata6_Morula_rep1

description: Library name: CUT and Tag Sample 16


title: GLC7-3xHA , KY5235 , Rapa , 8WG16 , Rep1

description:
Library name: GLC7_3xHA_KY5235_Rapa_8WG16_Rep1
MATalpha his3∆1 lys2∆0 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA


title: RBC-step2-4G-r1

description: Library name: RBC-step-2--4G-r1


title: GLC7-3xHA-FRB , KY5319 , Rapa , 8WG16 , Rep2

description:
Library name: GLC7_3xHA_FRB_KY5319_Rapa_8WG16_Rep2
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: RBC-step2-4F-r1

description: Library name: RBC-step-2--4F-r1


title: RBC-step2-4F-r2

description: Library name: RBC-step-2--4F-r2


title: RBC-step2-4E-r2

description: Library name: RBC-step-2--4E-r2


title: GLC7-3xHA-FRB , KY5319 , DMSO , 8WG16 , Rep2

description:
Library name: GLC7_3xHA_FRB_KY5319_DMSO_8WG16_Rep2
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: RBC-step2-5D-r1

description: Library name: RBC-step-2--5D-r1


title: Gata6_8C_rep1

description: Library name: CUT and Tag Sample 13


title: RBC-step2-4D-r2

description: Library name: RBC-step-2--4D-r2


title: Gata6_8C_rep2

description: Library name: CUT and Tag Sample 14


title: RBC-step2-4E-r1

description: Library name: RBC-step-2--4E-r1


title: GLC7-3xHA-FRB , KY5318 , Rapa , 8WG16 , Rep1

description:
Library name: GLC7_3xHA_FRB_KY5318_Rapa_8WG16_Rep1
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: Klf5_morula_rep2

description: Library name: CUT and Tag Sample 12

value: Proteintech, 21017-1-AP


title: RBC-step2-4C-r2

description: Library name: RBC-step-2--4C-r2


title: RBC-step2-4D-r1

description: Library name: RBC-step-2--4D-r1


title: RBC-step2-4B-r2

description: Library name: RBC-step-2--4B-r2


title: GLC7-3xHA , KY5236 , Rapa , Spt5 , Rep2

description:
Library name: GLC7_3xHA_KY5236_Rapa_Spt5_Rep2
MATalpha his3∆1 lys2∆0 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA


title: GLC7-3xHA-FRB , KY5318 , DMSO , 8WG16 , Rep1

description:
Library name: GLC7_3xHA_FRB_KY5318_DMSO_8WG16_Rep1
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: RBC-step2-4C-r1

description: Library name: RBC-step-2--4C-r1


title: Klf5_morula_rep1

description: Library name: CUT and Tag Sample 11


title: Klf5_8C_rep2

description: Library name: CUT and Tag Sample 10


title: RBC-step2-4B-r1

description: Library name: RBC-step-2--4B-r1


title: RBC-step2-4A-r2

description: Library name: RBC-step-2--4A-r2


title: GLC7-3xHA , KY5235 , Rapa , Spt5 , Rep1

description:
Library name: GLC7_3xHA_KY5235_Rapa_Spt5_Rep1
MATalpha his3∆1 lys2∆0 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA


title: RBC-step2-4A-r1

description: Library name: RBC-step-2--4A-r1


title: RBC-step2-3H-r2

description: Library name: RBC-step-2--3H-r2


title: GLC7-3xHA-FRB , KY5319 , Rapa , Spt5 , Rep2

description:
Library name: GLC7_3xHA_FRB_KY5319_Rapa_Spt5_Rep2
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: RBC-step2-3H-r1

description: Library name: RBC-step-2--3H-r1


title: Nr5a2_Morula_rep1

description: Library name: CUT and Tag Sample 7

value: R&D Systems, PP-H2325-00


title: RBC-step2-3G-r2

description: Library name: RBC-step-2--3G-r2


title: RBC-step2-3G-r1

description: Library name: RBC-step-2--3G-r1


title: Nr5a2_8C_rep2

description: Library name: CUT and Tag Sample 6

value: preimplantation embryo


title: GLC7-3xHA-FRB , KY5319 , DMSO , Spt5 , Rep2

description:
Library name: GLC7_3xHA_FRB_KY5319_DMSO_Spt5_Rep2
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: RBC-step2-3F-r2

description: Library name: RBC-step-2--3F-r2


title: GLC7-3xHA-FRB , KY5318 , Rapa , Spt5 , Rep1

description:
Library name: GLC7_3xHA_FRB_KY5318_Rapa_Spt5_Rep1
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: RBC-step2-3F-r1

description: Library name: RBC-step-2--3F-r1


title: GLC7-3xHA-FRB , KY5318 , DMSO , Spt5 , Rep1

description:
Library name: GLC7_3xHA_FRB_KY5318_DMSO_Spt5_Rep1
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: RBC-step2-3E-r1

description: Library name: RBC-step-2--3E-r1


title: RBC-step2-3E-r2

description: Library name: RBC-step-2--3E-r2


title: RBC-step2-3D-r2

description: Library name: RBC-step-2--3D-r2


title: GLC7-3xHA , KY5236 , Rapa , Rtf1 , Rep2

description:
Library name: GLC7_3xHA_KY5236_Rapa_Rtf1_Rep2
MATalpha his3∆1 lys2∆0 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA


title: RBC-step2-3D-r1

description: Library name: RBC-step-2--3D-r1


title: Nr5a2_4C_rep1

description: Library name: CUT and Tag Sample 3

value: 4-cell embryo


title: RBC-step2-3C-r2

description: Library name: RBC-step-2--3C-r2


title: RBC-step2-3C-r1

description: Library name: RBC-step-2--3C-r1


title: GLC7-3xHA , KY5235 , Rapa , Rtf1 , Rep1

description:
Library name: GLC7_3xHA_KY5235_Rapa_Rtf1_Rep1
MATalpha his3∆1 lys2∆0 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA