title: Het KO 4 LFD Periportal Bio Rep 3

description:
Library name: DSP-1001660015952-G-B08
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from adrenal gland (ENCLB773HVF)

status: Public on Jan 14 2025

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR176KEW/
***************
biological replicate number: 1
technical replicate number: 1
description: W73 adrenal gland
experiment encode accession: ENCSR176KEW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2023-01-25
lab: Barbara Wold, Caltech
library encode accession: ENCLB773HVF
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

library_source: transcriptomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens female adult (59 years) adrenal gland tissue, preserved by flash-freezing

value: adrenal gland

value: tissue

tag: biosample encode accession

tag: Sex

value: female

tag: health state

value: DM:yes; HTN:yes; CAD:no

tag: dev stage

value: adult

tag: age

value: 59 year

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Yiing Lin, MD, PhD

tag: collection date

value: not applicable

tag: geographic location

tag: link

value: ENCBS826JAI at ENCODE; https://www.encodeproject.org/ENCBS826JAI/


title: RIP-seq from K562 (ENCLB893QNN)

description:
https://www.encodeproject.org/experiments/ENCSR192OSC/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR192OSC
assay title: RIP-seq
assembly: hg19
possible controls: ENCSR067RXF
encode release date: 2016-05-04
lab: John Rinn, Broad
library encode accession: ENCLB893QNN
fragmentation methods: sonication (generic)
size range: 150-150

source_name: Homo sapiens K562 cell line

tag: antibody

tag: line

value: cell line

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Bradley Bernstein, Broad

value: ATCC

value: ENCBS354VJM at ENCODE; https://www.encodeproject.org/ENCBS354VJM/


title: Het KO 4 LFD Perivenous Bio Rep 3

city: Baton Rouge

first: Tim

last: Heden*

state: LA

address: 6400 Perkins Road

institute: Pennington Biomedical Research Center

description:
Library name: DSP-1001660015952-G-B05
FFPE Spatial Transcriptome Sequencing

data_processing:
The GeoMx NGS Pipeline was used to process FASTQ sequencing files from Nanostring GeoMx libraries to produce digital count conversion files. The DCC files were packed into a zip file and uploaded into the GeoMx Digital Spatial Profiler system for spatially resolved expression analysis and visualizations.
Assembly: Mm10
Supplementary files format and content: Slide_Image_with_ROIs_Study_2_Blk_1.tiff
Supplementary files format and content: Slide_Image_with_ROIs_Study_2_Blk_2.tiff
Supplementary files format and content: Information_Summary_for_each_ROI.xlsx
Supplementary files format and content: GeneExpression_CountData.xlsx
Library strategy: Spatial Transcriptomics

organism: Mus musculus

source_name: Liver

extract_protocol:
Formalin Fixed Paraffin Embedded Tissue was sectioned to a 5 micron thickness.
Spatial transcriptome sequencing libraries were prepared with Nanostring GeoMx Mouse NGS Whole Transcritpome Atlas RNA panel.

tag: tissue

value: Liver


title: total RNA-seq from HCT116 (ENCLB591TGB)

description:
https://www.encodeproject.org/experiments/ENCSR146GSS/
***************
biological replicate number: 2
technical replicate number: 1
description: HCT116-SMARCA5-clone1-treated-new_bulk-E3
experiment encode accession: ENCSR146GSS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB591TGB
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SMARCA5 treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS965YHW at ENCODE; https://www.encodeproject.org/ENCBS965YHW/


title: Het KO 4 LFD Perivenous Bio Rep 2

description:
Library name: DSP-1001660015952-G-B04
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from HCT116 (ENCLB362LKI)

description:
https://www.encodeproject.org/experiments/ENCSR146GSS/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116-SMARCA5-clone1-treated-new_bulk-E3
experiment encode accession: ENCSR146GSS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB362LKI
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: adult

value: ENCBS641JLV at ENCODE; https://www.encodeproject.org/ENCBS641JLV/


title: Het KO 4 LFD Periportal Bio Rep 1

description:
Library name: DSP-1001660015952-G-B06
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from heart left ventricle (ENCLB024BTV)

description:
https://www.encodeproject.org/experiments/ENCSR131FDP/
***************
biological replicate number: 1
technical replicate number: 1
description: UW040 heart left ventricle
experiment encode accession: ENCSR131FDP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2023-01-25
lab: Barbara Wold, Caltech
library encode accession: ENCLB024BTV
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (69 years) heart left ventricle tissue

value: heart left ventricle

value: tissue

value: ischemic (EF 25% LVEDD 5.7; RV mildly dilated, moderate dysfunction)

value: 69 year

value: Michael Snyder, Stanford

value: Shin Lin

value: not applicable

value: ENCBS199BOZ at ENCODE; https://www.encodeproject.org/ENCBS199BOZ/


title: Het KO 4 LFD Perivenous Bio Rep 1

description:
Library name: DSP-1001660015952-G-B03
FFPE Spatial Transcriptome Sequencing

value: Liver


title: total RNA-seq from HCT116 (ENCLB886DSJ)

description:
https://www.encodeproject.org/experiments/ENCSR113CCF/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116-MED14-clone1-untreated-new_bulk-4C
experiment encode accession: ENCSR113CCF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB886DSJ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens MED14

value: cell line

value: male

value: colorectal carcinoma

value: ENCBS265FNK at ENCODE; https://www.encodeproject.org/ENCBS265FNK/


title: Het KO 3 LFD Periportal Bio Rep 1

description:
Library name: DSP-1001660015952-G-A12
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from HCT116 (ENCLB892RFT)

description:
https://www.encodeproject.org/experiments/ENCSR113CCF/
***************
biological replicate number: 2
technical replicate number: 1
description: HCT116-MED14-clone1-untreated-new_bulk-4C
experiment encode accession: ENCSR113CCF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB892RFT
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS003KVP at ENCODE; https://www.encodeproject.org/ENCBS003KVP/


title: Het KO 3 LFD Perivenious Bio Rep 1

description:
Library name: DSP-1001660015952-G-A09
FFPE Spatial Transcriptome Sequencing


title: Het KO 3 LFD Perivenious Bio Rep 2

description:
Library name: DSP-1001660015952-G-A10
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from HCT116 (ENCLB334GGS)

description:
https://www.encodeproject.org/experiments/ENCSR094RQC/
***************
biological replicate number: 2
technical replicate number: 1
description: HCT116-RAD21-clone1-treated-new_bulk-C1
experiment encode accession: ENCSR094RQC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB334GGS
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21 treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: adult

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS068GZX at ENCODE; https://www.encodeproject.org/ENCBS068GZX/


title: Het KO 3 LFD Perivenious Bio Rep 3

description:
Library name: DSP-1001660015952-G-A11
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from HCT116 (ENCLB517HFT)

description:
https://www.encodeproject.org/experiments/ENCSR094RQC/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116-RAD21-clone1-treated-new_bulk-C1
experiment encode accession: ENCSR094RQC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB517HFT
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: ENCBS590FGJ at ENCODE; https://www.encodeproject.org/ENCBS590FGJ/


title: total RNA-seq from pancreas (ENCLB749PHP)

description:
https://www.encodeproject.org/experiments/ENCSR075ZTG/
***************
biological replicate number: 1
technical replicate number: 1
description: W64 pancreas
experiment encode accession: ENCSR075ZTG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2023-01-25
lab: Barbara Wold, Caltech
library encode accession: ENCLB749PHP
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (26 years) pancreas tissue, preserved by flash-freezing

value: pancreas

value: tissue

value: DM:no; HTN:no; CAD:no

value: 26 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS375HYG at ENCODE; https://www.encodeproject.org/ENCBS375HYG/


title: Control 1 LFD Perivenous Bio Rep 2

description:
Library name: DSP-1001660015952-G-B10
FFPE Spatial Transcriptome Sequencing

value: Liver


title: total RNA-seq from HCT116 (ENCLB189VUN)

description:
https://www.encodeproject.org/experiments/ENCSR096UGR/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116-SUPT16H-clone1-treated-new_bulk-F1
experiment encode accession: ENCSR096UGR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB189VUN
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SUPT16H treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: cell line

value: male

value: colorectal carcinoma

value: not applicable

value: ENCBS956LYW at ENCODE; https://www.encodeproject.org/ENCBS956LYW/


title: Het KO 2 LFD Periportal Bio Rep 3

description:
Library name: DSP-1001660015952-G-A08
FFPE Spatial Transcriptome Sequencing


title: Het KO 3 LFD Periportal Bio Rep 2

description:
Library name: DSP-1001660015952-G-B01
FFPE Spatial Transcriptome Sequencing


title: Het KO 2 LFD Periportal Bio Rep 2

description:
Library name: DSP-1001660015952-G-A07
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from HCT116 (ENCLB812YWT)

description:
https://www.encodeproject.org/experiments/ENCSR034DEZ/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116-SUPT16H-clone1-untreated-new_bulk-F1
experiment encode accession: ENCSR034DEZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB812YWT
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SUPT16H

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS249OII at ENCODE; https://www.encodeproject.org/ENCBS249OII/


title: Het KO 2 LFD Periportal Bio Rep 1

description:
Library name: DSP-1001660015952-G-A06
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from HCT116 (ENCLB424XXW)

description:
https://www.encodeproject.org/experiments/ENCSR034DEZ/
***************
biological replicate number: 2
technical replicate number: 1
description: HCT116-SUPT16H-clone1-untreated-new_bulk-F1
experiment encode accession: ENCSR034DEZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB424XXW
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: ENCBS171WOQ at ENCODE; https://www.encodeproject.org/ENCBS171WOQ/


title: Het KO 2 LFD Perivenous Bio Rep 3

description:
Library name: DSP-1001660015952-G-A05
FFPE Spatial Transcriptome Sequencing


title: RIP-seq from K562 (ENCLB472UWZ)

description:
https://www.encodeproject.org/experiments/ENCSR026JZX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR026JZX
assay title: RIP-seq
assembly: hg19
possible controls: ENCSR067RXF
encode release date: 2016-05-04
lab: John Rinn, Broad
library encode accession: ENCLB472UWZ
fragmentation methods: sonication (generic)
size range: 150-150

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Bradley Bernstein, Broad

value: ATCC

value: ENCBS354VJM at ENCODE; https://www.encodeproject.org/ENCBS354VJM/


title: Het KO 2 LFD Perivenous Bio Rep 2

description:
Library name: DSP-1001660015952-G-A04
FFPE Spatial Transcriptome Sequencing

value: Liver


title: RIP-seq from K562 (ENCLB329YGV)

description:
https://www.encodeproject.org/experiments/ENCSR026JZX/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR026JZX
assay title: RIP-seq
assembly: hg19
possible controls: ENCSR067RXF
encode release date: 2016-05-04
lab: John Rinn, Broad
library encode accession: ENCLB329YGV
fragmentation methods: sonication (generic)
size range: 150-150

value: cell line

value: ENCBS378DFU at ENCODE; https://www.encodeproject.org/ENCBS378DFU/


title: RIP-seq from K562 (ENCLB242FWB)

description:
https://www.encodeproject.org/experiments/ENCSR026JZX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR026JZX
assay title: RIP-seq
assembly: hg19
possible controls: ENCSR067RXF
encode release date: 2016-05-04
lab: John Rinn, Broad
library encode accession: ENCLB242FWB
fragmentation methods: sonication (generic)
size range: 150-150

value: not applicable

value: ENCBS005AIZ at ENCODE; https://www.encodeproject.org/ENCBS005AIZ/


title: Het KO 2 LFD Perivenous Bio Rep 1

description:
Library name: DSP-1001660015952-G-A03
FFPE Spatial Transcriptome Sequencing


title: Het KO 3 LFD Periportal Bio Rep 3

description:
Library name: DSP-1001660015952-G-B02
FFPE Spatial Transcriptome Sequencing


title: rnjA_depletion_rnjB_rendseq

city: Boston

first: James

middle: Christopher

last: Taggart

state: MA

address: 200 Longwood Avenue

department: Systems Biology

institute: Harvard Medical School

data_processing:
Adapter or poly(A) sequence was trimmed from end sequencing and Rend-seq libraries using CutAdapt (Martin, 2011) with parameters “-a 'CTGTAGGCACCATCAAT' -m 15”.
Trimmed reads were then mapped to the S. cerevisiae genome (SacCer3) using bowtie v1.1.2 with parameters “-v 1 -k 1 –best –un” with retained unmapped reads subsequently mapped to the B. subtilis genome (NC_000964.3) with the same parameters (Langmead et al., 2009).
Using custom Python scripts, we converted the bowtie output to wig files, attributing signal from reads with a mismatch at their first position to the adjacent nucleotide to address mismatches due to non-templated addition during reverse transcription.
Assembly: B. subtilis NC000964.3
Supplementary files format and content: Wiggle file with two columns: first column contains chromosome positions and second column contains the number of reads its 5' or 3' end mapped to the position.

organism: Bacillus subtilis

source_name: bacterial cell

growth_protocol: All Rend-seq sequencing experiments were performed using cells grown in 2xYT, supplemented with 2% xylose or glucose for RNase J1 induction or depletion as necessary. Except when we sought to deplete RNase J1, strains with an inducible RNase J1 allele were consistently grown in the presence of 2% xylose. For all sequencing experiments, overnight cultures in 2xYT were back-diluted to an OD600 of 0.0002 in 20 mL prewarmed 2xYT and grown to an OD600 of 0.2, at which point they were harvested. For any strain with an RNase J1 knockout, cultures were vortexed prior to and following inoculation to minimize clumping. To achieve RNase J1 depletion, 10 times the required volume of overnight culture was collected, washed twice with 1 mL pre-warmed 2xYT, and resuspended in 1 mL 2xYT. 100 µL of this resuspension was used to inoculate the final culture. Samples were harvested for sequencing by adding 7 mL of culture to 7 mL of ice cold methanol, pelleting, decanting, and flash freezing with liquid nitrogen. Cell pellets were stored at -80°C prior to RNA extraction.

extract_protocol:
Prior to RNA extraction, cell pellets were washed with 10-15 mL ice cold 10 mM Tris pH 7.0 to remove contaminating nucleic acids that precipitate from 2xYT in methanol. For Rend-seq, RNA was extracted from cell pellets using either an RNeasy Mini Kit (Qiagen) with on-column DNase treatment, an RNeasy Plus Mini Kit (Qiagen) or through RNAsnap extraction (Stead et al., 2012) followed by Turbo DNase treatment. Following RNA extraction and gDNA depletion, 20 µg of purified RNA was treated with MICROBExpress Bacterial mRNA Enrichment Kit (ThermoFisher) per the manufacturer’s instructions and precipitated with isopropanol.
Libraries were constructed as per the Rend-seq protocol described in Lalanne et al., Cell 2018.

tag: cell type

value: bacterial cell

tag: strain

tag: genotype

value: 168 (trpC2) rnjB::lox72, amyE::{Pspank-rnjA spc}, rnjA::kan


title: Het KO 1 LFD Periportal Bio Rep 3

description:
Library name: DSP-1001660015952-G-A02
FFPE Spatial Transcriptome Sequencing


title: Het KO 1 LFD Periportal Bio Rep 2

description:
Library name: DSP-1001660015953-F-H12
FFPE Spatial Transcriptome Sequencing


title: A7_1_S19_End_vivo_R2

city: Québec

first: Ricardo

middle: Perecin

last: Nociti

state: Québec

address: 2425, Rue de l'Agriculture

department: Animal Science

country: Canada

institute: Université Laval

description: Bridi_CLs_Count_Table_BRIDI_etal_2024.csv

data_processing:
Trimgalore / cutadapt
STAR
featurecounts
DESEQ2
PCIT / CETF
Assembly: ARS-UCD 1.2
Supplementary files format and content: Raw counts for each sample in .csv file

molecule: polyA RNA

organism: Bos taurus

extract_protocol:
The total RNA of corpus luteum  (CM_EE, CM_EE_AI, CM_EE_IVF, NC) was extracted using miRNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions. The total RNA was treated with DNase I (Invitrogen; Carlsbad, CA) to avoid DNA contamination.
The RNA library preparation of three replicates of endometrial  explants co-cultured in the presence or absence of in vivoorin vitroproduced bovine embryos were performed with 0.1- 4 µg the total RNA using Illumina TruSeq Stranded mRNA Sample Prep kit. The libraries were quantified by qPCR using the KAPA Library Quantification kit (Illumina; KAPA Biosystems). The sequencing was performed in 1 lane of Hiseq 2500 V4 (2x100pb).

tag: cell line

value: slaughterhouse

value: Cls

tag: group

tag: batch


title: Het KO 1 LFD Periportal Bio Rep 1

description:
Library name: DSP-1001660015953-F-H11
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from HCT116 (ENCLB522XQG)

description:
https://www.encodeproject.org/experiments/ENCSR096UGR/
***************
biological replicate number: 2
technical replicate number: 1
description: HCT116-SUPT16H-clone1-treated-new_bulk-F1
experiment encode accession: ENCSR096UGR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB522XQG
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

tag: biosample encode accession

tag: Sex

value: male

tag: health state

value: colorectal carcinoma

tag: dev stage

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS561STX at ENCODE; https://www.encodeproject.org/ENCBS561STX/


title: A8_1_S20_End_vitro_R2


title: A6_1_S18_End_R2


title: Het KO 1 LFD Perivenous Bio Rep 3

description:
Library name: DSP-1001660015953-F-H10
FFPE Spatial Transcriptome Sequencing

value: Liver


title: A11_S11_End_vitro_R4


title: A10_S10_End_vivo_R4


title: Het KO 1 LFD Perivenous Bio Rep 1

description:
Library name: DSP-1001660015953-F-H08
FFPE Spatial Transcriptome Sequencing


title: A9_S9_End_R4


title: KYSE450 shHMGB2_3

city: Zhengzhou

first: Ting

last: Wang

address: No. 100 Keke Avenue, Zhengzhou City, Henan Province

country: China

institute: Zhengzhou University

description: Library name: samples 6

data_processing:
Read counts were processed and aligned using Bowtie2 v2.2.5 and RSEM v1.2.12.
Differential gene expression analysis was conducted with a fold change > 1.2 and adjusted P < 0.05 using the DEGSeq software.
Assembly: hg38
Supplementary files format and content: csv files include FPKM values for each sample

growth_protocol: KYSE450 cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidifined atmosphere with 5% CO2 at 37 ℃

extract_protocol:
RNA was harvested using Trizol. 1ug of total RNA was used for the construction of sequencing libraries
RNA  libraries for RNA-seq were prepared using Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit following manufacturer's protocols

value: ESCC

value: HMGB2 knockdown

tag: treatment

value: shHMGB2 Virus infection repeat sample


title: KYSE450 shHMGB2_2

description: Library name: samples 5


title: KYSE450 shHMGB2_1

description: Library name: samples 4

value: shHMGB2 Virus infection


title: A7_S7_DMEN_R5

value: NC


title: KYSE450 mock_3

description: Library name: samples 3

value: WT

value: mock Virus infection repeat sample


title: A6_S6_End_vitro_R5

value: slaughterhouse

value: Cls


title: KYSE450 mock_2

description: Library name: samples 2


title: A5_S5_End_vivo_R5


title: KYSE450 mock_1

description: Library name: samples 1

value: mock Virus infection


title: A4_S4_End_R5


title: X11_S11_End_vitro_R4


title: LCPMuscle，rep3

city: TianJin

first: Lu

last: chuang

address: BinHai

institute: Northwest Normal University

description: Library name: sample36

data_processing:
fastp
Assembly: ZAAS_Lpoly_2.0
Supplementary files format and content: All_samples.GeneExpression.FPKM.xls

organism: Larimichthys

source_name: Muscle

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen, USA) according to the manufacturer’s instructions. The concentration of RNA was assessed using a NanoDrop (Thermo Fisher Scientific, USA), and the quality was evaluated on an Agilent 2100 bioanalyzer (Thermo Fisher Scientific, USA). All samples with an RNA integrity number (RIN) ≥ 7.0 were used to prepare sequencing libraries to ensure high-quality sequencing data.
mRNA was purified using oligo (dT)-attached magnetic beads and fragmented into small pieces. cDNA was synthesized using random hexamer-primed reverse transcription. Subsequently, A-Tailing Mix and RNA Index Adapters were added and incubated for end repair. The cDNA fragments obtained from the previous step were amplified by PCR, and the double-stranded PCR products were heated, denatured and circularized by the splint oligo sequence to obtain the final library.

value: Muscle


title: X10_S10_End_vivo_R4


title: X9_S9_End_R4


title: LCPMuscle，rep1

description: Library name: sample34


title: LCPLiver，rep3

description: Library name: sample33


title: LCPLiver，rep2

description: Library name: sample32


title: A5_1_S17_DMEN_R2


title: X7_S7_DMEN_R5


title: Het KO 1 LFD Perivenous Bio Rep 2

description:
Library name: DSP-1001660015953-F-H09
FFPE Spatial Transcriptome Sequencing


title: X6_S6_End_vitro_R5


title: X8_S8_DMEN_R4


title: LCPBrain，rep3

description: Library name: sample30

source_name: Brain

value: Brain


title: LCPLiver，rep1

description: Library name: sample31


title: X5_S5_End_vivo_R5


title: X4_S4_End_R5


title: LCPBrain，rep2

description: Library name: sample29


title: LCPBrain，rep1

description: Library name: sample28


title: A8_S8_DMEN_R4


title: EE-IVF [27_EndVitro-6]

data_processing:
Trimgalore / cutadapt
STAR
featurecounts
DESEQ2
PCIT / CETF
Assembly: ARS-UCD 1.2
Supplementary files format and content: Count_Table_BRIDI_etal_2023.csv
Supplementary files format and content: FPKM_Table_BRIDI_etal_2023.csv

source_name: Endometrium

extract_protocol:
The total RNA of endometrial explants (EE, EE-AI, and EE-IVF) was extracted using miRNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions. The total RNA was treated with DNase I (Invitrogen; Carlsbad, CA) to avoid DNA contamination.
The RNA library preparation of three replicates of endometrial explants co-cultured in the presence or absence of in vivoorin vitroproduced bovine embryos were performed with 0.1- 4 µg the total RNA using Illumina TruSeq Stranded mRNA Sample Prep kit. The libraries were quantified by qPCR using the KAPA Library Quantification kit (Illumina; KAPA Biosystems). The sequencing was performed in 1 lane of Hiseq 2500 V4 (2x100pb).

value: Endometrium

value: IVF


title: LPCMuscle，rep3

description: Library name: sample27


title: LPCMuscle，rep1

description: Library name: sample25


title: EE-AI [21_EndVivo-6]

value: AI


title: LPCLiver，rep3

description: Library name: sample24


title: EE-AI [20_EndVivo-6]


title: EE-IVF [26_EndVitro-6]


title: EE-AI [19_EndVivo-6]


title: LPCLiver，rep2

description: Library name: sample23


title: LCPMuscle，rep2

description: Library name: sample35


title: LPCMuscle，rep2

description: Library name: sample26


title: EEs [15_End-6]

value: CTRL


title: LPCBrain，rep3

description: Library name: sample21


title: EEs [14_End-6]


title: LPCBrain，rep2

description: Library name: sample20


title: LPCBrain，rep1

description: Library name: sample19


title: EEs [13_End-6]


city: London

first: Sarah

middle: J

last: Marzi

address: Maurice Wohl Clinical Neuroscience Institute

department: Basic and Clinical Neuroscience

country: United Kingdom

institute: King's College London

description: Library name: CST9733, 1/100, 13 PCR, column [H3K27me3]

library_source: genomic

data_processing:
Sequenced on HiSeq 4000 (PE75); bcl2fastq used for basecalling.
Sequenced reads were 1) trimmed for adaptor sequences using TrimGalore 0.6.6; 2) mapped to hg19 whole genome using bowtie v2.2.9 with parameters --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700; 3) duplicate reads were removed with picard v2.6.0 ; 4) deduplicated sam files were converted to bam format using samtools v1.3.1, keeping mapped read pairs. Where applicable bam files were downsampled with samtools v1.3.1
bam files were converted to fragment bed files with bedtools v2.25.0. Fragment bed files were converted to fragment bedgraph files with bedtools v2.25.0
MACS2 peaks were called on bam files with parameters -f BAMPE -g hs -q 1e-5 --keep-dup all –nolambda --nomodel. To call H3K27me3 peaks, the --broad flag was also used.
SEACR peaks were called on fragment bedgraph files with parameters 0.01 non stringent. To call H3K27me3 peaks, a threshold of 0.1 was used.
Assembly: hg19
Supplementary files format and content: bed peak files
Library strategy: CUT&Tag

molecule: genomic DNA

extract_protocol:
Bench top CUT&Tag was performed as previously described (https://www.protocols.io/view/bench-top-cut-amp-tag-bcuhiwt6) using 500,000 exponentially growing K562 cells per experiment. Following tagmentation, either SDS- or column- based DNA extraction was conducted. SDS-based DNA extraction: PCR tubes were placed on a magnetic rack and solution allowed to clear. Supernatant was removed and beads resuspended in 50 μL TAPS Buffer (10 mM TAPS pH 8.5, 0.2 mM EDTA) at RT. Tubes were returned to a magnetic rack and supernatant removed. 5 μL SDS Release Buffer (10 mM TAPS pH 8.5, 0.1% SDS) was added to each tube at RT. After a quick spin, samples were incubated at 58°C for 1 hour. Next, 15 μL SDS Quench Buffer (0.67% Triton-X 100 in Molecular grade H2O) was added at RT. Column-based DNA extraction: 1.68 μL 0.5M EDTA, 0.5 μL 10% SDS, 0.44 μL 10 mg/mL Proteinase K were added to each 50uL sample. Samples were incubated at 55°C for 1 hour and spun quickly. Sample tubes were then placed on a magnetic rack and solutions allowed to clear. Supernatant was transferred to a new microcentrifuge tube and processed according to the ChIP DNA Clean & Concentrator (Zymo Research D5205) protocol.
For library amplification in PCR tube format, 21 μL DNA was combined with 2 μL of universal i5 and uniquely barcoded i7 primer where a different barcode was used for each sample that was intended to be pooled together. 25 μL NEBNext HiFi 2× PCR Master mix was added, then the sample was gently mixed through and spun down. The sample was placed in a Thermocycler with heated lid following these conditions: 72°C for 5 min (gap filling); 98°C for 30 s; 11-15 cycles of 98°C for 10 s and 63°C for 30 s; final extension at 72°C for 1 min; and hold at 4°C. Following PCR, bead cleanup was conducted by addition of 1.1x Ampure XP beads (Beckman Coulter). Library and beads were mixed thoroughly, then spun down and incubated at RT for 10-15 min. Beads were gently washed twice with freshly prepared 80% ethanol using a magnetic rack, then the library was eluted with 20-30 μL 10 mM Tris-HCl pH 8.0 at RT.

tag: histone mark

tag: antibody dilution

tag: tsa

value: No TSA

tag: dna extraction_method

value: column

tag: pcr cycles


description: Library name: Diagenode C15410196, 1/50, 13 PCR, column [H3K27ac]

tag: antibody

value: Diagenode C15410196


title: rmpA overexpression sample 3 of Escherichia coli

city: Beijing

first: Jiangqing

last: Huang

address: No 3, 1st Beichen West Road, Chaoyang District

institute: Chinese Academy of Sciences

description: Library name: PLB1K-rmpA-3

data_processing:
Initial quantification was performed using Qubit2.0 Fluorometer, diluting the library to 1.5ng/ul, followed by an Agilent 2100 bioanalyzer for the insert size of the library.
After qualified library check, different libraries are pooled according to the requirements of effective concentration and target data volume for Illumina sequencing. The basic principle of Sequencing is Sequencing by Synthesis.
Fastq software was used for quality control analysis of the sequenced data.
Bowtie2 software was used to conduct genomic localization analysis of the filtered sequencing columns.
Subread software was used to count the number of reads covered by each gene (including new predicted genes) from inception to termination.
Assembly: Reference genome of Klebsiella RJF293 strain (accession number: GCF_001530015.1) and Escherichia coli K-12 strain (accession number:GCF_000005845.2).
Supplementary files format and content: gene_fpkm_RmpA_Klebsiella.xls
Supplementary files format and content: gene_fpkm_RmpA_Escherichia.xls

organism: Escherichia coli

source_name: RNA-seq of Escherichia coli PLB1K-rmpA-rmpA overexpression sample

growth_protocol: Strain was cultured at 37°C condition and routinely cultured in lysogeny broth (LB), or on LB agar Kanamycin (Kan, 50 μg/mL), gentamicin (Gm, 10 μg/mL) or dehydrated tetracycline (aTc, 2 μM) were used for selection when application.

extract_protocol:
The RNA of strains was extracted using the High Purity RNA Extraction Kit (Qiagen, China) according to manufactured protocol. Then agarose gel electrophoresis and Nanodrop were performed to verify the RNA content and concentration, respectively.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit follow ing manufacturer's protocols.

treatment_protocol: No application.

tag: cell type

value: bacterial cells


description: Library name: Active Motif 39133, 1/100, 13 PCR, column [H3K27ac]

value: Active Motif 39133


title: rmpA overexpression sample 2 of Escherichia coli

description: Library name: PLB1K-rmpA-2

tag: strain


description: Library name: Abcam-ab4729, 1/100, 13 PCR, column [H3K27ac]


title: rmpA overexpression sample 1 of Escherichia coli

description: Library name: PLB1K-rmpA-1


description: Library name: Abcam-ab177178, 1/100, 13 PCR, column [H3K27ac]


title: EE-IVF [25_EndVitro-6]

tag: tissue


description: Library name: Diagenode C15410196, 1/50, 13 PCR, SDS [H3K27ac]

tag: cell line

value: SDS


title: Control sample 2 of Escherichia coli

description: Library name: PLB1K-2

source_name: RNA-seq of Escherichia coli PLB1K-control sample


title: Control sample 1 of Escherichia coli

description: Library name: PLB1K-1


title: ONT_PCR_plasmid_libraries_DXYB6C_2_sample_2

city: Montreal

first: Jean-Benoit

last: Lalanne

state: QC

address: 5155 Chem. de la Rampe

department: Biochemistry and Molecular Medicine

institute: University of Montreal

description:
Library name: ONT_PCR_plasmid_libraries
Long-read ONT data from plasmid DNA (PCR-libraries). Pool of PCR products from libraries p146 & p149-p154.

library_source: other

data_processing:
ONT reads were processed by first searching for ‘signpost’ sequences, corresponding to constant regions flanking our barcodes, within the reads.   Signpost sequences: Left BC1 upstream: CGCGTTTAAT Left BC1 downstream: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG Right BC2 upstream: GATCCGTCGATCGACTGAGT Right BC2 downstream: TAGCGCGCCATTAGGCATGA   To do so, we ran Smith-Waterman (ssw-align17, option -r) using the nanopore reads as target and signposts as query, and reformatted the output to collate alignment scores from all signposts for each target read. Reads for which all 4/4 signposts were detected (75% match or higher) in the concordant orientations and expected barcode order (BC1 position < BC2 for + strand, and vice versa). The sequences corresponding to barcodes, insert index (one for each library), and insert were obtained based on local position reference frames set by signpost positions and length and strand. All sequences were then converted for forward strand for downstream analysis (reverse complement for reads mapped to - orientation). Reads were demultiplexed based on the insert index by calculating the Levenshtein distance to the closest index from the expected list:  Insert class Insert index Primer used for insert amplification p146 (parental) , CTCTTCAGAT, NA Short, homologous, AGACTCAAGT, o937 Short, non-homologous, GAGACGGTCA, o941 Mid-sized, homologous, AGACGATCTG, o938 Mid-sized, non-homologous, GAGACCCTAA, o942 Long, homologous, AGACATTGGC, o939 Long, non-homologous, GAGACCATCG, o943  The second best match was also retained. Any reads for which the best match was within a Levenshtein distance 1, and the difference to the second best match was at least 2 was deemed unambiguously demultiplexable. Finally, only reads with BC1 and BC2 (separately, i.e., irrespective of whether their pairing is correct) corresponding to exact match in our final set of barcodes in our dictionary of valid pairs were retained from quantification. Reads were deemed ‘full length’ with regards to BC-to-BC distance if they fell within the 1% to 99% size distribution from the size selected & digested reads. Only full BC-to-BC length reads were considered for quantification of main figure. Full ITR-to-ITR length boundaries for classification as full length read  were taken to be: plasmids parental p146: 800 to 1050 nt; plasmids all others: 2000 to 2500 nt, AAV all except p153×-mid and p153×-short: 2250 to 2750 nt, AAV p153×-mid: 1100 to 1400 nt, and AAV p153×-short: 500 to 750 nt.  To collate metadata on insert sequences, we aligned the inserts to both the E. coli genome (GCF000005845.2) and plasmid CN1839 (Addgene #163509) using minimap2 (version 2.28, option -x map-ont). Alignments with >0.65 fraction of matching bases (matching bases in alignment/alignment length including gaps) were retained. For a given read and start alignment position within the read, the best scoring (fraction of matching bases) alignment was retained. To further reduce redundant alignments to homologous sections, each read with multiple listed alignments was considered. Overlap (in the read reference frame) between alignments was computed, and alignments were considered redundant if they overlapped by >50% (in practice, the distribution of overlap was nearly perfectly bimodal between 0% and 100%), and the best alignment was retained. To properly categorize inserts overlapping with the end of the plasmid (minimap does not deal with circular chromosomes), reads with two disjoint alignments and one starting within position 5 or ending within 5 of the end of the plasmid were re-categorized as non-composite (unique overlapping the circular junction). Based on these, read inserts were then categorized based on whether they contained a non-mapped (based on our stringent procedure), a unique alignment (to either the E. coli genome or CN1839), or a composite alignment (two or more non-overlapping alignments to either the E. coli genome, CN1839, or both). Quantification  from the plasmid inserts aligned with expectations (homologous libraries entirely comprised of simple fragments mapping to the plasmid, non-homologous libraries coming from a mixture of both given the source material used for tagmentation).
Assembly: Custom constructs, N/A.
Supplementary files format and content: ONT_reads_all_signposts_plasmid_PCR_20250103.txt.gz & ONT_reads_all_signposts_AAV_PCR_20250103.txt.gz: column 1: ONT read ID column 2: read length (nt) column 3: position left BC upstream signpost alignment column 4: position left BC downstream signpost alignment column 5: position right BC upstream signpost alignment column 6: position right BC downstream signpost alignment column 7: read strand column 8: position of middle of left BC column 9: position of middle of right BC column 10: insert sequence parsed in read column 11: left BC1 sequence parsed in read column 12: right BC2 sequence parsed in read column 13: insert index sequence parsed in read column 14: ONT sample name (Plasmidsaurus project ID)
Supplementary files format and content: ONT_final_valid_BCs_reads_plasmid_PCR_20250103.txt.gz & ONT_final_valid_BCs_reads_AAV_PCR_20250103.txt.gz: column 1: ONT read ID column 2: read length (nt) column 3: position left BC upstream signpost alignment column 4: position left BC downstream signpost alignment column 5: position right BC upstream signpost alignment column 6: position right BC downstream signpost alignment column 7: read strand column 8: position of middle of left BC column 9: position of middle of right BC column 10: classified as full BC-to-BC length (falling within the 1% to 99% of the respective digested plasmid insert size) column 11: insert sequence parsed in read column 12: left BC1 sequence parsed in read column 13: right BC2 sequence parsed in read column 14: BC1_BC2 pair column 15: boolean marking valid BC1_BC2 pair column 16: insert index sequence parsed in read column 17: library ID (from demultiplexing of insert index) column 18: ONT sample name (Plasmidsaurus project ID) column 19: fraction of insert covered by alignment(s) column 20: fraction of matches in insert from alignment(s) column 21: string describing alignment (sequence_strand_start_end, if composite, multiple alignments are separated by ::) column 22: marks composite alignments likely coming from inserts overlapping circular junction column 23: alignment category (simple_Ecoli, simple_CN1839, composite_Ecoli, composite_CN1839, composite_Ecoli_CN1839, not_mappable)
Library strategy: Custom amplicons

molecule: other

organism: synthetic construct

source_name: AAV-293 cells for AAV packaging, PHP.eB serotype

extract_protocol:
Plasmids were purified with Zymo MidiPrep kit. AAV samples were sequenced by Plasmidsaurus.
See manuscript for details.  To generate libraries of barcoded insert by PCR from the AAV packaged DNA, we first extracted DNA by performing proteinase K treatment (3 uL crude AAV prep, 6 uL 10 mM Tris 8, 1 uL proteinase K [Thermo Scientific EO0491], 60 min at 50C, 5 min at 70C, then placed on ice), followed by phenol/chloroform extraction (add 190 uL 10 mM Tris 8, add 200 uL phenol-chloroform-isoamyl alcohol [Invitrogen 15593-031], vortex 30 s, spin at 16,000 g at room temperature for 5 min, take aqueous layer) and isopropanol precipitation (add 1 uL glycoblue, 50 uL NaOAc 3M, 250 uL isopropanol 100%, vortex, 45 min at -80C, 45 min at 21,000 g at 4C, 80% EtOH wash, air dry pellet, resuspend in 10 uL 10 mM Tris 8). 2 uL of the precipitated DNA was taken as template for PCR with primers oJBL949+oJBL950 (Kapa Robust Hot Start Ready mix [Roche], 60C annealing temperature, elongation time 2 min 30 s) and tracked by qPCR (SYBr green). PCR libraries were generated from all samples packaged with the PHP.eB serotype in standard (non-sparse) packaging conditions (i.e. samples 1 to 6, see Fig. S4f). Two separate reactions per sample (reaction 1: volume 20 uL, 16 cycles; reaction 2: volume 50 uL, 17 to 20 cycles) were pooled prior to submission. Of note, we tested the importance of adding a DNase treatment step by performing qPCR with primers targeting the insert between the AAV ITRs (oJBL905+oJBL906) vs. a sequence on the ampicillin cassette in the backbone (oJBL097+oJBL098) comparing with/without DNase treatment prior to proteinase K treatment but saw no difference (>30-fold lower backbone material relative to cargo), likely because of the benzonase treatment already having degraded the non-encapsidated DNA. PCR libraries from plasmids were prepared from 1 ng of template (with quantification possibly confounded by genomic DNA carryover), and reactions were stopped at 18 cycles (input starting material calibrated to still be in exponential phase before the inflection point). Plasmid-templated samples also included the parental p146 (which was pooled at 1/10-fold stoichiometry of other larger inserts to mitigate ONT size biases). In both plasmid- and AAV-templated conditions, PCR reactions were cleaned up with 0.4x Ampure clean, leaving predominantly >2 kb products, Fig. S5g (i.e., largely excluding p153×-short and p153×-mid samples). Two samples corresponding to pooled products (AAV pool sample 1, plasmid pool sample 2) were submitted to Plasmidsaurus for long-read sequencing (custom project ID: DXYB6C, target reads 1M per sample).  PCR amplicons were submitted to Plasmidsaurus for sequencing by Oxford Nanopore Technology.


description: Library name: Active Motif 39133, 1/100, 13 PCR, SDS [H3K27ac]


title: LPCLiver，rep1

description: Library name: sample22

value: Liver


title: ONT_PCR_AAV_libraries_DXYB6C_1_sample_1

description:
Library name: ONT_PCR_AAV_libraries
Long-read ONT data from packaged AAV (PCR-libraries). Pool of PCR products from packages libraries p149-p154.

value: AAV-293 cells for AAV packaging, PHP.eB serotype


title: CST9733, 1/100, 13 PCR, SDS [H3K27me3]

description: Library name: CST9733, 1/100, 13 PCR, SDS [H3K27me3]


description: Library name: Abcam-ab4729, 1/100, 13 PCR, SDS [H3K27ac]


description:
Library name: RP88L6_9_ONT_AAV_direct_assembly_and_non_assembly_reads
Long-reat ONT data from packaged AAV (direct). Library p153*, AAV2 serotype, sparse (90% CN2481).

data_processing:
Short-read data (p146 barcode pairs dictionary): Read counts corresponding to identical barcodes 1 and 2 were first piled up.  First, representation of barcodes (separately, summing reads from pairs with 3 or more counts) was inspected, revealing a trimodal distribution: low counts (<=5 reads) corresponding to likely sequencing or PCR errors (BC1: n=1010349, 2.5% of reads; BC2: n=1162035, 2.9% of reads), intermediate counts barcodes making up the bulk of the coverage (BC1=6345673 barcodes, 92.9% of reads; BC2: n=6596695 barcodes, 93.5% of reads), and high-count barcodes (BC1: n=827, 4.6% of reads; BC2: n=530 barcodes, 3.7% of reads), possibly emerging from low level of clonal expansion during cloning. In the case of BC2, a single sequence (ATAACGACTTGTGAGC) was drastically over-represented (2.5% of reads). This barcode and all other barcodes within a Levenshtein distance of 2 or less to it (n=402 barcode, 0.25% of reads) were not considered in downstream analysis to avoid spurious non-unique pairs. We note our barcode space was not saturated at that level of tolerance to mismatches (average of 3 BCs within our BC2 reads within Levenshtein distance of 2 to repeated 1-shufflings of the ATAACGACTTGTGAGC sequence). Further, barcodes with 10 or more consecutive Gs, or containing truncated BC (with the detected post-BC sequences: ATTAAAC for BC1, TAGCGCG for BC2) were removed, corresponding to a minute proportion of the library (BC1: n=9533, 1.1% of reads; BC2: n=3910 , 0.06% of reads). To avoid mismatches from high-representation barcodes being retained as spurious mid-counts barcodes, the list of mid-counts barcode was pruned by removing those within Levenshtein distance of 2 from the high-counts barcodes (number mid-counts barcodes removed in pruning process: BC1 n=16386; BC2 n=4747). All remaining pruned mid-counts barcodes were retained downstream (BC1: n=6321002; BC2: n=6588391). Finally, the high-counts barcodes were further error-corrected by generating an undirected graph connecting barcodes within Levenshtein distance of 2 or less. The most highly represented barcode from connected components were considered the valid barcode. Rare clusters composed of many well-represented barcodes (fold-change between max/min < 10 within cluster) were discarded as possibly ambiguous, leading respectively to n=609 and n=420 error-corrected high count BC1 and BC2 sets. All in all, these filtering steps generated a list of well-represented high quality barcodes (BC1: n=6321611, BC2: n=6588811). From these well-represented BC1 and BC2, we finally filtered on unique pairing between the two. Specifically, all paired barcodes with 2 or more reads were filtered for members present in both separately valid sets. Then, the proportion of reads to each barcode within a pair (e.g., number of reads to BC1 from a given pair over number of reads containing the same BC1 across all pairs in the library) was computed. Only pairs for which >99% of reads mapped to a unique pair were retained. This led to a final set of n=5586772 valid barcode pairs used for downstream assessment. Only exact matches to BC1 and BC2 constituents of these final pairs were used for filtering long-read data and setting the denominator in our barcode swap quantification.
ONT reads were processed by first searching for ‘signpost’ sequences, corresponding to constant regions flanking our barcodes, within the reads.
Signpost sequences:
Left BC1 upstream: CGCGTTTAAT
Left BC1 downstream: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
Right BC2 upstream: GATCCGTCGATCGACTGAGT
Right BC2 downstream: TAGCGCGCCATTAGGCATGA
To do so, we ran Smith-Waterman (ssw-align17, option -r) using the nanopore reads as target and signposts as query, and reformatted the output to collate alignment scores from all signposts for each target read. Reads for which all 4/4 signposts were detected (75% match or higher) in the concordant orientations and expected barcode order (BC1 position < BC2 for + strand, and vice versa). The sequences corresponding to barcodes, insert index (one for each library), and insert were obtained based on local position reference frames set by signpost positions and length and strand. All sequences were then converted for forward strand for downstream analysis (reverse complement for reads mapped to - orientation). Reads were demultiplexed based on the insert index by calculating the Levenshtein distance to the closest index from the expected list:
>>>>>>>>>>>>>>>
Insert class, Insert index, Primer used for insert amplification
p146 (parental), CTCTTCAGAT, NA
Short, homologous, AGACTCAAGT, o937
Short, non-homologous, GAGACGGTCA, o941
Mid-sized, homologous, AGACGATCTG, o938
Mid-sized, non-homologous, GAGACCCTAA, o942
Long, homologous, AGACATTGGC, o939
Long, non-homologous, GAGACCATCG, o943
>>>>>>>>>>>>>>>
The second best match was also retained. Any reads for which the best match was within a Levenshtein distance 1, and the difference to the second best match was at least 2 was deemed unambiguously demultiplexable. Finally, only reads with BC1 and BC2 (separately, i.e., irrespective of whether their pairing is correct) corresponding to exact match in our final set of barcodes in our dictionary of valid pairs were retained from quantification. Reads were deemed ‘full length’ with regards to BC-to-BC distance if they fell within the 1% to 99% size distribution from the size selected & digested reads. Only full BC-to-BC length reads were considered for quantification of main figure. Full ITR-to-ITR length boundaries for classification as full length read  were taken to be: plasmids parental p146: 800 to 1050 nt; plasmids all others: 2000 to 2500 nt, AAV all except p153×-mid and p153×-short: 2250 to 2750 nt, AAV p153×-mid: 1100 to 1400 nt, and AAV p153×-short: 500 to 750 nt.
To collate metadata on insert sequences, we aligned the inserts to both the E. coli genome (GCF000005845.2) and plasmid CN1839 (Addgene #163509) using minimap2 (version 2.28, option -x map-ont). Alignments with >0.65 fraction of matching bases (matching bases in alignment/alignment length including gaps) were retained. For a given read and start alignment position within the read, the best scoring (fraction of matching bases) alignment was retained. To further reduce redundant alignments to homologous sections, each read with multiple listed alignments was considered. Overlap (in the read reference frame) between alignments was computed, and alignments were considered redundant if they overlapped by >50% (in practice, the distribution of overlap was nearly perfectly bimodal between 0% and 100%), and the best alignment was retained. To properly categorize inserts overlapping with the end of the plasmid (minimap does not deal with circular chromosomes), reads with two disjoint alignments and one starting within position 5 or ending within 5 of the end of the plasmid were re-categorized as non-composite (unique overlapping the circular junction). Based on these, read inserts were then categorized based on whether they contained a non-mapped (based on our stringent procedure), a unique alignment (to either the E. coli genome or CN1839), or a composite alignment (two or more non-overlapping alignments to either the E. coli genome, CN1839, or both). Quantification  from the plasmid inserts aligned with expectations (homologous libraries entirely comprised of simple fragments mapping to the plasmid, non-homologous libraries coming from a mixture of both given the source material used for tagmentation).
Assembly: Custom constructs, N/A.
Library strategy: Custom amplicons

source_name: AAV-293 cells for AAV packaging, AAV2 serotype

extract_protocol:
Plasmids were purified with Zymo MidiPrep kit. AAV samples were sequenced by Plasmidsaurus.
See manuscript for details on cloning of libraries p149-p154 (dually barcoded inserts flanked by AAV2 ITRs, with different insert lengths and class [homologous/non-homologous] between barcodes).  The library for barcode dictionary generation from parental backbone p146 was generated by amplifying by PCR (primers o945+o946v2 containing P5 and P7 Illumina adapters) the GFP stuffer insert flanked by the two barcodes using 5 ng starting template (50 uL reaction, Kapa Robust, standard conditions, 10 cycles) and followed by 1x ampure beads cleanup. The resulting library was sequenced using custom primers as a fraction of a NextSeq2000 P2 100 cycles run (read1: 42 cycles with o947, index1: 20 cycles with o761 Nextera_read1 [into SapI restriction site and GFP, not used], index2: 20 cycles with o948 [into GFP, not used], read2: 16 cycles with o762 Nextera_index2). Sequencing data was demultiplexed from other samples based on the first 10 indices of read1 (GATCCGTCGA) using bcl2fastq with base mask i10y*,y*,y*,y*, yielding 195.6M reads to associate barcodes from p146. BC1 (5’/left of insert) was on cycles 1 to 16 within read 2, BC2 (3’/right of insert) was on cycles 21 to 36 within read1.  For long read sequencing, inserts from the barcoded plasmids were released by MluI+NotI digestion and size selected on agarose (Zymoclean kit). Size selected inserts were pooled and submitted to Plasmidsaurus for a custom Oxford Nanopore sequencing project.  AAV preps were submitted to Plasmidsaurus for direct sequencing (which involves an annealing step, end-repair and adapter ligation) with Oxford Nanopore.


description:
Library name: RP88L6_8_ONT_AAV_direct_assembly_and_non_assembly_reads
Long-reat ONT data from packaged AAV (direct). Library p153*, PHP.eB serotype, sparse (90% CN2481).


description:
Library name: RP88L6_7_ONT_AAV_direct_assembly_and_non_assembly_reads
Long-reat ONT data from packaged AAV (direct). Library p153*, AAV2 serotype, standard.

value: AAV-293 cells for AAV packaging, AAV2 serotype


description: Library name: CST9733, 1/100, 11 PCR, column [H3K27me3]


description:
Library name: RP88L6_6_ONT_AAV_direct_assembly_and_non_assembly_reads
Long-reat ONT data from packaged AAV (direct). Library p154, PHP.eB serotype, standard.


description: Library name: Diagenode C15410196, 1/50, 11 PCR, column [H3K27ac]


description: Library name: Abcam-ab177178, 1/100, 13 PCR, SDS [H3K27ac]


description: Library name: Active Motif 39133, 1/100, 11 PCR, column [H3K27ac]


description:
Library name: RP88L6_4_ONT_AAV_direct_assembly_and_non_assembly_reads
Long-reat ONT data from packaged AAV (direct). Library p152, PHP.eB serotype, standard.


description: Library name: Abcam-ab4729, 1/100, 11 PCR, column [H3K27ac]


description:
Library name: RP88L6_3_ONT_AAV_direct_assembly_and_non_assembly_reads
Long-reat ONT data from packaged AAV (direct). Library p151, PHP.eB serotype, standard.


description: Library name: Diagenode C15410196, 1/50, 11 PCR, SDS [H3K27ac]


title: Control sample 3 of Escherichia coli

description: Library name: PLB1K-3


description: Library name: Abcam-ab177178, 1/100, 11 PCR, column [H3K27ac]


description:
Library name: RP88L6_2_ONT_AAV_direct_assembly_and_non_assembly_reads
Long-reat ONT data from packaged AAV (direct). Library p150, PHP.eB serotype, standard.


title: CST9733, 1/100, 11 PCR, SDS [H3K27me3]

description: Library name: CST9733, 1/100, 11 PCR, SDS [H3K27me3]


title: 75 mg metformin, Liver, 65 weeks, Sample 5

city: University Park

first: Evelyn

middle: Anne

last: Weaver

state: PA

address: 439 Shortlidge Rd

institute: Penn State University

description:
Library name: Sample 10
Column name in MetforminReadCounts_0vs75.txt: Met_5

data_processing:
Library quality checked (fastQC, V 0.12.0)
Trimming raw reads (trim galore! V 0.6.4, default setting)
Alignment (STAR V2.7.11b) against reference chicken genome
Raw read count (Htseq 0.12.3, htseq-count) extracted from each aligned bam file
Assembly: GRCg6a (galGal6)
Supplementary files format and content: txt, raw read counts from alignment bam files

organism: Gallus gallus

extract_protocol:
Total RNA was isolated using TRIzol and purified using the Qiagen RNeasy Mini kit. 200 ng of RNA. 200 ng of total RNA was used to construct sequencing libraries.
TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: Broiler breeder hens (n=45 hens/treatment group) were supplemented with metformin (0 or 75 mg/kg body weight) in the diet for 40 weeks (25-65 weeks of age)

value: Metformin

tag: time

value: 65 weeks


title: 75 mg metformin, Liver, 65 weeks, Sample 3

description:
Library name: Sample 8
Column name in MetforminReadCounts_0vs75.txt: Met_3


description:
Library name: RP88L6_1_ONT_AAV_direct_assembly_and_non_assembly_reads
Long-reat ONT data from packaged AAV (direct). Library p149, PHP.eB serotype, standard.


description: Library name: Active Motif 39133, 1/100, 11 PCR, SDS [H3K27ac]


title: 75 mg metformin, Liver, 65 weeks, Sample 2

description:
Library name: Sample 7
Column name in MetforminReadCounts_0vs75.txt: Met_2


title: 8Y6YSQ_ONT_2BC_plasmid_digest

description:
Library name: 8Y6YSQ_ONT_2BC_plasmid_digest
Long-reat ONT data from dually barcoded inserts size selected from digested plasmids (pooled libraries p146, p149-p154).

source_name: Escherichia coli (for plasmid amplification)


description: Library name: Abcam-ab4729, 1/100, 11 PCR, SDS [H3K27ac]


title: 75 mg metformin, Liver, 65 weeks, Sample 1

description:
Library name: Sample 6
Column name in MetforminReadCounts_0vs75.txt: Met_1

source_name: Liver


title: 0 mg metformin, Liver, 65 weeks, Sample 5

description:
Library name: Sample 5
Column name in MetforminReadCounts_0vs75.txt: Control_5


title: 0 mg metformin, Liver, 65 weeks, Sample 3

description:
Library name: Sample 3
Column name in MetforminReadCounts_0vs75.txt: Control_3


title: mCherry, naive, ATAC-seq, rep 2

city: Halifax

first: Spencer

middle: Gordon

last: Jones

state: NS

address: 5850 College St

department: Biochemistry and Molecular Biology

institute: Dalhousie University

data_processing:
Raw sequence reads were trimmed using trimmomatic (version 0.39) to remove low quality leading and tailing bases (below quality 3).
Trimmed reads were aligned to D. melanogaster genome (dm6) using Bowtie (version 2.4.1), with the very-sensitive settings.
Reads were shifted , +4 bp for the forward strand and -5 bp for the negative strand, to account for the DNA repair nick of the Tn5 transpose. Duplicate reads, as well as reads that aligned to multiple loci, had a low mapping quality (<4), aligned to mitochondrial chromosomes, or scaffolds were removed.
ATAC-seq peaks were identified with macs2 (version 2.1.2), using q<0.01.
Assembly: dm6
Supplementary files format and content: narrowPeak

organism: Drosophila melanogaster

source_name: Mushroom body

extract_protocol:
Fly heads were obtained from samples of 50-60 flies through flash freezing with liquid nitrogen, followed by vortexing and separation through a series of a sieves. Fly heads were then suspended in homogenization buffer and nuclei released into solution through chemical and physical agitation of the cell membrane. Anti-GFP bound beads were then used to isolate GFP-positive nuclei from the whole head homogenate to represent the mushroom body-specific fraction (MB). DNA was isolated using a Qiagen MinElute Kit.
ATAC-Seq libraries were generated by mixing purified DNA with custom Nextera primers and High-Fidelity PCR Mastermix (NEB) and amplified as per manufacturer's instructions. Final libraries were purified using a Qiagen PCR purification kit.

value: Mushroom body

tag: genotype


title: 0 mg metformin, Liver, 65 weeks, Sample 4

description:
Library name: Sample 4
Column name in MetforminReadCounts_0vs75.txt: Control_4


title: 0 mg metformin, Liver, 65 weeks, Sample 2

description:
Library name: Sample 2
Column name in MetforminReadCounts_0vs75.txt: Control_2


description: Library name: Abcam-ab177178, 1/100, 11 PCR, SDS [H3K27ac]


title: 0 mg metformin, Liver, 65 weeks, Sample 1

description:
Library name: Sample 1
Column name in MetforminReadCounts_0vs75.txt: Control_1


description:
Library name: RP88L6_5_ONT_AAV_direct_assembly_and_non_assembly_reads
Long-reat ONT data from packaged AAV (direct). Library p153*, PHP.eB serotype, standard.


title: mCherry, naive, ATAC-seq, rep 1


description: Library name: Diagenode C15410196, 1/100, 15 PCR, SDS +TSA [H3K27ac]

value: TSA


title: AF, WT, rep5

city: Los Angeles

first: Audrey

last: Nickle

address: 2250 Alcazar St

department: Center for Craniofacial Molecular Biology

institute: University of Southern California

description: Library name: 1313-Z10_S13

data_processing:
Analysis was performed using Partek Flow
Assembly: mm10 GENCODE (release M25)
Supplementary files format and content: text file includes raw counts for each sample

source_name: Anterior Fontanelle

extract_protocol:
RNA was isolated using the Zymo Quick-RNA Miniprep Plus kit according to manufacturer's instructions. QC was performed via TapeStation and all samples had RIN scores >8
Library construction was performed using the Kapa Stranded Kit from Roche according to manufacturer's instructions and sequencing was performed using Illumina Hiseq3000, 1x50 read length with single reads.

value: Anterior Fontanelle

value: WT


description: Library name: Diagenode C15410196, 1/50, 15 PCR, SDS +TSA [H3K27ac]


title: AF, WT, rep4

description: Library name: 1313-Z9_S12


title: AF, NCC Fgfr2 KO, rep5

description: Library name: 1313-Z8_S11

value: Wnt1-Cre; Fgfr2fl/fl


title: IVF_NC_scRNA-seq_H2

city: Odense

first: Jan

middle: Wilhelm

last: Kornfeld

address: Campusbej 50

country: Denmark

institute: University of Southern Denmark

library_source: transcriptomic single cell

data_processing:
Sequencing reads were aligned to the mouse reference genome from Gencode (vM25) using STAR aligner and gene features were counted by using featureCountsv (2.0.3).
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files includes raw reads for each sample.
Supplementary files format and content: tab-delimited text files includes RPKM values for each sample.

growth_protocol: MicroRNA microinjected zygotes were kept until 8-cell-stage and then disassociated for further sequencing.

extract_protocol:
Custom-made Smart-seq2 protocol was implemented as before.
RNA libraries for scRNA-seq were prepared using Dual-indexed Illumina Nextera XT sequencing librarie kit.

treatment_protocol: Zygote were microinjected with miR-let-7d/e, mi699a-5p or negative control.

tag: mouse id

value: blastomeres

value: NC


title: AF, NCC Fgfr2 KO, rep4

description: Library name: 1313-Z7_S10


title: 75 mg metformin, Liver, 65 weeks, Sample 4

description:
Library name: Sample 9
Column name in MetforminReadCounts_0vs75.txt: Met_4


description: Library name: Abcam-ab4729, 1/100, 15 PCR, SDS +TSA [H3K27ac]


description: Library name: Abcam-ab177178, 1/100, 15 PCR, SDS +TSA [H3K27ac]


title: AF, WT, rep3

description: Library name: 1313-Z6_S9


title: AF, NCC Fgfr2 KO, rep3

description: Library name: 1313-Z5_S8


description: Library name: Diagenode C15410196, 1/50, 15 PCR, SDS [H3K27ac]

value: No TSA


title: AF, WT, rep1

description: Library name: 1313-Z2_S5


title: AF, WT, rep2

description: Library name: 1313-Z3_S6


title: IVF_NC_scRNA-seq_G2


description: Library name: Diagenode C15410196, 1/100, 15 PCR, SDS [H3K27ac]

value: Diagenode C15410196


title: WGS from transverse colon (ENCLB109VNU)

description:
https://www.encodeproject.org/experiments/ENCSR664TEU/
***************
biological replicate number: 1
technical replicate number: 1
description: The data contained in this Experiment correspond to PacBio Sequel generated 10Kb DNA libraries of ENCODE donor ENCDO793LXB.
experiment encode accession: ENCSR664TEU
assay title: WGS
assembly: GRCh38
encode release date: 2020-03-04
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB109VNU
size range: >1000

source_name: Homo sapiens transverse colon tissue female adult (53 years)

extract_protocol: not provided

value: transverse colon

value: tissue

tag: description

value: Transverse colon tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

tag: biosample encode accession

value: adult

tag: Sex

value: female

tag: age

value: 53 year

tag: lab

value: Thomas Gingeras, CSHL

tag: link

value: ENCBS974EYF at ENCODE; https://www.encodeproject.org/ENCBS974EYF/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: AF, NCC Fgfr2 KO, rep1

description: Library name: 1313-Z1_S4


title: IVF_NC_scRNA-seq_G3

tag: treatment


title: AF, NCC Fgfr2 KO, rep2

description: Library name: 1313-Z4_S7


title: IVF_NC_scRNA-seq_F3


title: gastric cancer [G69T__VDJ]

city: Fukuoka

first: Naoki

last: Katayama

address: 3-1-1 Maidashi, Higashi-ku

country: Japan

institute: Kyushu University

data_processing:
Raw sequencing reads were aligned to the human reference genome GRCh38 and processed to a matrix representing the UMI’s per cell barcode per gene using Cell Ranger v7.1.0 (10x Genomics)
Output files were analyzed with the R v4.2.1 package "Seurat v4.3.0".
Assembly: GRCh38
Supplementary files format and content: To merge the data of all samples, we used the "SCTransform" package for the normalization and variance stabilization of molecular count data.

source_name: MID

extract_protocol:
Single-cell library preparation was performed according to the manual of the Chromium Next GEM Single-cell 3' Reagent Kits v3.1 the Chromium Next GEM Single Cell 5′ Kit v2 for Dual Index (10x Genomics). The cell suspensions were loaded on the Single-cell G Chip for gel bead-in-emulsion (GEM) generation and barcoding. cDNA library thus was generated with a droplet-based sequencing platform (10X Genomics). Next, reverse transcription, RT cleanup cDNA amplification, and quantification was performed to construct the 3’ and 5’ gene library.
The libraries were sequenced on NovaSeq6000 (Illumina) or DNBSEQ-G400 (MGI Tech).

tag: tissue type

value: gastric cancer

value: stomach

tag: gender

value: Female


title: gastric cancer [G76T__VDJ]

source_name: LOW

value: Male


title: gastric cancer [G75T__VDJ]


title: CST9733, 1/100, 15 PCR, SDS [H3K27me3]

description: Library name: CST9733, 1/100, 15 PCR, SDS [H3K27me3]

tag: histone mark

tag: antibody

tag: antibody dilution

tag: tsa

tag: dna extraction_method

value: SDS

tag: pcr cycles


description: Library name: Active Motif 39133, 1/100, 15 PCR, SDS [H3K27ac]

tag: cell line

value: Active Motif 39133


title: IVF_NC_scRNA-seq_F2

tag: tissue

tag: mouse id

tag: cell type

value: blastomeres

tag: genotype

value: WT

tag: strain

value: NC


title: IVF_NC_scRNA-seq_G1


title: IVF_NC_scRNA-seq_H1


description: Library name: Abcam-ab4729, 1/100, 15 PCR, SDS [H3K27ac]

value: No TSA


title: gastric cancer [G68T__VDJ]

source_name: HIGH

tag: age


title: IVF_NC_scRNA-seq_F1


title: gastric cancer [G66T__VDJ]


title: gastric cancer [G68N__VDJ]

source_name: normal

value: Adjacent normal gastric mucosa


description: Library name: Abcam-ab177178, 1/100, 15 PCR, SDS [H3K27ac]


title: gastric cancer [G68N]


title: gastric cancer [G67T__VDJ]


title: gastric cancer [G48N]


title: IVF_NC_scRNA-seq_E3


title: IVF_NC_scRNA-seq_E2


title: Control sample 1 of Klebsiella pneumonia RJF293

description: Library name: dCas9-sgRNA-1

organism: Klebsiella pneumoniae

source_name: RNA-seq of Klebsiella strain RJF293 dCas9-sgRNA-control sample

value: bacterial cells


title: rmpA knochdown sample 2 of Klebsiella pneumonia RJF293

description: Library name: dcas9-rmpA-2

source_name: RNA-seq of Klebsiella strain RJF293 dCas9-rmpA-rmpA knockdown sample


title: IVF_NC_scRNA-seq_E1


title: rmpA knochdown sample 1 of Klebsiella pneumonia RJF293

description: Library name: dcas9-rmpA-1


description:
Library name: Diagenode C15410196, 1/50, 15 PCR, SDS, replicate 2 [H3K27ac]
diag-2

value: Diagenode C15410196


title: IVF_NC_scRNA-seq_D2


title: rmpA knochdown sample 3 of Klebsiella pneumonia RJF293

description: Library name: dcas9-rmpA-3


description:
Library name: Abcam-ab4729, 1/100, 15 PCR, SDS, replicate 2 [H3K27ac]
ab4729-2


title: Control sample 2 of Klebsiella pneumonia RJF293

description: Library name: dCas9-sgRNA-2


title: Control sample 3 of Klebsiella pneumonia RJF293

description: Library name: dCas9-sgRNA-3


title: AHL_T2

city: Nedlands WA

first: Wenna

last: Lee

state: WA

address: Perth Children's Hospital, 15 Hospital Ave, 15 Hospital Ave

country: Australia

institute: The Kids Research Institute Australia

description: Library name: AHL_T2

data_processing:
The raw FASTQ data were transferred via RSYNC into a Linux virtual machine for pre-processing and FASTQ sequence reads with more than one file was concatenated.
Quality control was performed using FastQC v0.12.0 and MultiQC v1.13.
STAR v2.7.10b was used to align the untrimmed FASTQ sequences (inclusive of adapters and indexes) to hg38 transcripts.
The BAM files generated by STAR were indexed by Samtools 1.16.1 and SAM files.
HTseq v2.0.2 was used to perform read counts on the SAM files and generate raw RNA count files.
Assembly: Ensembl GRCh38.86
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: whole blood

extract_protocol:
Cellular RNA was manually extracted from whole blood collected in PAXgene blood RNA tubes using PAXgene blood miRNA kit (PreAnalytiX GmbH; Hombrechtikon, Switzerland) following manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using Illumina stranded mRNA Library Prep (Illumina; San Diego, CA, USA) following manufacturer's protocols.

value: whole blood

tag: time

value: 3 month post-intake

value: tick-bitten participant

tag: batch


description:
Library name: CST 9733, 1/100, 15 PCR, SDS, replicate 1 [H3K27me3]
ab9733-1


description:
Library name: Abcam-ab177178, 1/100, 15 PCR, SDS, replicate 2 [H3K27ac]
ab177-2


title: AHE_T0

description: Library name: AHE_T0

value: Intake

tag: treatment


title: IVF_NC_scRNA-seq_D1


description:
Library name: Abcam-ab4729, 1/100, 15 PCR, SDS, replicate 1 [H3K27ac]
ab4729-1


title: AHL_T0

description: Library name: AHL_T0


title: AHE_T2

description: Library name: AHE_T2


description:
Library name: CST 9733, 1/100, 15 PCR, SDS, replicate 2 [H3K27me3]
ab9733-2


title: AHN_T1

description: Library name: AHN_T1

value: 1 week post-intake


title: IVF_NC_scRNA-seq_C3


title: AHE_T1

description: Library name: AHE_T1


title: IVF_NC_scRNA-seq_C2


title: AHN_T0

description: Library name: AHN_T0


title: gastric cancer [G46T]

tag: tissue type

value: gastric cancer

value: stomach

tag: gender


title: IVF_NC_scRNA-seq_D3


description:
Library name: Diagenode C15410196, 1/50, 15 PCR, SDS, replicate 1 [H3K27ac]
diag-1

tag: histone mark

tag: antibody


title: AHL_T1

description: Library name: AHL_T1


title: IVF_NC_scRNA-seq_C1


title: IVF_NC_scRNA-seq_B3


title: K562, daunorubicin 10 µM, 4h, CTCF ChIP-seq, biol rep 2

city: Leiden

first: Minkang

last: Tan

address: Einthovenweg 20

department: Department of Cell and Chemical Biology

country: Netherlands

institute: Leiden University Medical Center

description: Library name: K562-CTCF ChIP-seq - Daun-2

data_processing:
The ChIP-seq data were processed using the ENCODE Data Coordination Center (DCC) ChIP-seq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2) (v1.9.0).
ChIP-seq reads were aligned to the human reference genome (GRCh37/hg19) using Bowtie2. Duplicate reads were removed using Picard MarkDuplicates.
Peaks of each biological replicate were called using SPP with the parameters ‘-npeak 300000 -speak 155 -fdr 0.01’. Reproducible peaks were intersected from two biological replicates. The blacklisted regions described by ENCODE were discarded.
The ChIP-seq signal tracks were generated from BAM files using the command ‘bedtools genomecov -scale’ with read count per million (CPM) normalization and converted to bigwig files using bedGraphToBigWig.
Assembly: hg19
Supplementary files format and content: bigwig, bed

source_name: Blood

growth_protocol: K562 cells were cultured in RPMI 1640 + L-Glutamine (Gibco), 10% fetal bovine serum (Biowest), and 1% Penicillin-Streptomycin (Gibco).

extract_protocol:
ChIP samples were processed as described in PMID 19275939 and 25961671.
The ChIP DNA was cleaned up using  QIAquick PCR Purification Kit (QIAGEN, 28106) and eluted in 35 µl EB. 34 µl ChIP DNA was end-repaired in a 50 µl reaction, with 5 µl 10x Beads were reclaimed and washed once with 70% ethanol without mixing followed by aspirating ethanol.  End-Repair Buffer, 5 µl 2.5 mM dNTP Mix, 5 µl,10 mM ATP, and 1 µl End-Repair Enzyme Mix (Lucigen,14422-5). Incubated at room temperature for 45 mins and purified using the QIAquick PCR Purification Kit (QIAGEN, 28106), eluting in 35 µl of EB. Then the 34 µl end-repaired ChIP DNA was added of ‘A’ base to 3’ Ends in a 50 µl reaction, with 5 µl Klenow buffer (NEB2), 10 µl 1 mM dATP, 1 µl Klenow (3’ to 5’ exo minus). Incubated for 30 mins at 37°C and purified using the QIAquick PCR Purification Kit (QIAGEN, 28106) eluting in 12 µl of EB. The 12 µl purified DNA was ligated with an adapter in a 30 µl reaction, with 15 µl 2x DNA ligase buffer,1 µl Adapter oligo mix (40 ng/µl), and 2 µl T4 DNA ligase. Incubated at room temperature for 15 minutes and purified using the QIAquick PCR Purification Kit (QIAGEN, 28106), eluting in 25 µl of EB. The 23 µl purified DNA was combined and mixed with 25 μl Phusion High-Fidelity PCR Master Mix (Thermofisher, F531L), 1 µl 10 µM PCR primer 1.1, 1 µl 10 µM PCR primer 2.1 to a total 50 µl reaction volume. PCR procedures were 98 °C for 30 s, 15 cycles of 98 °C for 10 s, 65 °C for 30 s, 72 °C for 30 s, and 72 °C for 5 min (15 cycles could be used for high abundant ChIPed DNA, 17 cycles could be used for low abundant ChIPed DNA). The PCR product was purified using the QIAquick PCR Purification Kit (QIAGEN, 28106), and eluted in 19 µl of EB. The adapter-ligated DNA was run on a 2% Agarose E-gel (ThermoFisher, G402022) and excised DNA of the most abundant band (should be around 300 bp, within the range of 450 bp-600 bp) from the gel with a clean scalpel (be sure to take photos of the gel before and after the gel slices are excised). The cut of gel was purified using MinElute Gel Extraction Kit (QIAGEN, 28606), and eluting in 15 µl of EB. Measure the DNA concentration (ng/µl) using Qbit, and assess the quality of purified libraries using a Bioanalyzer High-Sensitivity DNA Analysis kit (Agilent).

treatment_protocol: 100 miilion K562 cells were treated with 10 µM of indicated drug for 4 hours.

value: Blood

value: human erythroleukemia cell

value: daunorubicin 10 µM, 4h


title: K562, daunorubicin 10 µM, 4h, CTCF ChIP-seq, biol rep 1

description: Library name: K562-CTCF ChIP-seq - Daun-1


title: AJK_T2

description: Library name: AJK_T2


title: AHR_T2

description: Library name: AHR_T2


title: AHR_T1

description: Library name: AHR_T1


title: K562, aclarubicin 10 µM, 4h, CTCF ChIP-seq, biol rep 2

description: Library name: K562-CTCF ChIP-seq - Acla-2

value: aclarubicin 10 µM, 4h


title: AHR_T0

description: Library name: AHR_T0


description:
Library name: Abcam-ab177178, 1/100, 15 PCR, SDS, replicate 1 [H3K27ac]
ab177-1

tag: antibody dilution

tag: tsa

value: SDS


title: K562, aclarubicin 10 µM, 4h, CTCF ChIP-seq, biol rep 1

description: Library name: K562-CTCF ChIP-seq - Acla-1


title: IVF_NC_scRNA-seq_B2

value: blastomeres

value: WT

value: NC


title: AHP_T0

description: Library name: AHP_T0


title: AHP_T1

description: Library name: AHP_T1


title: IVF_NC_scRNA-seq_B1


title: AHP_T2

description: Library name: AHP_T2


title: Control eCLIP from K562 (ENCLB304MRR)

description:
https://www.encodeproject.org/experiments/ENCSR961NOR/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP control experiment on K562 against SRSF1
experiment encode accession: ENCSR961NOR
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2022-12-17
lab: Gene Yeo, UCSD
library encode accession: ENCLB304MRR
fragmentation methods: see document
size range: 175-300

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens K562 cell line

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: adult

value: 53 year

tag: passage number

tag: lab

value: Gene Yeo, UCSD

tag: source

value: ATCC

tag: collection date

value: not applicable

tag: geographic location

tag: link

value: ENCBS177POD at ENCODE; https://www.encodeproject.org/ENCBS177POD/


title: IVF_NC_scRNA-seq_A2

tag: tissue

tag: mouse id

tag: cell type

tag: genotype

tag: strain

tag: treatment


title: IVF_NC_scRNA-seq_A3


title: AJS_T0

description: Library name: AJS_T0

value: whole blood

tag: time

value: Intake

value: tick-bitten participant

tag: batch


title: AJS_T1

description: Library name: AJS_T1

value: 1 week post-intake


title: Control eCLIP from K562 (ENCLB110CYE)

description:
https://www.encodeproject.org/experiments/ENCSR961NOR/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against SRSF1
experiment encode accession: ENCSR961NOR
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2022-12-17
lab: Gene Yeo, UCSD
library encode accession: ENCLB110CYE
fragmentation methods: see document
size range: 175-300

tag: line

tag: biosample encode accession

tag: Sex

tag: age

value: ENCBS344MAK at ENCODE; https://www.encodeproject.org/ENCBS344MAK/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: 100x CRISPR-Cas9-low-4

city: Tianjin

first: Shuai

last: Li

state: Tianjin

address: Huanhuxi Road

institute: Tianjin Tumor Hospital

description: Library name: 100x CRISPR-Cas9-low-4

data_processing:
Clean reads were obtained by filtering out low-quality sequences and subsequently merged using FLASH software (v1.2.11).
In-house Perl scripts were developed to analyze the library sequences.
Supplementary files format and content: Tab-delimited text files. Column 1 (TIS sequence): This column contains the unique translation initiation site (TIS) sequences identified in our analysis. Column 2 (read count): This column indicates the number of sequencing reads.

growth_protocol: The HEK293T cell line (American Type Culture Collection, ATCC, USA) is cultured in Dulbecco's Modified Eagle Medium (DMEM) (Thermo Fisher Scientific, USA) supplemented with 10% Fetal Bovine Serum (FBS) (Corning, USA) and 1% Penicillin-Streptomycin Solution (Thermo Fisher Scientific, USA), and maintained in an incubator at 37°C with 5% CO2.

extract_protocol:
Genomic DNA was extracted with the TaKaRa MiniBEST Universal Genomic DNA Extraction Kit (TaKaRa, Japan). Library sequences were amplified using high-fidelity KOD-Plus-Neo DNA polymerase (TOYOBO, Japan). For each library, the number of PCR cycles has been determined to ensure that the amplification is in the exponential phase.
Library construction and high-throughput sequencing were performed by Novogene (China). The PCR products were processed for sequencing library preparation using the NEBNext Ultra II FS DNA PCR-free Library Prep Kit for Illumina (NEB, USA), following the High Inputs (100–500 ng) protocol.

treatment_protocol: HEK293T cells were seeded into 10 cm dishes one day before transfection (60-70% confluency). Using Lipofectamine 2000 (Thermo Fisher Scientific, USA), 6 μg of the dsDNA-assembly-PCR library and 6 μg of the px330-sgAAVS1 plasmid or hyPBase plasmid were co-transfected into HEK293T cells. Forty-eight hours post-transfection, the cell culture medium was supplemented with 2 μg/ml puromycin (Selleck Chemicals, USA) to select for cells with stable library integration. The selection process was maintained for a minimum of 10 days.


title: AHN_T2

description: Library name: AHN_T2

value: 3 month post-intake


title: Control eCLIP from K562 (ENCLB690OJP)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR660DRN/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP control experiment on K562 against EIF4E
experiment encode accession: ENCSR660DRN
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB690OJP
fragmentation methods: see document
size range: 175-300

tag: health state

tag: dev stage

tag: passage number

tag: lab


title: AJK_T0

description: Library name: AJK_T0


title: AJS_T2

description: Library name: AJS_T2


title: 100x CRISPR-Cas9-low-3

description: Library name: 100x CRISPR-Cas9-low-3


title: IVF_mi699a-5p_scRNA-seq_H3

value: blastomeres

value: WT


title: 100x CRISPR-Cas9-low-1

description: Library name: 100x CRISPR-Cas9-low-1


title: 100x CRISPR-Cas9-medium-4

description: Library name: 100x CRISPR-Cas9-medium-4


title: IVF_mi699a-5p_scRNA-seq_H1


title: 100x CRISPR-Cas9-high-4

description: Library name: 100x CRISPR-Cas9-high-4


title: IVF_mi699a-5p_scRNA-seq_G3


title: 100x CRISPR-Cas9-medium-2

description: Library name: 100x CRISPR-Cas9-medium-2


title: 100x CRISPR-Cas9-high-3

description: Library name: 100x CRISPR-Cas9-high-3


title: Control eCLIP from K562 (ENCLB776DKO)

description:
https://www.encodeproject.org/experiments/ENCSR660DRN/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against EIF4E
experiment encode accession: ENCSR660DRN
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB776DKO
fragmentation methods: see document
size range: 175-300

value: cell line

value: female

tag: source

tag: link


title: eCLIP from K562 (ENCLB272VSK)

description:
https://www.encodeproject.org/experiments/ENCSR440MSY/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against ELAC2
experiment encode accession: ENCSR440MSY
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR545KBT
encode release date: 2022-11-16
lab: Gene Yeo, UCSD
library encode accession: ENCLB272VSK
fragmentation methods: see document
size range: 175-300

tag: antibody

value: chronic myelogenous leukemia (CML)

value: adult

tag: collection date

tag: geographic location

value: ENCBS592SHU at ENCODE; https://www.encodeproject.org/ENCBS592SHU/


title: eCLIP from K562 (ENCLB382NGG)

description:
https://www.encodeproject.org/experiments/ENCSR953ZOA/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against HNRNPK
experiment encode accession: ENCSR953ZOA
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR143CTS
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB382NGG
fragmentation methods: see document
size range: 175-300

value: HNRNPK

value: 53 year

value: Gene Yeo, UCSD

value: ATCC


title: IVF_mi699a-5p_scRNA-seq_H2

tag: tissue

tag: mouse id

tag: cell type

tag: genotype

tag: strain


title: eCLIP from K562 (ENCLB270TXG)

description:
https://www.encodeproject.org/experiments/ENCSR440MSY/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against ELAC2
experiment encode accession: ENCSR440MSY
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR545KBT
encode release date: 2022-11-16
lab: Gene Yeo, UCSD
library encode accession: ENCLB270TXG
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

tag: line

tag: biosample encode accession

value: ENCBS175JIH at ENCODE; https://www.encodeproject.org/ENCBS175JIH/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: IVF_NC_scRNA-seq_A1

tag: treatment

value: NC


title: IVF_mi699a-5p_scRNA-seq_G1


title: IVF_mi699a-5p_scRNA-seq_G2


title: 100x CRISPR-Cas9-high-2

description: Library name: 100x CRISPR-Cas9-high-2


title: 100x CRISPR-Cas9-high-1

description: Library name: 100x CRISPR-Cas9-high-1


title: eCLIP from K562 (ENCLB805GYM)

description:
https://www.encodeproject.org/experiments/ENCSR953ZOA/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against HNRNPK
experiment encode accession: ENCSR953ZOA
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR143CTS
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB805GYM
fragmentation methods: see document
size range: 175-300

tag: Sex

tag: age

tag: health state

value: ENCBS039CVO at ENCODE; https://www.encodeproject.org/ENCBS039CVO/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: eCLIP from K562 (ENCLB219XMW)

description:
https://www.encodeproject.org/experiments/ENCSR937RSF/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against RPS10
experiment encode accession: ENCSR937RSF
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR701KRV
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB219XMW
fragmentation methods: see document
size range: 175-300

tag: dev stage

tag: passage number

tag: lab


title: 100x CRISPR-Cas9-ultra high-4

description: Library name: 100x CRISPR-Cas9-ultra high-4


title: 100x CRISPR-Cas9-ultra high-3

description: Library name: 100x CRISPR-Cas9-ultra high-3


title: IVF_mi699a-5p_scRNA-seq_F3

value: blastomeres


title: 100x CRISPR-Cas9-ultra high-1

description: Library name: 100x CRISPR-Cas9-ultra high-1


title: IVF_mi699a-5p_scRNA-seq_F2

value: WT


title: eCLIP from K562 (ENCLB810VQD)

description:
https://www.encodeproject.org/experiments/ENCSR937RSF/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against RPS10
experiment encode accession: ENCSR937RSF
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR701KRV
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB810VQD
fragmentation methods: see document
size range: 175-300

tag: antibody

value: cell line

tag: link

value: ENCBS505ILK at ENCODE; https://www.encodeproject.org/ENCBS505ILK/


title: 100x CRISPR-Cas9-background-4

description: Library name: 100x CRISPR-Cas9-background-4


title: 100x CRISPR-Cas9-ultra high-2

description: Library name: 100x CRISPR-Cas9-ultra high-2


title: 100x CRISPR-Cas9-medium-3

description: Library name: 100x CRISPR-Cas9-medium-3


title: Control eCLIP from K562 (ENCLB056WFA)

description:
https://www.encodeproject.org/experiments/ENCSR407QDZ/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP control experiment on K562 against RYBP
experiment encode accession: ENCSR407QDZ
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2023-01-24
lab: Gene Yeo, UCSD
library encode accession: ENCLB056WFA
fragmentation methods: see document
size range: 175-300

value: female

value: chronic myelogenous leukemia (CML)

tag: source

tag: collection date

value: not applicable

tag: geographic location


title: 100x CRISPR-Cas9-medium-1

description: Library name: 100x CRISPR-Cas9-medium-1

tag: cell type


title: 100x CRISPR-Cas9-background-2

description: Library name: 100x CRISPR-Cas9-background-2


title: Control eCLIP from K562 (ENCLB107ZXT)

description:
https://www.encodeproject.org/experiments/ENCSR407QDZ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against RYBP
experiment encode accession: ENCSR407QDZ
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2023-01-24
lab: Gene Yeo, UCSD
library encode accession: ENCLB107ZXT
fragmentation methods: see document
size range: 175-300

value: adult


title: 100x CRISPR-Cas9-background-3

description: Library name: 100x CRISPR-Cas9-background-3


title: IVF_mi699a-5p_scRNA-seq_E3

tag: tissue

tag: mouse id

tag: genotype


title: Piggybac-low-4

description: Library name: Piggybac-low-4


title: IVF_mi699a-5p_scRNA-seq_F1

tag: strain


title: Control eCLIP from K562 (ENCLB466LVX)

description:
https://www.encodeproject.org/experiments/ENCSR911RWF/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP control experiment on K562 against RPS6
experiment encode accession: ENCSR911RWF
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB466LVX
fragmentation methods: see document
size range: 175-300

tag: line

tag: biosample encode accession

value: 53 year

value: ENCBS177POD at ENCODE; https://www.encodeproject.org/ENCBS177POD/


title: Control eCLIP from K562 (ENCLB354PHR)

description:
https://www.encodeproject.org/experiments/ENCSR911RWF/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against RPS6
experiment encode accession: ENCSR911RWF
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB354PHR
fragmentation methods: see document
size range: 175-300

tag: Sex

tag: age

value: Gene Yeo, UCSD


title: Piggybac-medium-3

description: Library name: Piggybac-medium-3


title: Piggybac-low-2

description: Library name: Piggybac-low-2


title: Piggybac-low-3

description: Library name: Piggybac-low-3


title: Piggybac-low-1

description: Library name: Piggybac-low-1


title: Piggybac-medium-4

description: Library name: Piggybac-medium-4


title: Piggybac-medium-2

description: Library name: Piggybac-medium-2


title: IVF_mi699a-5p_scRNA-seq_D3

tag: treatment


title: eCLIP from K562 (ENCLB950DNW)

description:
https://www.encodeproject.org/experiments/ENCSR391BBA/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against EIF4E
experiment encode accession: ENCSR391BBA
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR660DRN
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB950DNW
fragmentation methods: see document
size range: 175-300

tag: health state

tag: dev stage

value: ATCC

tag: passage number

value: ENCBS344MAK at ENCODE; https://www.encodeproject.org/ENCBS344MAK/


title: eCLIP from K562 (ENCLB231NRG)

description:
https://www.encodeproject.org/experiments/ENCSR391BBA/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against EIF4E
experiment encode accession: ENCSR391BBA
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR660DRN
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB231NRG
fragmentation methods: see document
size range: 175-300

tag: antibody

tag: lab

tag: link


title: IVF_mi699a-5p_scRNA-seq_D2


title: Piggybac-medium-1

description: Library name: Piggybac-medium-1


title: Piggybac-high-4

description: Library name: Piggybac-high-4


title: eCLIP from K562 (ENCLB298ALX)

description:
https://www.encodeproject.org/experiments/ENCSR631HUN/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against DDX47
experiment encode accession: ENCSR631HUN
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR058PIY
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB298ALX
fragmentation methods: see document
size range: 175-300

tag: source

tag: collection date

tag: geographic location


title: Piggybac-high-3

description: Library name: Piggybac-high-3

tag: cell type


title: IVF_mi699a-5p_scRNA-seq_D1

tag: tissue

tag: mouse id

tag: genotype


title: Piggybac-high-2

description: Library name: Piggybac-high-2


title: Piggybac-high-1

description: Library name: Piggybac-high-1


title: 100x CRISPR-Cas9-background-1

description: Library name: 100x CRISPR-Cas9-background-1


title: IVF_mi699a-5p_scRNA-seq_E2

tag: strain


title: 100x CRISPR-Cas9-low-2

description: Library name: 100x CRISPR-Cas9-low-2


title: IVF_mi699a-5p_scRNA-seq_C3


title: IVF_mi699a-5p_scRNA-seq_C2


title: PiggyBac-ultra high-2

description: Library name: PiggyBac-ultra high-2


title: PiggyBac-ultra high-4

description: Library name: PiggyBac-ultra high-4


title: IVF_mi699a-5p_scRNA-seq_E1


title: PiggyBac-ultra high-3

description: Library name: PiggyBac-ultra high-3


title: eCLIP from K562 (ENCLB736IEC)

description:
https://www.encodeproject.org/experiments/ENCSR381VNR/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against SRSF9
experiment encode accession: ENCSR381VNR
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR219TIG
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB736IEC
fragmentation methods: see document
size range: 175-300

tag: line

tag: biosample encode accession

tag: Sex

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: PiggyBac-ultra high-1

description: Library name: PiggyBac-ultra high-1


title: eCLIP from K562 (ENCLB953RHA)

description:
https://www.encodeproject.org/experiments/ENCSR381VNR/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against SRSF9
experiment encode accession: ENCSR381VNR
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR219TIG
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB953RHA
fragmentation methods: see document
size range: 175-300

tag: health state

tag: age

value: ENCBS592SHU at ENCODE; https://www.encodeproject.org/ENCBS592SHU/


title: Piggybac-background-2

description: Library name: Piggybac-background-2


title: Piggybac-background-3

description: Library name: Piggybac-background-3


title: Piggybac-background-4

description: Library name: Piggybac-background-4


title: IVF_mi699a-5p_scRNA-seq_B3

tag: treatment


title: IVF_mi699a-5p_scRNA-seq_C1


title: IVF_mi699a-5p_scRNA-seq_B2


title: eCLIP from HepG2 (ENCLB890XNW)

description:
https://www.encodeproject.org/experiments/ENCSR379GZS/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against NSUN2
experiment encode accession: ENCSR379GZS
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR293CFE
encode release date: 2022-11-16
lab: Gene Yeo, UCSD
library encode accession: ENCLB890XNW
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens HepG2 cell line

tag: antibody

value: male

value: hepatocellular carcinoma

tag: dev stage

value: child

value: 15 year

tag: passage number

value: ENCBS133LVQ at ENCODE; https://www.encodeproject.org/ENCBS133LVQ/


title: Piggybac-background-1

description: Library name: Piggybac-background-1


title: CRISPR-Cas9-low-4

description: Library name: CRISPR-Cas9-low-4


title: IVF_mi699a-5p_scRNA-seq_B1

value: blastomeres

value: WT


title: CRISPR-Cas9-low-3

description: Library name: CRISPR-Cas9-low-3


title: Control eCLIP from K562 (ENCLB175DEY)

description:
https://www.encodeproject.org/experiments/ENCSR821ESG/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against NFX1
experiment encode accession: ENCSR821ESG
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2017-11-28
lab: Gene Yeo, UCSD
library encode accession: ENCLB175DEY
fragmentation methods: see document
size range: 175-300

value: cell line

value: female

tag: lab

value: chronic myelogenous leukemia (CML)

tag: link

value: ENCBS517UIR at ENCODE; https://www.encodeproject.org/ENCBS517UIR/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: eCLIP from K562 (ENCLB204LRA)

description:
https://www.encodeproject.org/experiments/ENCSR631HUN/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against DDX47
experiment encode accession: ENCSR631HUN
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR058PIY
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB204LRA
fragmentation methods: see document
size range: 175-300

value: adult

value: 53 year

value: Gene Yeo, UCSD

tag: source

value: ATCC