title: 1d6_Participant_110_week_7


title: snATAC-seq from forebrain (ENCLB675KOC)

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/ENCSR937PSF/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of mouse forebrain
experiment encode accession: ENCSR937PSF
assay title: snATAC-seq
assembly: mm10
encode release date: 2019-04-19
lab: Bing Ren, UCSD
library encode accession: ENCLB675KOC
fragmentation methods: chemical (Nextera tagmentation)
size range: 200-750

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (11.5 days)

value: forebrain

value: tissue

tag: description

value: Forebrain from 109 embyronic 11.5 day mice

tag: biosample encode accession

tag: age

tag: dev stage

value: embryonic

tag: Sex

value: pooled male and female

tag: health state

value: healthy

tag: lab

value: Len Pennacchio, LBNL

tag: link

value: ENCBS745VOM at ENCODE; https://www.encodeproject.org/ENCBS745VOM/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: F0_HF1_LIV

city: Odense

first: Jan

middle: Wilhelm

last: Kornfeld

address: Campusbej 50

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

library_source: transcriptomic

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.

molecule: total RNA

source_name: liver

growth_protocol: C57BL/6 male F0 mice were fed with chow diet from weaning to 6-week-old and then kept with specific diet until 24-week-old.

extract_protocol:
RNA was harvested using TRI reagent (Sigma) followed by clean-up with RPE buffer (Qiagen, Germany). 1 ug of total RNA was used for the consturction of sequncing libraries.
RNA libraries for RNA-seq were prepared using NovaSeq 6000 SP Reagent Kit.

treatment_protocol: 6-week-old mice were fed with LFD (18 weeks), HLD (18 weeks) or HFD (9 weeks) followed by LFD (9 weeks).

tag: tissue

value: liver

tag: strain

tag: genotype

value: WT

tag: generation

tag: age weeks

tag: diet

value: HFD

value: male


title: RNA_quant_MPRA_1a

city: Boston

first: James

middle: Christopher

last: Taggart

state: MA

address: 200 Longwood Avenue

department: Systems Biology

institute: Harvard Medical School

data_processing:
Barcodes were counted by directly parsing the single-end sequencing reads derived from both gDNA and RNA in a FASTQ format, with the barcode appearing at a fixed position within the read. As before, any variant with mutations in the constant sequence proceeding the barcode was discarded. Additionally, any two barcodes of identical sequence and unique molecular identifier were counted as a single read. The number of unique reads mapping to each variant barcode was calculated for both the RNA and gDNA-derived samples, and the ratio of RNA to gDNA-derived reads was calculated to extract the relative accumulation of processed mRNA for each variant. Barcodes can then be grouped by associated mutations, thresholded based on read count, and normalized to the median wild-type barcode’s ratio.
Assembly: N/A
Supplementary files format and content: .txt files are tab-separated tables summarizing data including counts for each detected variant, integrating information from all three datasets (barcode-to-sequence mapping, RNA quantification, and gDNA quantification).

organism: Bacillus subtilis

source_name: bacterial cell

growth_protocol: To collect samples, a single cryovial of a B. subtilis library was thawed, washed twice with 10 mL LB to remove glycerol, and grown overnight in 200 mL of LB at 37°C in a 2.8 L flask with vigorous shaking. These cultures were then back-diluted to an OD600 of 0.0003 in 200 mL LB with library inducer and grown at 37°C until an OD600 of 0.3, at which point samples were harvested.

extract_protocol:
RNA was extracted from frozen cell pellets with gDNA depletion using an RNeasy Plus Mini Kit (Qiagen). gDNA was prepared from a frozen cell pellet using the Wizard Genomic DNA Purification Kit (Promega).
For RNA-derived libraries from experiments 1a, 1b, 2a, 2b, and 9 (see Table S7), 40 µg of total RNA was reverse transcribed using primer oJT442 and SuperScript III. This cDNA was then run on a 6% TBE-Urea gel, and the following size selection ranges were gel purified: 300-500 nt for full-length cggR and glnR constructs (experiments 1a, 2a, 9) and 100-250 nt for cleaved cggR constructs (experiments 1b and 2b). For the remaining experiments, cleaved RNA was isolated by size selection of RNAs ranging from 200-400 nt for tetM-cggR sites, 150-300 nt for aprE-cggR sites, and 150-350 nt for aprE-glnR sites on a 6% TBE-Urea gel (Novex). The size selected product was reverse transcribed using primer oJT442 and SuperScript III (Thermo Fisher) and size selected on 6% TBE-Urea gel, extracting approximately 120 to 200 nucleotides for cggR libraries and 100 to 200 for glnR. For all experiments, size-selected cDNA was amplified using Phusion DNA polymerase (NEB), adding a barcode and Illumina adapters with a Truseq indexing primer and an isoform-specific primer (see Table S2 for primer sequences). These isoform-specific primers were oJT441/oJT1290 for cleaved/full-length products from cggR constructs or oJT890/oJT1291 for cleaved/full-length products from glnR constructs. gDNA-derived libraries were generated using a two-step Phusion PCR protocol. An initial amplicon was performed generated through 2 cycles of PCR using from 4 µg of purified nucleic acid per 50 µL PCR reaction (reaction scaled up as needed to minimize UMI collapse in more complex libraries) with primers oJT444/445 for cggR upstream mutations, oJT1125/445 for cggR downstream mutations, and oJT891/445 for glnR downstream mutations. The untranslated cggR library required a longer amplicon to capture the upstream stop codon and was instead amplified with oJT942 and oJT445. This first PCR reaction was cleaned up with a double-sided Select-a-Size DNA Clean & Concentrator column (Zymo) and a DNA Clean & Concentrator 5 column (Zymo). A quarter of this reaction was then used for the second round of PCR, using the same primers as used for quantifying cleaved RNA abundance (oJT441 or oJT890 with our Truseq indexing primer) and size selected on an 8% TBE gel.

treatment_protocol: For all MPRA experiments, cells were grown in LB medium with an inducer (20 ng/mL anhydrotetracycline or 2% xylose) when noted. For all experiments in an inducible RNase J1 background, 2% xylose was consistently used to maintain RNase J1 expression, which was substituted for 2% glucose when RNase J1 depletion was required.

tag: cell type

value: bacterial cell

value: W168 ganA::{comK kan}


title: F0_LF5_LIV

value: LFD


title: snATAC-seq from forebrain (ENCLB811TNC)

description:
https://www.encodeproject.org/experiments/ENCSR937PSF/
***************
biological replicate number: 2
technical replicate number: 1
description: snATAC-seq of mouse forebrain
experiment encode accession: ENCSR937PSF
assay title: snATAC-seq
assembly: mm10
encode release date: 2019-04-19
lab: Bing Ren, UCSD
library encode accession: ENCLB811TNC
fragmentation methods: chemical (Nextera tagmentation)
size range: 200-750

value: Forebrain from 88 embyronic 11.5 day mice

value: ENCBS720JOH at ENCODE; https://www.encodeproject.org/ENCBS720JOH/


title: 1d5_Participant_110_week_6

city: Adelaide

first: Feargal

middle: J

last: Ryan

state: Adelaide

address: North Terrace

country: Australia

institute: SAHMRI

description: Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination

data_processing:
Quality control with Trimmomatic version 0.38
Gene count matrix was generated with FeatureCounts version 1.5.0-p2 and Ensembl 101
Aligned to genome using HISAT2 version 2.1.0
Assembly: GRCh38
Supplementary files format and content: FeatureCounts per gene counts

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol:
RNA extraction and genomic DNA elimination was carried out using the PAXgene® Blood RNA kit (762164, Qiagen, Feldbachstrasse, Germany) as per the manufacturer’s instructions
Total RNA was converted to strand-specific Illumina compatible sequencing libraries using the Nugen Universal Plus Total RNA-Seq library kit from Tecan (Mannedorf, Switzerland) as per the manufacturer’s instructions (MO1523 v2) using 12 cycles of PCR amplification for the final libraries. An Anydeplete probe mix targeting both human ribosomal and adult globin transcripts (HBA1, HBA2, HBB, HBD) was used to deplete these transcripts.

value: M

tag: timepoint

tag: sample number

value: Peripheral blood


title: snATAC-seq from forebrain (ENCLB454MDS)

description:
https://www.encodeproject.org/experiments/ENCSR836VNN/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of mouse forebrain
experiment encode accession: ENCSR836VNN
assay title: snATAC-seq
assembly: mm10
encode release date: 2019-04-19
lab: Bing Ren, UCSD
library encode accession: ENCLB454MDS
fragmentation methods: chemical (Nextera tagmentation)
size range: 200-750

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (12.5 days)

value: forebrain

value: tissue

tag: description

value: Forebrain from 120 embryonic 12.5 day mice

value: embryonic

value: ENCBS974GPH at ENCODE; https://www.encodeproject.org/ENCBS974GPH/


title: 1d4_Participant_016_week_7


title: 1d3_Participant_016_week_6


title: F0_LF4_LIV


title: 4exo_3end_pooled

description: Pooled data from two sequencing lanes with the same library, run on a HiSeq2000 and NextSeq500.

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 with a 3' end mapped to the position.

growth_protocol: All 3′-end sequencing experiments were performed using cells grown in 2xYT. 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. 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. All 3′ end sequencing samples were purified through RNAsnap. In the RNAsnap protocol, cells were resuspended in 500 µL extraction solution (95% Formamide, 1% BME, 0.025% SDS, 18 mM EDTA) and transferred to a 2 mL tube containing 200 µL chilled 0.1 mm diameter zirconia beads. These tubes were vortexed for 10 minutes using a horizontal vortex adapter and subsequently incubated at 95 °C for 7 minutes. Samples were spun at 15,000 g, after which 400 µL was removed and diluted 1:5 with 1.6 mL DEPC-treated water. This mixture was precipitated with isopropanol and resuspended in 10 mM Tris, pH 7.0. At least 30 µg of RNA was then treated for 30 minutes at 37°C with 10 µL Turbo DNase in a 100 µL reaction. 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.
3′ end sequencing libraries were prepared in a manner similar to Rend-seq (Lalanne et al., Cell 2018), with deviation in the order of reactions (for full protocol, see Herzel et al., NAR 2022). Prior to fragmentation, 1.8 µg of rRNA depleted RNA was ligated to an adenylated adapter as described for Rend-seq. This ligation product was then fragmented and RNA species of sizes 33-63 nt were purified via denaturing polyacrylamide gel extraction. From this point onwards, the library preparation is identical to Rend-seq (Lalanne et al., 2018).

value: rph::spc rnr::tc yhaM::Pm pnp::kan


title: snATAC-seq from forebrain (ENCLB501ZEG)

description:
https://www.encodeproject.org/experiments/ENCSR750EXW/
***************
biological replicate number: 2
technical replicate number: 1
description: snATAC-seq of mouse forebrain
experiment encode accession: ENCSR750EXW
assay title: snATAC-seq
assembly: mm10
encode release date: 2019-04-19
lab: Bing Ren, UCSD
library encode accession: ENCLB501ZEG
fragmentation methods: chemical (Nextera tagmentation)
size range: 200-750

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (16.5 days)

value: Forebrain from 41 embyonic 16.5 day mice

tag: biosample encode accession

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS512LKA at ENCODE; https://www.encodeproject.org/ENCBS512LKA/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: snATAC-seq from forebrain (ENCLB702KXQ)

description:
https://www.encodeproject.org/experiments/ENCSR836VNN/
***************
biological replicate number: 2
technical replicate number: 1
description: snATAC-seq of mouse forebrain
experiment encode accession: ENCSR836VNN
assay title: snATAC-seq
assembly: mm10
encode release date: 2019-04-19
lab: Bing Ren, UCSD
library encode accession: ENCLB702KXQ
fragmentation methods: chemical (Nextera tagmentation)
size range: 200-750

value: Forebrain from 68 embryonic 12.5 day mice

tag: age

value: ENCBS617DPG at ENCODE; https://www.encodeproject.org/ENCBS617DPG/


title: F0_LF3_LIV

value: liver

value: WT

value: LFD

value: male


title: F0_LF2_LIV


title: ylbF_rendseq_pooled

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.

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.

value: bacterial cell

value: W168 ylbF::erm


title: snATAC-seq from forebrain (ENCLB585MWS)

description:
https://www.encodeproject.org/experiments/ENCSR750EXW/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of mouse forebrain
experiment encode accession: ENCSR750EXW
assay title: snATAC-seq
assembly: mm10
encode release date: 2019-04-19
lab: Bing Ren, UCSD
library encode accession: ENCLB585MWS
fragmentation methods: chemical (Nextera tagmentation)
size range: 200-750

value: forebrain

value: tissue

value: Forebrain pooled from embyonic 16.5 day mice

tag: dev stage

value: embryonic

value: ENCBS156DHU at ENCODE; https://www.encodeproject.org/ENCBS156DHU/


title: 1d2_Participant_088_week_7

tag: Sex

value: M

value: Peripheral blood


title: rnjA_depletion_rny_rendseq_pooled

value: W168 Pspac-rnjA ery rny::spc


title: 1d1_Participant_088_week_6


title: snATAC-seq from forebrain (ENCLB710NFW)

description:
https://www.encodeproject.org/experiments/ENCSR580SVE/
***************
biological replicate number: 2
technical replicate number: 1
description: snATAC-seq of mouse forebrain
experiment encode accession: ENCSR580SVE
assay title: snATAC-seq
assembly: mm10
encode release date: 2019-04-19
lab: Bing Ren, UCSD
library encode accession: ENCLB710NFW
fragmentation methods: chemical (Nextera tagmentation)
size range: 200-750

source_name: Mus musculus strain B6NTac;B6NCrl/Lap forebrain tissue mixed sex postnatal (0 days)

value: Forebrain of pooled postnatal 0 day mice

value: 0 day

value: postnatal

value: pooled male and female

tag: health state

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS554AAA at ENCODE; https://www.encodeproject.org/ENCBS554AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: F0_LF1_LIV

value: liver

value: WT

value: LFD

value: male


title: WT_rendseq_pooled

value: bacterial cell


title: 1c6_Participant_084_week_7

value: F


title: snATAC-seq from forebrain (ENCLB866UFV)

description:
https://www.encodeproject.org/experiments/ENCSR580SVE/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of mouse forebrain
experiment encode accession: ENCSR580SVE
assay title: snATAC-seq
assembly: mm10
encode release date: 2019-04-19
lab: Bing Ren, UCSD
library encode accession: ENCLB866UFV
fragmentation methods: chemical (Nextera tagmentation)
size range: 200-750

value: forebrain

value: tissue

value: Forebrain from 15 postnatal 0 day mice

tag: lab

value: ENCBS038AAA at ENCODE; https://www.encodeproject.org/ENCBS038AAA/


title: 4exo_ylbF_rendseq_pooled

value: W168 rph::spc rnr::tc yhaM::Pm pnp::kan ylbF::erm


title: snATAC-seq from forebrain (ENCLB653FWK)

description:
https://www.encodeproject.org/experiments/ENCSR374QZJ/
***************
biological replicate number: 2
technical replicate number: 1
description: snATAC-seq of mouse forebrain
experiment encode accession: ENCSR374QZJ
assay title: snATAC-seq
assembly: mm10
encode release date: 2019-04-19
lab: Bing Ren, UCSD
library encode accession: ENCLB653FWK
fragmentation methods: chemical (Nextera tagmentation)
size range: 200-750

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (15.5 days)

value: Forebrain from 62 embryonic 15.5 day mice

value: embryonic

tag: link

value: ENCBS841GER at ENCODE; https://www.encodeproject.org/ENCBS841GER/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: Fetal Liver, maternal circadian disruption, rep2

city: Tokyo

first: Kenichiro

last: Kinouchi

address: 35 Shinanomachi, Shinjuku-ku

country: Japan

institute: Keio University School of Medicine

data_processing:
Reads are mapped to the genome using Bismark and Bowtie 2 allowing for no mismatches (-N 0) and a seed substring length of 20 (-L 20). Following alignment, PCR duplicates are removed using a custom analysis script. Each read has a randomized 6-mer barcode and if more than one read has the same start and end coordinates and the same barcode, all but one of the reads are discarded. Alignment information of the remaining reads are stored in BAM files. Methylation at CpG sites is then extracted from the BAM files using Bismark.
Assembly: mm10
Supplementary files format and content: Files with the extension *.bedGraph.gz. Compressed files containing the methylation percentage at covered CpG sites. There are four columns in these files: chromosome, start coordinate (0-based), end coordinate (1-based), and percent methylation.

source_name: Liver

extract_protocol:
Genomic DNA was extracted using the MagMAX™ DNA Multi-Sample Kit (ThermoFisher 4413020) on the KingFisher Apex instrument (ThermoFisher 5400930) following manufacturer’s instructions.
100 ng of gDNA was digested with TaqaI (NEB R0149) at 65⁰C for 2 h followed by MspI (NEB R0106) at 37⁰C overnight. Following enzymatic digestion, samples were used for library generation using the Ovation RRBS Methyl-Seq System (Tecan 0353-32) following manufacturer’s instructions.

tag: tissue

value: Liver

value: wild-type

tag: treatment

value: chronic phase shifting during pregancy


title: rnjA+ylbF_rendseq_pooled

tag: strain

tag: genotype

value: W168 rnjA::spc ylbF::erm


title: Fetal liver, maternal circadian disruption, rep1


title: 1c5_Participant_084_week_6

value: Peripheral blood


title: snATAC-seq from forebrain (ENCLB709KUO)

description:
https://www.encodeproject.org/experiments/ENCSR374QZJ/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of mouse forebrain
experiment encode accession: ENCSR374QZJ
assay title: snATAC-seq
assembly: mm10
encode release date: 2019-04-19
lab: Bing Ren, UCSD
library encode accession: ENCLB709KUO
fragmentation methods: chemical (Nextera tagmentation)
size range: 200-750

value: Forebrain from 78 embryonic 15.5 day mice

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS811RMD at ENCODE; https://www.encodeproject.org/ENCBS811RMD/


title: 4exo_ylbF_3exo_pooled

value: bacterial cell


title: Fetal liver, control, rep2

value: control


title: 1c4_Participant_100_week_7

value: F


title: snATAC-seq from forebrain (ENCLB401VNO)

description:
https://www.encodeproject.org/experiments/ENCSR205OEF/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of mouse forebrain
experiment encode accession: ENCSR205OEF
assay title: snATAC-seq
assembly: mm10
encode release date: 2019-04-19
lab: Bing Ren, UCSD
library encode accession: ENCLB401VNO
fragmentation methods: chemical (Nextera tagmentation)
size range: 200-750

source_name: Mus musculus strain B6NTac;B6NCrl/Lap forebrain tissue mixed sex embryo (14.5 days)

value: forebrain

value: tissue

value: Forebrain from 24 embyonic 14.5 day mice

value: ENCBS002AAA at ENCODE; https://www.encodeproject.org/ENCBS002AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: Fetal liver, control, rep1

value: Liver

value: wild-type


title: 1c2_Participant_134_week_7


title: snATAC-seq from forebrain (ENCLB394GQB)

description:
https://www.encodeproject.org/experiments/ENCSR205OEF/
***************
biological replicate number: 2
technical replicate number: 1
description: snATAC-seq of mouse forebrain
experiment encode accession: ENCSR205OEF
assay title: snATAC-seq
assembly: mm10
encode release date: 2019-04-19
lab: Bing Ren, UCSD
library encode accession: ENCLB394GQB
fragmentation methods: chemical (Nextera tagmentation)
size range: 200-750

value: Forebrain from 34 embryonic 14.5 day mice

value: embryonic

value: ENCBS014AAA at ENCODE; https://www.encodeproject.org/ENCBS014AAA/


title: rnjA_depletion_rendseq_pooled

value: W168 amyE::{Pxyl-rnjA Cm} rnjA::spc


title: Liver, maternal circadian disruption, rep2

value: chronic phase shifting during pregancy


title: 1c1_Participant_134_week_6

value: Peripheral blood


title: Phage_cured_rnjA+rnc_rendseq_pooled

value: W168 {delta}Skin {delta}SP{beta}::PIID-sspB kan rnc::ery rnjA::spc


title: 1b6_Participant_072_week_7

value: M


title: Liver, control, rep2

value: control


title: Phage_cured_rnjA_rendseq_pooled

value: bacterial cell

value: W168 {delta}Skin {delta}SP{beta}::PIID-sspB kan rnjA::spc


title: total RNA-seq from monocyte (ENCLB266SOJ)

description:
https://www.encodeproject.org/experiments/ENCSR959ZHO/
***************
biological replicate number: 1
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.monocytes_spleen_M_59days
experiment encode accession: ENCSR959ZHO
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB266SOJ
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: Mus musculus strain B6CASTF1/J male adult (59.00 days) monocyte primary cell

value: monocyte

value: primary cell

value: male

value: adult

value: John Stamatoyannopoulos, UW

tag: source

value: Mark Groudine

tag: model organism mating status

value: virgin

tag: collection date

value: not applicable

tag: geographic location

value: ENCBS277BDX at ENCODE; https://www.encodeproject.org/ENCBS277BDX/


title: rnjA_rendseq_pooled

tag: cell type

value: W168 rnjA::spc


title: Liver, maternal circadian disruption, rep1

value: Liver

value: wild-type

value: chronic phase shifting during pregancy


title: 1b5_Participant_072_week_6

value: M

tag: timepoint

tag: sample number

value: Peripheral blood


title: total RNA-seq from CD4-positive naive resting alpha-beta T cell (ENCLB414OYA)

description:
https://www.encodeproject.org/experiments/ENCSR968ZOA/
***************
biological replicate number: 1
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD4 naive_spleen_F_57days
experiment encode accession: ENCSR968ZOA
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB414OYA
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: Mus musculus strain B6CASTF1/J female adult (57.00 days) CD4-positive naive resting alpha-beta T primary cell

tag: biosample encode accession

value: female

tag: age

value: ENCBS958MXN at ENCODE; https://www.encodeproject.org/ENCBS958MXN/


title: 1c3_Participant_100_week_6

tag: Sex

value: F


title: rnjA_depletion_rppH_5end_seq

data_processing:
poly(A) sequence was trimmed from 5end sequencing libraries using CutAdapt (Martin, 2011) with parameters “-a A{15} -m 15 -u 8 --rename='{id} UMI={cut_prefix}’”.
5′ end sequencing reads were collapsed using the 8 bp unique molecular identifier (UMI) at the start of each read using custom Python scripts, requiring identical UMI sequences and read sequences within a hamming distance of 1 to be considered duplicates.
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.
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 with a 5' end mapped to the position.

growth_protocol: All 5end-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 all 5′ end sequencing samples, RNA was extracted using the RNAsnap protocol and Turbo DNase treated as described for the Rend-seq and 3′ end sequencing experiments. rRNA was depleted from 10 µg of purified RNA with the MICROBExpress Bacterial mRNA Enrichment Kit, per manufacturer’s instructions, precipitated, and resuspended in 10 mM Tris pH 7.0.
600 ng rRNA depleted RNA was then ligated to 260 pmol of an RNA adapter for 18 hours at 22 °C using T4 RNA Ligase 1. Following ligation, RNA was fragmented for 2 minutes using RNA fragmentation reagents (ThermoFisher) and fragments of either size 41-71 or 60-90 were isolated through denaturing polyacrylamide gel extraction. RNA fragments were dephosphorylated, polyadenylated, and reverse transcribed following the BaM-seq multiplexed RNA sequencing protocol (Johnson et al., 2023). To add Illumina adapters, pooled cDNA was amplified between 5-10 cycles with primers oDP128 and oDP161 (Johnson et al., 2023) using Q5 DNA polymerase and purified by polyacrylamide gel electrophoresis.

value: bacterial cell

value: W168 amyE::{Pxyl-rnjA Cm} rnjA::spc rppH::erm


title: 1b4_Participant_071_week_7


title: 1b3_Participant_071_week_6


title: total RNA-seq from T-cell (ENCLB732XBI)

description:
https://www.encodeproject.org/experiments/ENCSR377UPT/
***************
biological replicate number: 3
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD3_spleen_M_66days
experiment encode accession: ENCSR377UPT
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB732XBI
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: Mus musculus strain B6CASTF1/J male adult (66.00 days) T-cell primary cell

value: T-cell

value: primary cell

value: male

tag: dev stage

value: adult

value: ENCBS742VKS at ENCODE; https://www.encodeproject.org/ENCBS742VKS/


title: total RNA-seq from T-cell (ENCLB382IQB)

description:
https://www.encodeproject.org/experiments/ENCSR377UPT/
***************
biological replicate number: 2
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD3_spleen_M_66days
experiment encode accession: ENCSR377UPT
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB382IQB
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

tag: lab

value: John Stamatoyannopoulos, UW

value: Mark Groudine

value: virgin

value: not applicable

value: ENCBS380IYP at ENCODE; https://www.encodeproject.org/ENCBS380IYP/


title: 4exo_rendseq_pooled

value: W168 rph::spc rnr::tc yhaM::Pm pnp::kan


title: rnjA_depletion_ndoA_rendseq

value: W168 amyE::{Pxyl-rnjA Cm} rnjA::spc ndoA::kan


title: liver, PXR-CAR-CYP3A4/3A7_ MI-883_3

city: Hradec Kralove

first: Alena

last: Mrkvicova

address: Simkova

country: Czech Republic

institute: LFHK

data_processing:
Universal Illumina adaptors were trimmed using fastp v0.23.0
Fastq files were aligned to the mouse reference genome (mm10) using RNASTAR
FeatureCounts was used to make count matrices
Assembly: mm10
Supplementary files format and content: tab delimited file includes raw counts for each sample

growth_protocol: Humanized PXR-CAR-CYP3A4/3A7 mice (model 11585, Taconic, Rensselaer, NY, USA) were housed in a temperature-controlled environment (22 ± 2°C) with 12-hour light/dark cycle and free access to water.

extract_protocol:
Total RNA from liver samples has been isolated using TRIZOL®. Total RNA was purified using Agencourt RNAClean XP Beads (Beckman Coulter, Inc.) and then the diluted RNA was quantified using Qubit 2.0 Fluorometer with Qubit RNA BR Assay Kit (Invitrogen) for precise measurement. The integrity of purified RNA was evaluated based on RIN (>7) acquired using the 2100 Bioanalyzer System with Total RNA Nano Chip (Agilent Technologies) according to the manufacturer's protocol. The input amount of total RNA used in the libraries was 520 ng.
Libraries were constructed with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs Inc., Ipswich, MA, USA). The whole procedure was performed according to the protocol suggested by the manufacturer. The samples were multiplexed using suitable molecular barcodes by using the NEBNext Multiplex Oligos from Illumina. Adaptor enrichment was performed by using eight cycles of PCR. The concentration of molecular libraries was measured using Qubit 2.0 Fluorometer with Qubit dsDNA HS Assay Kit (Invitrogen).

treatment_protocol: Either p.o. gavage 3x per week -MI-883 5mg/kg dissolved in vehicle (5%DMSO/5%PEG300/90%corn oil)  or  p.o. gavage 3x per week -vehicle (5%DMSO/5%PEG300/90%corn oil).

value: liver


title: rnjA_depletion_ndoA_5end_seq


title: liver, PXR-CAR-CYP3A4/3A7_ MI-883_4

value: Humanized PXR-CAR-CYP3A4/3A7 mice (model 11585, Taconic, Rensselaer, NY, USA)


title: total RNA-seq from T-cell (ENCLB364ZDD)

description:
https://www.encodeproject.org/experiments/ENCSR377UPT/
***************
biological replicate number: 1
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD3_spleen_M_66days
experiment encode accession: ENCSR377UPT
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB364ZDD
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

tag: link

value: ENCBS598TMX at ENCODE; https://www.encodeproject.org/ENCBS598TMX/


title: rnjA+ylbF_5end_seq_pooled

value: bacterial cell

value: W168 rnjA::spc ylbF::erm


title: 1b1_Participant_141_week_6

description: Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination

value: F

tag: tissue

value: Peripheral blood


title: liver, PXR-CAR-CYP3A4/3A7_ MI-883_2

tag: treatment


title: total RNA-seq from CD4-positive naive resting alpha-beta T cell (ENCLB558ULM)

description:
https://www.encodeproject.org/experiments/ENCSR835KFT/
***************
biological replicate number: 1
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD4 naive_spleen_M_76days
experiment encode accession: ENCSR835KFT
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB558ULM
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: Mus musculus strain B6CASTF1/J male adult (76.00 days) CD4-positive naive resting alpha-beta T primary cell

value: primary cell

value: male

value: ENCBS997RQF at ENCODE; https://www.encodeproject.org/ENCBS997RQF/


title: 1a6_Participant_078_week_7

value: M


title: total RNA-seq from neutrophil (ENCLB005XLE)

description:
https://www.encodeproject.org/experiments/ENCSR309GVQ/
***************
biological replicate number: 1
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.neutrophil_spleen_F_83days
experiment encode accession: ENCSR309GVQ
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-19
lab: Barbara Wold, Caltech
library encode accession: ENCLB005XLE
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: Mus musculus strain B6CASTF1/J female adult (83.00 days) neutrophil primary cell

value: neutrophil

value: female

value: adult

value: John Stamatoyannopoulos, UW

value: Mark Groudine

value: ENCBS430REP at ENCODE; https://www.encodeproject.org/ENCBS430REP/


title: rnjA_depletion_5end_seq_pooled

tag: strain

value: W168 amyE::{Pxyl-rnjA Cm} rnjA::spc


title: total RNA-seq from T-cell (ENCLB182FNT)

description:
https://www.encodeproject.org/experiments/ENCSR377UPT/
***************
biological replicate number: 4
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD3_spleen_M_66days
experiment encode accession: ENCSR377UPT
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB182FNT
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: T-cell

value: virgin

value: not applicable

value: ENCBS460IRW at ENCODE; https://www.encodeproject.org/ENCBS460IRW/


title: Liver, control, rep1

value: Liver

tag: genotype

value: wild-type

value: control


title: liver, PXR-CAR-CYP3A4/3A7_control_5

value: liver

value: Humanized PXR-CAR-CYP3A4/3A7 mice (model 11585, Taconic, Rensselaer, NY, USA)


title: 1a4_Participant_087_week_7

value: F

value: Peripheral blood


title: liver, PXR-CAR-CYP3A4/3A7_ MI-883_5


title: Phage_cured_rnjA+rnc_5end_seq_pooled

value: bacterial cell

value: W168 {delta}Skin {delta}SP{beta}::PIID-sspB kan rnc::ery rnjA::spc


title: total RNA-seq from monocyte (ENCLB944MRQ)

description:
https://www.encodeproject.org/experiments/ENCSR536HHA/
***************
biological replicate number: 1
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.monocytes_spleen_F_59days
experiment encode accession: ENCSR536HHA
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB944MRQ
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: Mus musculus strain B6CASTF1/J female adult (59.00 days) monocyte primary cell

value: monocyte

value: primary cell

value: female

value: adult

value: John Stamatoyannopoulos, UW

tag: source

value: ENCBS606RYO at ENCODE; https://www.encodeproject.org/ENCBS606RYO/


title: 1b2_Participant_141_week_7


title: 1a3_Participant_087_week_6


title: liver, PXR-CAR-CYP3A4/3A7_control_3


title: liver, PXR-CAR-CYP3A4/3A7_control_4


title: rnjA_5end_seq_pooled

value: W168 rnjA::spc


title: total RNA-seq from B cell (ENCLB521FDN)

description:
https://www.encodeproject.org/experiments/ENCSR788PEE/
***************
biological replicate number: 4
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD19_spleen_F_67days
experiment encode accession: ENCSR788PEE
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB521FDN
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: Mus musculus strain B6CASTF1/J female adult (67.00 days) B primary cell

value: B cell

value: Mark Groudine

tag: model organism mating status

value: virgin

value: not applicable

value: ENCBS575JXK at ENCODE; https://www.encodeproject.org/ENCBS575JXK/


title: rnjA_depletion_rny_5end_seq_pooled

value: W168 Pspac-rnjA ery rny::spc


title: Phage_cured_rnjA_5end_seq_pooled

value: W168 {delta}Skin {delta}SP{beta}::PIID-sspB kan rnjA::spc


title: total RNA-seq from B cell (ENCLB500YSM)

description:
https://www.encodeproject.org/experiments/ENCSR788PEE/
***************
biological replicate number: 1
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD19_spleen_F_67days
experiment encode accession: ENCSR788PEE
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB500YSM
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

tag: collection date

value: ENCBS982OLT at ENCODE; https://www.encodeproject.org/ENCBS982OLT/


title: liver, PXR-CAR-CYP3A4/3A7_control_2

value: liver

value: Humanized PXR-CAR-CYP3A4/3A7 mice (model 11585, Taconic, Rensselaer, NY, USA)

value: control


title: 1a2_Participant_086_week_7

value: M

value: Peripheral blood


title: total RNA-seq from B cell (ENCLB595PNZ)

description:
https://www.encodeproject.org/experiments/ENCSR788PEE/
***************
biological replicate number: 3
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD19_spleen_F_67days
experiment encode accession: ENCSR788PEE
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB595PNZ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: primary cell

value: female

value: adult

tag: geographic location

value: ENCBS661EAT at ENCODE; https://www.encodeproject.org/ENCBS661EAT/


title: 1a1_Participant_086_week_6


title: total RNA-seq from B cell (ENCLB966SVH)

description:
https://www.encodeproject.org/experiments/ENCSR788PEE/
***************
biological replicate number: 2
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD19_spleen_F_67days
experiment encode accession: ENCSR788PEE
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB966SVH
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: B cell

value: John Stamatoyannopoulos, UW

value: ENCBS904RDT at ENCODE; https://www.encodeproject.org/ENCBS904RDT/


title: mESC RCMC 3hr DMSO Rep 2

first: Martin

last: Aryee

address: 3 Blackfan Circle, 11th Floor

department: Data Science

institute: Dana Farber Cancer Institute

description: Library name: RCMC_3hrDMSO_TRep3

data_processing:
Two replicates each of mESC RCMC WT, mESC RCMC DMSO, and mESC RCMC IAA were aligned to the reference genome (mm10) using the BWA-MEM algorithm (with -5SP -T0). Ligation events were then recorded using pairtools parse v. 0.3.0 (with --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --add-columns pos5, pos3, dist_to_5, dist_to_3, read_len). Parsed reads were then sorted (pairtools sort) and PCR duplicates were removed (pairtools dedup). Final pairs and bam files were then generated using pairtools split --nproc-in 8 --nproc-out 8 --output-pairs ${filename}.mapped.pairs --output-sam -|samtools view -bS -@16 | samtools sort -@16 -o ${filename}.mapped.PT.bam; samtools index ${filename}.mapped.PT.bam We used a Terra pipeline to keep data processing consistent. Replicates were merged using pairtools merge and we then filtered to both fragments of an interaction pair in the captured regions using pairtools select (captured regions (mm10): Fbn2 (chr18: 57,899,000 - 58,901,000), Ppm1g (chr5: 31,100,000 - 32,225,000), and Klf1 (chr8: 84,120,000 - 85,130,000)). For example, pairtools select '(chrom1=="chr18") and (chrom2=="chr18") and (57899000 <= pos1 <= 58901000) and (57899000 <= pos2 <= 58901000)' RCMC_WT.mapped.pairs > RCMC_WT_Fbn2.mapped.pairs. Balanced contact maps were created using the merged replicate captured region pairs files. To create .mcool files, we compressed the combined replicate pairs files (bgzip), indexed the compressed pairs files (pairix), created cool files (cooler cload pairix), and then obtained ICE-balanced mcool files (cooler zoomify --balance).
Assembly: mm10
Supplementary files format and content: Genome-wide pairs files for each individual replicate, balanced .mcool files for combined replicates for each perturbation (WT, DMSO, IAA) and each captured locus (Fbn2, Klf1, Ppm1g), and RDS files (which can be loaded into R with readRDS) for each experimental perturbation (WT, DMSO, IAA). RDS files include only reads contained in the three captured loci (Fbn2, Klf1, Ppm1g.) For further clarification, see https://github.com/aryeelab/cohesin_extrusion_reproducibility/blob/main/Protocol_Revisions.md

growth_protocol: Protocol as specified in GSE207225: Mouse embryonic stem cells (JM8.N4 mESCs) were cultured on plates coated with 0.1% gelatin solution (Sigma-Aldrich) under feeder-free conditions in medium consisting of KnockOut DMEM (Thermofisher) with 15% FBS (HyClone, SH30396.03, Lot. No. AE28209315) and 1000U/mL LIF (home-made), 1 mM MEM Non-Essential Amino Acid Solution (Thermofisher), 2 mM GlutaMAX (Thermofisher), 100 μg/ml Penicillin-Streptomycin (Thermofisher), and 0.1 mM 2-mercapoethanol (Sigma) supplemented with 2i, 10 μM MEK inhibitor (Tocris) and 3 μM GSK inhibitor (Sigma). mESCs were fed daily by replacing half the medium and passaged every two days with 0.05% Trypsin-EDTA (Thermo Fisher Scientific). 1 day prior to harvesting, cells were swapped to medium as described above without 2i.

extract_protocol: WT, 3 hour DMSO, and 3 hour IAA libraries (two replicates of each) at the Fbn2 (chr18: 57,899,000 - 58,901,000), Ppm1g (chr5: 31,100,000 - 32,225,000), and Klf1 (chr8: 84,120,000 - 85,130,000) loci from Goel et al. Nature Genetics 2023 were re-sequenced with 150bp reads. Protocol as specified in GSE207225: Cells were fixed with 3 mM DSG for 35 minutes, followed by an additional 10 minutes with 1% formaldehyde. Following quenching, nuclei were prepared from fixed cells. Chromatin was digested in situ using MNase, DNA 3' ends were chewed back and biotinylated, and then free DNA ends were proximity ligated. Unligated ends were digested, and followed by reverse crosslinking of the chromatin and Protease K digestion. DNA was purified by phenol chloroform extraction and DNA Clean and Concentrator kit (Zymo), and then size selected for dinucleosomal fragments on an agarose gel. Following end polishing of DNA fragments, a streptavidin pulldown was used to enrich for ligated dinucleosomal fragments. Size selected DNA fragments bound to streptavidin coated beads were used to prepare Micro-C libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), using NEBNext Multiplex Oligos for Illumina for indexing samples. Libraries were amplified with 7-8 PCR cycles on the thermocycler using KAPA HiFi HotStart ReadyMix (Roche) and purified using AMPure XP beads (Beckman Coulter). Purified libraries were quantified using qPCR and pooled in a 1:1 ratio to a total of 2-4 µg of DNA. Following the Twist Standard Hybridization Target Enrichment Protocol (Twist Biosciences) with the inclusion of Mouse Cot-1 DNA (Invitrogen) blocker solution, this library pool was hybridized to custom probe panels for loci of interest and bound to streptavidin coated beads. Bead-bound fragments were pulled down, amplified with 6 PCR cycles on the thermocycler using Equinox Library Amp Mix (Twist), and purified using Twist Binding and Purification Beads (Twist). Following qPCR quantification, the target enriched library pool was submitted for sequencing.

tag: cell line

tag: cell type

value: mouse embryonic stem cell

value: Homozygous RAD21-mAID-BFP-V5

value: DMSO (3 hours)


title: 75 mg metformin, Liver, 65 weeks, Sample 10

city: University Park

first: Evelyn

middle: Anne

last: Weaver

state: PA

address: 439 Shortlidge Rd

department: Animal Science

institute: Penn State University

description:
Library name: Sample 15
Column name in MetforminReadCounts_0vs75.txt: Met_10

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: Liver

value: Metformin

tag: time

value: 65 weeks


title: liver, PXR-CAR-CYP3A4/3A7_ MI-883_1

value: liver

value: Humanized PXR-CAR-CYP3A4/3A7 mice (model 11585, Taconic, Rensselaer, NY, USA)


title: 1a5_Participant_078_week_6

value: M

tag: timepoint

tag: sample number


title: liver, PXR-CAR-CYP3A4/3A7_control_1

value: control


title: total RNA-seq from CD8-positive naive resting alpha-beta T cell (ENCLB855OQR)

description:
https://www.encodeproject.org/experiments/ENCSR769LJY/
***************
biological replicate number: 1
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD8 naive_spleen_M_57days
experiment encode accession: ENCSR769LJY
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB855OQR
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: Mus musculus strain B6CASTF1/J male adult (57.00 days) CD8-positive naive resting alpha-beta T primary cell

value: primary cell

tag: biosample encode accession

tag: Sex

value: male

tag: age

value: Mark Groudine

value: virgin

value: not applicable

value: ENCBS099LIC at ENCODE; https://www.encodeproject.org/ENCBS099LIC/


title: mESC RCMC 3hr IAA Rep 2

description: Library name: RCMC_3hrIAA_TRep3

value: IAA (3 hours)


title: 75 mg metformin, Liver, 65 weeks, Sample 9

description:
Library name: Sample 14
Column name in MetforminReadCounts_0vs75.txt: Met_9


title: Stim_1

city: Bunkyo-ku

first: Manami

last: Katoh

state: Tokyo

address: 7-3-1 Hongo

department: Department of Cardiovascular Medicine

institute: The University of Tokyo

description: 10x Genomics Chromium Single Cell 3' Reagent Kits

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10

molecule: nuclear RNA

source_name: placenta

extract_protocol:
Nuclei were extracted from fresh-frozen placentas using the singulator 100 (S2 Genomics).
Sample 1-4,library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: placenta

value: placental cell

value: 8-10 weeks old

value: CPS


title: total RNA-seq from neutrophil (ENCLB831KZD)

description:
https://www.encodeproject.org/experiments/ENCSR293FRO/
***************
biological replicate number: 1
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.neutrophil_spleen_F_59days
experiment encode accession: ENCSR293FRO
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-19
lab: Barbara Wold, Caltech
library encode accession: ENCLB831KZD
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: Mus musculus strain B6CASTF1/J female adult (59.00 days) neutrophil primary cell

value: neutrophil

value: female

tag: dev stage

value: adult

tag: lab

value: John Stamatoyannopoulos, UW

tag: link

value: ENCBS928RPJ at ENCODE; https://www.encodeproject.org/ENCBS928RPJ/


title: CTRL_2

tag: tissue

tag: strain

tag: treatment

value: no treat


title: 75 mg metformin, Liver, 65 weeks, Sample 8

description:
Library name: Sample 13
Column name in MetforminReadCounts_0vs75.txt: Met_8

value: Liver

value: Metformin

value: 65 weeks


title: mESC RCMC 3hr IAA Rep 1

description: Library name: RCMC_3hrIAA_TRep2

value: mouse embryonic stem cell

tag: genotype

value: Homozygous RAD21-mAID-BFP-V5


title: total RNA-seq from neutrophil (ENCLB410LYO)

description:
https://www.encodeproject.org/experiments/ENCSR251XVY/
***************
biological replicate number: 1
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.neutrophil_spleen_M_59days
experiment encode accession: ENCSR251XVY
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-19
lab: Barbara Wold, Caltech
library encode accession: ENCLB410LYO
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: Mus musculus strain B6CASTF1/J male adult (59.00 days) neutrophil primary cell

value: primary cell

value: male

tag: source

value: Mark Groudine

tag: model organism mating status

value: virgin

tag: collection date

value: not applicable

value: ENCBS159CLP at ENCODE; https://www.encodeproject.org/ENCBS159CLP/


title: mESC RCMC WT Rep 2

description: Library name: RCMC_WT_TRep3

tag: cell line

tag: cell type

value: WT


title: 75 mg metformin, Liver, 65 weeks, Sample 7

description:
Library name: Sample 12
Column name in MetforminReadCounts_0vs75.txt: Met_7

tag: time


title: mESC RCMC WT Rep 1

description: Library name: RCMC_WT_TRep2


title: total RNA-seq from neutrophil (ENCLB636AMD)

description:
https://www.encodeproject.org/experiments/ENCSR251XVY/
***************
biological replicate number: 2
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.neutrophil_spleen_M_59days
experiment encode accession: ENCSR251XVY
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-19
lab: Barbara Wold, Caltech
library encode accession: ENCLB636AMD
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: neutrophil

tag: geographic location

value: ENCBS236AZT at ENCODE; https://www.encodeproject.org/ENCBS236AZT/


title: CTRL_1

value: placenta

value: placental cell

value: 8-10 weeks old


title: 75 mg metformin, Liver, 65 weeks, Sample 6

description:
Library name: Sample 11
Column name in MetforminReadCounts_0vs75.txt: Met_6

value: Liver


title: total RNA-seq from B cell (ENCLB331FZF)

description:
https://www.encodeproject.org/experiments/ENCSR243UCH/
***************
biological replicate number: 3
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD19_spleen_M_62days
experiment encode accession: ENCSR243UCH
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB331FZF
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: Mus musculus strain B6CASTF1/J male adult (62.00 days) B primary cell

value: B cell

tag: biosample encode accession

value: adult

value: John Stamatoyannopoulos, UW

value: ENCBS012ASP at ENCODE; https://www.encodeproject.org/ENCBS012ASP/


title: mESC RCMC 3hr DMSO Rep 1

description: Library name: RCMC_3hrDMSO_TRep2

value: mouse embryonic stem cell

value: Homozygous RAD21-mAID-BFP-V5

value: DMSO (3 hours)


title: Liver from non-humanized mouse

type: RNA

city: Albuquerque

first: Kathryn

last: Brayer

state: New Mexico

address: 1 University of New Mexico, MSC07 4025

institute: University of New Mexico

description: Formalin fixed parafin embedded tissues were sectioned to 5um and mounted on 10X Genomics Xenium slides. Slides were prepared for imaging on a Xenium Analyzer (10X Genomics, Pleasanton, CA) following the manufacturers protocols (CG000580 Rev C, CG000582 Rev E, CG000584 Rev C). Probes used included the pre-designed 377-gene Human Multi-Tissue and Cancer Panel and an additional 22-gene custom panel.

hyb_protocol: Fixed tissue was routinely processed and paraffin embedded. Paraffin sections were cut at 5um and mounted on Xenium slides per 10x Genomics Demonstrated Protocol. Slides were incubated at 42C for 3 hours prior to being stored in a desiccator until ready for Xenium processing.

scan_protocol: Xenium slides were prepared with 10xGenomics Xenium In Situ Gene Expression Reagent kit according to manufacturer's construction

data_processing: Seurat v5 was used to perform quality filtering, dimensionality reduction, clustering, and visualization with SCTransform for Normalization.

label: Xenium

source_name: Liver sample from non-humanized mouse

label_protocol: Xenium mouse Probe Set

growth_protocol: mouse water and food was changed on regular basis

extract_protocol: After 6 weeks, 5 MBM male and 5 MBM female mice from both cohorts (humanized and non-humanized) were euthanized and necropsied. Samples from huNBSGW with MBM were re-injected into a second generation of HuNBSGW hosts, while samples from non-HuNBSGW with MBM were re-injected into non-huNBSGW hosts. Blood was collected and re-injected retro-orbitally (350 µL) into second generation mice (“blood-

treatment_protocol: CDXs were generated using 6-12 weeks old NBSGW (NOD.Cg-KitW-41J Tyr + Prkdcscid Il2rgtm1Wjl/ThomJ) mice. Twenty four huNBSGW and twenty four NBSGW mice were injected retro-orbitally with 50 µL (4 mg/mL) of low-molecular weight heparin (NDC, Cat# 63323-533-01) prior to intracardiac injection to avoid thromboembolism.

value: liver


title: Intestine from humanized mouse

source_name: Intestine sample from humanized mouse

value: intestine


title: BC_mapping_MPRA_7

data_processing:
Barcode quantification and variant sequence identification was handled using custom scripts written in Python. To determine the variant sequence associated with each barcode, the paired end reads from the gDNA-derived libraries were directly parsed as FASTQ files, with one read capturing the barcode and the other the variable region of the construct. Variants with at least one mutation in the constant region proceeding the barcode were discarded. To avoid rare mutations or sequencing errors confounding our variant sequence mapping, variant sequence assignment required at least three reads per barcode. If, among these reads, the second-most frequent sequence was at least 25% as frequent as the top sequence, the barcode was discarded entirely.
Assembly: N/A
Supplementary files format and content: .txt files are tab-separated tables containing information and counts for each detected variant, integrating information from all three datasets (barcode-to-sequence mapping, RNA quantification, and gDNA quantification).

source_name: bacterial cell

extract_protocol:
gDNA was prepared from a frozen cell pellet using the Wizard Genomic DNA Purification Kit (Promega).
gDNA-derived libraries were generated using a two-step Phusion PCR protocol. An initial amplicon was generated through 2 cycles of PCR using from 4 µg of purified nucleic acid per 50 µL PCR reaction (reaction scaled up as needed to minimize UMI collapse in more complex libraries) with primers oJT444/445 for cggR upstream mutations, oJT1125/445 for cggR downstream mutations, and oJT891/445 for glnR downstream mutations. The untranslated cggR library required a longer amplicon to capture the upstream stop codon and was instead amplified with oJT942 and oJT445. This first PCR reaction was cleaned up with a double-sided Select-a-Size DNA Clean & Concentrator column (Zymo) and a DNA Clean & Concentrator 5 column (Zymo). A quarter of this reaction was then used for the second round of PCR, using primers oJT446/447. This product was size selected on an 8% TBE gel and sequenced.

value: bacterial cell


title: BC_mapping_MPRA_9

value: W168 amyE::{Pxyl-rnjA Cm} rnjA::spc ganA::{comK kan}

value: 2% xylose (RNase J1 induction)


title: Internal_1

first: Yoshitaka

last: Matsuo

address: 4-6-1, Shirokanedai, Minato-Ku

department: IMSUT

institute: The University of Tokyo,

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with Cutadapt v2.8
random barcode triming with UMI-tool v1.0.1
rRNA alignment with bowtie2 v2.0.6
Alignment with STAR v2.7.8
Read quantitation using plastid v0.4.7
Assembly: STAR v2.7.8 using C. merilae genome ASM9120v1
Supplementary files format and content: Count file at coding region of each gene
Library strategy: Ribo-seq

organism: Cyanidioschyzon merolae

source_name: Internal

extract_protocol:
The lysate was treated with RNase I and then subjected to ultracentrifugation for ribosome profiling. Total RNA was extracted by TRIzol reagent from the ribosome pellet.
Ribosome profiling libraries were generated as described in MGlincy, N.J. and Ingolia, N.T., 2017, Methods, 126:112-129 .

value: Internal

value: WT


title: Internal_2


title: Division_1

source_name: Division

value: Division


title: total RNA-seq from B cell (ENCLB341GIS)

description:
https://www.encodeproject.org/experiments/ENCSR243UCH/
***************
biological replicate number: 1
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD19_spleen_M_62days
experiment encode accession: ENCSR243UCH
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB341GIS
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: primary cell

tag: Sex

value: male

value: Mark Groudine

value: virgin

value: not applicable

value: ENCBS278JYA at ENCODE; https://www.encodeproject.org/ENCBS278JYA/


title: total RNA-seq from B cell (ENCLB218EWD)

description:
https://www.encodeproject.org/experiments/ENCSR243UCH/
***************
biological replicate number: 4
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD19_spleen_M_62days
experiment encode accession: ENCSR243UCH
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB218EWD
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: B cell

value: adult

tag: age

value: John Stamatoyannopoulos, UW

value: ENCBS871ZJQ at ENCODE; https://www.encodeproject.org/ENCBS871ZJQ/


title: Instestine from non-humanized mouse

source_name: Intestine sample from non-humanized mouse

value: intestine


title: Liver from humanized mouse

source_name: Liver sample from humanized mouse

value: liver


title: Stim_2

value: placenta

value: placental cell

value: 8-10 weeks old

value: CPS


title: BC_mapping_MPRA_8a+b

value: bacterial cell

value: W168 amyE::{Pxyl-rnjA Cm} rnjA::spc ganA::{comK kan}

value: 2% xylose (RNase J1 induction)


title: Brain from non-humanized mouse

source_name: Brain sample from non-humanized mouse

value: brain


title: BC_mapping_MPRA_5


title: Division_2

value: Division

value: WT


title: total RNA-seq from B cell (ENCLB463ELW)

description:
https://www.encodeproject.org/experiments/ENCSR703ACF/
***************
biological replicate number: 1
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD19_spleen_F_62days
experiment encode accession: ENCSR703ACF
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB463ELW
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: Mus musculus strain B6CASTF1/J female adult (62.00 days) B primary cell

value: primary cell

value: female

tag: dev stage

value: Mark Groudine

value: virgin

value: not applicable

value: ENCBS032CJY at ENCODE; https://www.encodeproject.org/ENCBS032CJY/


title: total RNA-seq from B cell (ENCLB440HZR)

description:
https://www.encodeproject.org/experiments/ENCSR703ACF/
***************
biological replicate number: 4
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD19_spleen_F_62days
experiment encode accession: ENCSR703ACF
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB440HZR
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: Mus musculus strain B6CASTF1/J female adult (55.00 days) B primary cell

value: B cell

value: adult

tag: lab

value: John Stamatoyannopoulos, UW

value: ENCBS285KOP at ENCODE; https://www.encodeproject.org/ENCBS285KOP/


title: LCMuscle，rep1

city: TianJin

first: Lu

last: chuang

address: BinHai

country: China

institute: Northwest Normal University

description: Library name: sample16

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

organism: Larimichthys crocea

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: LCMuscle，rep2

description: Library name: sample17


title: BC_mapping_MPRA_4a+b

value: bacterial cell


title: Brain from humanized mouse

source_name: Brain sample from humanized mouse


title: LPMuscle，rep3

description: Library name: sample9

organism: Larimichthys polyactis


title: LCMuscle，rep3

description: Library name: sample18


title: total RNA-seq from B cell (ENCLB153WUB)

description:
https://www.encodeproject.org/experiments/ENCSR703ACF/
***************
biological replicate number: 3
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD19_spleen_F_62days
experiment encode accession: ENCSR703ACF
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB153WUB
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

tag: link

value: ENCBS397NDI at ENCODE; https://www.encodeproject.org/ENCBS397NDI/


title: BC_mapping_MPRA_6


title: total RNA-seq from B cell (ENCLB070YRV)

description:
https://www.encodeproject.org/experiments/ENCSR243UCH/
***************
biological replicate number: 2
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD19_spleen_M_62days
experiment encode accession: ENCSR243UCH
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB070YRV
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: male

value: ENCBS493EYM at ENCODE; https://www.encodeproject.org/ENCBS493EYM/


title: BC_mapping_MPRA_1a+b_3

value: W168 ganA::{comK kan}


title: LCLiver，rep3

description: Library name: sample15

source_name: Liver

tag: tissue

value: Liver


title: Embryo 5, lens removed, 6h

city: Aberdeen

first: Lynda

last: Erskine

address: Foresterhill

department: School of Medicine, Medical Sciences and Nutrition

country: United Kingdom

institute: University of Aberdeen

description:
Library name: E5-LR
Column name in Normalised_Counts_Sex.txt: E5.LR

data_processing:
To assess the quality of the sequencing data, the reads were analysed with FastQC (version 0.11.8). All samples were shown to have a majority of high-quality reads and no evidence of adapter contamination. To remove any lower quality sequences, TrimGalore! (version 0.6.4)  was used to filter the reads with a phred quality score threshold of 30.
Reads were aligned to the chicken genome using HISAT2 (version 2.1.0) and SAMtools (version 1.9) used to process the alignments. Reads were quantified at gene regions using FeatureCounts (subread version 1.6.2) utilising the parameter to split multi-mapped reads as a fraction across all genes that they align to, and the parameter for stranded analysis.
Assembly: GRCg6a
Supplementary files format and content: tab-delimited text file includes normalised counts for each sample

source_name: optic cup

growth_protocol: Fertilised Dekalb white chicken eggs were incubated on their side in a humidified incubator at 37˚ C until Hamburger and Hamilton (HH) 23 (~E4).

extract_protocol:
RNA was prepared using TRIzol (Fisher Scientific) followed by purification and removal of genomic DNA using the Qiagen RNeasy mini kit with on-column DNase I digestion (Qiagen), according to the manufacturers’ instructions.
Libraries were prepared using the Illumina TruSeq Stranded mRNA kit with unique dual indices and sequenced on an Illumina NextSeq 500 with v2.5 chemistry and 75 bp paired end reads.

treatment_protocol: Lenses were removed from one eye of HH23 (~E4) chicken embryos. The eggs were windowed and the membranes around the eye removed. Using forceps, a slit was made in the dorsal side of the eye and the lens grasped and gently removed. The eggs were sealed and reincubated for 6 hours. The retinas were dissected from the operated and contralateral, unoperated eyes and collected individually in RNAlater. Paired samples of operated and contralateral (unoperated) retinas were collected, with 5 biological replicates from different embryos.

value: optic cup

value: WT

value: Lens removal at E4 (HH23)

tag: batch


title: LPMuscle，rep2

description: Library name: sample8


title: total RNA-seq from neutrophil (ENCLB233AHN)

description:
https://www.encodeproject.org/experiments/ENCSR698PIS/
***************
biological replicate number: 1
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.neutrophil_spleen_M_65days
experiment encode accession: ENCSR698PIS
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-19
lab: Barbara Wold, Caltech
library encode accession: ENCLB233AHN
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

source_name: Mus musculus strain B6CASTF1/J male adult (65.00 days) neutrophil primary cell

value: neutrophil

value: primary cell

value: Mark Groudine

value: virgin

value: ENCBS597TMV at ENCODE; https://www.encodeproject.org/ENCBS597TMV/


title: LPLiver，rep3

description: Library name: sample6


title: LPMuscle，rep1

description: Library name: sample7


title: Embryo 4, lens removed, 6h

description:
Library name: E4-LR
Column name in Normalised_Counts_Sex.txt: E4.LR

tag: treatment


title: Embryo 5, control unoperated, 6h

description:
Library name: E5-Control
Column name in Normalised_Counts_Sex.txt: E5.Control

tag: genotype

value: control


title: total RNA-seq from neutrophil (ENCLB371CSY)

description:
https://www.encodeproject.org/experiments/ENCSR698PIS/
***************
biological replicate number: 2
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.neutrophil_spleen_M_65days
experiment encode accession: ENCSR698PIS
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-19
lab: Barbara Wold, Caltech
library encode accession: ENCLB371CSY
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: John Stamatoyannopoulos, UW

tag: source

value: not applicable

value: ENCBS646YRX at ENCODE; https://www.encodeproject.org/ENCBS646YRX/


title: BC_mapping_MPRA_2a+b

tag: strain

value: bacterial cell


title: LPLiver，rep2

description: Library name: sample5


title: Embryo 4, control unoperated, 6h

description:
Library name: E4-Control
Column name in Normalised_Counts_Sex.txt: E4.Control


title: LCLiver，rep2

description: Library name: sample14


title: total RNA-seq from B cell (ENCLB716BHS)

description:
https://www.encodeproject.org/experiments/ENCSR703ACF/
***************
biological replicate number: 2
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD19_spleen_F_62days
experiment encode accession: ENCSR703ACF
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB716BHS
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: B cell

value: female

tag: model organism mating status

tag: collection date

value: ENCBS652PQK at ENCODE; https://www.encodeproject.org/ENCBS652PQK/


title: LCBrain，rep3

description: Library name: sample12

source_name: Brain

value: Brain


title: LPLiver，rep1

description: Library name: sample4

value: Liver


title: total RNA-seq from neutrophil (ENCLB242ZXF)

description:
https://www.encodeproject.org/experiments/ENCSR167IUG/
***************
biological replicate number: 1
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.neutrophil_spleen_M_83days
experiment encode accession: ENCSR167IUG
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-19
lab: Barbara Wold, Caltech
library encode accession: ENCLB242ZXF
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: Mus musculus strain B6CASTF1/J male adult (83.00 days) neutrophil primary cell

value: male

value: ENCBS517LJD at ENCODE; https://www.encodeproject.org/ENCBS517LJD/


title: LCLiver，rep1

description: Library name: sample13


title: LPBrain，rep3

description: Library name: sample3


title: Embryo 3, lens removed, 6h

description:
Library name: E3-LR
Column name in Normalised_Counts_Sex.txt: E3.LR

value: optic cup

value: WT

value: Lens removal at E4 (HH23)


title: total RNA-seq from B cell (ENCLB842IIL)

description:
https://www.encodeproject.org/experiments/ENCSR092BBW/
***************
biological replicate number: 3
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD19_spleen_M_67days
experiment encode accession: ENCSR092BBW
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB842IIL
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: Mus musculus strain B6CASTF1/J male adult (67.00 days) B primary cell

value: primary cell

value: Mark Groudine

value: virgin

value: ENCBS718WEQ at ENCODE; https://www.encodeproject.org/ENCBS718WEQ/


title: LCBrain，rep1

description: Library name: sample10


title: total RNA-seq from B cell (ENCLB726UHG)

description:
https://www.encodeproject.org/experiments/ENCSR092BBW/
***************
biological replicate number: 2
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD19_spleen_M_67days
experiment encode accession: ENCSR092BBW
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB726UHG
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: John Stamatoyannopoulos, UW

value: not applicable

value: ENCBS489PFJ at ENCODE; https://www.encodeproject.org/ENCBS489PFJ/


title: Embryo 3, control unoperated, 6h

description:
Library name: E3-Control
Column name in Normalised_Counts_Sex.txt: E3.Control

value: control


title: total RNA-seq from B cell (ENCLB289BPC)

description:
https://www.encodeproject.org/experiments/ENCSR092BBW/
***************
biological replicate number: 1
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD19_spleen_M_67days
experiment encode accession: ENCSR092BBW
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB289BPC
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: B cell

value: ENCBS821FUE at ENCODE; https://www.encodeproject.org/ENCBS821FUE/


title: LPBrain，rep2

description: Library name: sample2

value: Brain


title: OAd-IFN, Less-responder-2

city: Minneapolis

first: Julia

last: Davydova

state: MN

address: 420 Delaware St. SE, MMC 195

department: Surgery

institute: University of Minnesota

description:
Library name: V13F06-354_D1
Fresh frozen spatial transcriptome sequencing

data_processing:
A reference was created using the combined MesAur1.0 and the Human Adenovirus 5 isolate HAdV-C5/USA/26107/2012 (accession GCA_029237105.1) genomes with SpaceRanger 2.0.0
Raw fastq files were aligned to the reference and the gene expression was estimated using SpaceRanger 2.0.0 with default parameters
Gene - barcode matrices of the SpaceRanger filtered data were merged and analyzed with custom R scripts
Assembly: MesAur1.0
Supplementary files format and content: aligned_fiducials.jpg: generated by SpaceRanger
Supplementary files format and content: barcodes.tsv.gz : SpaceRanger filtered barcodes
Supplementary files format and content: detected_tissue_image.jpg: generated by SpaceRanger
Supplementary files format and content: features.tsv.gz: genes included in the SpaceRanger count command
Supplementary files format and content: matrix.mtx.gz: resulting gene by barcode count matrix
Supplementary files format and content: scalefactors_json.json: generated by SpaceRanger
Supplementary files format and content: tissue_hires_image.png: high resolution image of the tissue section
Supplementary files format and content: tissue_lowres_image.png: low resolution image of the tissue section
Supplementary files format and content: tissue_positions.csv: lilst of barcode coordinates
Supplementary files format and content: merged.rds: compressed object containing the 4 tissue samples merged and analyzed with Seurat 4.3.0.1
Library strategy: Spatial Transcriptomics

organism: Mesocricetus auratus

source_name: HP-1 pancreatic cancer cell line-derived tumor

growth_protocol: HP-1 pancreatic cancer tumors were established by injecting 2 x 10^6 cells in the left flanks of 6-7-week-old male Syrian hamsters.

extract_protocol:
Tumors were snap-frozen in isopentane and liquid nitrogen, embedded in O.C.T. compound. A 10 µm section from each sample was placed within a capture area on the Visium Spatial slide.
Library construction was performed following the manufacturer’s instruction (CG000239, Visium Spatial Gene Expression Reagent Kits, 10x Genomics).

treatment_protocol: Twelve days after tumor cell inoculation, tumors were treated intratumorally with OAd-IFN or OAd-Luc (2.5x10^9 pfu/50 µL/injection) every three days for a total of four injections.

value: OAd-IFN


title: total RNA-seq from B cell (ENCLB015UQP)

description:
https://www.encodeproject.org/experiments/ENCSR092BBW/
***************
biological replicate number: 4
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD19_spleen_M_67days
experiment encode accession: ENCSR092BBW
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB015UQP
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: male

value: ENCBS496IKI at ENCODE; https://www.encodeproject.org/ENCBS496IKI/


title: Embryo 2, lens removed, 6h

description:
Library name: E2-LR
Column name in Normalised_Counts_Sex.txt: E2.LR

value: optic cup

value: WT


title: LCBrain，rep2

description: Library name: sample11


title: LPBrain，rep1

description: Library name: sample1


title: total RNA-seq from T-cell (ENCLB667AGY)

description:
https://www.encodeproject.org/experiments/ENCSR034MGF/
***************
biological replicate number: 2
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD3_spleen_F_66days
experiment encode accession: ENCSR034MGF
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB667AGY
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: Mus musculus strain B6CASTF1/J female adult (66.00 days) T-cell primary cell

value: T-cell

value: primary cell

value: female

value: ENCBS899UQX at ENCODE; https://www.encodeproject.org/ENCBS899UQX/


title: Embryo 1, lens removed, 6h

description:
Library name: E1-LR
Column name in Normalised_Counts_Sex.txt: E1.LR

value: Lens removal at E4 (HH23)


title: RmpA Input sample

city: Beijing

first: Jiangqing

last: Huang

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

institute: Chinese Academy of Sciences

description:
Library name: RmpA_Input
ChIP-seq of Klebsiella strain RJF293

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The clean reads were used for protein binding site analysis. They were mapped to the reference genome of Klebsiella RJF293 strain using STAR software (version 2.5.3a) with default parameters.
The RSeQC（version 2.6）was used for reads distribution analysis.The MACS2 software（Version 2.1.1）was used for peak calling.
The bedtools（Version 2.25.0）was used for peaks annotation and peak distribution analysis.
The differentially binding peaks were identified by a python script，using fisher test.
Assembly: Reference genome of Klebsiella RJF293 strain (accession number: GCF_001530015.1).
Supplementary files format and content: bigWig

organism: Klebsiella pneumoniae

source_name: bacterial cells

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.

extract_protocol:
Cells were crosslinked with formaldehyde (1% final concentration) for 20 min at room temperature with continuous shaking. Crosslinking was stopped by addition of 500 mM glycine.The DNA was sonicated to sizes of 200-500 bp on ice (50% total output, 30-s on, 5 min off, twice), following by centrifugation to remove the insoluble cellular debris.The 10% lysis sonicated chromatin was stored and named “Input”, and 80% was used in immunoprecipitation reactions with monoclonal ANTI-FLAG® M2 antibody (Sigma-Aldrich,F1804-50UG) and named “IP”.
The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3（Catalog NO. ND607, Vazyme）. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.

tag: cell type

value: bacterial cells

tag: chip target

value: none (input)


title: OAd-IFN, Less-responder-1

description:
Library name: V13F06-354_B1
Fresh frozen spatial transcriptome sequencing

value: HP-1 pancreatic cancer cell line-derived tumor


title: RmpA ChIP sample

description:
Library name: RmpA_IP
ChIP-seq of Klebsiella strain RJF293

value: RmpA


title: OAd-Luc

description:
Library name: V13F06-354_A1
Fresh frozen spatial transcriptome sequencing

value: OAd-Luc


title: OAd-IFN, Responder

description:
Library name: V13F06-354_C1
Fresh frozen spatial transcriptome sequencing


title: 4sU_ADE_d4G+_rep3

status: Public on Jan 13 2025

city: Edinburgh

first: Rob

middle: S

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

institute: The University of Edinburgh

description:
Library name: Sample 12
4sU-seq. 4sU labelled RNA isolated from ADE differentiated cells (ADE Day 4 GSC Positive Population)

library_source: other

data_processing:
Mapping and manipulation of 4sU-seq data from the ADE differentiation. Following demultiplexing (performed by the sequencing facility - BGI), .Fastq files were aligned to the mouse genome (mm9 build) using Bowtie2 v2.2.6 for paired-end sequence data with default settings. The resulting .SAM alignment files were converted into tag directories using the HOMER package (v4.8) using the ‘makeTagDirectory’ function with the following parameters (-format sam -flip –sspe; PMID: 20513432). Genomic intervals that extended beyond the end of the chromosomes were removed using the ‘removeOutOfBoundsReads.pl’ function. Strand-specific browser track files in .bigWig format were generated per replicate using ‘makeUCSCfile’ with the following parameters (-fsize 1e20 -strand +/− -norm 5e7 -lastTag -color 25,50,200).
Assembly: mm9
Supplementary files format and content: .bigWig files contain information on both the genomic distribution, strand-specific expression and signal strength of the mapped reads (representative of the sample composition). .bigWig files are in an indexed binary format.

molecule: other

source_name: Hex-RS; Gsc-GFP (B6) Dual Fluoresecent Reporter mESCs

growth_protocol: Dual reporter ESCs were cultured in ESC medium + LIF as previously described (PMID: 27723457) and differentiated according to our standard ADE differentiation protocol (PMID: 26840225). To generate sufficient cells for Fluorescence Activated Cell Sorting (FACS), ADE differentiation was performed in T75 flasks alongside a 6-well plate that was analysed by flow cytometry at ADE day 6 to monitor differentiation.

extract_protocol:
4sU incubation was performed in ADE differentiation medium (ADEM; see PMID: 26840225) from the T75 flasks to be used for FACS sorting. To obtain the ADEM, 15 ml of ADEM was pipetted from each T75 flask, flasks were returned to the incubator and the extracted ADEM was pooled and centrifuged at 1000 g for 5 mins to remove cell debris. In the following steps, flasks were treated in the same order for every action taken in batches of up to 6 flasks to avoid timing differences between flasks. After aspiration, 5 ml pooled ADEM (negative control; 1-2 flasks per sort) or 5 ml pooled ADEM containing 500 μM 4sU were added and flasks were then returned to the incubator. After exactly 20 mins, flasks were aspirated, washed with 10 ml PBS (Merck, D8537), aspirated again and incubated for 3 min at 37°C in 2 ml per flask of attenuated trypsin (0.025% (v/v) trypsin (Thermo Fisher Scientific, 15090–046), 1.27 mM EDTA, and 1% (v/v) Chicken serum (Merck C5405) in PBS (Merck D8537)). Cells were then released from the flask by tapping and attenuated trypsin was inactivated by adding 8 ml ice-cold flow cytometry buffer (FC buffer - 10% FCS in PBS). Cell suspensions from all flasks with the same treatment in the batch were then pooled, pipetted repeatedly to obtain a single cell suspension, counted using a hemocytometer (Neubauer) and stored on ice. This process was repeated when required (for day 3 & day 4 samples) until a sufficient number of cells were obtained for the sorting procedure 100M cells). All centrifugation steps hereafter were performed at 400 g for 3 mins. Samples were centrifuged, aspirated, resuspended in ice-cold FC buffer at 1-1.5 x 107 cells/ml and passed through a cell strainer (Corning, 352235). Negative control cells were not sorted and kept on ice during the sorting procedure. 4sU-labelled cells were sorted on a BD FACSAriaIII into 5 ml Falcon tubes (Corning) at 4°C containing 1 ml of ice-cold FC buffer. After sorting 1 million cells, the tube was transferred to ice in the dark and replaced with a fresh 5 ml Falcon tube containing 1 ml of ice-cold FC buffer and this process was repeated until all 4sU-labelled cells were sorted. Samples were centrifuged, resuspended in 100 μl of ice-cold PBS and cells from the same population were pooled to obtain an equal number of cells for each population, equivalent to the population that generated the lowest number of cells and an identical number of cells was taken from the unsorted and unlabelled negative control sample. All samples were then transferred to 1.5 ml DNA LoBind tubes (Eppendorf, Enfield, CT 06082), added up to 1 ml using ice-cold PBS, centrifuged, aspirated and agitated to resuspend cells in the remaining PBS (<10 μl). Cells were lysed by adding 1 ml of Trizol reagent (Thermo Fisher Scientific) equilibrated to RT. After 5 mins of incubation at RT, samples were stored at -20 ºC. 4sU incorporated RNAs were isolated as previously described (PMID: 32439634; as adapted from PMID: 25811895).
Ribosomal RNA was depleted from the purified RNA using the low-input RiboMinus eukaryote system v2 kit according to the manufacturer's instructions (Ambion A15027). Libraries were constructed using the NEBNext Ultra II directional RNA library preparation kit for Illumina according to the protocol for ribosome-depleted RNA and with an 11-min RNA fragmentation step (NEB E7760). Library PCRs were supplemented with 2× SYBR dye (Sigma S9430) so that amplification could be monitored by quantitative PCR on a Roche LightCycler 480. Individual libraries were pooled into two six-sample equimolar pools containing the indexes 3-8 (NEBNext multiplex oligos for Illumina, set 1, E7335) and deep-sequenced at BGI on a HiSeq4000 (paired-end 100-bp reads).

tag: cell line

value: ADE Day 4 GSC Positive Population

value: ADE Differentiation


title: total RNA-seq from T-cell (ENCLB740JTB)

description:
https://www.encodeproject.org/experiments/ENCSR034MGF/
***************
biological replicate number: 1
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD3_spleen_F_66days
experiment encode accession: ENCSR034MGF
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB740JTB
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

value: adult

value: John Stamatoyannopoulos, UW

value: Mark Groudine

value: virgin

value: not applicable

tag: geographic location

value: ENCBS359DHS at ENCODE; https://www.encodeproject.org/ENCBS359DHS/


title: 4sU_ADE_d4G+_rep2

description:
Library name: Sample 11
4sU-seq. 4sU labelled RNA isolated from ADE differentiated cells (ADE Day 4 GSC Positive Population)

value: Hex-RS; Gsc-GFP (B6) Dual Fluoresecent Reporter mESCs


title: 4sU_ADE_d4G-_rep2

description:
Library name: Sample 8
4sU-seq. 4sU labelled RNA isolated from ADE differentiated cells (ADE Day 4 GSC Negative Population)

value: ADE Day 4 GSC Negative Population


title: 4sU_ADE_d3G+_rep2

description:
Library name: Sample 5
4sU-seq. 4sU labelled RNA isolated from ADE differentiated cells (ADE Day 3 GSC Positive Population)

value: ADE Day 3 GSC Positive Population


title: 4sU_ADE_d4G-_rep3

description:
Library name: Sample 9
4sU-seq. 4sU labelled RNA isolated from ADE differentiated cells (ADE Day 4 GSC Negative Population)


title: 4sU_ADE_d3G+_rep1

description:
Library name: Sample 4
4sU-seq. 4sU labelled RNA isolated from ADE differentiated cells (ADE Day 3 GSC Positive Population)


title: 4sU_ADE_d4G+_rep1

description:
Library name: Sample 10
4sU-seq. 4sU labelled RNA isolated from ADE differentiated cells (ADE Day 4 GSC Positive Population)


title: total RNA-seq from T-cell (ENCLB695NMT)

description:
https://www.encodeproject.org/experiments/ENCSR034MGF/
***************
biological replicate number: 3
technical replicate number: 1
description: MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD3_spleen_F_66days
experiment encode accession: ENCSR034MGF
assay title: total RNA-seq
assembly: mm10
encode release date: 2023-01-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB695NMT
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: T-cell

value: primary cell

tag: Sex

value: female

tag: age

value: ENCBS462YUX at ENCODE; https://www.encodeproject.org/ENCBS462YUX/


title: 4sU_ADE_d3G-_rep3

description:
Library name: Sample 3
4sU-seq. 4sU labelled RNA isolated from ADE differentiated cells (ADE Day 3 GSC Negative Population)

value: ADE Day 3 GSC Negative Population


title: 4sU_ADE_d3G-_rep2

description:
Library name: Sample 2
4sU-seq. 4sU labelled RNA isolated from ADE differentiated cells (ADE Day 3 GSC Negative Population)


title: 4sU_ADE_d3G-_rep1

description:
Library name: Sample 1
4sU-seq. 4sU labelled RNA isolated from ADE differentiated cells (ADE Day 3 GSC Negative Population)


title: 4sU_ADE_d3G+_rep3

description:
Library name: Sample 6
4sU-seq. 4sU labelled RNA isolated from ADE differentiated cells (ADE Day 3 GSC Positive Population)